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Conserved domains on  [gi|2020930311|ref|NP_001381050|]
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RNA-binding protein 41 isoform 11 [Homo sapiens]

Protein Classification

RNA-binding protein( domain architecture ID 106745)

RNA-binding protein containing an RNA recognition motif (RRM)

CATH:  3.30.70.330
Gene Ontology:  GO:0003723
PubMed:  15853797
SCOP:  3000110

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
RRM_SF super family cl17169
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
287-361 1.02e-23

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).


The actual alignment was detected with superfamily member cd12239:

Pssm-ID: 473069 [Multi-domain]  Cd Length: 82  Bit Score: 93.45  E-value: 1.02e-23
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2020930311 287 RLSEEEIRKIpmFSSYnpgEPNKEKKGPPIQFRMMT-GRMRGQAFITFPNKEIAWQALHLVNGYKLHGKILVIEFG 361
Cdd:cd12239    12 RVSEKDLKYI--FGRF---VDSSSEEKNMFDIRLMTeGRMKGQAFITFPSEELAEKALNLTNGYVLHGKPMVVQFA 82
 
Name Accession Description Interval E-value
RRM2_RBM40_like cd12239
RNA recognition motif 2 (RRM2) found in RNA-binding protein 40 (RBM40) and similar proteins; ...
287-361 1.02e-23

RNA recognition motif 2 (RRM2) found in RNA-binding protein 40 (RBM40) and similar proteins; This subfamily corresponds to the RRM2 of RBM40 and the RRM of RBM41. RBM40, also known as RNA-binding region-containing protein 3 (RNPC3) or U11/U12 small nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K protein). It serves as a bridging factor between the U11 and U12 snRNPs. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), connected by a linker that includes a proline-rich region. It binds to the U11-associated 59K protein via its RRM1 and employs the RRM2 to bind hairpin III of the U12 small nuclear RNA (snRNA). The proline-rich region might be involved in protein-protein interactions. RBM41 contains only one RRM. Its biological function remains unclear.


Pssm-ID: 409685 [Multi-domain]  Cd Length: 82  Bit Score: 93.45  E-value: 1.02e-23
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2020930311 287 RLSEEEIRKIpmFSSYnpgEPNKEKKGPPIQFRMMT-GRMRGQAFITFPNKEIAWQALHLVNGYKLHGKILVIEFG 361
Cdd:cd12239    12 RVSEKDLKYI--FGRF---VDSSSEEKNMFDIRLMTeGRMKGQAFITFPSEELAEKALNLTNGYVLHGKPMVVQFA 82
RRM smart00360
RNA recognition motif;
289-358 5.88e-08

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 49.51  E-value: 5.88e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2020930311  289 SEEEIRKIpmFSSYnpgepnkekkGPPIQFRMM----TGRMRGQAFITFPNKEIAWQALHLVNGYKLHGKILVI 358
Cdd:smart00360  12 TEEELREL--FSKF----------GKVESVRLVrdkeTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
288-356 1.88e-05

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: 42.22  E-value: 1.88e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2020930311 288 LSEEEIRKIpmFSSYnpgepnkekkGPPIQFRMM---TGRMRGQAFITFPNKEIAWQALHLVNGYKLHGKIL 356
Cdd:pfam00076  10 TTEEDLKDL--FSKF----------GPIKSIRLVrdeTGRSKGFAFVEFEDEEDAEKAIEALNGKELGGREL 69
hnRNP-R-Q TIGR01648
heterogeneous nuclear ribonucleoprotein R, Q family; Sequences in this subfamily include the ...
288-356 1.89e-04

heterogeneous nuclear ribonucleoprotein R, Q family; Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q, and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.


Pssm-ID: 273732 [Multi-domain]  Cd Length: 578  Bit Score: 43.45  E-value: 1.89e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2020930311 288 LSEEEIrkIPMFssynpgepnkEKKGPPIQFRMM---TGRMRGQAFITFPNKEIAWQALHLVNGYKLH-GKIL 356
Cdd:TIGR01648  70 LYEDEL--VPLF----------EKAGPIYELRLMmdfSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRpGRLL 130
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
287-368 2.72e-04

RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 39.31  E-value: 2.72e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020930311 287 RLSEEEIRKipMFSSYnpgepnkekkGPPIQFRMM----TGRMRGQAFITFPNKEIAWQALHLVNGYKLHGKILVIEFGK 362
Cdd:COG0724    12 SVTEEDLRE--LFSEY----------GEVTSVKLItdreTGRSRGFGFVEMPDDEEAQAAIEALNGAELMGRTLKVNEAR 79

                  ....*.
gi 2020930311 363 NKKQRS 368
Cdd:COG0724    80 PREERP 85
 
Name Accession Description Interval E-value
RRM2_RBM40_like cd12239
RNA recognition motif 2 (RRM2) found in RNA-binding protein 40 (RBM40) and similar proteins; ...
287-361 1.02e-23

RNA recognition motif 2 (RRM2) found in RNA-binding protein 40 (RBM40) and similar proteins; This subfamily corresponds to the RRM2 of RBM40 and the RRM of RBM41. RBM40, also known as RNA-binding region-containing protein 3 (RNPC3) or U11/U12 small nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K protein). It serves as a bridging factor between the U11 and U12 snRNPs. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), connected by a linker that includes a proline-rich region. It binds to the U11-associated 59K protein via its RRM1 and employs the RRM2 to bind hairpin III of the U12 small nuclear RNA (snRNA). The proline-rich region might be involved in protein-protein interactions. RBM41 contains only one RRM. Its biological function remains unclear.


Pssm-ID: 409685 [Multi-domain]  Cd Length: 82  Bit Score: 93.45  E-value: 1.02e-23
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2020930311 287 RLSEEEIRKIpmFSSYnpgEPNKEKKGPPIQFRMMT-GRMRGQAFITFPNKEIAWQALHLVNGYKLHGKILVIEFG 361
Cdd:cd12239    12 RVSEKDLKYI--FGRF---VDSSSEEKNMFDIRLMTeGRMKGQAFITFPSEELAEKALNLTNGYVLHGKPMVVQFA 82
RRM1_U1A_like cd12246
RNA recognition motif 1 (RRM1) found in the U1A/U2B"/SNF protein family; This subfamily ...
287-362 1.14e-08

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: 51.38  E-value: 1.14e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2020930311 287 RLSEEEIRKI--PMFSSYnpgepnkekkGPPIQFRMM-TGRMRGQAFITFPNKEIAWQALHLVNGYKLHGKILVIEFGK 362
Cdd:cd12246    10 KIKKDELKRSlyALFSQF----------GPVLDIVASkSLKMRGQAFVVFKDVESATNALRALQGFPFYGKPMRIQYAK 78
RRM smart00360
RNA recognition motif;
289-358 5.88e-08

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 49.51  E-value: 5.88e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2020930311  289 SEEEIRKIpmFSSYnpgepnkekkGPPIQFRMM----TGRMRGQAFITFPNKEIAWQALHLVNGYKLHGKILVI 358
Cdd:smart00360  12 TEEELREL--FSKF----------GKVESVRLVrdkeTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
288-359 1.14e-06

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: 45.74  E-value: 1.14e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2020930311 288 LSEEEIRKIpmFSSYnpgepnkekkGPPIQFRMMT---GRMRGQAFITFPNKEIAWQALHLVNGYKLHGKILVIE 359
Cdd:cd00590    10 TTEEDLREL--FSKF----------GEVVSVRIVRdrdGKSKGFAFVEFESPEDAEKALEALNGTELGGRPLKVS 72
RRM_CSTF2_RNA15_like cd12398
RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), yeast ...
288-360 3.28e-06

RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins; This subfamily corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64. The family also includes yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins. RNA15 is a core subunit of cleavage factor IA (CFIA), an essential transcriptional 3'-end processing factor from Saccharomyces cerevisiae. RNA recognition by CFIA is mediated by an N-terminal RRM, which is contained in the RNA15 subunit of the complex. The RRM of RNA15 has a strong preference for GU-rich RNAs, mediated by a binding pocket that is entirely conserved in both yeast and vertebrate RNA15 orthologs.


Pssm-ID: 409832 [Multi-domain]  Cd Length: 77  Bit Score: 44.43  E-value: 3.28e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2020930311 288 LSEEEIRKIpmFSsynpgepnkeKKGPPIQFRMM----TGRMRGQAFITFPNKEIAWQALHLVNGYKLHGKILVIEF 360
Cdd:cd12398    12 ATEEQLKEI--FS----------EVGPVVSFRLVtdreTGKPKGYGFCEFRDAETALSAVRNLNGYELNGRPLRVDF 76
RRM_eIF3G_like cd12408
RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit G ...
322-360 1.53e-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: 42.50  E-value: 1.53e-05
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 2020930311 322 TGRMRGQAFITFPNKEIAWQALHLVNGYKLHGKILVIEF 360
Cdd:cd12408    37 TGQSKGFAFVTFETREDAERAIEKLNGFGYDNLILSVEW 75
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
288-356 1.88e-05

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: 42.22  E-value: 1.88e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2020930311 288 LSEEEIRKIpmFSSYnpgepnkekkGPPIQFRMM---TGRMRGQAFITFPNKEIAWQALHLVNGYKLHGKIL 356
Cdd:pfam00076  10 TTEEDLKDL--FSKF----------GPIKSIRLVrdeTGRSKGFAFVEFEDEEDAEKAIEALNGKELGGREL 69
RRM1_hnRNPR cd12482
RNA recognition motif 1 (RRM1) found in vertebrate heterogeneous nuclear ribonucleoprotein R ...
278-351 4.44e-05

RNA recognition motif 1 (RRM1) found in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R); This subgroup corresponds to the RRM1 of hnRNP R, which is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. It is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, and in retinal development and light-elicited cellular activities. hnRNP R contains an acidic auxiliary N-terminal region, followed by two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; it binds RNA through its RRM domains.


Pssm-ID: 409909 [Multi-domain]  Cd Length: 79  Bit Score: 41.50  E-value: 4.44e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2020930311 278 VPEDeiqrnrLSEEEIrkIPMFssynpgepnkEKKGPPIQFRMM----TGRMRGQAFITFPNKEIAWQALHLVNGYKL 351
Cdd:cd12482     9 IPRD------LYEDEL--VPLF----------EKAGPIWDLRLMmdplSGQNRGYAFITFCNKEAAQEAVKLCDNYEI 68
RRM_CSTF2_CSTF2T cd12671
RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), cleavage ...
289-359 1.06e-04

RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), cleavage stimulation factor subunit 2 tau variant (CSTF2T) and similar proteins; This subgroup corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64.


Pssm-ID: 410072 [Multi-domain]  Cd Length: 85  Bit Score: 40.57  E-value: 1.06e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2020930311 289 SEEEIRKIpmFSSYnpgepnkekkGPPIQFRMM----TGRMRGQAFITFPNKEIAWQALHLVNGYKLHGKILVIE 359
Cdd:cd12671    19 TEEQLKDI--FSEV----------GPVVSFRLVydreTGKPKGYGFCEYQDQETALSAMRNLNGYELNGRALRVD 81
hnRNP-R-Q TIGR01648
heterogeneous nuclear ribonucleoprotein R, Q family; Sequences in this subfamily include the ...
288-356 1.89e-04

heterogeneous nuclear ribonucleoprotein R, Q family; Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q, and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.


Pssm-ID: 273732 [Multi-domain]  Cd Length: 578  Bit Score: 43.45  E-value: 1.89e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2020930311 288 LSEEEIrkIPMFssynpgepnkEKKGPPIQFRMM---TGRMRGQAFITFPNKEIAWQALHLVNGYKLH-GKIL 356
Cdd:TIGR01648  70 LYEDEL--VPLF----------EKAGPIYELRLMmdfSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRpGRLL 130
RRM1_RBM40_like cd12238
RNA recognition motif 1 (RRM1) found in RNA-binding protein 40 (RBM40) and similar proteins; ...
323-360 2.54e-04

RNA recognition motif 1 (RRM1) found in RNA-binding protein 40 (RBM40) and similar proteins; This subfamily corresponds to the RRM1 of RBM40, also known as RNA-binding region-containing protein 3 (RNPC3) or U11/U12 small nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K protein), It serves as a bridging factor between the U11 and U12 snRNPs. It contains two repeats of RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), connected by a linker that includes a proline-rich region. It binds to the U11-associated 59K protein via its RRM1 and employs the RRM2 to bind hairpin III of the U12 small nuclear RNA (snRNA). The proline-rich region might be involved in protein-protein interactions.


Pssm-ID: 409684 [Multi-domain]  Cd Length: 73  Bit Score: 39.16  E-value: 2.54e-04
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 2020930311 323 GRMRGQAFITFPNKEIAWQALHLVNGYKLHGKILVIEF 360
Cdd:cd12238    35 GKLKHTAFATFDNEQAASKALSRLHQLKILGKRLVVEY 72
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
287-368 2.72e-04

RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 39.31  E-value: 2.72e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020930311 287 RLSEEEIRKipMFSSYnpgepnkekkGPPIQFRMM----TGRMRGQAFITFPNKEIAWQALHLVNGYKLHGKILVIEFGK 362
Cdd:COG0724    12 SVTEEDLRE--LFSEY----------GEVTSVKLItdreTGRSRGFGFVEMPDDEEAQAAIEALNGAELMGRTLKVNEAR 79

                  ....*.
gi 2020930311 363 NKKQRS 368
Cdd:COG0724    80 PREERP 85
RRM1_hnRNPR_like cd12249
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein R (hnRNP R) ...
283-351 3.42e-04

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins; This subfamily corresponds to the RRM1 in hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF), and dead end protein homolog 1 (DND1). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. It has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. DND1 is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members in this family, except for DND1, contain three conserved RNA recognition motifs (RRMs); DND1 harbors only two RRMs.


Pssm-ID: 409695 [Multi-domain]  Cd Length: 78  Bit Score: 38.72  E-value: 3.42e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2020930311 283 IQRNrLSEEEIrkIPMFssynpgepnkEKKGPPIQFRMM---TGRMRGQAFITFPNKEIAWQALHLVNGYKL 351
Cdd:cd12249     9 IPRD-VFEDEL--VPLF----------EKCGKIYELRLMmdfSGLNRGYAFVTYTNKEAAQRAVKTLNNYEI 67
RRM_RBM18 cd12355
RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 18 and similar proteins; ...
287-358 7.87e-04

RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 18 and similar proteins; This subfamily corresponds to the RRM of RBM18, a putative RNA-binding protein containing a well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The biological role of RBM18 remains unclear.


Pssm-ID: 409791 [Multi-domain]  Cd Length: 80  Bit Score: 38.05  E-value: 7.87e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2020930311 287 RLSEEEIRKIpmFSSYnpGEPNK-----EKKGPpiqfrmMTGRMRGQAFITFPNKEIAWQALHLVNGYKLHGKILVI 358
Cdd:cd12355    10 RLTEYHLLKL--LSKY--GKIKKfdflfHKTGP------LKGQPRGYCFVTFETKEEAEKAIECLNGKLALGKKLVV 76
RRM3_RBM47 cd12497
RNA recognition motif 3 (RRM3) found in vertebrate RNA-binding protein 47 (RBM47); This ...
289-362 1.40e-03

RNA recognition motif 3 (RRM3) found in vertebrate RNA-binding protein 47 (RBM47); This subgroup corresponds to the RRM3 of RBM47, a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM47 contains two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409920 [Multi-domain]  Cd Length: 74  Bit Score: 37.25  E-value: 1.40e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2020930311 289 SEEEIRKIpmFSSYNPGEPNKEKKgppiqfrmmtgrMRGQAFITFPNKEIAWQALHLVNGYKLHGKILVIEFGK 362
Cdd:cd12497    14 TEDTIKKI--FGQFNPGCVERVKK------------IRDYAFVHFASRDDAVVAMNNLNGTELEGSCIEVTLAK 73
RRM3_HuR cd12653
RNA recognition motif 3 (RRM3) found in vertebrate Hu-antigen R (HuR); This subgroup ...
322-367 1.65e-03

RNA recognition motif 3 (RRM3) found in vertebrate Hu-antigen R (HuR); This subgroup corresponds to the RRM3 of HuR, also termed ELAV-like protein 1 (ELAV-1), the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Like other Hu proteins, HuR contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410056 [Multi-domain]  Cd Length: 85  Bit Score: 37.34  E-value: 1.65e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 2020930311 322 TGRMRGQAFITFPNKEIAWQALHLVNGYKLHGKILVIEFGKNKKQR 367
Cdd:cd12653    40 TNKCKGFGFVTMTNYEEAAMAIASLNGYRLGDKILQVSFKTNKSHK 85
RRM1_ACF cd12486
RNA recognition motif 1 (RRM1) found in vertebrate APOBEC-1 complementation factor (ACF); This ...
307-356 1.82e-03

RNA recognition motif 1 (RRM1) found in vertebrate APOBEC-1 complementation factor (ACF); This subgroup corresponds to the RRM1 of ACF, also termed APOBEC-1-stimulating protein, an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. ACF shuttles between the cytoplasm and nucleus. It contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which display high affinity for an 11 nucleotide AU-rich mooring sequence 3' of the edited cytidine in apoB mRNA. All three RRMs may be required for complementation of editing activity in living cells. RRM2/3 are implicated in ACF interaction with APOBEC-1.


Pssm-ID: 409912 [Multi-domain]  Cd Length: 78  Bit Score: 36.88  E-value: 1.82e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2020930311 307 PNKEKKGPPIQFRMM---TGRMRGQAFITFPNKEIAWQALHLVNGYKL-HGKIL 356
Cdd:cd12486    20 PLCEKIGKIYEMRMMmdfNGNNRGYAFVTFSNKQEARNAIKQLNNYEIrNGRLL 73
RRM3_Hu cd12377
RNA recognition motif 3 (RRM3) found in the Hu proteins family; This subfamily corresponds to ...
322-360 2.00e-03

RNA recognition motif 3 (RRM3) found in the Hu proteins family; This subfamily corresponds to the RRM3 of the Hu proteins family which represent a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 409811 [Multi-domain]  Cd Length: 76  Bit Score: 36.53  E-value: 2.00e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 2020930311 322 TGRMRGQAFITFPNKEIAWQALHLVNGYKLHGKILVIEF 360
Cdd:cd12377    37 TNKCKGYGFVTMTNYDEAAVAIASLNGYRLGGRVLQVSF 75
RRM1_Nop4p cd12674
RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; ...
322-362 2.13e-03

RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; This subgroup corresponds to the RRM1 of Nop4p (also known as 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 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 410075 [Multi-domain]  Cd Length: 80  Bit Score: 36.67  E-value: 2.13e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 2020930311 322 TGRMRGQAFITFPNKEIAWQALHLVNGYKLHGKILVIEFGK 362
Cdd:cd12674    38 TKKSRGYGFVSFSTHDDAEEALAKLKNRKLSGHILKLDFAK 78
RRM_SRSF10_SRSF12 cd12312
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF10, SRSF12 and ...
315-360 2.68e-03

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: 36.58  E-value: 2.68e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 2020930311 315 PIQFRmmTGRMRGQAFITFPNKEIAWQALHLVNGYKLHGKILVIEF 360
Cdd:cd12312    33 PLDFY--TRRPRGFAYIQFEDVRDAEDALYYLDRTRFLGREIEIQF 76
RRM1_RBM28_like cd12413
RNA recognition motif 1 (RRM1) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
322-364 2.69e-03

RNA recognition motif 1 (RRM1) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM1 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: 409847 [Multi-domain]  Cd Length: 79  Bit Score: 36.42  E-value: 2.69e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 2020930311 322 TGRMRGQAFITFPNKEIAWQALHLVNGYKLHGKILVIEFGKNK 364
Cdd:cd12413    37 KDKCRGFGYVTFALAEDAQRALEEVKGKKFGGRKIKVELAKKK 79
RRM1_Crp79 cd21619
RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe mRNA export factor Crp79 and ...
287-358 3.87e-03

RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe mRNA export factor Crp79 and similar proteins; Crp79, also called meiotic expression up-regulated protein 5 (Mug5), or polyadenylate-binding protein crp79, or PABP, or poly(A)-binding protein, is an auxiliary mRNA export factor that binds the poly(A) tail of mRNA and is involved in the export of mRNA from the nucleus to the cytoplasm. 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: 410198 [Multi-domain]  Cd Length: 78  Bit Score: 35.96  E-value: 3.87e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2020930311 287 RLSEEEIRKIpmFSSYNPGEPNKEkkgpPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLHGKILVI 358
Cdd:cd21619    12 TINEDALEKI--FSRYGQVESVRR----PPIHTDKADRTTGFGFIKYTDAESAERAMQQADGILLGRRRLVV 77
RRM1_PHIP1 cd12271
RNA recognition motif 1 (RRM1) found in Arabidopsis thaliana phragmoplastin interacting ...
313-359 6.03e-03

RNA recognition motif 1 (RRM1) found in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins; This subfamily corresponds to the RRM1 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA.


Pssm-ID: 409714 [Multi-domain]  Cd Length: 72  Bit Score: 35.38  E-value: 6.03e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2020930311 313 GPPIQFRMMT----GRMRGQAFITFPNKEIAWQALHLvNGYKLHGKILVIE 359
Cdd:cd12271    23 GEVRSVDLMRfpdsGNFRGIAFITFKTEEAAKRALAL-DGEMLGNRFLKVE 72
RRM1_hnRNPQ cd12483
RNA recognition motif 1 (RRM1) found in vertebrate heterogeneous nuclear ribonucleoprotein Q ...
288-351 6.60e-03

RNA recognition motif 1 (RRM1) found in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q); This subgroup corresponds to the RRM1 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP, a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains.


Pssm-ID: 409910 [Multi-domain]  Cd Length: 84  Bit Score: 35.33  E-value: 6.60e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2020930311 288 LSEEEIrkIPMFssynpgepnkEKKGPPIQFRMM----TGRMRGQAFITFPNKEIAWQALHLVNGYKL 351
Cdd:cd12483    17 LFEDEL--VPLF----------EKAGPIWDLRLMmdplTGLNRGYAFVTFCTKEAAQEAVKLCNNHEI 72
RRM2_RBM23_RBM39 cd12284
RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein RBM23, RBM39 and ...
288-354 6.65e-03

RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins; This subfamily corresponds to the RRM2 of RBM39 (also termed HCC1), a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor.


Pssm-ID: 409726 [Multi-domain]  Cd Length: 78  Bit Score: 35.29  E-value: 6.65e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2020930311 288 LSEEEIRKIpmFSSYNPGEPNKEKKGPPiqfrmmTGRMRGQAFITFPNKEIAWQALHLVNGYKLHGK 354
Cdd:cd12284    10 ITEDMLRGI--FEPFGKIEFVQLQKDPE------TGRSKGYGFIQFRDAEDAKKALEQLNGFELAGR 68
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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