histone-lysine N-methyltransferase SETD1B isoform X1 [Homo sapiens]
Protein Classification
List of domain hits
| Name | Accession | Description | Interval | E-value | ||||
| SET_SETD1 | cd19169 | SET domain (including post-SET domain) found in SET domain-containing protein 1 (SETD1) and ... |
1815-1962 | 1.46e-103 | ||||
SET domain (including post-SET domain) found in SET domain-containing protein 1 (SETD1) and similar proteins; This family includes SET domain-containing protein 1A (SETD1A) and SET domain-containing protein 1B (SETD1B). These proteins are histone-lysine N-methyltransferases that specifically methylate 'Lys-4' of histone H3 (H3K4me) when part of the SET1 histone methyltransferase (HMT) complex, but not if the neighboring 'Lys-9' residue is already methylated. : Pssm-ID: 380946 Cd Length: 148 Bit Score: 327.37 E-value: 1.46e-103
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| RRM_Set1B | cd12549 | RNA recognition motif in vertebrate histone-lysine N-methyltransferase Setd1B (Set1B); This ... |
101-193 | 3.77e-63 | ||||
RNA recognition motif in vertebrate histone-lysine N-methyltransferase Setd1B (Set1B); This subgroup corresponds to the RRM of Setd1B, also termed SET domain-containing protein 1B (Set1B), or lysine N-methyltransferase 2G, a ubiquitously expressed vertebrates histone methyltransferase that exhibits high homology to yeast Set1. Set1B is localized to euchromatic nuclear speckles and associates with a complex containing six human homologs of the yeast Set1/COMPASS complex, including CXXC finger protein 1 (CFP1; homologous to yeast Spp1), Rbbp5 (homologous to yeast Swd1), Ash2 (homologous to yeast Bre2), Wdr5 (homologous to yeast Swd3), and Wdr82 (homologous to yeast Swd2). Set1B complex is a histone methyltransferase that produces trimethylated histone H3 at Lys4. Set1B contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), an N- SET domain, and a C-terminal catalytic SET domain followed by a post-SET domain. : Pssm-ID: 409965 [Multi-domain] Cd Length: 93 Bit Score: 209.81 E-value: 3.77e-63
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| N-SET super family | cl13245 | COMPASS (Complex proteins associated with Set1p) component N; The n-SET or N-SET domain is a ... |
1679-1821 | 3.95e-35 | ||||
COMPASS (Complex proteins associated with Set1p) component N; The n-SET or N-SET domain is a component of the COMPASS complex, associated with SET1, conserved in yeasts and in other eukaryotes up to humans. The COMPASS complex functions to methylate the fourth lysine of Histone 3 and for the silencing of genes close to the telomeres of chromosomes. This domain promotes trimethylation in conjunction with an RRM domain and is necessary for binding of the Spp1 component of COMPASS into the complex. The actual alignment was detected with superfamily member pfam11764: Pssm-ID: 463344 Cd Length: 172 Bit Score: 132.41 E-value: 3.95e-35
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| Name | Accession | Description | Interval | E-value | ||||
| SET_SETD1 | cd19169 | SET domain (including post-SET domain) found in SET domain-containing protein 1 (SETD1) and ... |
1815-1962 | 1.46e-103 | ||||
SET domain (including post-SET domain) found in SET domain-containing protein 1 (SETD1) and similar proteins; This family includes SET domain-containing protein 1A (SETD1A) and SET domain-containing protein 1B (SETD1B). These proteins are histone-lysine N-methyltransferases that specifically methylate 'Lys-4' of histone H3 (H3K4me) when part of the SET1 histone methyltransferase (HMT) complex, but not if the neighboring 'Lys-9' residue is already methylated. Pssm-ID: 380946 Cd Length: 148 Bit Score: 327.37 E-value: 1.46e-103
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| RRM_Set1B | cd12549 | RNA recognition motif in vertebrate histone-lysine N-methyltransferase Setd1B (Set1B); This ... |
101-193 | 3.77e-63 | ||||
RNA recognition motif in vertebrate histone-lysine N-methyltransferase Setd1B (Set1B); This subgroup corresponds to the RRM of Setd1B, also termed SET domain-containing protein 1B (Set1B), or lysine N-methyltransferase 2G, a ubiquitously expressed vertebrates histone methyltransferase that exhibits high homology to yeast Set1. Set1B is localized to euchromatic nuclear speckles and associates with a complex containing six human homologs of the yeast Set1/COMPASS complex, including CXXC finger protein 1 (CFP1; homologous to yeast Spp1), Rbbp5 (homologous to yeast Swd1), Ash2 (homologous to yeast Bre2), Wdr5 (homologous to yeast Swd3), and Wdr82 (homologous to yeast Swd2). Set1B complex is a histone methyltransferase that produces trimethylated histone H3 at Lys4. Set1B contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), an N- SET domain, and a C-terminal catalytic SET domain followed by a post-SET domain. Pssm-ID: 409965 [Multi-domain] Cd Length: 93 Bit Score: 209.81 E-value: 3.77e-63
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| SET | smart00317 | SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain; Putative methyl transferase, based on ... |
1834-1949 | 7.49e-37 | ||||
SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain; Putative methyl transferase, based on outlier plant homologues Pssm-ID: 214614 [Multi-domain] Cd Length: 124 Bit Score: 135.54 E-value: 7.49e-37
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| N-SET | pfam11764 | COMPASS (Complex proteins associated with Set1p) component N; The n-SET or N-SET domain is a ... |
1679-1821 | 3.95e-35 | ||||
COMPASS (Complex proteins associated with Set1p) component N; The n-SET or N-SET domain is a component of the COMPASS complex, associated with SET1, conserved in yeasts and in other eukaryotes up to humans. The COMPASS complex functions to methylate the fourth lysine of Histone 3 and for the silencing of genes close to the telomeres of chromosomes. This domain promotes trimethylation in conjunction with an RRM domain and is necessary for binding of the Spp1 component of COMPASS into the complex. Pssm-ID: 463344 Cd Length: 172 Bit Score: 132.41 E-value: 3.95e-35
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| SET | COG2940 | SET domain-containing protein (function unknown) [General function prediction only]; |
1834-1964 | 9.24e-34 | ||||
SET domain-containing protein (function unknown) [General function prediction only]; Pssm-ID: 442183 [Multi-domain] Cd Length: 134 Bit Score: 127.39 E-value: 9.24e-34
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| SET | pfam00856 | SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be ... |
1839-1944 | 1.73e-29 | ||||
SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure. Pssm-ID: 459965 [Multi-domain] Cd Length: 115 Bit Score: 114.16 E-value: 1.73e-29
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| RRM | smart00360 | RNA recognition motif; |
110-176 | 2.60e-13 | ||||
RNA recognition motif; Pssm-ID: 214636 [Multi-domain] Cd Length: 73 Bit Score: 66.46 E-value: 2.60e-13
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| RRM_1 | pfam00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ... |
96-175 | 3.76e-09 | ||||
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease. Pssm-ID: 425453 [Multi-domain] Cd Length: 70 Bit Score: 54.93 E-value: 3.76e-09
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| Name | Accession | Description | Interval | E-value | ||||
| SET_SETD1 | cd19169 | SET domain (including post-SET domain) found in SET domain-containing protein 1 (SETD1) and ... |
1815-1962 | 1.46e-103 | ||||
SET domain (including post-SET domain) found in SET domain-containing protein 1 (SETD1) and similar proteins; This family includes SET domain-containing protein 1A (SETD1A) and SET domain-containing protein 1B (SETD1B). These proteins are histone-lysine N-methyltransferases that specifically methylate 'Lys-4' of histone H3 (H3K4me) when part of the SET1 histone methyltransferase (HMT) complex, but not if the neighboring 'Lys-9' residue is already methylated. Pssm-ID: 380946 Cd Length: 148 Bit Score: 327.37 E-value: 1.46e-103
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| SET_SETD1B | cd19205 | SET domain (including post-SET domain) found in SET domain-containing protein 1B (SETD1B) and ... |
1814-1966 | 4.61e-103 | ||||
SET domain (including post-SET domain) found in SET domain-containing protein 1B (SETD1B) and similar proteins; SETD1B (EC2.1.1.43), also termed lysine N-methyltransferase 2G, is a histone-lysine N-methyltransferase that specifically methylates 'Lys-4' of histone H3 (H3K4me) when part of the SET1 histone methyltransferase (HMT) complex, but not if the neighboring 'Lys-9' residue is already methylated. Loss of SETD1B occurs in up to half the gastric and colorectal cancers, most commonly via SETD1B mutations, while de novo variants in SETD1B are associated with intellectual disability, epilepsy and autism. Pssm-ID: 380982 [Multi-domain] Cd Length: 153 Bit Score: 326.24 E-value: 4.61e-103
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| SET_SETD1A | cd19204 | SET domain (including post-SET domain) found in SET domain-containing protein 1A (SETD1A) and ... |
1814-1966 | 2.91e-90 | ||||
SET domain (including post-SET domain) found in SET domain-containing protein 1A (SETD1A) and similar proteins; SETD1A (EC2.1.1.43), also termed lysine N-methyltransferase 2F, or Set1/Ash2 histone methyltransferase complex subunit SET1, is a histone-lysine N-methyltransferase that specifically methylates 'Lys-4' of histone H3 (H3K4me), when part of the SET1 histone methyltransferase (HMT) complex, but not if the neighboring 'Lys-9' residue is already methylated. Human SET domain containing protein 1A (hSETD1A) expression occurs at a high rate in hepatocellular carcinoma patients and controls tumor metastasis in breast cancer by activating MMP expression. Pssm-ID: 380981 [Multi-domain] Cd Length: 153 Bit Score: 289.62 E-value: 2.91e-90
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| SET_SETD1-like | cd10518 | SET domain (including post-SET domain) found in SET domain-containing proteins (SETD1A/SETD1B), ... |
1834-1962 | 1.01e-82 | ||||
SET domain (including post-SET domain) found in SET domain-containing proteins (SETD1A/SETD1B), histone-lysine N-methyltransferases (KMT2A/KMT2B/KMT2C/KMT2D) and similar proteins; This family includes SET domain-containing protein 1A (SETD1A), 1B (SETD1B), as well as histone-lysine N-methyltransferase 2A (KMT2A), 2B (KMT2B), 2C (KMT2C), 2D (KMT2D). These proteins are histone-lysine N-methyltransferases (EC 2.1.1.43) that specifically methylate 'Lys-4' of histone H3 (H3K4me). Pssm-ID: 380916 Cd Length: 150 Bit Score: 267.93 E-value: 1.01e-82
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| SET_SET1 | cd20072 | SET domain (including post-SET domain) found in catalytic component of the Saccharomyces ... |
1815-1962 | 7.81e-77 | ||||
SET domain (including post-SET domain) found in catalytic component of the Saccharomyces cerevisiae COMPASS complex and similar proteins; The family contains mostly fungal SET domains, including SET1 found in the catalytic component of the Saccharomyces cerevisiae COMPASS (complex of proteins associated with Set1). SET1 is a histone-lysine N-methyltransferase that specifically methylates 'Lys-4' of histone H3 (H3K4me), when part of the SET1 histone methyltransferase (HMT) complex. The activity of this catalytic domain is established through forming a complex with a set of core proteins; it is extensively contacted by Cps60 (Bre2), Cps50 (Swd1), and Cps30 (Swd3). Pssm-ID: 380998 Cd Length: 148 Bit Score: 251.19 E-value: 7.81e-77
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| SET_KMT2A_2B | cd19170 | SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2A (KMT2A), ... |
1834-1966 | 2.70e-64 | ||||
SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2A (KMT2A), 2B (KMT2B) and similar proteins; This family includes KMT2A and KMT2B. Both KMT2A (also termed ALL-1 or CXXC7 or MLL or MLL1 or TRX1 or HRX) and KMT2B (also termed MLL4 or TRX2) act as histone methyltransferases that methylate 'Lys-4' of histone H3 (H3K4me). Pssm-ID: 380947 [Multi-domain] Cd Length: 152 Bit Score: 215.33 E-value: 2.70e-64
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| RRM_Set1B | cd12549 | RNA recognition motif in vertebrate histone-lysine N-methyltransferase Setd1B (Set1B); This ... |
101-193 | 3.77e-63 | ||||
RNA recognition motif in vertebrate histone-lysine N-methyltransferase Setd1B (Set1B); This subgroup corresponds to the RRM of Setd1B, also termed SET domain-containing protein 1B (Set1B), or lysine N-methyltransferase 2G, a ubiquitously expressed vertebrates histone methyltransferase that exhibits high homology to yeast Set1. Set1B is localized to euchromatic nuclear speckles and associates with a complex containing six human homologs of the yeast Set1/COMPASS complex, including CXXC finger protein 1 (CFP1; homologous to yeast Spp1), Rbbp5 (homologous to yeast Swd1), Ash2 (homologous to yeast Bre2), Wdr5 (homologous to yeast Swd3), and Wdr82 (homologous to yeast Swd2). Set1B complex is a histone methyltransferase that produces trimethylated histone H3 at Lys4. Set1B contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), an N- SET domain, and a C-terminal catalytic SET domain followed by a post-SET domain. Pssm-ID: 409965 [Multi-domain] Cd Length: 93 Bit Score: 209.81 E-value: 3.77e-63
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| SET_KMT2C_2D | cd19171 | SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2C (KMT2C), ... |
1834-1963 | 4.11e-53 | ||||
SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2C (KMT2C), 2D (KMT2D) and similar proteins; This family includes KMT2C and KMT2D. Both, KMT2C (also termed HALR or MLL3) and KMT2D (also termed ALR or MLL2), act as histone methyltransferases that methylate 'Lys-4' of histone H3 (H3K4me). They are subunits of MLL2/3 complex, a coactivator complex of nuclear receptors, involved in transcriptional coactivation. Pssm-ID: 380948 [Multi-domain] Cd Length: 153 Bit Score: 183.40 E-value: 4.11e-53
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| RRM_Set1 | cd12304 | RNA recognition motif in the Set1-like family of histone-lysine N-methyltransferases; This ... |
101-193 | 7.88e-52 | ||||
RNA recognition motif in the Set1-like family of histone-lysine N-methyltransferases; This subfamily corresponds to the RRM of the Set1-like family of histone-lysine N-methyltransferases which includes Set1A and Set1B that are ubiquitously expressed vertebrates histone methyltransferases exhibiting high homology to yeast Set1. Set1A and Set1B proteins exhibit a largely non-overlapping subnuclear distribution in euchromatic nuclear speckles, strongly suggesting that they bind to a unique set of target genes and thus make non-redundant contributions to the epigenetic control of chromatin structure and gene expression. With the exception of the catalytic component, the subunit composition of the Set1A and Set1B histone methyltransferase complexes are identical. Each complex contains six human homologs of the yeast Set1/COMPASS complex, including Set1A or Set1B, Ash2 (homologous to yeast Bre2), CXXC finger protein 1 (CFP1; homologous to yeast Spp1), Rbbp5 (homologous to yeast Swd1), Wdr5 (homologous to yeast Swd3), and Wdr82 (homologous to yeast Swd2). The genomic targeting of these complexes is determined by the identity of the catalytic subunit present in each histone methyltransferase complex. Thus, the Set1A and Set1B complexes may exhibit both overlapping and non-redundant properties. Both Set1A and Set1B contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), an N- SET domain, and a C-terminal catalytic SET domain followed by a post-SET domain. In contrast to Set1B, Set1A additionally contains an HCF-1 binding motif that interacts with HCF-1 in vivo. Pssm-ID: 409745 [Multi-domain] Cd Length: 93 Bit Score: 177.16 E-value: 7.88e-52
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| RRM_Set1A | cd12548 | RNA recognition motif in vertebrate histone-lysine N-methyltransferase Setd1A (Set1A); This ... |
101-195 | 1.40e-49 | ||||
RNA recognition motif in vertebrate histone-lysine N-methyltransferase Setd1A (Set1A); This subgroup corresponds to the RRM of Setd1A, also termed SET domain-containing protein 1A (Set1A), or lysine N-methyltransferase 2F, or Set1/Ash2 histone methyltransferase complex subunit Set1, a ubiquitously expressed vertebrates histone methyltransferase that exhibits high homology to yeast Set1. Set1A is localized to euchromatic nuclear speckles and associates with a complex containing six human homologs of the yeast Set1/COMPASS complex, including CXXC finger protein 1 (CFP1; homologous to yeast Spp1), Rbbp5 (homologous to yeast Swd1), Ash2 (homologous to yeast Bre2), Wdr5 (homologous to yeast Swd3), and Wdr82 (homologous to yeast Swd2). Set1A contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), an N- SET domain, and a C-terminal catalytic SET domain followed by a post-SET domain. In contrast to Set1B, Set1A additionally contains an HCF-1 binding motif that interacts with HCF-1 in vivo. Pssm-ID: 409964 [Multi-domain] Cd Length: 95 Bit Score: 170.92 E-value: 1.40e-49
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| SET_KMT2A | cd19206 | SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2A (KMT2A) ... |
1834-1966 | 1.14e-47 | ||||
SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2A (KMT2A) and similar proteins; KMT2A (EC2.1.1.43; also termed lysine N-methyltransferase 2A, ALL-1, CXXC-type zinc finger protein 7 (CXXC7), myeloid/lymphoid or mixed-lineage leukemia (MLL), myeloid/lymphoid or mixed-lineage leukemia protein 1 (MLL1), trithorax-like protein (TRX1), or zinc finger protein HRX) acts as a histone methyltransferase that plays an essential role in early development and hematopoiesis. It is a catalytic subunit of the MLL1/MLL complex, a multiprotein complex that mediates both methylation of 'Lys-4' of histone H3 (H3K4me) complex and acetylation of 'Lys-16' of histone H4 (H4K16ac). Pssm-ID: 380983 [Multi-domain] Cd Length: 154 Bit Score: 167.89 E-value: 1.14e-47
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| SET_KMT2B | cd19207 | SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2B (KMT2B) ... |
1834-1966 | 2.20e-42 | ||||
SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2B (KMT2B) and similar proteins; KMT2B (EC2.1.1.43; also termed lysine N-methyltransferase 2B, myeloid/lymphoid or mixed-lineage leukemia protein 4 (MLL2/MLL4), trithorax homolog 2 (TRX2), or WW domain-binding protein 7 (WBP-7)), acts as a histone methyltransferase that methylates 'Lys-4' of histone H3 (H3K4me). It is required during the transcriptionally active period of oocyte growth for the establishment and/or maintenance of bulk H3K4 trimethylation (H3K4me3), global transcriptional silencing that precedes resumption of meiosis, oocyte survival and normal zygotic genome activation. Pssm-ID: 380984 [Multi-domain] Cd Length: 154 Bit Score: 152.87 E-value: 2.20e-42
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| SET_KMT2C | cd19208 | SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2C (KMT2C) ... |
1834-1962 | 1.44e-37 | ||||
SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2C (KMT2C) and similar proteins; KMT2C (EC2.1.1.43; also termed lysine N-methyltransferase 2C, homologous to ALR protein (HALR) myeloid/lymphoid, or mixed-lineage leukemia protein 3 (MLL3)), acts as a histone methyltransferase that methylates 'Lys-4' of histone H3 (H3K4me) and may be involved in leukemogenesis and developmental disorder. KMT2C is a catalytic subunit of MLL2/3 complex, a coactivator complex of nuclear receptors, involved in transcriptional coactivation. Overexpression of KMT2C is associated with estrogen receptor-positive breast cancer; KMT2C mediates the estrogen dependence of breast cancer through regulation of estrogen receptor alpha (ERalpha) enhancer function. KMT2C is frequently mutated in certain populations with diffuse-type gastric adenocarcinomas (DGA); its loss promotes epithelial-to-mesenchymal transition (EMT) and is associated with worse overall survival. Pssm-ID: 380985 [Multi-domain] Cd Length: 154 Bit Score: 138.99 E-value: 1.44e-37
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| SET_SETD2-like | cd10531 | SET domain (including post-SET domain) found in SET domain-containing protein 2 (SETD2), ... |
1839-1962 | 1.98e-37 | ||||
SET domain (including post-SET domain) found in SET domain-containing protein 2 (SETD2), nuclear SETD2 (NSD2), ASH1-like protein (ASH1L) and similar proteins; This family includes SET domain-containing protein 2 (SETD2), nuclear SETD2 (NSD2) and ASH1-like protein (ASH1L), which function as histone-lysine N-methyltransferases. SETD2 specifically trimethylates 'Lys-36' of histone H3 (H3K36me3) using demethylated 'Lys-36' (H3K36me2) as substrate. NSD2 shows histone H3 'Lys-27' (H3K27me) methyltransferase activity. ASH1L specifically methylates 'Lys-36' of histone H3 (H3K36me). The family also includes Arabidopsis thaliana ASH1-related protein 3 (ASHR3) and similar proteins. Pssm-ID: 380929 Cd Length: 136 Bit Score: 137.77 E-value: 1.98e-37
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| SET_EZH | cd10519 | SET domain found in enhancer of zeste homolog 1 (EZH1), zeste homolog 2 (EZH2) and similar ... |
1834-1943 | 6.92e-37 | ||||
SET domain found in enhancer of zeste homolog 1 (EZH1), zeste homolog 2 (EZH2) and similar proteins; The family includes EZH1 and EZH2. EZH1 (EC 2.1.1.43; also termed ENX-2, or histone-lysine N-methyltransferase EZH1) is a catalytic subunit of the PRC2/EED-EZH1 complex, which methylates 'Lys-27' of histone H3, leading to transcriptional repression of the affected target gene. EZH2 (EC 2.1.1.43; also termed lysine N-methyltransferase 6, ENX-1, or histone-lysine N-methyltransferase EZH2) is a catalytic subunit of the PRC2/EED-EZH2 complex, which methylates 'Lys-9' (H3K9me) and 'Lys-27' (H3K27me) of histone H3, leading to transcriptional repression of the affected target gene. Both, EZH1 and EZH2, can mono-, di- and trimethylate 'Lys-27' of histone H3 to form H3K27me1, H3K27me2 and H3K27me3, respectively. Pssm-ID: 380917 Cd Length: 117 Bit Score: 135.45 E-value: 6.92e-37
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| SET | smart00317 | SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain; Putative methyl transferase, based on ... |
1834-1949 | 7.49e-37 | ||||
SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain; Putative methyl transferase, based on outlier plant homologues Pssm-ID: 214614 [Multi-domain] Cd Length: 124 Bit Score: 135.54 E-value: 7.49e-37
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| SET_SETD2 | cd19172 | SET domain (including post-SET domain) found in SET domain-containing protein 2 (SETD2) and ... |
1839-1965 | 3.44e-36 | ||||
SET domain (including post-SET domain) found in SET domain-containing protein 2 (SETD2) and similar proteins; SETD2 (also termed HIF-1, huntingtin yeast partner B, huntingtin-interacting protein 1 (HIP-1), huntingtin-interacting protein B, lysine N-methyltransferase 3A or protein-lysine N-methyltransferase SETD2) acts as histone-lysine N-methyltransferase that specifically trimethylates 'Lys-36' of histone H3 (H3K36me3) using demethylated 'Lys-36' (H3K36me2) as substrate. It has been shown that methylation is a posttranslational modification of dynamic microtubules and that SETD2 methylates alpha-tubulin at lysine 40, the same lysine that is marked by acetylation on microtubules. Methylation of microtubules occurs during mitosis and cytokinesis and can be ablated by SETD2 deletion, which causes mitotic spindle and cytokinesis defects, micronuclei, and polyploidy. Pssm-ID: 380949 [Multi-domain] Cd Length: 142 Bit Score: 134.63 E-value: 3.44e-36
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| N-SET | pfam11764 | COMPASS (Complex proteins associated with Set1p) component N; The n-SET or N-SET domain is a ... |
1679-1821 | 3.95e-35 | ||||
COMPASS (Complex proteins associated with Set1p) component N; The n-SET or N-SET domain is a component of the COMPASS complex, associated with SET1, conserved in yeasts and in other eukaryotes up to humans. The COMPASS complex functions to methylate the fourth lysine of Histone 3 and for the silencing of genes close to the telomeres of chromosomes. This domain promotes trimethylation in conjunction with an RRM domain and is necessary for binding of the Spp1 component of COMPASS into the complex. Pssm-ID: 463344 Cd Length: 172 Bit Score: 132.41 E-value: 3.95e-35
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| SET_KMT2D | cd19209 | SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2D (KMT2D) ... |
1834-1962 | 4.90e-35 | ||||
SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2D (KMT2D) and similar proteins; KMT2D (EC2.1.1.43; also termed lysine N-methyltransferase 2D, ALL1-related protein (ALR), or myeloid/lymphoid or mixed-lineage leukemia protein 2 (MLL2)), acts as histone methyltransferase that methylates 'Lys-4' of histone H3 (H3K4me). It is a coactivator for estrogen receptor by being recruited by ESR1, thereby activating transcription. KMT2D is a subunit of MLL2/3 complex, a coactivator complex of nuclear receptors, involved in transcriptional coactivation. Pssm-ID: 380986 [Multi-domain] Cd Length: 155 Bit Score: 131.74 E-value: 4.90e-35
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| SET_ASHR3-like | cd19175 | SET domain (including post-SET domain) found in Arabidopsis thaliana ASH1-related protein 3 ... |
1839-1965 | 1.77e-34 | ||||
SET domain (including post-SET domain) found in Arabidopsis thaliana ASH1-related protein 3 (ASHR3) and similar proteins; This family includes Arabidopsis thaliana ASH1-related protein 3 (ASHR3, also termed protein SET DOMAIN GROUP 4 or protein stamen loss), ASH1 homolog 3 (ASHH3, also termed protein SET DOMAIN GROUP 7) and homolog 4 (ASHH4, also termed protein SET DOMAIN GROUP 24). They all function as histone-lysine N-methyltransferases (EC 2.1.1.43). Pssm-ID: 380952 [Multi-domain] Cd Length: 139 Bit Score: 129.46 E-value: 1.77e-34
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| SET | COG2940 | SET domain-containing protein (function unknown) [General function prediction only]; |
1834-1964 | 9.24e-34 | ||||
SET domain-containing protein (function unknown) [General function prediction only]; Pssm-ID: 442183 [Multi-domain] Cd Length: 134 Bit Score: 127.39 E-value: 9.24e-34
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| SET_NSD | cd19173 | SET domain (including post-SET domain) found in nuclear SET domain-containing proteins, NSD1, ... |
1839-1965 | 7.96e-33 | ||||
SET domain (including post-SET domain) found in nuclear SET domain-containing proteins, NSD1, NSD2, NSD3 and similar proteins; The nuclear receptor-binding SET Domain (NSD) family of histone H3 lysine 36 methyltransferases is comprised of NSD1, NSD2, and NSD3, which are primarily known to be involved in chromatin integrity and gene expression through mono-, di-, or tri-methylating lysine 36 of histone H3 (H3K36), respectively. NSD1 (EC 2.1.1.43; also termed histone-lysine N-methyltransferase H3 lysine-36 and H4 lysine-20 specific, androgen receptor coactivator 267 kDa protein (ARA267), androgen receptor-associated protein of 267 kDa, H3-K36-HMTase, H4-K20-HMTase, lysine N-methyltransferase 3B (KMT3B) or NR-binding SET domain-containing protein 1) functions as a histone-lysine N-methyltransferase that preferentially methylates 'Lys-36' of histone H3 and 'Lys-20' of histone H4. NSD2 (EC 2.1.1.43; also termed multiple myeloma SET domain-containing protein (MMSET), protein trithorax-5 (TRX5), or wolf-Hirschhorn syndrome candidate 1 protein (WHSC1)) acts as histone-lysine N-methyltransferase with histone H3 'Lys-27' (H3K27me) methyltransferase activity. NSD3 (EC 2.1.1.43; also termed protein whistle, WHSC1-like 1 isoform 9 with methyltransferase activity to lysine, Wolf-Hirschhorn syndrome candidate 1-like protein 1 (WHSC1L1), or WHSC1-like protein 1) functions as a histone-lysine N-methyltransferase that preferentially methylates 'Lys-4' and 'Lys-27' of histone H3. Pssm-ID: 380950 [Multi-domain] Cd Length: 142 Bit Score: 124.73 E-value: 7.96e-33
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| SET | pfam00856 | SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be ... |
1839-1944 | 1.73e-29 | ||||
SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure. Pssm-ID: 459965 [Multi-domain] Cd Length: 115 Bit Score: 114.16 E-value: 1.73e-29
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| SET_ASH1L | cd19174 | SET domain (including post-SET domain) found in ASH1-like protein (ASH1L) and similar proteins; ... |
1839-1966 | 7.29e-29 | ||||
SET domain (including post-SET domain) found in ASH1-like protein (ASH1L) and similar proteins; ASH1L (EC 2.1.1.43; also termed absent small and homeotic disks protein 1 homolog, KMT2H, or lysine N-methyltransferase 2H) acts as histone-lysine N-methyltransferase that specifically methylates 'Lys-36' of histone H3 (H3K36me). It plays important roles in development; heterozygous mutation of ASH1L is associated with severe intellectual disability (ID) and multiple congenital anomaly (MCA). Pssm-ID: 380951 [Multi-domain] Cd Length: 141 Bit Score: 113.54 E-value: 7.29e-29
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| SET_SUV39H | cd10542 | SET domain (including pre-SET and post-SET domains) found in suppressor of variegation 3-9 ... |
1839-1965 | 7.66e-27 | ||||
SET domain (including pre-SET and post-SET domains) found in suppressor of variegation 3-9 homologs, SUV39H1, SUV39H2 and similar proteins; This family includes SUV39H1 (also termed histone H3-K9 methyltransferase 1, H3-K9-HMTase 1, lysine N-methyltransferase 1A, KMT1A, position-effect variegation 3-9 homolog, SUV39H, or Su(var)3-9 homolog 1) and SUV39H2 (also termed histone H3-K9 methyltransferase 2, H3-K9-HMTase 2, lysine N-methyltransferase 1B, KMT1B, or Su(var)3-9 homolog 2), both act as histone-lysine N-methyltransferases that specifically trimethylate 'Lys-9' of histone H3 (H3K9me3) using monomethylated H3 'Lys-9' as substrate. They mainly function in heterochromatin regions, thereby playing central roles in the establishment of constitutive heterochromatin at pericentric and telomere regions. Also included are Schizosaccharomyces pombe H3K9 methyltransferase Clr4 (SUV39H homolog) and Neurospora crassa DIM-5, both of which also methylate 'Lys-9' of histone H3. Pssm-ID: 380940 [Multi-domain] Cd Length: 245 Bit Score: 111.23 E-value: 7.66e-27
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| SET_EZH2 | cd19218 | SET domain found in enhancer of zeste homolog 2 (EZH2) and similar proteins; EZH2 (EC 2.1.1.43) ... |
1834-1945 | 1.23e-25 | ||||
SET domain found in enhancer of zeste homolog 2 (EZH2) and similar proteins; EZH2 (EC 2.1.1.43), also termed lysine N-methyltransferase 6, or ENX-1, or histone-lysine N-methyltransferase EZH2, is a catalytic subunit of the polycomb repressive complex 2 (PRC2)/EED-EZH2 complex, which methylates 'Lys-9' (H3K9me) and 'Lys-27' (H3K27me) of histone H3, leading to transcriptional repression of the affected target gene. It can mono-, di- and trimethylate 'Lys-27' of histone H3 to form H3K27me1, H3K27me2 and H3K27me3, respectively. PRC2 is involved in several cancers; EZH2 is overexpressed in breast, liver and prostate cancer, while point mutations in EZH2 alter the substrate preference and product specificity of PRC2 in Non-Hodgkin lymphomas (NHLs). Thus, PRC2 is a popular target for cancer therapeutics. Pssm-ID: 380995 Cd Length: 120 Bit Score: 103.45 E-value: 1.23e-25
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| SET_EZH1 | cd19217 | SET domain found in enhancer of zeste homolog 1 (EZH1) and similar proteins; EZH1 (EC 2.1.1.43) ... |
1834-1949 | 2.62e-24 | ||||
SET domain found in enhancer of zeste homolog 1 (EZH1) and similar proteins; EZH1 (EC 2.1.1.43), also termed ENX-2, or histone-lysine N-methyltransferase EZH1, is a catalytic subunit of the PRC2/EED-EZH1 complex, which methylates 'Lys-27' of histone H3, leading to transcriptional repression of the affected target gene. It can mono-, di- and trimethylate 'Lys-27' of histone H3 to form H3K27me1, H3K27me2 and H3K27me3, respectively. Pssm-ID: 380994 Cd Length: 136 Bit Score: 100.53 E-value: 2.62e-24
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| SET_NSD2 | cd19211 | SET domain (including post-SET domain) found in nuclear SET domain-containing protein 2 (NSD2) ... |
1839-1965 | 1.35e-23 | ||||
SET domain (including post-SET domain) found in nuclear SET domain-containing protein 2 (NSD2) and similar proteins; NSD2 (EC 2.1.1.43; also termed multiple myeloma SET domain-containing protein (MMSET), protein trithorax-5 (TRX5), or wolf-Hirschhorn syndrome candidate 1 protein (WHSC1)) acts as histone-lysine N-methyltransferase with histone H3 'Lys-36' (H3K36me) methyltransferase activity. NSD2 has been shown to mediate di- and trimethylation of H3K36 and dimethylation of H4K20 in different systems, and has been characterized as a transcriptional repressor interacting with histone deacetylase HDAC1 and histone demethylase LSD1. NSD2 mediates constitutive NF-kappaB signaling for cancer cell proliferation, survival and tumor growth. It is highly overexpressed in several types of human cancers, including small-cell lung cancers, neuroblastoma, carcinomas of stomach and colon, and bladder cancers, and its overexpression tends to be associated with tumor aggressiveness. WHSC1 is frequently deleted in Wolf-Hirschhorn syndrome (WHS). Pssm-ID: 380988 [Multi-domain] Cd Length: 142 Bit Score: 98.52 E-value: 1.35e-23
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| SET_SETDB-like | cd10538 | SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1) ... |
1839-1943 | 1.06e-22 | ||||
SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1) and 2 (SETDB2), suppressor of variegation 3-9 homologs, SUV39H1 and SUV39H2, euchromatic histone-lysine N-methyltransferase EHMT1 and EHMT2, and similar proteins; The family includes SET domain bifurcated 1 (SETDB1) and 2 (SETDB2), suppressor of variegation 3-9 homologs, SUV39H1 and SUV39H2, euchromatic histone-lysine N-methyltransferase EHMT1 and EHMT2. SETDB1 (EC 2.1.1.43; also termed ERG-associated protein with SET domain (ESET), histone H3-K9 methyltransferase 4, H3-K9-HMTase 4, or lysine N-methyltransferase 1E (KMT1E)) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). It mainly functions in euchromatin regions, thereby playing a central role in the silencing of euchromatic genes. SETDB2 (EC 2.1.1.43; also termed chronic lymphocytic leukemia deletion region gene 8 protein (CLLD8), or lysine N-methyltransferase 1F (KMT1F)) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). It is involved in left-right axis specification in early development and mitosis. SUV39H1 (also termed histone H3-K9 methyltransferase 1, H3-K9-HMTase 1, lysine N-methyltransferase 1A, KMT1A, position-effect variegation 3-9 homolog, SUV39H, or Su(var)3-9 homolog 1) and SUV39H2 (also termed histone H3-K9 methyltransferase 2, H3-K9-HMTase 2, lysine N-methyltransferase 1B, KMT1B, or Su(var)3-9 homolog 2), both act as histone-lysine N-methyltransferases that specifically trimethylate 'Lys-9' of histone H3 (H3K9me3) using monomethylated H3 'Lys-9' as substrate. They mainly function in heterochromatin regions, thereby playing central roles in the establishment of constitutive heterochromatin at pericentric and telomere regions. EHMT1 (also termed Eu-HMTase1, G9a-like protein 1, GLP, GLP1, histone H3-K9 methyltransferase 5, H3-K9-HMTase 5, lysine N-methyltransferase 1D, or KMT1D) and EHMT2 (also termed Eu-HMTase2, HLA-B-associated transcript 8, histone H3-K9 methyltransferase 3, H3-K9-HMTase 3, lysine N-methyltransferase 1C, KMT1C, or protein G9a), both act as histone-lysine N-methyltransferases that specifically mono- and dimethylate 'Lys-9' of histone H3 (H3K9me1 and H3K9me2, respectively) in euchromatin. This family also includes the pre-SET domain, which is found in a number of histone methyltransferases (HMTase), N-terminal to the SET domain. Pre-SET domain is a zinc binding motif which contains 9 conserved cysteines that coordinate three zinc ions. It is thought that this region plays a structural role in stabilizing SET domains. Most family members, except for Arabidopsis thaliana SUVH9, contain a post-SET domain which harbors a zinc-binding site. Pssm-ID: 380936 [Multi-domain] Cd Length: 217 Bit Score: 98.60 E-value: 1.06e-22
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| SET_NSD3 | cd19212 | SET domain (including post-SET domain) found in nuclear receptor-binding SET domain-containing ... |
1839-1965 | 1.33e-22 | ||||
SET domain (including post-SET domain) found in nuclear receptor-binding SET domain-containing protein 3 (NSD3) and similar proteins; NSD3 (EC 2.1.1.43; also termed protein whistle, WHSC1-like 1 isoform 9 with methyltransferase activity to lysine, Wolf-Hirschhorn syndrome candidate 1-like protein 1 (WHSC1L1), or WHSC1-like protein 1) functions as a histone-lysine N-methyltransferase that preferentially methylates 'Lys-4' and 'Lys-27' of histone H3. NSD3 is amplified and overexpressed in multiple cancer types, including acute myeloid leukemia (AML), breast, lung, pancreatic and bladder cancers, as well as squamous cell carcinoma of the head and neck (SCCHN). NSD3 contributes to tumorigenesis by interacting with bromodomain-containing protein 4 (BRD4), the bromodomain and extraterminal (BET) protein, which is a potential therapeutic target in acute myeloid leukemia (AML). NSD3 is amplified in primary tumors and cell lines from breast carcinoma, and can promote the cell viability of small-cell lung cancer and pancreatic ductal adenocarcinoma. High NSD3 expression is implicated in poor grade and heavy smoking history in SCCHN. Thus, NSD3 may serve as a potential druggable target for selective cancer therapy. Pssm-ID: 380989 [Multi-domain] Cd Length: 142 Bit Score: 95.76 E-value: 1.33e-22
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| SET_NSD1 | cd19210 | SET domain (including post-SET domain) found in nuclear receptor-binding SET domain-containing ... |
1839-1965 | 1.01e-21 | ||||
SET domain (including post-SET domain) found in nuclear receptor-binding SET domain-containing protein 1 (NSD1) and similar proteins; NSD1 (EC 2.1.1.43; also termed Histone-lysine N-methyltransferase H3 lysine-36 and H4 lysine-20 specific, androgen receptor coactivator 267 kDa protein (ARA267), androgen receptor-associated protein of 267 kDa, H3-K36-HMTase, H4-K20-HMTase, lysine N-methyltransferase 3B (KMT3B), or NR-binding SET domain-containing protein 1) functions as a histone-lysine N-methyltransferase that preferentially methylates 'Lys-36' of histone H3 and 'Lys-20' of histone H4. NSD1 is altered in approximately 10% of head and neck cancer patients with 55% decrease in risk of death in NSD1-mutated versus non-mutated patients; its disruption promotes favorable chemotherapeutic responses linked to hypomethylation. Pssm-ID: 380987 [Multi-domain] Cd Length: 142 Bit Score: 93.07 E-value: 1.01e-21
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| SET_LegAS4-like | cd10522 | SET domain found in Legionella pneumophila type IV secretion system effector LegAS4 and ... |
1840-1943 | 2.29e-21 | ||||
SET domain found in Legionella pneumophila type IV secretion system effector LegAS4 and similar proteins; LegAS4 is a type IV secretion system effector of Legionella pneumophila. It contains a SET domain that is involved in the modification of Lys4 of histone H3 (H3K4) in the nucleolus of the host cell, thereby enhancing heterochromatic rDNA transcription. It also contains an ankyrin repeat domain of unknown function at its C-terminal region. Pssm-ID: 380920 [Multi-domain] Cd Length: 122 Bit Score: 91.25 E-value: 2.29e-21
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| SET_SETDB1 | cd10517 | SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1) ... |
1839-1965 | 1.48e-19 | ||||
SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1) and similar proteins; SETDB1 (EC 2.1.1.43; also termed ERG-associated protein with SET domain (ESET), histone H3-K9 methyltransferase 4, H3-K9-HMTase 4, or lysine N-methyltransferase 1E (KMT1E)) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). It mainly functions in euchromatin regions, thereby playing a central role in the silencing of euchromatic genes. Pssm-ID: 380915 [Multi-domain] Cd Length: 288 Bit Score: 91.20 E-value: 1.48e-19
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| SET_SETMAR | cd10544 | SET domain (including pre-SET and post-SET domains) found in SET domain and mariner ... |
1839-1965 | 2.81e-19 | ||||
SET domain (including pre-SET and post-SET domains) found in SET domain and mariner transposase fusion protein (SETMAR) and similar proteins; SETMAR (also termed metnase) is a DNA-binding protein that is indirectly recruited to sites of DNA damage through protein-protein interactions. It has a sequence-specific DNA-binding activity recognizing the 19-mer core of the 5'-terminal inverted repeats (TIRs) of the Hsmar1 element and displays a DNA nicking and end joining activity. SETMAR also acts as a histone-lysine N-methyltransferase that methylates 'Lys-4' and 'Lys-36' of histone H3. It specifically mediates dimethylation of H3 'Lys-36' at sites of DNA double-strand break and may recruit proteins required for efficient DSB repair through non-homologous end-joining. Pssm-ID: 380942 [Multi-domain] Cd Length: 254 Bit Score: 89.67 E-value: 2.81e-19
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| SET_SETD8 | cd10528 | SET domain found in SET domain-containing protein 8 (SETD8) and similar proteins; SETD8 (EC 2. ... |
1840-1943 | 3.43e-19 | ||||
SET domain found in SET domain-containing protein 8 (SETD8) and similar proteins; SETD8 (EC 2.1.1.43; also termed N-lysine methyltransferase KMT5A, H4-K20-HMTase KMT5A, lysine N-methyltransferase 5A, lysine-specific methylase 5A, PR/SET domain-containing protein 07, PR-Set7 or PR/SET07) is a nucleosomal histone-lysine N-methyltransferase that specifically monomethylates 'Lys-20' of histone H4 (H4K20me1). It plays a central role in the silencing of euchromatic genes. Pssm-ID: 380926 [Multi-domain] Cd Length: 141 Bit Score: 85.71 E-value: 3.43e-19
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| SET_SETD5-like | cd10529 | SET domain found in SET domain-containing protein 5 (SETD5), inactive histone-lysine ... |
1840-1943 | 1.95e-18 | ||||
SET domain found in SET domain-containing protein 5 (SETD5), inactive histone-lysine N-methyltransferase 2E (KMT2E) and similar proteins; SETD5 is a probable transcriptional regulator that acts via the formation of large multiprotein complexes that modify and/or remodel the chromatin. KMT2E (also termed inactive lysine N-methyltransferase 2E or myeloid/lymphoid or mixed-lineage leukemia protein 5 (MLL5)) associates with chromatin regions downstream of transcriptional start sites of active genes and thus regulates gene transcription. The family also includes Saccharomyces cerevisiae SET domain-containing proteins, SET3 and SET4, and Schizosaccharomyces pombe SET3. Most of these family members contain a post-SET domain which harbors a zinc-binding site. Pssm-ID: 380927 Cd Length: 127 Bit Score: 83.09 E-value: 1.95e-18
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| SET_EHMT | cd10543 | SET domain (including pre-SET and post-SET domains) found in euchromatic histone-lysine ... |
1839-1962 | 2.70e-18 | ||||
SET domain (including pre-SET and post-SET domains) found in euchromatic histone-lysine N-methyltransferase EHMT1, EHMT2 and similar proteins; This family includes EHMT1 (also termed Eu-HMTase1, G9a-like protein 1, GLP, GLP1, histone H3-K9 methyltransferase 5, H3-K9-HMTase 5, lysine N-methyltransferase 1D, or KMT1D) and EHMT2 (also termed Eu-HMTase2, HLA-B-associated transcript 8, histone H3-K9 methyltransferase 3, H3-K9-HMTase 3, lysine N-methyltransferase 1C, KMT1C, or protein G9a), both act as histone-lysine N-methyltransferases that specifically mono- and dimethylate 'Lys-9' of histone H3 (H3K9me1 and H3K9me2, respectively) in euchromatin. Pssm-ID: 380941 [Multi-domain] Cd Length: 231 Bit Score: 85.85 E-value: 2.70e-18
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| SET_EZH-like | cd19168 | SET domain found in enhancer of zeste homolog 1 (EZH1) and zeste homolog 2 (EZH2) of polycomb ... |
1834-1943 | 5.89e-18 | ||||
SET domain found in enhancer of zeste homolog 1 (EZH1) and zeste homolog 2 (EZH2) of polycomb repressive complex 2 (PRC2), and similar proteins; The family includes EZH1 and EZH2. EZH1 (EC 2.1.1.43; also termed ENX-2, or histone-lysine N-methyltransferase EZH1) is a catalytic subunit of the PRC2/EED-EZH1 complex, which methylates 'Lys-27' of histone H3, leading to transcriptional repression of the affected target gene. EZH2 (EC 2.1.1.43; also termed lysine N-methyltransferase 6, ENX-1, or histone-lysine N-methyltransferase EZH2) is a catalytic subunit of the PRC2/EED-EZH2 complex, which methylates 'Lys-9' (H3K9me) and 'Lys-27' (H3K27me) of histone H3, leading to transcriptional repression of the affected target gene. Both EZH1 and EZH2 can mono-, di- and trimethylate 'Lys-27' of histone H3 to form H3K27me1, H3K27me2 and H3K27me3, respectively. PRC2 is involved in several cancers; EZH2 is overexpressed in breast, liver and prostate cancer, while point mutations in EZH2 alter the substrate preference and product specificity of PRC2 in Non-Hodgkin lymphomas (NHLs). Thus, PRC2 is a popular target for cancer therapeutics. Pssm-ID: 380945 Cd Length: 124 Bit Score: 81.85 E-value: 5.89e-18
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| SET_SUV39H2 | cd10532 | SET domain (including pre-SET and post-SET domains) found in suppressor of variegation 3-9 ... |
1839-1965 | 8.24e-18 | ||||
SET domain (including pre-SET and post-SET domains) found in suppressor of variegation 3-9 homolog 2 (SUV39H2) and similar proteins; SUV39H2 (EC 2.1.1.43; also termed histone H3-K9 methyltransferase 2, H3-K9-HMTase 2, lysine N-methyltransferase 1B (KMT1B), or Su(var)3-9 homolog 2) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3) using monomethylated H3 'Lys-9' as substrate. It mainly functions in heterochromatin regions, thereby playing a central role in the establishment of constitutive heterochromatin at pericentric and telomere regions. Pssm-ID: 380930 [Multi-domain] Cd Length: 243 Bit Score: 84.94 E-value: 8.24e-18
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| SET_SUV39H_Clr4-like | cd20073 | SET domain (including pre-SET and post-SET domains) found in of Schizosaccharomyces pombe H3K9 ... |
1839-1965 | 1.42e-17 | ||||
SET domain (including pre-SET and post-SET domains) found in of Schizosaccharomyces pombe H3K9 methyltransferase Clr4, and similar proteins; This subfamily contains fission yeast Schizosaccharomyces pombe H3K9 methyltransferase Clr4 (also known as Suv39h), the sole homolog of the mammalian SUV39H1 and SUV39H2 enzymes, that has a critical role in preventing aberrant heterochromatin formation. It is known to di- and tri-methylate Lys-9 of histone H3, a central heterochromatic histone modification, with its specificity profile most similar to that of the human SUV39H2 homolog. Pssm-ID: 380999 [Multi-domain] Cd Length: 259 Bit Score: 84.55 E-value: 1.42e-17
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| SET_EHMT1 | cd10535 | SET domain (including pre-SET and post-SET domains) found in euchromatic histone-lysine ... |
1838-1962 | 2.21e-17 | ||||
SET domain (including pre-SET and post-SET domains) found in euchromatic histone-lysine N-methyltransferase 1 (EHMT1) and similar proteins; EHMT1 (also termed Eu-HMTase1, G9a-like protein 1, GLP, GLP1, histone H3-K9 methyltransferase 5, H3-K9-HMTase 5, or lysine N-methyltransferase 1D (KMT1D)) acts as a histone-lysine N-methyltransferase that specifically mono- and dimethylates 'Lys-9' of histone H3 (H3K9me1 and H3K9me2, respectively) in euchromatin. Pssm-ID: 380933 [Multi-domain] Cd Length: 231 Bit Score: 83.44 E-value: 2.21e-17
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| SET_SUV39H1 | cd10525 | SET domain (including pre-SET and post-SET domains) found in suppressor of variegation 3-9 ... |
1839-1965 | 4.54e-16 | ||||
SET domain (including pre-SET and post-SET domains) found in suppressor of variegation 3-9 homolog 1 (SUV39H1) and similar proteins; SUV39H1 (EC 2.1.1.43; also termed histone H3-K9 methyltransferase 1, H3-K9-HMTase 1, lysine N-methyltransferase 1A (KMT1A), position-effect variegation 3-9 homolog (SUV39H), or Su(var)3-9 homolog 1) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3) using monomethylated H3 'Lys-9' as substrate. It mainly functions in heterochromatin regions, thereby playing a central role in the establishment of constitutive heterochromatin at pericentric and telomere regions. Pssm-ID: 380923 [Multi-domain] Cd Length: 255 Bit Score: 80.32 E-value: 4.54e-16
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| SET_SpSET3-like | cd19183 | SET domain (including post-SET domain) found in Schizosaccharomyces pombe SET ... |
1834-1947 | 5.07e-16 | ||||
SET domain (including post-SET domain) found in Schizosaccharomyces pombe SET domain-containing protein 3 (SETD3) and similar proteins; Schizosaccharomyces pombe SETD3 functions as a transcriptional regulator that acts via the formation of large multiprotein complexes that modify and/or remodel the chromatin. It is required for both, gene activation and repression. Pssm-ID: 380960 Cd Length: 173 Bit Score: 77.83 E-value: 5.07e-16
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| SET_EHMT2 | cd10533 | SET domain (including pre-SET and post-SET domains) found in euchromatic histone-lysine ... |
1839-1962 | 6.08e-16 | ||||
SET domain (including pre-SET and post-SET domains) found in euchromatic histone-lysine N-methyltransferase 2 (EHMT2) and similar proteins; EHMT2 (also termed Eu-HMTase2, HLA-B-associated transcript 8, histone H3-K9 methyltransferase 3, H3-K9-HMTase 3, lysine N-methyltransferase 1C (KMT1C), or protein G9a) acts as a histone-lysine N-methyltransferase that specifically mono- and dimethylates 'Lys-9' of histone H3 (H3K9me1 and H3K9me2, respectively) in euchromatin. Pssm-ID: 380931 [Multi-domain] Cd Length: 239 Bit Score: 79.29 E-value: 6.08e-16
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| SET_SETDB2 | cd10523 | SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 2 (SETDB2) ... |
1887-1965 | 1.79e-14 | ||||
SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 2 (SETDB2) and similar proteins; SETDB2 (EC 2.1.1.43; also termed chronic lymphocytic leukemia deletion region gene 8 protein (CLLD8), or lysine N-methyltransferase 1F (KMT1F)) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). It is involved in left-right axis specification in early development and mitosis. Pssm-ID: 380921 [Multi-domain] Cd Length: 266 Bit Score: 75.64 E-value: 1.79e-14
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| SET | cd08161 | SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily; The Su(var)3-9, ... |
1834-1943 | 7.25e-14 | ||||
SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily; The Su(var)3-9, Enhancer-of-zeste, Trithorax (SET) domain superfamily corresponds to SET domain-containing lysine methyltransferases, which catalyze site and state-specific methylation of lysine residues in histones that are fundamental in epigenetic regulation of gene activation and silencing in eukaryotic organisms. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains has been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as N-SET and C-SET. C-SET forms an unusual and conserved knot-like structure of probable functional importance. In addition to N-SET and C-SET, an insert region (I-SET) and flanking regions of high structural variability form part of the overall structure. Some family members contain a pre-SET domain, which is found in a number of histone methyltransferases (HMTase), and a post-SET domain, which harbors a zinc-binding site. Pssm-ID: 380914 [Multi-domain] Cd Length: 72 Bit Score: 68.05 E-value: 7.25e-14
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| RRM | smart00360 | RNA recognition motif; |
110-176 | 2.60e-13 | ||||
RNA recognition motif; Pssm-ID: 214636 [Multi-domain] Cd Length: 73 Bit Score: 66.46 E-value: 2.60e-13
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| SET_SETDB | cd10541 | SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1), ... |
1839-1965 | 2.60e-13 | ||||
SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1), SET domain bifurcated 2 (SETDB2), and similar proteins; SETDB1 (EC 2.1.1.43; also termed ERG-associated protein with SET domain (ESET), histone H3-K9 methyltransferase 4, H3-K9-HMTase 4, or lysine N-methyltransferase 1E (KMT1E)) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). It mainly functions in euchromatin regions, thereby playing a central role in the silencing of euchromatic genes. SETDB2 (EC 2.1.1.43; also termed chronic lymphocytic leukemia deletion region gene 8 protein (CLLD8), or lysine N-methyltransferase 1F (KMT1F)) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). It is involved in left-right axis specification in early development and mitosis. Pssm-ID: 380939 [Multi-domain] Cd Length: 236 Bit Score: 71.42 E-value: 2.60e-13
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| RRM_SF | cd00590 | RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ... |
110-177 | 4.58e-12 | ||||
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs). Pssm-ID: 409669 [Multi-domain] Cd Length: 72 Bit Score: 63.07 E-value: 4.58e-12
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| SET_AtSUVH-like | cd10545 | SET domain found in Arabidopsis thaliana histone H3-K9 methyltransferases (SUVHs) and similar ... |
1839-1943 | 7.27e-12 | ||||
SET domain found in Arabidopsis thaliana histone H3-K9 methyltransferases (SUVHs) and similar proteins; Arabidopsis thaliana SUVH protein (also termed suppressor of variegation 3-9 homolog protein) is a histone-lysine N-methyltransferase that methylates 'Lys-9' of histone H3. H3 'Lys-9' methylation represents a specific tag for epigenetic transcriptional repression. Some family members contain a post-SET domain which binds a Zn2+ ion. Most family members, except for Arabidopsis thaliana SUVH9, contain a post-SET domain which harbors a zinc-binding site. Pssm-ID: 380943 [Multi-domain] Cd Length: 232 Bit Score: 67.04 E-value: 7.27e-12
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| SET_SUV39H_DIM5-like | cd19473 | SET domain (including pre-SET domain) found in Neurospora crassa (DIM-5) and similar proteins; ... |
1838-1965 | 4.80e-10 | ||||
SET domain (including pre-SET domain) found in Neurospora crassa (DIM-5) and similar proteins; This subfamily contains Neurospora crassa DIM-5 (also termed H3-K9-HMTase dim-5, or HKMT) which functions as histone-lysine N-methyltransferase that specifically trimethylates histone H3 to form H3K9me3. Pssm-ID: 380996 [Multi-domain] Cd Length: 274 Bit Score: 62.72 E-value: 4.80e-10
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| RRM_1 | pfam00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ... |
96-175 | 3.76e-09 | ||||
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease. Pssm-ID: 425453 [Multi-domain] Cd Length: 70 Bit Score: 54.93 E-value: 3.76e-09
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| RRM_FOX1_like | cd12407 | RNA recognition motif (RRM) found in vertebrate RNA binding protein fox-1 homologs and similar ... |
115-180 | 2.08e-08 | ||||
RNA recognition motif (RRM) found in vertebrate RNA binding protein fox-1 homologs and similar proteins; This subfamily corresponds to the RRM of several tissue-specific alternative splicing isoforms of vertebrate RNA binding protein Fox-1 homologs, which show high sequence similarity to the Caenorhabditis elegans feminizing locus on X (Fox-1) gene encoding Fox-1 protein. RNA binding protein Fox-1 homolog 1 (RBFOX1), also termed ataxin-2-binding protein 1 (A2BP1), or Fox-1 homolog A, or hexaribonucleotide-binding protein 1 (HRNBP1), is predominantly expressed in neurons, skeletal muscle and heart. It regulates alternative splicing of tissue-specific exons by binding to UGCAUG elements. Moreover, RBFOX1 binds to the C-terminus of ataxin-2 and forms an ataxin-2/A2BP1 complex involved in RNA processing. RNA binding protein fox-1 homolog 2 (RBFOX2), also termed Fox-1 homolog B, or hexaribonucleotide-binding protein 2 (HRNBP2), or RNA-binding motif protein 9 (RBM9), or repressor of tamoxifen transcriptional activity, is expressed in ovary, whole embryo, and human embryonic cell lines in addition to neurons and muscle. RBFOX2 activates splicing of neuron-specific exons through binding to downstream UGCAUG elements. RBFOX2 also functions as a repressor of tamoxifen activation of the estrogen receptor. RNA binding protein Fox-1 homolog 3 (RBFOX3 or NeuN or HRNBP3), also termed Fox-1 homolog C, is a nuclear RNA-binding protein that regulates alternative splicing of the RBFOX2 pre-mRNA, producing a message encoding a dominant negative form of the RBFOX2 protein. Its message is detected exclusively in post-mitotic regions of embryonic brain. Like RBFOX1, both RBFOX2 and RBFOX3 bind to the hexanucleotide UGCAUG elements and modulate brain and muscle-specific splicing of exon EIIIB of fibronectin, exon N1 of c-src, and calcitonin/CGRP. Members in this family also harbor one RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Pssm-ID: 409841 [Multi-domain] Cd Length: 76 Bit Score: 52.79 E-value: 2.08e-08
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| RRM_SAFB_like | cd12417 | RNA recognition motif (RRM) found in the scaffold attachment factor (SAFB) family; This ... |
110-177 | 1.29e-07 | ||||
RNA recognition motif (RRM) found in the scaffold attachment factor (SAFB) family; This subfamily corresponds to the RRM domain of the SAFB family, including scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), SAFB-like transcriptional modulator (SLTM), and similar proteins, which are ubiquitously expressed. SAFB1, SAFB2 and SLTM have been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. They share high sequence similarities and all contain a scaffold attachment factor-box (SAF-box, also known as SAP domain) DNA-binding motif, an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region rich in glutamine and arginine residues. SAFB1 is a nuclear protein with a distribution similar to that of SLTM, but unlike that of SAFB2, which is also found in the cytoplasm. To a large extent, SAFB1 and SLTM might share similar functions, such as the inhibition of an oestrogen reporter gene. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1 and SLTM. Pssm-ID: 409851 [Multi-domain] Cd Length: 74 Bit Score: 50.72 E-value: 1.29e-07
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| SET_SETD5 | cd19181 | SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and ... |
1841-1961 | 1.39e-07 | ||||
SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins; SETD5 is a probable transcriptional regulator that acts via the formation of large multiprotein complexes that modify and/or remodel the chromatin. SETD5 loss-of-function mutations are a likely cause of a familial syndromic intellectual disability with variable phenotypic expression. Pssm-ID: 380958 Cd Length: 150 Bit Score: 52.70 E-value: 1.39e-07
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| RRM_RBMX_like | cd12382 | RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y ... |
102-181 | 4.93e-07 | ||||
RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA recognition motif 1 (hRBMY), testis-specific heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T) and similar proteins; This subfamily corresponds to the RRM domain of hnRNP G, also termed glycoprotein p43 or RBMX, an RNA-binding motif protein located on the X chromosome. It is expressed ubiquitously and has been implicated in the splicing control of several pre-mRNAs. Moreover, hnRNP G may function as a regulator of transcription for SREBP-1c and GnRH1. Research has shown that hnRNP G may also act as a tumor-suppressor since it upregulates the Txnip gene and promotes the fidelity of DNA end-joining activity. In addition, hnRNP G appears to play a critical role in proper neural development of zebrafish and frog embryos. The family also includes several paralogs of hnRNP G, such as hRBMY and hnRNP G-T (also termed RNA-binding motif protein, X-linked-like-2). Both, hRBMY and hnRNP G-T, are exclusively expressed in testis and critical for male fertility. Like hnRNP G, hRBMY and hnRNP G-T interact with factors implicated in the regulation of pre-mRNA splicing, such as hTra2-beta1 and T-STAR. Although members in this family share a high conserved N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), they appear to recognize different RNA targets. For instance, hRBMY interacts specifically with a stem-loop structure in which the loop is formed by the sequence CA/UCAA. In contrast, hnRNP G associates with single stranded RNA sequences containing a CCA/C motif. In addition to the RRM, hnRNP G contains a nascent transcripts targeting domain (NTD) in the middle region and a novel auxiliary RNA-binding domain (RBD) in its C-terminal region. The C-terminal RBD exhibits distinct RNA binding specificity, and would play a critical role in the regulation of alternative splicing by hnRNP G. Pssm-ID: 409816 [Multi-domain] Cd Length: 80 Bit Score: 48.94 E-value: 4.93e-07
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| SET_SMYD | cd20071 | SET domain (including SET domain and post-SET domain) found in SET and MYND domain-containing ... |
1903-1943 | 6.71e-07 | ||||
SET domain (including SET domain and post-SET domain) found in SET and MYND domain-containing protein, and similar proteins; The family includes SET and MYND domain-containing proteins, SMYD1-SYMD5. SMYD1 (EC 2.1.1.43; also termed BOP) is a heart and muscle specific SET-MYND domain containing protein, which functions as a histone methyltransferase and regulates downstream gene transcription. It methylates histone H3 at 'Lys-4' (H3K4me), seems able to perform both mono-, di-, and trimethylation. SMYD2 (also termed HSKM-B, or lysine N-methyltransferase 3C (KMT3C)) functions as a histone methyltransferase that methylates both histones and non-histone proteins, including p53/TP53 and RB1. It specifically methylates histone H3 'Lys-4' (H3K4me) and dimethylates histone H3 'Lys-36' (H3K36me2). SMYD3 (also termed zinc finger MYND domain-containing protein 1) functions as a histone methyltransferase that specifically methylates 'Lys-4' of histone H3, inducing di- and tri-methylation, but not monomethylation. It also methylates 'Lys-5' of histone H4. SMYD3 plays an important role in transcriptional activation as a member of an RNA polymerase complex. SMYD4 functions as a potential tumor suppressor that plays a critical role in breast carcinogenesis at least partly through inhibiting the expression of PDGFR-alpha. SMYD5 (also termed protein NN8-4AG, or retinoic acid-induced protein 15) functions as histone lysine methyltransferase that mediates H4K20me3 at heterochromatin regions. Pssm-ID: 380997 [Multi-domain] Cd Length: 122 Bit Score: 50.07 E-value: 6.71e-07
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| RRM3_Prp24 | cd12298 | RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar ... |
103-178 | 3.04e-06 | ||||
RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins; This subfamily corresponds to the RRM3 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. Pssm-ID: 409739 [Multi-domain] Cd Length: 78 Bit Score: 46.87 E-value: 3.04e-06
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| SET_Suv4-20-like | cd10524 | SET domain (including post-SET domain) found in Drosophila melanogaster suppressor of ... |
1901-1943 | 3.53e-06 | ||||
SET domain (including post-SET domain) found in Drosophila melanogaster suppressor of variegation 4-20 (Suv4-20) and similar proteins; Suv4-20 (also termed Su(var)4-20) is a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-20' of histone H4. It acts as a dominant suppressor of position-effect variegation. The family also includes Suv4-20 homologs, lysine N-methyltransferase 5B (KMT5B) and lysine N-methyltransferase 5C (KMT5C). Both KMT5B (also termed lysine-specific methyltransferase 5B, or suppressor of variegation 4-20 homolog 1, or Su(var)4-20 homolog 1, or Suv4-20h1) and KMT5C (also termed lysine-specific methyltransferase 5C, or suppressor of variegation 4-20 homolog 2, or Su(var)4-20 homolog 2, or Suv4-20h2) are histone methyltransferases that specifically trimethylate 'Lys-20' of histone H4 (H4K20me3). They play central roles in the establishment of constitutive heterochromatin in pericentric heterochromatin regions. Pssm-ID: 380922 [Multi-domain] Cd Length: 141 Bit Score: 48.43 E-value: 3.53e-06
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| RRM_spSet1p_like | cd12303 | RNA recognition motif in fission yeast Schizosaccharomyces pombe SET domain-containing protein ... |
123-182 | 5.31e-06 | ||||
RNA recognition motif in fission yeast Schizosaccharomyces pombe SET domain-containing protein 1 (spSet1p) and similar proteins; This subfamily corresponds to the RRM of spSet1p, also termed H3 lysine-4 specific histone-lysine N-methyltransferase, or COMPASS component SET1, or lysine N-methyltransferase 2, or Set1 complex component, is encoded by SET1 from the fission yeast S. pombe. It is essential for the H3 lysine-4 methylation. in vivo, and plays an important role in telomere maintenance and DNA repair in an ATM kinase Rad3-dependent pathway. spSet1p is the homology counterpart of Saccharomyces cerevisiae Set1p (scSet1p). However, it is more closely related to Set1 found in mammalian. Moreover, unlike scSet1p, spSet1p is not required for heterochromatin assembly in fission yeast. spSet1p contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a conserved SET domain that may play a role in DNA repair and telomere function. Pssm-ID: 409744 [Multi-domain] Cd Length: 86 Bit Score: 46.23 E-value: 5.31e-06
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| RRM3_RBM19_RRM2_MRD1 | cd12316 | RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and RNA recognition ... |
107-176 | 5.76e-06 | ||||
RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and RNA recognition motif 2 found in multiple RNA-binding domain-containing protein 1 (MRD1); This subfamily corresponds to the RRM3 of RBM19 and RRM2 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. Pssm-ID: 409755 [Multi-domain] Cd Length: 74 Bit Score: 45.80 E-value: 5.76e-06
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| RRM_scSet1p_like | cd12302 | RNA recognition motif in budding yeast Saccharomyces cerevisiae SET domain-containing protein ... |
101-179 | 8.08e-06 | ||||
RNA recognition motif in budding yeast Saccharomyces cerevisiae SET domain-containing protein 1 (scSet1p) and similar proteins; This subfamily corresponds to the RRM of scSet1p, also termed H3 lysine-4 specific histone-lysine N-methyltransferase, or COMPASS component SET1, or lysine N-methyltransferase 2, which is encoded by SET1 from the yeast S. cerevisiae. It is a nuclear protein that may play a role in both silencing and activating transcription. scSet1p is closely related to the SET domain proteins of multicellular organisms, which are implicated in diverse aspects of cell morphology, growth control, and chromatin-mediated transcriptional silencing. scSet1p contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a conserved SET domain that may play a role in DNA repair and telomere function. Pssm-ID: 409743 [Multi-domain] Cd Length: 110 Bit Score: 46.56 E-value: 8.08e-06
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| RRM2_NsCP33_like | cd21608 | RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ... |
96-176 | 2.98e-05 | ||||
RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ribonucleoprotein (NsCP33) and similar proteins; The family includes NsCP33, Arabidopsis thaliana chloroplastic 31 kDa ribonucleoprotein (CP31A) and mitochondrial glycine-rich RNA-binding protein 2 (AtGR-RBP2). NsCP33 may be involved in splicing and/or processing of chloroplast RNA's. AtCP31A, also called RNA-binding protein 1/2/3 (AtRBP33), or RNA-binding protein CP31A, or RNA-binding protein RNP-T, or RNA-binding protein cp31, is required for specific RNA editing events in chloroplasts and stabilizes specific chloroplast mRNAs, as well as for normal chloroplast development under cold stress conditions by stabilizing transcripts of numerous mRNAs under these conditions. CP31A may modulate telomere replication through RNA binding domains. AtGR-RBP2, also called AtRBG2, or glycine-rich protein 2 (AtGRP2), or mitochondrial RNA-binding protein 1a (At-mRBP1a), plays a role in RNA transcription or processing during stress. It binds RNAs and DNAs sequence with a preference to single-stranded nucleic acids. AtGR-RBP2 displays strong affinity to poly(U) sequence. It exerts cold and freezing tolerance, probably by exhibiting an RNA chaperone activity during the cold and freezing adaptation process. Some members in this family contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the second RRM motif. Pssm-ID: 410187 [Multi-domain] Cd Length: 76 Bit Score: 44.08 E-value: 2.98e-05
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| RRM1_2_CELF1-6_like | cd12361 | RNA recognition motif 1 (RRM1) and 2 (RRM2) found in CELF/Bruno-like family of RNA binding ... |
96-170 | 3.45e-05 | ||||
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in CELF/Bruno-like family of RNA binding proteins and plant flowering time control protein FCA; This subfamily corresponds to the RRM1 and RRM2 domains of the CUGBP1 and ETR-3-like factors (CELF) as well as plant flowering time control protein FCA. CELF, also termed BRUNOL (Bruno-like) proteins, is a family of structurally related RNA-binding proteins involved in regulation of pre-mRNA splicing in the nucleus, and control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also known as BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4 (BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both, sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. This subfamily also includes plant flowering time control protein FCA that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RRMs, and a WW protein interaction domain. Pssm-ID: 409796 [Multi-domain] Cd Length: 77 Bit Score: 43.76 E-value: 3.45e-05
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| RRM1_2_CoAA_like | cd12343 | RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RRM-containing coactivator activator ... |
110-177 | 4.46e-05 | ||||
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RRM-containing coactivator activator/modulator (CoAA) and similar proteins; This subfamily corresponds to the RRM in CoAA (also known as RBM14 or PSP2) and RNA-binding protein 4 (RBM4). CoAA is a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner, and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. RBM4 is a ubiquitously expressed splicing factor with two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may also function as a translational regulator of stress-associated mRNAs as well as play a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RRMs, a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. This family also includes Drosophila RNA-binding protein lark (Dlark), a homolog of human RBM4. It plays an important role in embryonic development and in the circadian regulation of adult eclosion. Dlark shares high sequence similarity with RBM4 at the N-terminal region. However, Dlark has three proline-rich segments instead of three alanine-rich segments within the C-terminal region. Pssm-ID: 409779 [Multi-domain] Cd Length: 66 Bit Score: 42.99 E-value: 4.46e-05
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| RRM2_NUCLs | cd12451 | RNA recognition motif 2 (RRM2) found in nucleolin-like proteins mainly from plants; This ... |
112-178 | 5.30e-05 | ||||
RNA recognition motif 2 (RRM2) found in nucleolin-like proteins mainly from plants; This subfamily corresponds to the RRM2 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Pssm-ID: 409885 [Multi-domain] Cd Length: 79 Bit Score: 43.17 E-value: 5.30e-05
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| RRM1_PSRP2_like | cd21609 | RNA recognition motif 1 (RRM1) found in chloroplastic plastid-specific 30S ribosomal protein 2 ... |
94-176 | 5.51e-05 | ||||
RNA recognition motif 1 (RRM1) found in chloroplastic plastid-specific 30S ribosomal protein 2 (PSRP-2) and similar proteins; PSRP-2, also called chloroplastic 30S ribosomal protein 2, or chloroplastic small ribosomal subunit protein cS22, is a component of the chloroplast ribosome (chloro-ribosome), a dedicated translation machinery responsible for the synthesis of chloroplast genome-encoded proteins, including proteins of the transcription and translation machinery and components of the photosynthetic apparatus. It binds single strand DNA (ssDNA) and RNA in vitro. It exhibits RNA chaperone activity and regulates negatively resistance responses to abiotic stresses during seed germination (e.g. salt, dehydration, and low temperature) and seedling growth (e.g. salt). The family also includes Nicotiana sylvestris chloroplastic 33 kDa ribonucleoprotein (NsCP33) and Arabidopsis thaliana chloroplastic 31 kDa ribonucleoprotein (AtCP31A). NsCP33 may be involved in splicing and/or processing of chloroplast RNA's. AtCP31A, also called RNA-binding protein 1/2/3 (AtRBP33), or RNA-binding protein CP31A, or RNA-binding protein RNP-T, or RNA-binding protein cp31, is required for specific RNA editing events in chloroplasts and stabilizes specific chloroplast mRNAs, as well as for normal chloroplast development under cold stress conditions by stabilizing transcripts of numerous mRNAs under these conditions. CP31A may modulate telomere replication through RNA binding domains. Members in this family contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif. Pssm-ID: 410188 [Multi-domain] Cd Length: 80 Bit Score: 43.18 E-value: 5.51e-05
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| RRM_TRA2 | cd12363 | RNA recognition motif (RRM) found in transformer-2 protein homolog TRA2-alpha, TRA2-beta and ... |
110-177 | 6.29e-05 | ||||
RNA recognition motif (RRM) found in transformer-2 protein homolog TRA2-alpha, TRA2-beta and similar proteins; This subfamily corresponds to the RRM of two mammalian homologs of Drosophila transformer-2 (Tra2), TRA2-alpha, TRA2-beta (also termed SFRS10), and similar proteins found in eukaryotes. TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. Both, TRA2-alpha and TRA2-beta, contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. Pssm-ID: 409798 [Multi-domain] Cd Length: 80 Bit Score: 42.99 E-value: 6.29e-05
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| RRM_eIF3G_like | cd12408 | RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit G ... |
110-177 | 6.73e-05 | ||||
RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit G (eIF-3G) and similar proteins; This subfamily corresponds to the RRM of eIF-3G and similar proteins. eIF-3G, also termed eIF-3 subunit 4, or eIF-3-delta, or eIF3-p42, or eIF3-p44, is the RNA-binding subunit of eIF3, a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3G binds 18 S rRNA and beta-globin mRNA, and therefore appears to be a nonspecific RNA-binding protein. eIF-3G is one of the cytosolic targets and interacts with mature apoptosis-inducing factor (AIF). eIF-3G contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This family also includes yeast eIF3-p33, a homolog of vertebrate eIF-3G, plays an important role in the initiation phase of protein synthesis in yeast. It binds both, mRNA and rRNA, fragments due to an RRM near its C-terminus. Pssm-ID: 409842 [Multi-domain] Cd Length: 76 Bit Score: 42.88 E-value: 6.73e-05
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| PostSET | smart00508 | Cysteine-rich motif following a subset of SET domains; |
1950-1966 | 6.76e-05 | ||||
Cysteine-rich motif following a subset of SET domains; Pssm-ID: 214703 Cd Length: 17 Bit Score: 41.24 E-value: 6.76e-05
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| SET_SpSet7-like | cd10540 | SET domain found in Schizossacharomyces pombe Set7 and similar proteins; Schizosaccharomyces ... |
1840-1943 | 1.10e-04 | ||||
SET domain found in Schizossacharomyces pombe Set7 and similar proteins; Schizosaccharomyces pombe Set7 is a novel histone-lysine N-methyltransferase. The family also includes a viral histone H3 lysine 27 methyltransferase from Paramecium bursaria Chlorella virus 1 (PBCV-1). Pssm-ID: 380938 Cd Length: 112 Bit Score: 43.40 E-value: 1.10e-04
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| RRM_RNPS1 | cd12365 | RNA recognition motif (RRM) found in RNA-binding protein with serine-rich domain 1 (RNPS1) and ... |
108-177 | 1.40e-04 | ||||
RNA recognition motif (RRM) found in RNA-binding protein with serine-rich domain 1 (RNPS1) and similar proteins; This subfamily corresponds to the RRM of RNPS1 and its eukaryotic homologs. RNPS1, also termed RNA-binding protein prevalent during the S phase, or SR-related protein LDC2, was originally characterized as a general pre-mRNA splicing activator, which activates both constitutive and alternative splicing of pre-mRNA in vitro.It has been identified as a protein component of the splicing-dependent mRNP complex, or exon-exon junction complex (EJC), and is directly involved in mRNA surveillance. Furthermore, RNPS1 is a splicing regulator whose activator function is controlled in part by CK2 (casein kinase II) protein kinase phosphorylation. It can also function as a squamous-cell carcinoma antigen recognized by T cells-3 (SART3)-binding protein, and is involved in the regulation of mRNA splicing. RNPS1 contains an N-terminal serine-rich (S) domain, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and the C-terminal arginine/serine/proline-rich (RS/P) domain. Pssm-ID: 409800 [Multi-domain] Cd Length: 73 Bit Score: 41.77 E-value: 1.40e-04
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| RRM_SRSF10_SRSF12 | cd12312 | RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF10, SRSF12 and ... |
110-177 | 2.88e-04 | ||||
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF10, SRSF12 and similar proteins; This subfamily corresponds to the RRM of SRSF10 and SRSF12. SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). It is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19), is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. Both, SRSF10 and SRSF12, contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. Pssm-ID: 240758 [Multi-domain] Cd Length: 84 Bit Score: 41.21 E-value: 2.88e-04
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| RRM_HP0827_like | cd12399 | RNA recognition motif (RRM) found in Helicobacter pylori HP0827 protein and similar proteins; ... |
113-176 | 3.31e-04 | ||||
RNA recognition motif (RRM) found in Helicobacter pylori HP0827 protein and similar proteins; This subfamily corresponds to the RRM of H. pylori HP0827, a putative ssDNA-binding protein 12rnp2 precursor, containing one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The ssDNA binding may be important in activation of HP0827. Pssm-ID: 409833 [Multi-domain] Cd Length: 75 Bit Score: 40.97 E-value: 3.31e-04
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| SET_KMT2E | cd19182 | SET domain found in inactive histone-lysine N-methyltransferase 2E (KMT2E) and similar ... |
1841-1945 | 4.30e-04 | ||||
SET domain found in inactive histone-lysine N-methyltransferase 2E (KMT2E) and similar proteins; KMT2E (also termed inactive lysine N-methyltransferase 2E, myeloid/lymphoid or mixed-lineage leukemia protein 5 (MLL5)) plays a key role in hematopoiesis, spermatogenesis and cell cycle progression. It associates with chromatin regions downstream of transcriptional start sites of active genes and thus regulates gene transcription. Lack of key residues in the SET domain as well as the presence of an unusually large loop in the SET-I subdomain preclude the interaction of MLL5 SET with its cofactor and substrate thus making MLL5 devoid of any in vitro methyltransferase activity on full-length histones and histone H3 peptide. Pssm-ID: 380959 Cd Length: 129 Bit Score: 42.19 E-value: 4.30e-04
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| RRM3_PTBP1_like | cd12423 | RNA recognition motif 3 (RRM3) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) ... |
126-178 | 4.57e-04 | ||||
RNA recognition motif 3 (RRM3) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) and similar proteins; This subfamily corresponds to the RRM3 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), and similar proteins found in Metazoa. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. PTBP2 also contains four RRMs. ROD1 coding protein Rod1 is a mammalian PTB homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It may play a role controlling differentiation in mammals. All members in this family contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Pssm-ID: 409857 [Multi-domain] Cd Length: 74 Bit Score: 40.68 E-value: 4.57e-04
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| RRM_PPIE | cd12347 | RNA recognition motif (RRM) found in cyclophilin-33 (Cyp33) and similar proteins; This ... |
110-178 | 7.54e-04 | ||||
RNA recognition motif (RRM) found in cyclophilin-33 (Cyp33) and similar proteins; This subfamily corresponds to the RRM of Cyp33, also termed peptidyl-prolyl cis-trans isomerase E (PPIase E), or cyclophilin E, or rotamase E. Cyp33 is a nuclear RNA-binding cyclophilin with an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal PPIase domain. Cyp33 possesses RNA-binding activity and preferentially binds to polyribonucleotide polyA and polyU, but hardly to polyG and polyC. It binds specifically to mRNA, which can stimulate its PPIase activity. Moreover, Cyp33 interacts with the third plant homeodomain (PHD3) zinc finger cassette of the mixed lineage leukemia (MLL) proto-oncoprotein and a poly-A RNA sequence through its RRM domain. It further mediates downregulation of the expression of MLL target genes HOXC8, HOXA9, CDKN1B, and C-MYC, in a proline isomerase-dependent manner. Cyp33 also possesses a PPIase activity that catalyzes cis-trans isomerization of the peptide bond preceding a proline, which has been implicated in the stimulation of folding and conformational changes in folded and unfolded proteins. The PPIase activity can be inhibited by the immunosuppressive drug cyclosporin A. Pssm-ID: 409783 [Multi-domain] Cd Length: 75 Bit Score: 39.90 E-value: 7.54e-04
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| RRM_CIRBP_RBM3 | cd12449 | RNA recognition motif (RRM) found in cold inducible RNA binding protein (CIRBP), RNA binding ... |
110-177 | 9.34e-04 | ||||
RNA recognition motif (RRM) found in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) and similar proteins; This subfamily corresponds to the RRM domain of two structurally related heterogenous nuclear ribonucleoproteins, CIRBP (also termed CIRP or A18 hnRNP) and RBM3 (also termed RNPL), both of which belong to a highly conserved cold shock proteins family. The cold shock proteins can be induced after exposure to a moderate cold-shock and other cellular stresses such as UV radiation and hypoxia. CIRBP and RBM3 may function in posttranscriptional regulation of gene expression by binding to different transcripts, thus allowing the cell to response rapidly to environmental signals. However, the kinetics and degree of cold induction are different between CIRBP and RBM3. Tissue distribution of their expression is different. CIRBP and RBM3 may be differentially regulated under physiological and stress conditions and may play distinct roles in cold responses of cells. CIRBP, also termed glycine-rich RNA-binding protein CIRP, is localized in the nucleus and mediates the cold-induced suppression of cell cycle progression. CIRBP also binds DNA and possibly serves as a chaperone that assists in the folding/unfolding, assembly/disassembly and transport of various proteins. RBM3 may enhance global protein synthesis and the formation of active polysomes while reducing the levels of ribonucleoprotein complexes containing microRNAs. RBM3 may also serve to prevent the loss of muscle mass by its ability to decrease cell death. Furthermore, RBM3 may be essential for cell proliferation and mitosis. Both, CIRBP and RBM3, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), that is involved in RNA binding, and C-terminal glycine-rich domain (RGG motif) that probably enhances RNA-binding via protein-protein and/or protein-RNA interactions. Like CIRBP, RBM3 can also bind to both RNA and DNA via its RRM domain. Pssm-ID: 409883 [Multi-domain] Cd Length: 80 Bit Score: 39.77 E-value: 9.34e-04
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| RRM2_DAZAP1 | cd12327 | RNA recognition motif 2 (RRM2) found in Deleted in azoospermia-associated protein 1 (DAZAP1) ... |
103-177 | 9.38e-04 | ||||
RNA recognition motif 2 (RRM2) found in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins; This subfamily corresponds to the RRM2 of DAZAP1 or DAZ-associated protein 1, also termed proline-rich RNA binding protein (Prrp), a multi-functional ubiquitous RNA-binding protein expressed most abundantly in the testis and essential for normal cell growth, development, and spermatogenesis. DAZAP1 is a shuttling protein whose acetylated is predominantly nuclear and the nonacetylated form is in cytoplasm. DAZAP1 also functions as a translational regulator that activates translation in an mRNA-specific manner. DAZAP1 was initially identified as a binding partner of Deleted in Azoospermia (DAZ). It also interacts with numerous hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1, hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate and cooperate with hnRNP particles to regulate adenylate-uridylate-rich elements (AU-rich element or ARE)-containing mRNAs. DAZAP1 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal proline-rich domain. Pssm-ID: 409765 [Multi-domain] Cd Length: 80 Bit Score: 39.79 E-value: 9.38e-04
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| RRM2_MRD1 | cd12566 | RNA recognition motif 2 (RRM2) found in yeast multiple RNA-binding domain-containing protein 1 ... |
115-176 | 1.28e-03 | ||||
RNA recognition motif 2 (RRM2) found in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subgroup corresponds to the RRM2 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. Pssm-ID: 409982 [Multi-domain] Cd Length: 79 Bit Score: 39.32 E-value: 1.28e-03
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| RRM2_TatSF1_like | cd12282 | RNA recognition motif 2 (RRM2) found in HIV Tat-specific factor 1 (Tat-SF1) and similar ... |
90-178 | 1.43e-03 | ||||
RNA recognition motif 2 (RRM2) found in HIV Tat-specific factor 1 (Tat-SF1) and similar proteins; This subfamily corresponds to the RRM2 of Tat-SF1 and CUS2. Tat-SF1 is the cofactor for stimulation of transcriptional elongation by human immunodeficiency virus-type 1 (HIV-1) Tat. It is a substrate of an associated cellular kinase. Tat-SF1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a highly acidic carboxyl-terminal half. The family also includes CUS2, a yeast homolog of human Tat-SF1. CUS2 interacts with U2 RNA in splicing extracts and functions as a splicing factor that aids assembly of the splicing-competent U2 snRNP in vivo. CUS2 also associates with PRP11 that is a subunit of the conserved splicing factor SF3a. Like Tat-SF1, CUS2 contains two RRMs as well. Pssm-ID: 409724 [Multi-domain] Cd Length: 91 Bit Score: 39.53 E-value: 1.43e-03
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| RRM1_Mug28 | cd21620 | RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe meiotically up-regulated ... |
96-177 | 1.82e-03 | ||||
RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe meiotically up-regulated gene 28 protein (Mug28) and similar proteins; Mug28 is a meiosis-specific protein that regulates spore wall formation. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif. Pssm-ID: 410199 [Multi-domain] Cd Length: 84 Bit Score: 39.03 E-value: 1.82e-03
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| RRM_Aly_REF_like | cd12418 | RNA recognition motif (RRM) found in the Aly/REF family; This subfamily corresponds to the RRM ... |
110-178 | 2.33e-03 | ||||
RNA recognition motif (RRM) found in the Aly/REF family; This subfamily corresponds to the RRM of Aly/REF family which includes THO complex subunit 4 (THOC4, also termed Aly/REF), S6K1 Aly/REF-like target (SKAR, also termed PDIP3 or PDIP46) and similar proteins. THOC4 is an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus, and was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid, and might be a novel transcription cofactor for erythroid-specific genes. SKAR shows high sequence homology with THOC4 and possesses one RRM as well. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion. Pssm-ID: 409852 [Multi-domain] Cd Length: 75 Bit Score: 38.33 E-value: 2.33e-03
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| RRM2_4_MRN1 | cd12262 | RNA recognition motif 2 (RRM2) and 4 (RRM4) found in RNA-binding protein MRN1 and similar ... |
103-164 | 2.74e-03 | ||||
RNA recognition motif 2 (RRM2) and 4 (RRM4) found in RNA-binding protein MRN1 and similar proteins; This subgroup corresponds to the RRM2 and RRM4 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, and is an RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Pssm-ID: 409706 [Multi-domain] Cd Length: 78 Bit Score: 38.53 E-value: 2.74e-03
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| RRM2_CELF3_4_5_6 | cd12635 | RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, ... |
110-170 | 3.29e-03 | ||||
RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins; This subgroup corresponds to the RRM2 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, being highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, both RRM1 and RRM2 of CELF-4 can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, being strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in a muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In addition to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. Pssm-ID: 410043 [Multi-domain] Cd Length: 81 Bit Score: 38.16 E-value: 3.29e-03
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| RRM2_RBM28_like | cd12414 | RNA recognition motif 2 (RRM2) found in RNA-binding protein 28 (RBM28) and similar proteins; ... |
113-176 | 3.83e-03 | ||||
RNA recognition motif 2 (RRM2) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM2 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. Pssm-ID: 409848 [Multi-domain] Cd Length: 76 Bit Score: 37.92 E-value: 3.83e-03
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| RRM_ZCRB1 | cd12393 | RNA recognition motif (RRM) found in Zinc finger CCHC-type and RNA-binding motif-containing ... |
117-174 | 4.79e-03 | ||||
RNA recognition motif (RRM) found in Zinc finger CCHC-type and RNA-binding motif-containing protein 1 (ZCRB1) and similar proteins; This subfamily corresponds to the RRM of ZCRB1, also termed MADP-1, or U11/U12 small nuclear ribonucleoprotein 31 kDa protein (U11/U12 snRNP 31 or U11/U12-31K), a novel multi-functional nuclear factor, which may be involved in morphine dependence, cold/heat stress, and hepatocarcinoma. It is located in the nucleoplasm, but outside the nucleolus. ZCRB1 is one of the components of U11/U12 snRNPs that bind to U12-type pre-mRNAs and form a di-snRNP complex, simultaneously recognizing the 5' splice site and branchpoint sequence. ZCRB1 is characterized by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a CCHC-type Zinc finger motif. In addition, it contains core nucleocapsid motifs, and Lys- and Glu-rich domains. Pssm-ID: 409827 [Multi-domain] Cd Length: 76 Bit Score: 37.65 E-value: 4.79e-03
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| RRM1_RBM45 | cd12366 | RNA recognition motif 1 (RRM1) found in RNA-binding protein 45 (RBM45) and similar proteins; ... |
101-165 | 5.61e-03 | ||||
RNA recognition motif 1 (RRM1) found in RNA-binding protein 45 (RBM45) and similar proteins; This subfamily corresponds to the RRM1 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Pssm-ID: 409801 [Multi-domain] Cd Length: 81 Bit Score: 37.68 E-value: 5.61e-03
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| RRM_SRSF2_SRSF8 | cd12311 | RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF2, SRSF8 and ... |
112-176 | 6.33e-03 | ||||
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF2, SRSF8 and similar proteins; This subfamily corresponds to the RRM of SRSF2 and SRSF8. SRSF2, also termed protein PR264, or splicing component, 35 kDa (splicing factor SC35 or SC-35), is a prototypical SR protein that plays important roles in the alternative splicing of pre-mRNA. It is also involved in transcription elongation by directly or indirectly mediating the recruitment of elongation factors to the C-terminal domain of polymerase II. SRSF2 is exclusively localized in the nucleus and is restricted to nuclear processes. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. The RRM is responsible for the specific recognition of 5'-SSNG-3' (S=C/G) RNA. In the regulation of alternative splicing events, it specifically binds to cis-regulatory elements on the pre-mRNA. The RS domain modulates SRSF2 activity through phosphorylation, directly contacts RNA, and promotes protein-protein interactions with the spliceosome. SRSF8, also termed SRP46 or SFRS2B, is a novel mammalian SR splicing factor encoded by a PR264/SC35 functional retropseudogene. SRSF8 is localized in the nucleus and does not display the same activity as PR264/SC35. It functions as an essential splicing factor in complementing a HeLa cell S100 extract deficient in SR proteins. Like SRSF2, SRSF8 contains a single N-terminal RRM and a C-terminal RS domain. Pssm-ID: 409751 [Multi-domain] Cd Length: 73 Bit Score: 37.25 E-value: 6.33e-03
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| RRM_TRA2B | cd12641 | RNA recognition motif (RRM) found in Transformer-2 protein homolog beta (TRA-2 beta) and ... |
116-182 | 7.30e-03 | ||||
RNA recognition motif (RRM) found in Transformer-2 protein homolog beta (TRA-2 beta) and similar proteins; This subgroup corresponds to the RRM of TRA2-beta or TRA-2-beta, also termed splicing factor, arginine/serine-rich 10 (SFRS10), or transformer-2 protein homolog B, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. It contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. TRA2-beta specifically binds to two types of RNA sequences, the CAA and (GAA)2 sequences, through the RRMs in different RNA binding modes. Pssm-ID: 410046 [Multi-domain] Cd Length: 87 Bit Score: 37.68 E-value: 7.30e-03
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| RRM2_FCA | cd12637 | RNA recognition motif 2 (RRM2) found in plant flowering time control protein FCA and similar ... |
109-172 | 7.58e-03 | ||||
RNA recognition motif 2 (RRM2) found in plant flowering time control protein FCA and similar proteins; This subgroup corresponds to the RRM2 of FCA, a gene controlling flowering time in Arabidopsis, which encodes a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. The flowering time control protein FCA contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNP (ribonucleoprotein domains), and a WW protein interaction domain. Pssm-ID: 410045 [Multi-domain] Cd Length: 81 Bit Score: 37.36 E-value: 7.58e-03
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| RRM3_U2AF65 | cd12232 | RNA recognition motif 3 (RRM3) found in U2 large nuclear ribonucleoprotein auxiliary factor ... |
110-165 | 8.46e-03 | ||||
RNA recognition motif 3 (RRM3) found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins; This subfamily corresponds to the RRM3 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs. Pssm-ID: 409679 [Multi-domain] Cd Length: 89 Bit Score: 37.18 E-value: 8.46e-03
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| RRM1_U1A_like | cd12246 | RNA recognition motif 1 (RRM1) found in the U1A/U2B"/SNF protein family; This subfamily ... |
110-177 | 9.67e-03 | ||||
RNA recognition motif 1 (RRM1) found in the U1A/U2B"/SNF protein family; This subfamily corresponds to the RRM1 of U1A/U2B"/SNF protein family which contains Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs), connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. Moreover, U2B" does not require an auxiliary protein for binding to RNA, and its nuclear transport is independent of U2 snRNA binding. Pssm-ID: 409692 [Multi-domain] Cd Length: 78 Bit Score: 36.74 E-value: 9.67e-03
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