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RecName: Full=AT-rich interactive domain-containing protein 4A; Short=ARID domain-containing protein 4A; AltName: Full=Retinoblastoma-binding protein 1; Short=RBBP-1
List of domain hits
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Name | Accession | Description | Interval | E-value | |||
ARID_ARID4A | cd16882 | ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 4A (ARID4A) ... |
311-397 | 3.96e-57 | |||
ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 4A (ARID4A) and similar proteins; ARID4A, also called retinoblastoma-binding protein 1 (RBBP1, or RBP1), is a leukemia and tumor suppressor involved in epigenetic regulation in leukemia and Prader-Willi/Angelman syndrome. It associates with the mSIN3A histone deacetylase (HDAC) chromatin remodeling complex through the interaction with the breast cancer associated tumor suppressor ING1, the breast cancer metastasis suppressor BRMS1, and the ARID4 family homolog ARID4B (also known as RBP1L1). ARID4A specifically interacts with retinoblastoma protein (pRb) and shows both HDAC-dependent and -independent repression activities. It is also involved in the pocket domain of pRb-mediated repression of E2F-dependent transcription and cellular proliferation. Moreover, it acts as a Runx2 coactivator and is involved in the regulation of osteoblastic differentiation in Runx2-osterix transcriptional cascade. ARID4A contains a Tudor domain, a PWWP domain (also known as HATH domain or RBB1NT domain), an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a chromobarrel domain, and a C-terminal R2 domain. The ARID and R2 domains are responsible for the repression activities. The Tudor, PWWP, and chromobarrel domains are all Royal Family domains, but only chromobarrel domain of ARID4A is responsible for recognizing both dsDNA and methylated histone tails, particularly H4K20me3, in chromatin remodeling and epigenetic regulation. : Pssm-ID: 350646 Cd Length: 87 Bit Score: 191.73 E-value: 3.96e-57
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RBB1NT | pfam08169 | RBB1NT (NUC162) domain; This domain is found N terminal to the ARID/BRIGHT domain in ... |
170-262 | 7.81e-46 | |||
RBB1NT (NUC162) domain; This domain is found N terminal to the ARID/BRIGHT domain in DNA-binding proteins of the Retinoblastoma-binding protein 1 family. : Pssm-ID: 462390 Cd Length: 93 Bit Score: 159.71 E-value: 7.81e-46
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Tudor_ARID4A_rpt1 | cd20459 | first Tudor domain found in AT-rich interactive domain-containing protein 4A (ARID4A) and ... |
4-61 | 2.34e-34 | |||
first Tudor domain found in AT-rich interactive domain-containing protein 4A (ARID4A) and similar proteins; ARID4A, also called retinoblastoma-binding protein 1 (RBBP1 or RBP1), is a leukemia and tumor suppressor involved in epigenetic regulation in leukemia and Prader-Willi/Angelman syndromes. It associates with the mSIN3A histone deacetylase (HDAC) chromatin remodeling complex through its interaction with the breast cancer associated tumor suppressor ING1, the breast cancer metastasis suppressor BRMS1, and the ARID4 family homolog ARID4B ( also known as RBP1L1). ARID4A specifically interacts with retinoblastoma protein (pRb) and shows both HDAC -dependent and -independent repression activities. It also acts as a Runx2 coactivator and is involved in the regulation of osteoblastic differentiation in Runx2-osterix transcriptional cascade. ARID4A contains tandem Tudor domains, a PWWP domain (also known as HATH domain or RBB1NT domain), an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a chromobarrel domain, and a C-terminal R2 domain. The ARID and R2 domains are responsible for the repression activities. The Tudor, PWWP, and chromobarrel domains are all Royal Family domains, but only the chromobarrel domain of ARID4A is responsible for recognizing both dsDNA and methylated histone tails, particularly H4K20me3, in chromatin remodeling and epigenetic regulation. The model corresponds to the first Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. : Pssm-ID: 410530 Cd Length: 58 Bit Score: 125.55 E-value: 2.34e-34
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CBD_RBP1_like | cd18641 | chromo barrel domain of retinoblastoma binding protein 1, and similar proteins; ... |
577-635 | 8.63e-33 | |||
chromo barrel domain of retinoblastoma binding protein 1, and similar proteins; Retinoblastoma-binding protein 1 (RBP1), also termed AT-rich interaction domain 4A, is a ubiquitously expressed nuclear protein. RBP1 is a tumor and leukemia suppressor that binds both methylated histone tails and DNA, and is involved in epigenetic regulation in leukemia and Prader-Willi/Angelman syndromes. The chromo barrel domain of RBP1 has been reported to recognize histone H4K20me3 weakly, and this binding is enhanced by the simultaneous binding of DNA. RBP1 binds directly, with several other proteins, to retinoblastoma protein (pRB) which regulates cell proliferation; pRB represses transcription by recruiting RBP1. SH3-fold-beta-barrel domains of the chromo-like superfamily include chromodomains, chromo shadow domains, and chromo barrel domains, and are implicated in the recognition of lysine-methylated histone tails and nucleic acids. The chromodomain differs, in that it lacks the first strand of the SH3-fold-beta-barrel. This first strand is altered by insertion in the chromo shadow domains, and chromo barrel domains are typical SH3-fold-beta-barrel domains with sequence similarity to the canonical chromodomain. : Pssm-ID: 350843 [Multi-domain] Cd Length: 59 Bit Score: 121.23 E-value: 8.63e-33
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Tudor_ARID4_rpt2 | cd20390 | second Tudor domain found in AT-rich interactive domain-containing protein ARID4 family; The ... |
62-114 | 5.04e-30 | |||
second Tudor domain found in AT-rich interactive domain-containing protein ARID4 family; The family contains ARID4A and its paralog ARID4B, both of which are retinoblastoma (RB)-binding proteins that function as coactivators to enhance the androgen receptor (AR) and RB transcriptional activity, and play important roles in the AR and RB pathways to control male fertility. They also act as the leukemia and tumor suppressors involved in epigenetic regulation in leukemia and Prader-Willi/Angelman syndromes. Moreover, they associate with the mSIN3A histone deacetylase (HDAC) chromatin remodeling complex through their interaction with each other, as well as with the breast cancer associated tumor suppressor ING1 and the breast cancer metastasis suppressor BRMS1. Both ARID4A and ARID4B contain tandem Tudor domains, a PWWP domain (also known as HATH domain or RBB1NT domain), an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a chromobarrel domain, and a C-terminal R2 domain. The model corresponds to the second Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. : Pssm-ID: 410461 Cd Length: 53 Bit Score: 113.14 E-value: 5.04e-30
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Name | Accession | Description | Interval | E-value | |||
ARID_ARID4A | cd16882 | ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 4A (ARID4A) ... |
311-397 | 3.96e-57 | |||
ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 4A (ARID4A) and similar proteins; ARID4A, also called retinoblastoma-binding protein 1 (RBBP1, or RBP1), is a leukemia and tumor suppressor involved in epigenetic regulation in leukemia and Prader-Willi/Angelman syndrome. It associates with the mSIN3A histone deacetylase (HDAC) chromatin remodeling complex through the interaction with the breast cancer associated tumor suppressor ING1, the breast cancer metastasis suppressor BRMS1, and the ARID4 family homolog ARID4B (also known as RBP1L1). ARID4A specifically interacts with retinoblastoma protein (pRb) and shows both HDAC-dependent and -independent repression activities. It is also involved in the pocket domain of pRb-mediated repression of E2F-dependent transcription and cellular proliferation. Moreover, it acts as a Runx2 coactivator and is involved in the regulation of osteoblastic differentiation in Runx2-osterix transcriptional cascade. ARID4A contains a Tudor domain, a PWWP domain (also known as HATH domain or RBB1NT domain), an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a chromobarrel domain, and a C-terminal R2 domain. The ARID and R2 domains are responsible for the repression activities. The Tudor, PWWP, and chromobarrel domains are all Royal Family domains, but only chromobarrel domain of ARID4A is responsible for recognizing both dsDNA and methylated histone tails, particularly H4K20me3, in chromatin remodeling and epigenetic regulation. Pssm-ID: 350646 Cd Length: 87 Bit Score: 191.73 E-value: 3.96e-57
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RBB1NT | pfam08169 | RBB1NT (NUC162) domain; This domain is found N terminal to the ARID/BRIGHT domain in ... |
170-262 | 7.81e-46 | |||
RBB1NT (NUC162) domain; This domain is found N terminal to the ARID/BRIGHT domain in DNA-binding proteins of the Retinoblastoma-binding protein 1 family. Pssm-ID: 462390 Cd Length: 93 Bit Score: 159.71 E-value: 7.81e-46
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Tudor_ARID4A_rpt1 | cd20459 | first Tudor domain found in AT-rich interactive domain-containing protein 4A (ARID4A) and ... |
4-61 | 2.34e-34 | |||
first Tudor domain found in AT-rich interactive domain-containing protein 4A (ARID4A) and similar proteins; ARID4A, also called retinoblastoma-binding protein 1 (RBBP1 or RBP1), is a leukemia and tumor suppressor involved in epigenetic regulation in leukemia and Prader-Willi/Angelman syndromes. It associates with the mSIN3A histone deacetylase (HDAC) chromatin remodeling complex through its interaction with the breast cancer associated tumor suppressor ING1, the breast cancer metastasis suppressor BRMS1, and the ARID4 family homolog ARID4B ( also known as RBP1L1). ARID4A specifically interacts with retinoblastoma protein (pRb) and shows both HDAC -dependent and -independent repression activities. It also acts as a Runx2 coactivator and is involved in the regulation of osteoblastic differentiation in Runx2-osterix transcriptional cascade. ARID4A contains tandem Tudor domains, a PWWP domain (also known as HATH domain or RBB1NT domain), an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a chromobarrel domain, and a C-terminal R2 domain. The ARID and R2 domains are responsible for the repression activities. The Tudor, PWWP, and chromobarrel domains are all Royal Family domains, but only the chromobarrel domain of ARID4A is responsible for recognizing both dsDNA and methylated histone tails, particularly H4K20me3, in chromatin remodeling and epigenetic regulation. The model corresponds to the first Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. Pssm-ID: 410530 Cd Length: 58 Bit Score: 125.55 E-value: 2.34e-34
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BRIGHT | smart00501 | BRIGHT, ARID (A/T-rich interaction domain) domain; DNA-binding domain containing a ... |
312-401 | 2.20e-33 | |||
BRIGHT, ARID (A/T-rich interaction domain) domain; DNA-binding domain containing a helix-turn-helix structure Pssm-ID: 128777 [Multi-domain] Cd Length: 93 Bit Score: 123.92 E-value: 2.20e-33
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CBD_RBP1_like | cd18641 | chromo barrel domain of retinoblastoma binding protein 1, and similar proteins; ... |
577-635 | 8.63e-33 | |||
chromo barrel domain of retinoblastoma binding protein 1, and similar proteins; Retinoblastoma-binding protein 1 (RBP1), also termed AT-rich interaction domain 4A, is a ubiquitously expressed nuclear protein. RBP1 is a tumor and leukemia suppressor that binds both methylated histone tails and DNA, and is involved in epigenetic regulation in leukemia and Prader-Willi/Angelman syndromes. The chromo barrel domain of RBP1 has been reported to recognize histone H4K20me3 weakly, and this binding is enhanced by the simultaneous binding of DNA. RBP1 binds directly, with several other proteins, to retinoblastoma protein (pRB) which regulates cell proliferation; pRB represses transcription by recruiting RBP1. SH3-fold-beta-barrel domains of the chromo-like superfamily include chromodomains, chromo shadow domains, and chromo barrel domains, and are implicated in the recognition of lysine-methylated histone tails and nucleic acids. The chromodomain differs, in that it lacks the first strand of the SH3-fold-beta-barrel. This first strand is altered by insertion in the chromo shadow domains, and chromo barrel domains are typical SH3-fold-beta-barrel domains with sequence similarity to the canonical chromodomain. Pssm-ID: 350843 [Multi-domain] Cd Length: 59 Bit Score: 121.23 E-value: 8.63e-33
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Tudor_ARID4_rpt2 | cd20390 | second Tudor domain found in AT-rich interactive domain-containing protein ARID4 family; The ... |
62-114 | 5.04e-30 | |||
second Tudor domain found in AT-rich interactive domain-containing protein ARID4 family; The family contains ARID4A and its paralog ARID4B, both of which are retinoblastoma (RB)-binding proteins that function as coactivators to enhance the androgen receptor (AR) and RB transcriptional activity, and play important roles in the AR and RB pathways to control male fertility. They also act as the leukemia and tumor suppressors involved in epigenetic regulation in leukemia and Prader-Willi/Angelman syndromes. Moreover, they associate with the mSIN3A histone deacetylase (HDAC) chromatin remodeling complex through their interaction with each other, as well as with the breast cancer associated tumor suppressor ING1 and the breast cancer metastasis suppressor BRMS1. Both ARID4A and ARID4B contain tandem Tudor domains, a PWWP domain (also known as HATH domain or RBB1NT domain), an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a chromobarrel domain, and a C-terminal R2 domain. The model corresponds to the second Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. Pssm-ID: 410461 Cd Length: 53 Bit Score: 113.14 E-value: 5.04e-30
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ARID | pfam01388 | ARID/BRIGHT DNA binding domain; This domain is know as ARID for AT-Rich Interaction Domain, ... |
312-397 | 7.53e-29 | |||
ARID/BRIGHT DNA binding domain; This domain is know as ARID for AT-Rich Interaction Domain, and also known as the BRIGHT domain. Pssm-ID: 460187 Cd Length: 87 Bit Score: 110.79 E-value: 7.53e-29
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Tudor-knot | pfam11717 | RNA binding activity-knot of a chromodomain; This is a novel knotted tudor domain which is ... |
576-628 | 4.76e-09 | |||
RNA binding activity-knot of a chromodomain; This is a novel knotted tudor domain which is required for binding to RNA. The know influences the loop conformation of the helical turn Ht2 - residues 61-6 3- that is located at the side opposite the knot in the tudor domain-chromodomain; stabilization of Ht2 is essential for RNA binding. Pssm-ID: 432022 [Multi-domain] Cd Length: 55 Bit Score: 53.36 E-value: 4.76e-09
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TUDOR | smart00333 | Tudor domain; Domain of unknown function present in several RNA-binding proteins. 10 copies in ... |
58-113 | 3.46e-07 | |||
Tudor domain; Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished). Pssm-ID: 197660 Cd Length: 57 Bit Score: 48.04 E-value: 3.46e-07
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CHROMO | smart00298 | Chromatin organization modifier domain; |
593-629 | 7.67e-06 | |||
Chromatin organization modifier domain; Pssm-ID: 214605 [Multi-domain] Cd Length: 55 Bit Score: 44.51 E-value: 7.67e-06
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PLN00104 | PLN00104 | MYST -like histone acetyltransferase; Provisional |
576-628 | 2.09e-03 | |||
MYST -like histone acetyltransferase; Provisional Pssm-ID: 215056 [Multi-domain] Cd Length: 450 Bit Score: 42.05 E-value: 2.09e-03
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Name | Accession | Description | Interval | E-value | |||
ARID_ARID4A | cd16882 | ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 4A (ARID4A) ... |
311-397 | 3.96e-57 | |||
ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 4A (ARID4A) and similar proteins; ARID4A, also called retinoblastoma-binding protein 1 (RBBP1, or RBP1), is a leukemia and tumor suppressor involved in epigenetic regulation in leukemia and Prader-Willi/Angelman syndrome. It associates with the mSIN3A histone deacetylase (HDAC) chromatin remodeling complex through the interaction with the breast cancer associated tumor suppressor ING1, the breast cancer metastasis suppressor BRMS1, and the ARID4 family homolog ARID4B (also known as RBP1L1). ARID4A specifically interacts with retinoblastoma protein (pRb) and shows both HDAC-dependent and -independent repression activities. It is also involved in the pocket domain of pRb-mediated repression of E2F-dependent transcription and cellular proliferation. Moreover, it acts as a Runx2 coactivator and is involved in the regulation of osteoblastic differentiation in Runx2-osterix transcriptional cascade. ARID4A contains a Tudor domain, a PWWP domain (also known as HATH domain or RBB1NT domain), an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a chromobarrel domain, and a C-terminal R2 domain. The ARID and R2 domains are responsible for the repression activities. The Tudor, PWWP, and chromobarrel domains are all Royal Family domains, but only chromobarrel domain of ARID4A is responsible for recognizing both dsDNA and methylated histone tails, particularly H4K20me3, in chromatin remodeling and epigenetic regulation. Pssm-ID: 350646 Cd Length: 87 Bit Score: 191.73 E-value: 3.96e-57
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ARID_ARID4B | cd16883 | ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 4B (ARID4B) ... |
312-402 | 9.24e-54 | |||
ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 4B (ARID4B) and similar proteins; ARID4B, also called 180 kDa Sin3-associated polypeptide (p180), breast cancer-associated antigen BRCAA1, histone deacetylase complex subunit SAP180, or retinoblastoma-binding protein 1-like 1 (RBP1L1, or RBBP1L1), is a tumor suppressor involved in epigenetic regulation in leukemia and Prader-Willi/Angelman syndrome. It associates with the mSIN3A histone deacetylase (HDAC) chromatin remodeling complex through the interaction with the breast cancer associated tumor suppressor ING1, the breast cancer metastasis suppressor BRMS1, and the ARID4 family homolog ARID4A ( also known as RBP1). ARID4B plays a causative role in metastatic progression of breast cancer. It may also be associated with regulating cell cycle. ARID4B contains a Tudor domain, a PWWP domain (also known as HATH domain or RBB1NT domain), an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a chromobarrel domain, and a C-terminal R2 domain. Pssm-ID: 350647 Cd Length: 92 Bit Score: 182.09 E-value: 9.24e-54
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ARID_ARID4 | cd16868 | ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing proteins ARID4A, ... |
312-397 | 4.08e-52 | |||
ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing proteins ARID4A, ARID4B and similar proteins; This subfamily contains ARID4A and its paralog ARID4B, both of which are retinoblastoma (Rb)-binding proteins that function as coactivators to enhance the androgen receptor (AR) and Rb transcriptional activity, and play important roles in the AR and Rb pathways to control male fertility. They also act as the leukemia and tumor suppressors involved in epigenetic regulation in leukemia and Prader-Willi/Angelman syndrome. Moreover, they associate with the mSIN3A histone deacetylase (HDAC) chromatin remodeling complex through the interaction with each other, as well as with the breast cancer associated tumor suppressor ING1 and the breast cancer metastasis suppressor BRMS1. Both ARID4A and ARID4B contain a Tudor domain, a PWWP domain (also known as HATH domain or RBB1NT domain), an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a chromobarrel domain, and a C-terminal R2 domain. Pssm-ID: 350632 Cd Length: 87 Bit Score: 177.20 E-value: 4.08e-52
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RBB1NT | pfam08169 | RBB1NT (NUC162) domain; This domain is found N terminal to the ARID/BRIGHT domain in ... |
170-262 | 7.81e-46 | |||
RBB1NT (NUC162) domain; This domain is found N terminal to the ARID/BRIGHT domain in DNA-binding proteins of the Retinoblastoma-binding protein 1 family. Pssm-ID: 462390 Cd Length: 93 Bit Score: 159.71 E-value: 7.81e-46
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Tudor_ARID4A_rpt1 | cd20459 | first Tudor domain found in AT-rich interactive domain-containing protein 4A (ARID4A) and ... |
4-61 | 2.34e-34 | |||
first Tudor domain found in AT-rich interactive domain-containing protein 4A (ARID4A) and similar proteins; ARID4A, also called retinoblastoma-binding protein 1 (RBBP1 or RBP1), is a leukemia and tumor suppressor involved in epigenetic regulation in leukemia and Prader-Willi/Angelman syndromes. It associates with the mSIN3A histone deacetylase (HDAC) chromatin remodeling complex through its interaction with the breast cancer associated tumor suppressor ING1, the breast cancer metastasis suppressor BRMS1, and the ARID4 family homolog ARID4B ( also known as RBP1L1). ARID4A specifically interacts with retinoblastoma protein (pRb) and shows both HDAC -dependent and -independent repression activities. It also acts as a Runx2 coactivator and is involved in the regulation of osteoblastic differentiation in Runx2-osterix transcriptional cascade. ARID4A contains tandem Tudor domains, a PWWP domain (also known as HATH domain or RBB1NT domain), an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a chromobarrel domain, and a C-terminal R2 domain. The ARID and R2 domains are responsible for the repression activities. The Tudor, PWWP, and chromobarrel domains are all Royal Family domains, but only the chromobarrel domain of ARID4A is responsible for recognizing both dsDNA and methylated histone tails, particularly H4K20me3, in chromatin remodeling and epigenetic regulation. The model corresponds to the first Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. Pssm-ID: 410530 Cd Length: 58 Bit Score: 125.55 E-value: 2.34e-34
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BRIGHT | smart00501 | BRIGHT, ARID (A/T-rich interaction domain) domain; DNA-binding domain containing a ... |
312-401 | 2.20e-33 | |||
BRIGHT, ARID (A/T-rich interaction domain) domain; DNA-binding domain containing a helix-turn-helix structure Pssm-ID: 128777 [Multi-domain] Cd Length: 93 Bit Score: 123.92 E-value: 2.20e-33
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CBD_RBP1_like | cd18641 | chromo barrel domain of retinoblastoma binding protein 1, and similar proteins; ... |
577-635 | 8.63e-33 | |||
chromo barrel domain of retinoblastoma binding protein 1, and similar proteins; Retinoblastoma-binding protein 1 (RBP1), also termed AT-rich interaction domain 4A, is a ubiquitously expressed nuclear protein. RBP1 is a tumor and leukemia suppressor that binds both methylated histone tails and DNA, and is involved in epigenetic regulation in leukemia and Prader-Willi/Angelman syndromes. The chromo barrel domain of RBP1 has been reported to recognize histone H4K20me3 weakly, and this binding is enhanced by the simultaneous binding of DNA. RBP1 binds directly, with several other proteins, to retinoblastoma protein (pRB) which regulates cell proliferation; pRB represses transcription by recruiting RBP1. SH3-fold-beta-barrel domains of the chromo-like superfamily include chromodomains, chromo shadow domains, and chromo barrel domains, and are implicated in the recognition of lysine-methylated histone tails and nucleic acids. The chromodomain differs, in that it lacks the first strand of the SH3-fold-beta-barrel. This first strand is altered by insertion in the chromo shadow domains, and chromo barrel domains are typical SH3-fold-beta-barrel domains with sequence similarity to the canonical chromodomain. Pssm-ID: 350843 [Multi-domain] Cd Length: 59 Bit Score: 121.23 E-value: 8.63e-33
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ARID | smart01014 | ARID/BRIGHT DNA binding domain; Members of the recently discovered ARID (AT-rich interaction ... |
312-397 | 1.50e-30 | |||
ARID/BRIGHT DNA binding domain; Members of the recently discovered ARID (AT-rich interaction domain) family of DNA-binding proteins are found in fungi and invertebrate and vertebrate metazoans. ARID-encoding genes are involved in a variety of biological processes including embryonic development, cell lineage gene regulation and cell cycle control. Although the specific roles of this domain and of ARID-containing proteins in transcriptional regulation are yet to be elucidated, they include both positive and negative transcriptional regulation and a likely involvement in the modification of chromatin structure. The basic structure of the ARID domain domain appears to be a series of six alpha-helices separated by beta-strands, loops, or turns, but the structured region may extend to an additional helix at either or both ends of the basic six. Based on primary sequence homology, they can be partitioned into three structural classes: Minimal ARID proteins that consist of a core domain formed by six alpha helices; ARID proteins that supplement the core domain with an N-terminal alpha-helix; and Extended-ARID proteins, which contain the core domain and additional alpha-helices at their N- and C-termini. Pssm-ID: 198082 [Multi-domain] Cd Length: 88 Bit Score: 115.79 E-value: 1.50e-30
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Tudor_ARID4_rpt2 | cd20390 | second Tudor domain found in AT-rich interactive domain-containing protein ARID4 family; The ... |
62-114 | 5.04e-30 | |||
second Tudor domain found in AT-rich interactive domain-containing protein ARID4 family; The family contains ARID4A and its paralog ARID4B, both of which are retinoblastoma (RB)-binding proteins that function as coactivators to enhance the androgen receptor (AR) and RB transcriptional activity, and play important roles in the AR and RB pathways to control male fertility. They also act as the leukemia and tumor suppressors involved in epigenetic regulation in leukemia and Prader-Willi/Angelman syndromes. Moreover, they associate with the mSIN3A histone deacetylase (HDAC) chromatin remodeling complex through their interaction with each other, as well as with the breast cancer associated tumor suppressor ING1 and the breast cancer metastasis suppressor BRMS1. Both ARID4A and ARID4B contain tandem Tudor domains, a PWWP domain (also known as HATH domain or RBB1NT domain), an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a chromobarrel domain, and a C-terminal R2 domain. The model corresponds to the second Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. Pssm-ID: 410461 Cd Length: 53 Bit Score: 113.14 E-value: 5.04e-30
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Tudor_ARID4B_rpt2 | cd20462 | second Tudor domain found in AT-rich interactive domain-containing protein 4B (ARID4B) and ... |
62-118 | 5.17e-30 | |||
second Tudor domain found in AT-rich interactive domain-containing protein 4B (ARID4B) and similar proteins; ARID4B, also called 180 kDa Sin3-associated polypeptide (p180), breast cancer-associated antigen BRCAA1, histone deacetylase complex subunit SAP180, or retinoblastoma-binding protein 1-like 1 (RBP1L1 or RBBP1L1), is a leukemia and tumor suppressor involved in epigenetic regulation in leukemia and Prader-Willi/Angelman syndromes. It associates with the mSIN3A histone deacetylase (HDAC) chromatin remodeling complex through its interaction with the breast cancer associated tumor suppressor ING1, the breast cancer metastasis suppressor BRMS1, and ARID4A ( also known as RBP1). ARID4B plays a causative role in metastatic progression of breast cancer. It may also be associated with regulating the cell cycle. ARID4B contains tandem Tudor domains, a PWWP domain (also known as HATH domain or RBB1NT domain), an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a chromobarrel domain, and a C-terminal R2 domain. The model corresponds to the second Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. Pssm-ID: 410533 Cd Length: 57 Bit Score: 113.23 E-value: 5.17e-30
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Tudor_ARID4A_rpt2 | cd20461 | second Tudor domain found in AT-rich interactive domain-containing protein 4A (ARID4A) and ... |
62-121 | 1.60e-29 | |||
second Tudor domain found in AT-rich interactive domain-containing protein 4A (ARID4A) and similar proteins; ARID4A, also called retinoblastoma-binding protein 1 (RBBP1 or RBP1), is a leukemia and tumor suppressor involved in epigenetic regulation in leukemia and Prader-Willi/Angelman syndromes. It associates with the mSIN3A histone deacetylase (HDAC) chromatin remodeling complex through its interaction with the breast cancer associated tumor suppressor ING1, the breast cancer metastasis suppressor BRMS1, and the ARID4 family homolog ARID4B ( also known as RBP1L1). ARID4A specifically interacts with retinoblastoma protein (pRb) and shows both HDAC -dependent and -independent repression activities. It also acts as a Runx2 coactivator and is involved in the regulation of osteoblastic differentiation in Runx2-osterix transcriptional cascade. ARID4A contains tandem Tudor domains, a PWWP domain (also known as HATH domain or RBB1NT domain), an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a chromobarrel domain, and a C-terminal R2 domain. The ARID and R2 domains are responsible for the repression activities. The Tudor, PWWP, and chromobarrel domains are all Royal Family domains, but only the chromobarrel domain of ARID4A is responsible for recognizing both dsDNA and methylated histone tails, particularly H4K20me3, in chromatin remodeling and epigenetic regulation. The model corresponds to the second Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. Pssm-ID: 410532 Cd Length: 60 Bit Score: 111.74 E-value: 1.60e-29
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ARID | pfam01388 | ARID/BRIGHT DNA binding domain; This domain is know as ARID for AT-Rich Interaction Domain, ... |
312-397 | 7.53e-29 | |||
ARID/BRIGHT DNA binding domain; This domain is know as ARID for AT-Rich Interaction Domain, and also known as the BRIGHT domain. Pssm-ID: 460187 Cd Length: 87 Bit Score: 110.79 E-value: 7.53e-29
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Tudor_ARID4B_rpt1 | cd20460 | first Tudor domain found in AT-rich interactive domain-containing protein 4B (ARID4B) and ... |
1-61 | 1.08e-27 | |||
first Tudor domain found in AT-rich interactive domain-containing protein 4B (ARID4B) and similar proteins; ARID4B, also called 180 kDa Sin3-associated polypeptide (p180), breast cancer-associated antigen BRCAA1, histone deacetylase complex subunit SAP180, or retinoblastoma-binding protein 1-like 1 (RBP1L1 or RBBP1L1), is a leukemia and tumor suppressor involved in epigenetic regulation in leukemia and Prader-Willi/Angelman syndromes. It associates with the mSIN3A histone deacetylase (HDAC) chromatin remodeling complex through its interaction with the breast cancer associated tumor suppressor ING1, the breast cancer metastasis suppressor BRMS1, and ARID4A ( also known as RBP1). ARID4B plays a causative role in metastatic progression of breast cancer. It may also be associated with regulating the cell cycle. ARID4B contains tandem Tudor domains, a PWWP domain (also known as HATH domain or RBB1NT domain), an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a chromobarrel domain, and a C-terminal R2 domain. The model corresponds to the first Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. Pssm-ID: 410531 Cd Length: 61 Bit Score: 106.67 E-value: 1.08e-27
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ARID | cd16100 | ARID/BRIGHT DNA binding domain family; The AT-rich interaction domain (ARID) family of ... |
312-397 | 1.26e-27 | |||
ARID/BRIGHT DNA binding domain family; The AT-rich interaction domain (ARID) family of transcription factors, found in a broad array of organisms from fungi to mammals, is characterized by a highly conserved, helix-turn-helix DNA binding domain that binds to the major groove of DNA. The ARID domain, also called BRIGHT, was first identified in the mouse B-cell-specific transcription factor Bright and in the product of the dead ringer (dri) gene of Drosophila melanogaster. ARID family members are implicated in normal development, differentiation, cell cycle regulation, transcriptional activation and chromatin remodeling. Different family members exhibit different DNA-binding properties. Drosophila Dri, mammalian ARID3A/3B/3C and ARID5A/5B, selectively bind AT-rich sites. However, ARID1A/1B, Drosophila Osa, yeast SWI1, ARID2, ARID4A/4B, JARID1A/1B/1C/1D, and JARID2, bind DNA without sequence specificity. Pssm-ID: 350627 Cd Length: 87 Bit Score: 107.44 E-value: 1.26e-27
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Tudor_ARID4_rpt1 | cd20389 | first Tudor domain found in AT-rich interactive domain-containing protein ARID4 family; The ... |
9-61 | 1.68e-26 | |||
first Tudor domain found in AT-rich interactive domain-containing protein ARID4 family; The family contains ARID4A and its paralog ARID4B, both of which are retinoblastoma (RB)-binding proteins that function as coactivators to enhance the androgen receptor (AR) and RB transcriptional activity, and play important roles in the AR and RB pathways to control male fertility. They also act as the leukemia and tumor suppressors involved in epigenetic regulation in leukemia and Prader-Willi/Angelman syndromes. Moreover, they associate with the mSIN3A histone deacetylase (HDAC) chromatin remodeling complex through their interaction with each other, as well as with the breast cancer associated tumor suppressor ING1 and the breast cancer metastasis suppressor BRMS1. Both ARID4A and ARID4B contain tandem Tudor domains, a PWWP domain (also known as HATH domain or RBB1NT domain), an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a chromobarrel domain, and a C-terminal R2 domain. The model corresponds to the first Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. Pssm-ID: 410460 Cd Length: 53 Bit Score: 103.11 E-value: 1.68e-26
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CBD | cd18643 | chromo barrel domain of MOF acetyltransferase, and similar proteins; This group includes the ... |
577-633 | 1.84e-21 | |||
chromo barrel domain of MOF acetyltransferase, and similar proteins; This group includes the chromo barrel domains found in human Tat-interactive protein 60 (TIP60, (also known as KAT5 or HTATIP), Drosophila melanogaster males-absent on the first (MOF) protein, human male-specific lethal (MSL) complex subunit 3 (MSL3), and retinoblastoma binding protein 1. SH3-fold-beta-barrel domains of the chromo-like superfamily include chromodomains, chromo shadow domains, and chromo barrel domains, and are implicated in the recognition of lysine-methylated histone tails and nucleic acids. The chromodomain differs, in that it lacks the first strand of the SH3-fold-beta-barrel. This first strand is altered by insertion in the chromo shadow domains, and chromo barrel domains are typical SH3-fold-beta-barrel domains with sequence similarity to the canonical chromo domain. The chromobarrel domains include a MOF-like subgroup which may be may be auto-inhibited, i.e. they seem to have occluded peptide binding sites. Pssm-ID: 350845 [Multi-domain] Cd Length: 61 Bit Score: 88.77 E-value: 1.84e-21
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ARID_ARID5 | cd16869 | ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing proteins ARID5A, ... |
314-397 | 1.96e-19 | |||
ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing proteins ARID5A, ARID5B, and similar proteins; This subfamily contains ARID5A and its paralog ARID5B. ARID5A, also called modulator recognition factor 1 (MRF-1), is an estrogen receptor alpha (ER alpha)-interacting protein that is expressed abundantly in cardiovascular tissues and suppresses ER alpha-induced transactivation. It also plays an important role in the promotion of inflammatory processes and autoimmune diseases. ARID5B, also called MRF1-like protein or modulator recognition factor 2 (MRF-2), is a DNA-binding protein that directly interacts with plant homeodomain (PHD) finger 2 (PHF2) to form a protein kinase A (PKA)-dependent PHF2-ARID5B histone H3K9Me2 demethylase complex. It also functions as a transcriptional co-regulator for the transcription factor sex determining region Y (SRY)-box protein 9 (Sox9) and promotes chondrogenesis through histone modification. Moreover, ARID5B is highly expressed in the cardiovascular system and may play essential roles in the phenotypic change of smooth muscle cells (SMCs) through its regulation of SMC differentiation. Both ARID5A and ARID5B contain an AT-rich DNA-interacting domain (ARID, also known as BRIGHT). Pssm-ID: 350633 Cd Length: 87 Bit Score: 83.88 E-value: 1.96e-19
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ARID_Swi1p-like | cd16871 | ARID/BRIGHT DNA binding domain of yeast SWI/SNF chromatin-remodeling complex subunit Swi1p and ... |
312-398 | 1.24e-17 | |||
ARID/BRIGHT DNA binding domain of yeast SWI/SNF chromatin-remodeling complex subunit Swi1p and similar proteins; Saccharomyces cerevisiae Swi1p, also called SWI/SNF chromatin-remodeling complex subunit SWI1, regulatory protein GAM3, or transcription regulatory protein ADR6, is a transcription regulatory protein that is a subunit of the SWI/SNF complex, which plays critical roles in the regulation of gene transcription and expression. It can exist as a prion, [SWI(+)], which demonstrates a link between prionogenesis and global transcriptional regulation. Swi1p contains an AT-rich DNA-interacting domain (ARID, also known as BRIGHT) that binds DNA nonspecifically. This subfamily also includes Schizosaccharomyces pombe SWI/SNF chromatin-remodeling complex subunit sol1 (sol1p, also known as switch one-like protein). sol1p is a homolog of S. cerevisiae Swi1p and is also a part of SWI/SNF chromatin-remodeling complex. Pssm-ID: 350635 Cd Length: 90 Bit Score: 78.83 E-value: 1.24e-17
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ARID_ARID1A-like | cd16865 | ARID/BRIGHT DNA binding domain found in AT-rich interactive domain-containing proteins ARID1A, ... |
312-401 | 4.68e-17 | |||
ARID/BRIGHT DNA binding domain found in AT-rich interactive domain-containing proteins ARID1A, ARID1B and similar proteins; This subfamily contains ARID1A and its paralog ARID1B. They are mutually exclusive components of human SWItch/Sucrose NonFermentable (SWI/SNF) chromatin remodeling protein complexes, but display different functions in development and cell-cycle control. SWI/SNF complexes containing ARID1A have an antiproliferative function, whereas the one harboring ARID1B shows a pro-proliferative function. ARID1A functions as an important tumor suppressor in various tumor types. It has been implicated in cell-cycle arrest, as well as in the interactions with p53 and BRG1/BRM and with topoisomerase II alpha. ARID1B may be considered as a potential therapeutic target for ARID1A-mutant cancers. Moreover, mutations in the ARID1B gene cause Coffin-Siris syndrome, exhibiting developmental defects, and haplo-insufficiency of ARID1B is a frequent cause of intellectual disability. Mutations in the ARID1B gene also have been found in many cancers. Both ARID1A and ARID1B contain an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), which binds DNA in a non-sequence-specific manner. Pssm-ID: 350629 Cd Length: 93 Bit Score: 77.32 E-value: 4.68e-17
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ARID_ARID3 | cd16867 | ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing proteins ARID3A, ... |
312-397 | 1.05e-16 | |||
ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing proteins ARID3A, ARID3B, ARID3C, dead ringer (Dri) from Drosophila melanogaster, and similar proteins; The ARID3 subfamily includes AT-rich interactive domain (ARID, also known as BRIGHT)-containing proteins ARID3A, ARID3B and ARID3C, which are the most direct mammalian counterparts of the Drosophila "dead ringer" protein Dri. They consist of an acidic N-terminal region of unknown function, the central ARID matrix association (or attachment) region (MAR)-DNA binding domain, a SUMO-I conjugation (SUMO) motif, and a multifunctional homomerization/nuclear export REKLES domain in the C-terminal third of the molecule. The ARID domain in this subfamily has been described as the "extended" or e-ARID due to additional conserved sequences at both the N and C termini of the core ARID region. The REKLES domain is found only in the ARID3 subfamily. It has co-evolved with and regulates functional properties of the ARID DNA-binding domain. Pssm-ID: 350631 Cd Length: 118 Bit Score: 77.53 E-value: 1.05e-16
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ARID_Dri-like | cd16881 | ARID/BRIGHT DNA binding domain of dead ringer (Dri) from Drosophila melanogaster and similar ... |
312-397 | 1.61e-16 | |||
ARID/BRIGHT DNA binding domain of dead ringer (Dri) from Drosophila melanogaster and similar proteins; Dri, also termed retained (retn), is a nuclear protein with a sequence-specific DNA-binding domain termed AT-rich DNA-interacting domain (ARID, also known as BRIGHT). It is a founding member of the ARID family. Sequence comparison shows that DRI belongs to the "extended" or e-ARID subfamily, which exhibits an extended region of similarity either side of the ARID. Dri plays an important role in embryogenesis. It functions as an essential transcription factor involved in aspects of dorsal/ventral and anterior/posterior axis patterning, as well as myogenesis and hindgut development. Pssm-ID: 350645 Cd Length: 125 Bit Score: 77.24 E-value: 1.61e-16
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ARID_ARID3C | cd16880 | ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 3C (ARID3C) ... |
312-397 | 3.32e-16 | |||
ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 3C (ARID3C) and similar proteins; ARID3C, also called Brightlike, is a new ARID3 family transcription factor that co-activates ARID3A-mediated immunoglobulin gene transcription. It also functions as a potential regulator of early events in B cell antigen receptor (BCR) signaling. ARID3C contains an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a SUMO-I conjugation (SUMO) motif and a multifunctional homomerization/nuclear export REKLES domain, which consists of two subdomains: a modestly conserved N-terminal REKLES alpha and a highly conserved (among ARID3 orthologous proteins) C-terminal REKLES beta. Pssm-ID: 350644 Cd Length: 127 Bit Score: 76.22 E-value: 3.32e-16
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MBT_PHF20L1-like | cd20104 | malignant brain tumor (MBT) repeat found in PHD finger protein 20-like protein 1 (PHF20L1) and ... |
576-631 | 7.53e-16 | |||
malignant brain tumor (MBT) repeat found in PHD finger protein 20-like protein 1 (PHF20L1) and similar domains; PHF20L1 associates with SOX2, antagonizes SOX2 ubiquitination and the sequential degradation induced by MLL1/WDR5 complexes. It binds both monomethylated Lys-42 and Lys-117 in SOX2 and thereby prevents SOX2 proteolysis. PHF20L1 also reads and controls enzyme levels of methylated DNMT1 in cells, thus representing a novel antagonist of DNMT1 degradation. PHF20L1 contains one MBT (malignant brain tumor) repeat. The MBT repeat is a protein module that recognizes methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine. This model corresponds to the MBT repeat of PHF20L1 and similar domains that contains the semi-aromatic cage that may bind methylated lysine residues. Pssm-ID: 439094 [Multi-domain] Cd Length: 60 Bit Score: 73.04 E-value: 7.53e-16
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ARID_ARID3B | cd16879 | ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 3B (ARID3B) ... |
312-397 | 8.30e-16 | |||
ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 3B (ARID3B) and similar proteins; ARID3B, also called Bright and dead ringer protein, or Bright-Dri-like protein (Bdp), is a DNA binding protein involved in cellular immortalization, epithelial-mesenchymal transition (EMT), and tumorigenesis. Its expression is differentially regulated in normal and malignant tissues. It is required for heart development by regulating the motility and differentiation of heart progenitors. ARID3B is overexpressed in neuroblastoma and ovarian cancer. It acts as a novel target with roles in cell motility in breast cancer cells, promotes migration of mouse embryo fibroblasts (MEFs) and breast cancer cells, and induces tumor necrosis factor alpha (TNFalpha)-mediated apoptosis. ARID3B contains an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a SUMO-I conjugation (SUMO) motif and a multifunctional homomerization/nuclear export REKLES domain, which consists of two subdomains: a modestly conserved N-terminal REKLES alpha and a highly conserved (among ARID3 orthologous proteins) C-terminal REKLES beta. Pssm-ID: 350643 Cd Length: 126 Bit Score: 75.05 E-value: 8.30e-16
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ARID_ARID3A | cd16878 | ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 3A (ARID3A) ... |
312-397 | 1.40e-14 | |||
ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 3A (ARID3A) and similar proteins; ARID3A, also called B-cell regulator of IgH transcription (Bright), dead ringer-like protein 1 (Dril1), or E2F-binding protein 1 (E2FBP1), is an ubiquitously expressed DNA-binding protein that has been implicated in embryonic patterning, cell lineage gene regulation, and cell cycle control, chromatin remodeling and transcriptional regulation. It was originally identified as a B cell-specific trans-activator of immunoglobulin heavy-chain (IgH) transcription, which increases immunoglobulin transcription in antigen-activated B cells and plays regulatory roles in hematopoiesis. It also functions as an E2F transcription regulator, inducing promyelocytic leukemia protein (PML) reduction and suppressing the formation of PML-nuclear bodies. It antagonizes the p16(INK4A)-Rb tumor suppressor machinery by regulating PML stability. ARID3A transcriptional activity can be modulated by SUMO (Small Ubiquitin-related Modifier) modification through the interaction with the SUMO-conjugating enzyme Ubc9. ARID3A also plays an important role in marginal zone B lymphocyte development and autoantibody production. Furthermore, ARID3A is a direct p53 target gene. It controls cell growth in a p53-dependent manner. ARID3A contains an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a SUMO-I conjugation (SUMO) motif and a multifunctional homomerization/nuclear export REKLES domain, which consists of two subdomains: a modestly conserved N-terminal REKLES alpha and a highly conserved (among ARID3 orthologous proteins) C-terminal REKLES beta. Pssm-ID: 350642 Cd Length: 133 Bit Score: 71.63 E-value: 1.40e-14
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ARID_ARID2 | cd16866 | ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 2 (ARID2) and ... |
312-397 | 1.38e-13 | |||
ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 2 (ARID2) and similar proteins; ARID2, also called BRG1-associated factor 200 (BAF200) or zinc finger protein with activation potential (Zipzap/p200), is a novel serum response factor (SRF)-binding protein with multiple conserved domains, including an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), RFX DNA-binding domain, a glutamine-rich domain, and two C2H2 zinc fingers. It binds DNA without sequence specificity. ARID2 is an intrinsic subunit of PBAF (SWI/SNF-B) remodeling complex, which needs ARID2 to play an essential role in promoting osteoblast differentiation, maintaining cellular identity and activating tissue-specific gene expression. Moreover, ARID2 may function as a tumor suppressor in many cancers. It may also serve as a transcription co-activator for the regulation of cardiac gene expression, and is required for heart morphogenesis and coronary artery development. Pssm-ID: 350630 Cd Length: 88 Bit Score: 67.29 E-value: 1.38e-13
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ARID_ARID5A | cd16884 | ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 5A (ARID5A) ... |
315-392 | 2.24e-13 | |||
ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 5A (ARID5A) and similar proteins; ARID5A, also called modulator recognition factor 1 (MRF-1), is an estrogen receptor alpha (ER alpha)-interacting protein that is expressed abundantly in cardiovascular tissues and suppresses ER alpha-induced transactivation. It also associates with thyroid receptor alpha (TR alpha) and retinoid X receptor alpha (RXR alpha) in a ligand-dependent manner, and with ER beta, androgen receptor (AR), and the retinoic acid receptor (RAR) in a ligand-independent manner. ARID5A functions as a negative regulator of RORgamma-induced Th17 cell differentiation and may be involved in the pathogenesis of rheumatoid arthritis (RA). Moreover, it is an important transcriptional partner of the transcription factor sex determining region Y (SRY)-box protein 9 (Sox9) in stimulation of chondrocyte-specific transcription. Meanwhile, ARID5A plays an important role in promotion of inflammatory processes and autoimmune diseases. It works as a unique RNA binding protein, which stabilizes interleukin-6 (IL-6) but not tumor necrosis factor-alpha (TNF-alpha) mRNA through binding to the 3' untranslated region (UTR) of IL-6 mRNA, and inhibits the destabilizing effect of regnase-1 on IL-6 mRNA. ARID5A contains an AT-rich DNA-interacting domain (ARID, also known as BRIGHT). Pssm-ID: 350648 Cd Length: 87 Bit Score: 66.95 E-value: 2.24e-13
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ARID_ARID5B | cd16885 | ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 5B (ARID5B) ... |
315-401 | 2.45e-11 | |||
ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 5B (ARID5B) and similar proteins; ARID5B, also called MRF1-like protein or modulator recognition factor 2 (MRF-2), is a DNA-binding protein that directly interacts with plant homeodomain (PHD) finger 2 (PHF2) to form a protein kinase A (PKA)-dependent PHF2-ARID5B histone H3K9Me2 demethylase complex, which is a signal-sensing modulator of histone methylation and gene transcription. It also functions as a transcriptional co-regulator for the transcription factor sex determining region Y (SRY)-box protein 9 (Sox9) and promotes chondrogenesis through histone modification. Moreover, ARID5B is highly expressed in the cardiovascular system and may play essential roles in the phenotypic change of smooth muscle cells (SMCs) through its regulation of SMC differentiation. Its polymorphism has been associated with risk for pediatric acute lymphoblastic leukemia (ALL). ARID5B contains an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), which can bind both the major and minor grooves of its target sequences. Pssm-ID: 350649 Cd Length: 95 Bit Score: 61.24 E-value: 2.45e-11
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ARID_ARID1B | cd16877 | ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 1B (ARID1B) ... |
312-397 | 3.23e-11 | |||
ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 1B (ARID1B) and similar proteins; ARID1B, also called BRG1-associated factor 250b (BAF250B), BRG1-binding protein ELD/OSA1, Osa homolog 2 (Osa2), or p250R, is the largest subunit of ATP-dependent SWItch/sucrose nonfermentable (SWI/SNF) chromatin remodeling complex, which plays a critical role in transcriptional control and gene expression. ARID1B exhibits tumour-suppressor activities in pancreatic cancer cell lines. Mutations in the ARID1B gene cause Coffin-Siris syndrome, exhibiting developmental defects, and haplo-insufficiency of ARID1B is a frequent cause of intellectual disability. Moreover, mutations in the ARID1B gene have been found in many cancers. ARID1B contains an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), which binds DNA in a non-sequence-specific manner similar to ARID1A. Pssm-ID: 350641 Cd Length: 93 Bit Score: 60.77 E-value: 3.23e-11
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CBD_MSL3_like | cd18983 | chromo barrel domain of human male-specific lethal complex subunit 3, and similar proteins; ... |
591-629 | 3.66e-09 | |||
chromo barrel domain of human male-specific lethal complex subunit 3, and similar proteins; This subgroup includes human male-specific lethal (MSL) complex subunit 3 (MSL3, also known as MSL3L1). The MSL3 chromodomain specifically recognizes the H4K20 monomethyl mark, in a DNA-dependent manner, and may be involved in chromosomal targeting of the MSL complex. Also included is MORF-related gene on chromosome 15 (MRG15, also known as MORF4L1) which specifically binds to Lys36-methylated histone H3 and plays a role in transcriptional regulation and in DNA repair. This subgroup also includes Arabidopsis thaliana Morf Related Gene 2 (MRG2) which acts as a H3K4me3/H3K36me3 reader involved in the regulation of Arabidopsis flowering. SH3-fold-beta-barrel domains of the chromo-like superfamily include chromodomains, chromo shadow domains and chromo barrel domains, and are implicated in the recognition of lysine-methylated histone tails and nucleic acids. The chromodomain differs, in that it lacks the first strand of the SH3-fold-beta-barrel. This first strand is altered by insertion in the chromo shadow domains, and chromo barrel domains are typical SH3-fold-beta-barrel domains with sequence similarity to the canonical chromo domain. Pssm-ID: 350846 Cd Length: 57 Bit Score: 53.99 E-value: 3.66e-09
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Tudor-knot | pfam11717 | RNA binding activity-knot of a chromodomain; This is a novel knotted tudor domain which is ... |
576-628 | 4.76e-09 | |||
RNA binding activity-knot of a chromodomain; This is a novel knotted tudor domain which is required for binding to RNA. The know influences the loop conformation of the helical turn Ht2 - residues 61-6 3- that is located at the side opposite the knot in the tudor domain-chromodomain; stabilization of Ht2 is essential for RNA binding. Pssm-ID: 432022 [Multi-domain] Cd Length: 55 Bit Score: 53.36 E-value: 4.76e-09
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ARID_JARID | cd16864 | ARID/BRIGHT DNA binding domain of JARID proteins; The JARID subfamily within the JmjC protein ... |
314-397 | 1.01e-08 | |||
ARID/BRIGHT DNA binding domain of JARID proteins; The JARID subfamily within the JmjC protein family includes lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and a Drosophila homolog, protein little imaginal discs (Lid). KDM5A was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interacting with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK and BMAL1. KDM5B has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of the pregnant female and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. Both KDM5A and KDM5B function as trimethylated histone H3 lysine 4 (H3K4me3) demethylases. KDM5C is a H3K4 trimethyl-histone demethylase that catalyzes demethylation of H3K4me3 and H3K4me2 to H3K4me1. It plays a role in neuronal survival and dendrite development. KDM5C defects are associated with X-linked mental retardation (XLMR). KDM5D is a male-specific antigen that shows a demethylase activity specific for di- and tri-methylated histone H3K4 (H3K4me3 and H3K4me2), and has a male-specific function as a histone H3K4 demethylase by recruiting a meiosis-regulatory protein, MSH5, to condensed DNA. KDM5D directly interacts with a polycomb-like protein Ring6a/MBLR, and plays a role in regulation of transcriptional initiation through H3K4 demethylation. The family also includes Drosophila melanogaster protein little imaginal discs (Lid) that functions as a JmjC-dependent trimethyl histone H3K4 (H3K4me3) demethylase, which is required for dMyc-induced cell growth. It positively regulates Hox gene expression in S2 cells. Members of this subfamily contain the catalytic JmjC domain, JmjN, the AT-rich domain interacting domain (ARID)/BRIGHT domain, a C5HC2 zinc finger, as well as two or three plant homeodomain (PHD) fingers. Pssm-ID: 350628 Cd Length: 87 Bit Score: 53.47 E-value: 1.01e-08
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ARID_ARID1A | cd16876 | ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 1A (ARID1A) ... |
312-397 | 2.70e-07 | |||
ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 1A (ARID1A) and similar proteins; ARID1A, also called B120, BRG1-associated factor 250a (BAF250A), Osa homolog 1(OSA1), SWI-like protein, SWI/SNF complex protein p270, or SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin subfamily F member 1 (SWI1), has been identified as a novel tumor suppressor in various tumor types. It interacts with BRG1 adenosine triphosphatase to form a SWItch/Sucrose NonFermentable (SWI/SNF) chromatin remodeling protein complex, which plays a critical role in transcriptional control and gene expression. ARID1A contains an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), and Eld/Osa homology domains (EHD) 1 and 2 within the C-terminus. The ARID in ARID1A binds nonspecific DNA in general and plays an important role in targeting SWI/SNF to chromatin. The EHD1 may be capable of mediating an intramolecular association with EHD2, and/or an intermolecular association resulting in homo- or hetero-dimerization. The EHD2 binds Swi2/Brahma homologue Brahma-related gene 1 (BRG1, also known as Snf2b), a human homologue of yeast Swi2. Pssm-ID: 350640 Cd Length: 93 Bit Score: 49.66 E-value: 2.70e-07
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TUDOR | smart00333 | Tudor domain; Domain of unknown function present in several RNA-binding proteins. 10 copies in ... |
58-113 | 3.46e-07 | |||
Tudor domain; Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished). Pssm-ID: 197660 Cd Length: 57 Bit Score: 48.04 E-value: 3.46e-07
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Tudor_SF | cd04508 | Tudor domain superfamily; The Tudor domain is a conserved structural domain, originally ... |
63-106 | 4.19e-06 | |||
Tudor domain superfamily; The Tudor domain is a conserved structural domain, originally identified in the Tudor protein of Drosophila, that adopts a beta-barrel-like core structure containing four short beta-strands followed by an alpha-helical region. It binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. Tudor domain-containing proteins may mediate protein-protein interactions required for various DNA-templated biological processes, such as RNA metabolism, as well as histone modification and the DNA damage response. Members of this superfamily contain one or more copies of the Tudor domain. Pssm-ID: 410449 [Multi-domain] Cd Length: 47 Bit Score: 44.88 E-value: 4.19e-06
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CHROMO | smart00298 | Chromatin organization modifier domain; |
593-629 | 7.67e-06 | |||
Chromatin organization modifier domain; Pssm-ID: 214605 [Multi-domain] Cd Length: 55 Bit Score: 44.51 E-value: 7.67e-06
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ARID_KDM5B | cd16874 | ARID/BRIGHT DNA binding domain of lysine-specific demethylase 5B (KDM5B); KDM5B, also called ... |
314-396 | 7.76e-05 | |||
ARID/BRIGHT DNA binding domain of lysine-specific demethylase 5B (KDM5B); KDM5B, also called cancer/testis antigen 31 (CT31), histone demethylase JARID1B, Jumonji/ARID domain-containing protein 1B (JARID1B), PLU-1, or retinoblastoma-binding protein 2 homolog 1 (RBP2-H1 or RBBP2H1A), is a member of the JARID subfamily within the JmjC proteins. It has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of the pregnant female and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. KDM5B acts as a histone demethylase that catalyzes the removal of trimethylation of lysine 4 on histone H3 (H3K4me3), induced by polychlorinated biphenyls (PCBs). It also mediates demethylation of H3K4me2 and H3K4me1. Moreover, KDM5B functions as a negative regulator of hematopoietic stem cell (HSC) self-renewal and progenitor cell activity. KDM5B has also been shown to interact with the DNA binding transcription factors BF-1 and PAX9, as well as TIEG1/KLF10 (transforming growth factor-beta inducible earlygene-1/Kruppel-like transcription factor 10), and possibly function as a transcriptional corepressor. KDM5B contains the catalytic JmjC domain, a JmjN domain, an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a C5HC2 zinc finger, as well as three plant homeodomain (PHD) fingers. Pssm-ID: 350638 Cd Length: 90 Bit Score: 42.62 E-value: 7.76e-05
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ARID_KDM5A | cd16873 | ARID/BRIGHT DNA binding domain of lysine-specific demethylase 5A (KDM5A); KDM5A, also called ... |
314-397 | 8.42e-05 | |||
ARID/BRIGHT DNA binding domain of lysine-specific demethylase 5A (KDM5A); KDM5A, also called histone demethylase JARID1A, Jumonji/ARID domain-containing protein 1A, or Retinoblastoma-binding protein 2 (RBBP-2 or RBP2), was originally identified as a retinoblastoma protein (Rb)-binding partner; its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interacting with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK and BMAL1. KDM5A functions as the trimethylated histone H3 lysine 4 (H3K4me3) demethylase that belongs to the JARID subfamily within the JmjC proteins. It also displays DNA-binding activities that can recognize the specific DNA sequence CCGCCC. KDM5A contains the catalytic JmjC domain, a JmjN domain, an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a C5HC2 zinc finger, as well as three plant homeodomain (PHD) fingers. Pssm-ID: 350637 Cd Length: 92 Bit Score: 42.56 E-value: 8.42e-05
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ARID_KDM5C_5D | cd16875 | ARID/BRIGHT DNA binding domain of lysine-specific demethylase KDM5C and KDM5D; This group ... |
314-399 | 3.43e-04 | |||
ARID/BRIGHT DNA binding domain of lysine-specific demethylase KDM5C and KDM5D; This group includes KDM5C and KDM5D, both of which belong to the JARID subfamily within the JmjC proteins. KDM5C, also called histone demethylase JARID1C, Jumonji/ARID domain-containing protein 1C, protein SmcX, or protein Xe169, is a H3K4 trimethyl-histone demethylase that catalyzes demethylation of H3K4me3 and H3K4me2 to H3K4me1. It plays a role in neuronal survival and dendrite development. KDM5C defects are associated with X-linked mental retardation (XLMR). KDM5D, also called histocompatibility Y antigen (H-Y), histone demethylase JARID1D, Jumonji/ARID domain-containing protein 1D, or protein SmcY, is a male-specific antigen that shows a demethylase activity specific for di- and tri-methylated histone H3K4 (H3K4me3 and H3K4me2), and has a male-specific function as a histone H3K4 demethylase by recruiting a meiosis-regulatory protein, MSH5, to condensed DNA. KDM5D directly interacts with a polycomb-like protein Ring6a/MBLR, and plays a role in regulation of transcriptional initiation through H3K4 demethylation. Both KDM5C and KDM5D contain the catalytic JmjC domain, a JmjN domain, an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a C5HC2 zinc finger, as well as two plant homeodomain (PHD) fingers. Pssm-ID: 350639 Cd Length: 92 Bit Score: 41.06 E-value: 3.43e-04
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Tudor_JMJD2_rpt2 | cd20392 | second Tudor domain found in Jumonji domain-containing protein 2 (JMJD2) family of histone ... |
62-112 | 3.98e-04 | |||
second Tudor domain found in Jumonji domain-containing protein 2 (JMJD2) family of histone demethylases; JMJD2 proteins, also called lysine-specific demethylase 4 histone demethylases (KDM4), have been implicated in various cellular processes including DNA damage response, transcription, cell cycle regulation, cellular differentiation, senescence, and carcinogenesis. They selectively catalyze the demethylation of di- and trimethylated H3K9 and H3K36. This model contains only three JMJD2 proteins, JMJD2A-C, which all contain jmjN and jmjC domains in the N-terminal region, followed by a canonical PHD domain, a noncanonical extended PHD domain, and tandem Tudor domains. The model corresponds to the second Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. JMJD2D is not included in this model, since it lacks both the PHD and Tudor domains and has a different substrate specificity. JMJD2A-C are required for efficient cancer cell growth. Pssm-ID: 410463 Cd Length: 56 Bit Score: 39.54 E-value: 3.98e-04
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ARID_HMGB9-like | cd16872 | ARID/BRIGHT DNA binding domain of Arabidopsis thaliana high mobility group B proteins HMGB9, ... |
315-397 | 6.17e-04 | |||
ARID/BRIGHT DNA binding domain of Arabidopsis thaliana high mobility group B proteins HMGB9, HMGB10, HMGB11, HMGB15 and similar proteins; This subfamily includes a group of conserved plant DNA-binding proteins, including HMGB9 (or ARID-HMG1), HMGB10 (or ARID-HMG2), HMGB11, and HMGB15. They have been termed ARID-HMG proteins, due to containing two DNA-binding domains, an N-terminal AT-rich DNA-interacting domain (ARID, also known as BRIGHT), and a C-terminal high mobility group (HMG)-box domain. They are widely expressed in Arabidopsis and localize primarily to the nucleus. HMGB9/ARID-HMG1 binds specifically to A/T-rich DNA. HMGB15 is a transcription factor predominantly expressed in mature pollen grains and pollen tubes. It may work in the form of a homodimer, or interact with HMGB9, HMGB10 and HMGB11 to form heteromultimers in plant cells. HMGB15 is required for pollen tube growth in Arabidopsis and is involved in transcriptional regulation through the interaction with AGL66 and AGL104. Pssm-ID: 350636 Cd Length: 86 Bit Score: 39.94 E-value: 6.17e-04
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PLN00104 | PLN00104 | MYST -like histone acetyltransferase; Provisional |
576-628 | 2.09e-03 | |||
MYST -like histone acetyltransferase; Provisional Pssm-ID: 215056 [Multi-domain] Cd Length: 450 Bit Score: 42.05 E-value: 2.09e-03
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CBD_MOF_like | cd18642 | chromo barrel domain of Drosophila melanogaster males-absent on the first protein, and similar ... |
596-628 | 7.48e-03 | |||
chromo barrel domain of Drosophila melanogaster males-absent on the first protein, and similar proteins; This subgroup includes the chromo barrel domains found in human Tat-interactive protein 60 (TIP60, (also known as KAT5 or HTATIP), Drosophila melanogaster males-absent on the first (MOF) protein, and Saccharomyces ESA1. SH3-fold-beta-barrel domains of the chromo-like superfamily include chromodomains, chromo shadow domains, and chromo barrel domains, and are implicated in the recognition of lysine-methylated histone tails and nucleic acids. The chromodomain differs, in that it lacks the first strand of the SH3-fold-beta-barrel. This first strand is altered by insertion in the chromo shadow domains, and chromo barrel domains are typical SH3-fold-beta-barrel domains with sequence similarity to the canonical chromo domain. The MOF-like chromo barrels may be may be auto-inhibited, i.e. they seem to have occluded peptide binding sites. Pssm-ID: 350844 [Multi-domain] Cd Length: 67 Bit Score: 36.26 E-value: 7.48e-03
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