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Conserved domains on  [gi|22035679|ref|NP_112739|]
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AT-rich interactive domain-containing protein 4B isoform 2 [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
ARID_ARID4B cd16883
ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 4B (ARID4B) ...
308-399 8.04e-64

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: 210.98  E-value: 8.04e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22035679  308 ERENFLQQLYKFMEDRGTPINKRPVLGYRNLNLFKLFRLVHKLGGFDNIESGAVWKQVYQDLGIPVLNSAAGYNVKCAYK 387
Cdd:cd16883    1 ERENFLQQLYKFMEDRGTPINKRPVLGYRNLNLFKLFRLVHKLGGFDNIESGAVWKQVYQDLGIPVLNSAAGYNVKCAYR 80
                         90
                 ....*....|..
gi 22035679  388 KYLYGFEEYCRS 399
Cdd:cd16883   81 KYLYGFEEYCTS 92
RBB1NT pfam08169
RBB1NT (NUC162) domain; This domain is found N terminal to the ARID/BRIGHT domain in ...
170-263 5.00e-42

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: 148.54  E-value: 5.00e-42
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22035679    170 DELLGKVVCVDyiSLDKKKAlWFPALVVCPDCSDEIAVKKDNILVRSFKDGKFTSVPRKDVHEITSDTAPKPDAVLKQAF 249
Cdd:pfam08169    3 DELLGKVVCVE--STDKKDN-WYPALVVSPSCQDDVTVKKDQCLVRSFKDGKFYTVPRKDVREFTRESGPKPESSLKPAL 79
                           90
                   ....*....|....
gi 22035679    250 EQALEFHKSRTIPA 263
Cdd:pfam08169   80 DAALEFLDTGEVPP 93
Tudor_ARID4B_rpt1 cd20460
first Tudor domain found in AT-rich interactive domain-containing protein 4B (ARID4B) and ...
1-61 1.47e-35

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: 129.01  E-value: 1.47e-35
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 22035679    1 MKALDEPPYLTVGTDVSAKYRGAFCEAKIKTAKRLVKVKVTFRHDSSTVEVQDDHIKGPLK 61
Cdd:cd20460    1 MKALDEPPYLTVGTDVSAKYRGAFCEAKIKTAKRLVKVKVTFRHDSSTVEVQDDHIKGPLK 61
Tudor_ARID4B_rpt2 cd20462
second Tudor domain found in AT-rich interactive domain-containing protein 4B (ARID4B) and ...
62-118 1.05e-33

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: 123.63  E-value: 1.05e-33
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 22035679   62 VGAIVEVKNLDGAYQEAVINKLTDASWYTVVFDDGDEKTLRRSSLCLKGERHFAESE 118
Cdd:cd20462    1 VGAVVEVKNPDGTYQEAVINKLTDASWYTVVFDDGDEKTLRRSSLCLKGERHFAESE 57
 
Name Accession Description Interval E-value
ARID_ARID4B cd16883
ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 4B (ARID4B) ...
308-399 8.04e-64

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: 210.98  E-value: 8.04e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22035679  308 ERENFLQQLYKFMEDRGTPINKRPVLGYRNLNLFKLFRLVHKLGGFDNIESGAVWKQVYQDLGIPVLNSAAGYNVKCAYK 387
Cdd:cd16883    1 ERENFLQQLYKFMEDRGTPINKRPVLGYRNLNLFKLFRLVHKLGGFDNIESGAVWKQVYQDLGIPVLNSAAGYNVKCAYR 80
                         90
                 ....*....|..
gi 22035679  388 KYLYGFEEYCRS 399
Cdd:cd16883   81 KYLYGFEEYCTS 92
RBB1NT pfam08169
RBB1NT (NUC162) domain; This domain is found N terminal to the ARID/BRIGHT domain in ...
170-263 5.00e-42

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: 148.54  E-value: 5.00e-42
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22035679    170 DELLGKVVCVDyiSLDKKKAlWFPALVVCPDCSDEIAVKKDNILVRSFKDGKFTSVPRKDVHEITSDTAPKPDAVLKQAF 249
Cdd:pfam08169    3 DELLGKVVCVE--STDKKDN-WYPALVVSPSCQDDVTVKKDQCLVRSFKDGKFYTVPRKDVREFTRESGPKPESSLKPAL 79
                           90
                   ....*....|....
gi 22035679    250 EQALEFHKSRTIPA 263
Cdd:pfam08169   80 DAALEFLDTGEVPP 93
Tudor_ARID4B_rpt1 cd20460
first Tudor domain found in AT-rich interactive domain-containing protein 4B (ARID4B) and ...
1-61 1.47e-35

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: 129.01  E-value: 1.47e-35
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 22035679    1 MKALDEPPYLTVGTDVSAKYRGAFCEAKIKTAKRLVKVKVTFRHDSSTVEVQDDHIKGPLK 61
Cdd:cd20460    1 MKALDEPPYLTVGTDVSAKYRGAFCEAKIKTAKRLVKVKVTFRHDSSTVEVQDDHIKGPLK 61
Tudor_ARID4B_rpt2 cd20462
second Tudor domain found in AT-rich interactive domain-containing protein 4B (ARID4B) and ...
62-118 1.05e-33

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: 123.63  E-value: 1.05e-33
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 22035679   62 VGAIVEVKNLDGAYQEAVINKLTDASWYTVVFDDGDEKTLRRSSLCLKGERHFAESE 118
Cdd:cd20462    1 VGAVVEVKNPDGTYQEAVINKLTDASWYTVVFDDGDEKTLRRSSLCLKGERHFAESE 57
ARID smart01014
ARID/BRIGHT DNA binding domain; Members of the recently discovered ARID (AT-rich interaction ...
311-394 5.01e-31

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: 116.95  E-value: 5.01e-31
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22035679     311 NFLQQLYKFMEDRGTPINKRPVLGYRNLNLFKLFRLVHKLGGFDNIESGAVWKQVYQDLGIPVLNSAAGYNVKCAYKKYL 390
Cdd:smart01014    5 LFLDRLRKFMEKRGTPLDKIPVIGGKPLDLYRLYRAVQKRGGFDKVTKKKKWKQVARELGIPPSATSAGTSLRKHYEKYL 84

                    ....
gi 22035679     391 YGFE 394
Cdd:smart01014   85 LPYE 88
ARID pfam01388
ARID/BRIGHT DNA binding domain; This domain is know as ARID for AT-Rich Interaction Domain, ...
311-394 9.10e-28

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: 107.71  E-value: 9.10e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22035679    311 NFLQQLYKFMEDRGTPINKRPVLGYRNLNLFKLFRLVHKLGGFDNIESGAVWKQVYQDLGIPVLNSAAGYNVKCAYKKYL 390
Cdd:pfam01388    4 LFLKSLRKFHEKRGTPLKQIPVIGGKPVDLYKLYKAVQKLGGYDKVTEKNLWREVAEKLGFPPSAASAATQLKQIYEKYL 83

                   ....
gi 22035679    391 YGFE 394
Cdd:pfam01388   84 LPYE 87
TUDOR smart00333
Tudor domain; Domain of unknown function present in several RNA-binding proteins. 10 copies in ...
58-113 1.25e-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: 49.58  E-value: 1.25e-07
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*..
gi 22035679      58 GPLKVGAIVEVKNLDGAYQEAVINKLTDASWYTVVFDD-GDEKTLRRSSLCLKGERH 113
Cdd:smart00333    1 PTFKVGDKVAARWEDGEWYRARIVKVDGEQLYEVFFIDyGNEEVVPPSDLRQLPEEL 57
PWWP_DNMT3 cd05835
PWWP domain found in the DNA (cytosine-5)-methyltransferase 3 (DNMT3) family; The DNMT3 family ...
191-260 1.29e-03

PWWP domain found in the DNA (cytosine-5)-methyltransferase 3 (DNMT3) family; The DNMT3 family includes DNMT3A and DNMT3B, which are required for genome-wide de novo methylation and is essential for the establishment of DNA methylation patterns during development. DNMT3A, also called DNA methyltransferase HsaIIIA, DNA MTase HsaIIIA, or M.HsaIIIA, modifies DNA in a non-processive manner and also methylates non-CpG sites. It may preferentially methylate DNA linker between 2 nucleosomal cores and is inhibited by histone H1. DNMT3A is recruited to trimethylated 'Lys-36' of histone H3 (H3K36me3) sites. DNMT3B, also called DNA methyltransferase HsaIIIB, DNA MTase HsaIIIB, or M.HsaIIIB, may preferentially methylate nucleosomal DNA within the nucleosome core region. DNMT3B may function as a transcriptional co-repressor by associating with CBX4 and independently of DNA methylation. Members of this family contains a PWWP domain that is responsible for establishing DNA methylation patterns during embryogenesis and gametogenesis. In tumorigenesis, DNA methylation by DNMT3B is known to play a role in the inactivation of tumor suppressor genes. In addition, a point mutation in the PWWP domain of DNMT3B has been identified in patients with ICF (immunodeficiency, centromeric instability, and facial anomalie) syndrome , a rare autosomal recessive disorder characterized by hypomethylation of classical satellite DNA.


Pssm-ID: 438960 [Multi-domain]  Cd Length: 89  Bit Score: 39.17  E-value: 1.29e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 22035679  191 WFPALVV-CPDCSDEIAvKKDNILVRSFKDGKFTSVPRKDVHEITSD-----TAPKPDAVLKQAFEQALEFHKSRT 260
Cdd:cd05835   15 WWPGIVVsHKDCGQKPP-AEGSVWVFWFGDHKVSEVPLDKILPFAEFfnkfyISKNSSKLYKKAVYEALKEAAERS 89
 
Name Accession Description Interval E-value
ARID_ARID4B cd16883
ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 4B (ARID4B) ...
308-399 8.04e-64

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: 210.98  E-value: 8.04e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22035679  308 ERENFLQQLYKFMEDRGTPINKRPVLGYRNLNLFKLFRLVHKLGGFDNIESGAVWKQVYQDLGIPVLNSAAGYNVKCAYK 387
Cdd:cd16883    1 ERENFLQQLYKFMEDRGTPINKRPVLGYRNLNLFKLFRLVHKLGGFDNIESGAVWKQVYQDLGIPVLNSAAGYNVKCAYR 80
                         90
                 ....*....|..
gi 22035679  388 KYLYGFEEYCRS 399
Cdd:cd16883   81 KYLYGFEEYCTS 92
ARID_ARID4 cd16868
ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing proteins ARID4A, ...
311-394 9.18e-50

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: 170.65  E-value: 9.18e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22035679  311 NFLQQLYKFMEDRGTPINKRPVLGYRNLNLFKLFRLVHKLGGFDNIESGAVWKQVYQDLGIPVLNSAAGYNVKCAYKKYL 390
Cdd:cd16868    4 NFLEQLYKFMEDRGTPINKPPVLGYKDLDLFKLYKLVQELGGMERVSQGAKWRSIYQQLGIPVLNSAASHNIKQAYKKYL 83

                 ....
gi 22035679  391 YGFE 394
Cdd:cd16868   84 YAFE 87
ARID_ARID4A cd16882
ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 4A (ARID4A) ...
311-394 1.03e-45

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: 158.98  E-value: 1.03e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22035679  311 NFLQQLYKFMEDRGTPINKRPVLGYRNLNLFKLFRLVHKLGGFDNIESGAVWKQVYQDLGIPVLNSAAGYNVKCAYKKYL 390
Cdd:cd16882    4 NFLQQLYKFMEDRGTPINKPPVLGYKDLNLFKLFRLVYQQGGCDNIESGSVWKQIYMDLGIPILNSAASYNVKTAYRKYL 83

                 ....
gi 22035679  391 YGFE 394
Cdd:cd16882   84 YGFE 87
RBB1NT pfam08169
RBB1NT (NUC162) domain; This domain is found N terminal to the ARID/BRIGHT domain in ...
170-263 5.00e-42

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: 148.54  E-value: 5.00e-42
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22035679    170 DELLGKVVCVDyiSLDKKKAlWFPALVVCPDCSDEIAVKKDNILVRSFKDGKFTSVPRKDVHEITSDTAPKPDAVLKQAF 249
Cdd:pfam08169    3 DELLGKVVCVE--STDKKDN-WYPALVVSPSCQDDVTVKKDQCLVRSFKDGKFYTVPRKDVREFTRESGPKPESSLKPAL 79
                           90
                   ....*....|....
gi 22035679    250 EQALEFHKSRTIPA 263
Cdd:pfam08169   80 DAALEFLDTGEVPP 93
Tudor_ARID4B_rpt1 cd20460
first Tudor domain found in AT-rich interactive domain-containing protein 4B (ARID4B) and ...
1-61 1.47e-35

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: 129.01  E-value: 1.47e-35
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 22035679    1 MKALDEPPYLTVGTDVSAKYRGAFCEAKIKTAKRLVKVKVTFRHDSSTVEVQDDHIKGPLK 61
Cdd:cd20460    1 MKALDEPPYLTVGTDVSAKYRGAFCEAKIKTAKRLVKVKVTFRHDSSTVEVQDDHIKGPLK 61
Tudor_ARID4B_rpt2 cd20462
second Tudor domain found in AT-rich interactive domain-containing protein 4B (ARID4B) and ...
62-118 1.05e-33

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: 123.63  E-value: 1.05e-33
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 22035679   62 VGAIVEVKNLDGAYQEAVINKLTDASWYTVVFDDGDEKTLRRSSLCLKGERHFAESE 118
Cdd:cd20462    1 VGAVVEVKNPDGTYQEAVINKLTDASWYTVVFDDGDEKTLRRSSLCLKGERHFAESE 57
ARID smart01014
ARID/BRIGHT DNA binding domain; Members of the recently discovered ARID (AT-rich interaction ...
311-394 5.01e-31

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: 116.95  E-value: 5.01e-31
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22035679     311 NFLQQLYKFMEDRGTPINKRPVLGYRNLNLFKLFRLVHKLGGFDNIESGAVWKQVYQDLGIPVLNSAAGYNVKCAYKKYL 390
Cdd:smart01014    5 LFLDRLRKFMEKRGTPLDKIPVIGGKPLDLYRLYRAVQKRGGFDKVTKKKKWKQVARELGIPPSATSAGTSLRKHYEKYL 84

                    ....
gi 22035679     391 YGFE 394
Cdd:smart01014   85 LPYE 88
BRIGHT smart00501
BRIGHT, ARID (A/T-rich interaction domain) domain; DNA-binding domain containing a ...
311-398 9.54e-31

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: 116.61  E-value: 9.54e-31
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22035679     311 NFLQQLYKFMEDRGTPINKRPVLGYRNLNLFKLFRLVHKLGGFDNIESGAVWKQVYQDLGIPVLNSAAGYNVKCAYKKYL 390
Cdd:smart00501    5 LFLDRLYKFMEERGSPLKKIPVIGGKPLDLYRLYRLVQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHYERYL 84

                    ....*...
gi 22035679     391 YGFEEYCR 398
Cdd:smart00501   85 LPYERFLR 92
Tudor_ARID4_rpt2 cd20390
second Tudor domain found in AT-rich interactive domain-containing protein ARID4 family; The ...
62-114 1.40e-29

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: 111.60  E-value: 1.40e-29
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 22035679   62 VGAIVEVKNLDGAYQEAVINKLTDASWYTVVFDDGDEKTLRRSSLCLKGERHF 114
Cdd:cd20390    1 VGATVEVKTPDGQFAEAVITKLTDASTYTVVFDDGDEKTLRRTSLCLKGERHF 53
Tudor_ARID4A_rpt2 cd20461
second Tudor domain found in AT-rich interactive domain-containing protein 4A (ARID4A) and ...
62-121 5.77e-28

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: 107.51  E-value: 5.77e-28
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 22035679   62 VGAIVEVKNLDGAYQEAVINKLTDASWYTVVFDDGDEKTLRRSSLCLKGERHFAESETLD 121
Cdd:cd20461    1 VGAIVETRTSDGSFQEAIISKLTDASWYTVVFDDGDERTLRRTSLCLKGERHFAESETLD 60
ARID pfam01388
ARID/BRIGHT DNA binding domain; This domain is know as ARID for AT-Rich Interaction Domain, ...
311-394 9.10e-28

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: 107.71  E-value: 9.10e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22035679    311 NFLQQLYKFMEDRGTPINKRPVLGYRNLNLFKLFRLVHKLGGFDNIESGAVWKQVYQDLGIPVLNSAAGYNVKCAYKKYL 390
Cdd:pfam01388    4 LFLKSLRKFHEKRGTPLKQIPVIGGKPVDLYKLYKAVQKLGGYDKVTEKNLWREVAEKLGFPPSAASAATQLKQIYEKYL 83

                   ....
gi 22035679    391 YGFE 394
Cdd:pfam01388   84 LPYE 87
Tudor_ARID4A_rpt1 cd20459
first Tudor domain found in AT-rich interactive domain-containing protein 4A (ARID4A) and ...
5-61 1.03e-27

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: 106.67  E-value: 1.03e-27
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 22035679    5 DEPPYLTVGTDVSAKYRGAFCEAKIKTAKRLVKVKVTFRHDSSTVEVQDDHIKGPLK 61
Cdd:cd20459    2 DEPAYLTVGTDVSAKYRGAFCEAKIKTVKRLVKVKVLLKGDNSTQLVQDDQVKGPLR 58
ARID cd16100
ARID/BRIGHT DNA binding domain family; The AT-rich interaction domain (ARID) family of ...
311-394 3.40e-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: 106.29  E-value: 3.40e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22035679  311 NFLQQLYKFMEDRGTPINKRPVLGYRNLNLFKLFRLVHKLGGFDNIESGAVWKQVYQDLGIPVLNSAAGYNVKCAYKKYL 390
Cdd:cd16100    4 EFLEQLRAFLESRGTPLLKPPTIGGKPLDLYKLYRAVVSRGGYEKVTEKKLWKEVARKLGLPTSSTSAAQALKRIYEKYL 83

                 ....
gi 22035679  391 YGFE 394
Cdd:cd16100   84 LPFE 87
Tudor_ARID4_rpt1 cd20389
first Tudor domain found in AT-rich interactive domain-containing protein ARID4 family; The ...
9-61 4.30e-25

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: 98.88  E-value: 4.30e-25
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 22035679    9 YLTVGTDVSAKYRGAFCEAKIKTAKRLVKVKVTFRHDSSTVEVQDDHIKGPLK 61
Cdd:cd20389    1 YLPVGTEVSAKYRGAFCEAKVKKVKKLVKCKVTFKDNGTSVVVSDDNIKGPLK 53
ARID_ARID5 cd16869
ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing proteins ARID5A, ...
311-394 4.73e-21

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: 88.51  E-value: 4.73e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22035679  311 NFLQQLYKFMEDRGTPINKRPVLGYRNLNLFKLFRLVHKLGGFDNIESGAVWKQVYQDLG-IPVLNSAAGYNVKcAYKKY 389
Cdd:cd16869    4 AFLKLLYKFMKDRGTPIERIPHLGFKQIDLYTFFKLVQKLGGYEQVTAKRLWKHVYDELGgNPSSTSAATCTRR-HYEKL 82

                 ....*
gi 22035679  390 LYGFE 394
Cdd:cd16869   83 LLPYE 87
ARID_ARID1A-like cd16865
ARID/BRIGHT DNA binding domain found in AT-rich interactive domain-containing proteins ARID1A, ...
312-398 2.78e-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: 78.09  E-value: 2.78e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22035679  312 FLQQLYKFMEDRGTPINKRPVLGYRNLNLFKLFRLVHKLGGFDNIESGAVWKQVYQDLGIPVlNSAAGYNVKCAYKKYLY 391
Cdd:cd16865    6 FLDRLLRFMEERGSPITNCPQISKQPLDLFRLYVTVKERGGVAEVTKNKKWKEICTELNIGA-SSSAAFTLRKNYIKYLL 84

                 ....*..
gi 22035679  392 GFEeyCR 398
Cdd:cd16865   85 AYE--CR 89
ARID_Swi1p-like cd16871
ARID/BRIGHT DNA binding domain of yeast SWI/SNF chromatin-remodeling complex subunit Swi1p and ...
311-395 3.92e-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: 77.68  E-value: 3.92e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22035679  311 NFLQQLYKFMEDRGTPINKRPVLGYRNLNLFKLFRLVHKLGGFDNIESGAVWKQVYQDLGIPV-LNSAAGYNVKCAYKKY 389
Cdd:cd16871    5 QFMKSLREFMAKRGTPIEQQPVIGGRPVNLFRLYQLVQKLGGSRQVTQNNQWPRVAQKLGFPPeQNPQVAQQLAQIYQRY 84

                 ....*.
gi 22035679  390 LYGFEE 395
Cdd:cd16871   85 LLPYEE 90
ARID_ARID5A cd16884
ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 5A (ARID5A) ...
312-389 2.68e-16

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: 75.04  E-value: 2.68e-16
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 22035679  312 FLQQLYKFMEDRGTPINKRPVLGYRNLNLFKLFRLVHKLGGFDNIESGAVWKQVYQDL-GIPVLNSAAgynvKCAYKKY 389
Cdd:cd16884    5 FLVNLYKFMKERNTPIERIPHLGFKQINLWKIYKAVEKLGGYELVTARRLWKNVYDELgGSPGSTSAA----TCTRRHY 79
ARID_ARID3C cd16880
ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 3C (ARID3C) ...
312-408 7.48e-15

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: 72.37  E-value: 7.48e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22035679  312 FLQQLYKFMEDRGTPINKRPVLGYRNLNLFKLFRLVHKLGGFDNIESGAVWKQVYQDLGIPVLNSAAGYNVKCAYKKYLY 391
Cdd:cd16880   19 FLDDLFSFMQKRGTPVNRIPIMAKQVLDLYTLYRLVTDKGGLVEVINKKIWREITKGLSLPTSITSAAFTLRTQYMKYLY 98
                         90
                 ....*....|....*....
gi 22035679  392 GFEEYCR--SANIEFQMAL 408
Cdd:cd16880   99 PYECEKRalSSPGELQAAI 117
ARID_ARID3 cd16867
ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing proteins ARID3A, ...
312-394 9.44e-15

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: 71.75  E-value: 9.44e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22035679  312 FLQQLYKFMEDRGTPINKRPVLGYRNLNLFKLFRLVHKLGGFDNIESGAVWKQVYQDLGIPVLNSAAGYNVKCAYKKYLY 391
Cdd:cd16867   16 FLDDLFSFMQKRGTPVNRIPIMAKQVLDLYELYRLVVEKGGLVEVINKKIWREITKGLNLPSSITSAAFTLRTQYMKYLY 95

                 ...
gi 22035679  392 GFE 394
Cdd:cd16867   96 PYE 98
ARID_Dri-like cd16881
ARID/BRIGHT DNA binding domain of dead ringer (Dri) from Drosophila melanogaster and similar ...
312-408 1.12e-14

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: 71.85  E-value: 1.12e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22035679  312 FLQQLYKFMEDRGTPINKRPVLGYRNLNLFKLFRLVHKLGGFDNIESGAVWKQVYQDLGIPVLNSAAGYNVKCAYKKYLY 391
Cdd:cd16881   23 FLDDLFSFMQKRGTPVNRIPIMAKQVLDLYELYNLVVARGGLVEVINKKLWREITKGLHLPSSITSAAFTLRTQYMKYLY 102
                         90       100
                 ....*....|....*....|.
gi 22035679  392 GFEeyCRSANI----EFQMAL 408
Cdd:cd16881  103 PYE--CEKLKLstpaELQAAI 121
ARID_ARID3B cd16879
ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 3B (ARID3B) ...
312-408 3.55e-14

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: 70.43  E-value: 3.55e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22035679  312 FLQQLYKFMEDRGTPINKRPVLGYRNLNLFKLFRLVHKLGGFDNIESGAVWKQVYQDLGIPVLNSAAGYNVKCAYKKYLY 391
Cdd:cd16879   18 FLDDLFAFMQKRGTPINRIPIMAKQVLDLYMLYKLVTEKGGLVEVINKKIWREITKGLNLPTSITSAAFTLRTQYMKYLY 97
                         90
                 ....*....|....*....
gi 22035679  392 GF--EEYCRSANIEFQMAL 408
Cdd:cd16879   98 PYecEKKSLSSPAELQAAI 116
ARID_ARID5B cd16885
ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 5B (ARID5B) ...
312-398 7.62e-14

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: 68.56  E-value: 7.62e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22035679  312 FLQQLYKFMEDRGTPINKRPVLGYRNLNLFKLFRLVHKLGGFDNIESGAVWKQVYQDLGIPVLNSAAGYNVKCAYKKYLY 391
Cdd:cd16885    5 FLVALYKYMKERKTPIERIPYLGFKQINLWTMFQAAQKLGGYETITARRQWKHIYDELGGNPGSTSAATCTRRHYERLIL 84

                 ....*..
gi 22035679  392 GFEEYCR 398
Cdd:cd16885   85 PYERFIK 91
ARID_ARID3A cd16878
ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 3A (ARID3A) ...
312-394 3.75e-13

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: 67.78  E-value: 3.75e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22035679  312 FLQQLYKFMEDRGTPINKRPVLGYRNLNLFKLFRLVHKLGGFDNIESGAVWKQVYQDLGIPVLNSAAGYNVKCAYKKYLY 391
Cdd:cd16878   26 FLDDLFSFMQKRGTPVNRIPIMAKQVLDLYMLYVLVTEKGGLVEVINKKLWREITKGLNLPTSITSAAFTLRTQYMKYLY 105

                 ...
gi 22035679  392 GFE 394
Cdd:cd16878  106 PYE 108
ARID_ARID2 cd16866
ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 2 (ARID2) and ...
311-394 6.42e-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: 65.36  E-value: 6.42e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22035679  311 NFLQQLYKFMEDRGTPINKRPVLGYRNLNLFKLFRLVHKLGGFDNIESGAVWKQVYQDLGIPVLNSAAGYNVKCAYKKYL 390
Cdd:cd16866    4 AFLNELRQFHASRGTPFKKIPVVGGKELDLYLLYSKVTALGGWAKVTDKNKWEEILEDFNFPRGCSNAAFALKQIYLRYL 83

                 ....
gi 22035679  391 YGFE 394
Cdd:cd16866   84 EAYE 87
ARID_JARID cd16864
ARID/BRIGHT DNA binding domain of JARID proteins; The JARID subfamily within the JmjC protein ...
311-394 8.93e-13

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: 65.02  E-value: 8.93e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22035679  311 NFLQQLYKFMEDRGTPInKRPVLGYRNLNLFKLFRLVHKLGGFDNIESGAVWKQVYQDLGIPvLNSAAGYNVKCAYKKYL 390
Cdd:cd16864    6 NFLDQIAKFWELQGSSL-KIPNVERKALDLFTLHKIVQEEGGFEEVTKERKWSKVARRLGYP-PGKGVGSLLRGHYERIL 83

                 ....
gi 22035679  391 YGFE 394
Cdd:cd16864   84 YPYD 87
ARID_ARID1B cd16877
ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 1B (ARID1B) ...
319-394 2.03e-10

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: 58.46  E-value: 2.03e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 22035679  319 FMEDRGTPINKRPVLGYRNLNLFKLFRLVHKLGGFDNIESGAVWKQVYQDLGIPVLNSAAGyNVKCAYKKYLYGFE 394
Cdd:cd16877   13 FMEERGTPVASLPAVGKKPLDLFRLYVCVKEIGGLAQVNKNKKWRELATNLNVGTSSSAAS-SLKKQYIQYLFAFE 87
TUDOR smart00333
Tudor domain; Domain of unknown function present in several RNA-binding proteins. 10 copies in ...
58-113 1.25e-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: 49.58  E-value: 1.25e-07
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*..
gi 22035679      58 GPLKVGAIVEVKNLDGAYQEAVINKLTDASWYTVVFDD-GDEKTLRRSSLCLKGERH 113
Cdd:smart00333    1 PTFKVGDKVAARWEDGEWYRARIVKVDGEQLYEVFFIDyGNEEVVPPSDLRQLPEEL 57
ARID_KDM5C_5D cd16875
ARID/BRIGHT DNA binding domain of lysine-specific demethylase KDM5C and KDM5D; This group ...
311-396 1.70e-06

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: 47.22  E-value: 1.70e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22035679  311 NFLQQLYKFMEDRGTPInKRPVLGYRNLNLFKLFRLVHKLGGFDNIESGAVWKQVYQDLGIPvlnsaAGYNV----KCAY 386
Cdd:cd16875    6 NYLDQIAKFWEIQGSSL-KIPNVERRILDLYSLSKIVQEEGGYEAICKDRRWARVAQRLGYP-----PGKNIgsllRSHY 79
                         90
                 ....*....|
gi 22035679  387 KKYLYGFEEY 396
Cdd:cd16875   80 ERIIYPYEMY 89
ARID_ARID1A cd16876
ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 1A (ARID1A) ...
312-394 3.39e-06

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: 46.58  E-value: 3.39e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22035679  312 FLQQLYKFMEDRGTPINKRPVLGYRNLNLFKLFRLVHKLGGFDNIESGAVWKQVYQDLGIPVLNSAAGyNVKCAYKKYLY 391
Cdd:cd16876    6 WVDRYLAFTEEKAMGMTNLPAVGRKPLDLYRLYVSVKEIGGLTQVNKNKKWRELATNLNVGTSSSAAS-SLKKQYIQCLY 84

                 ...
gi 22035679  392 GFE 394
Cdd:cd16876   85 AFE 87
ARID_KDM5A cd16873
ARID/BRIGHT DNA binding domain of lysine-specific demethylase 5A (KDM5A); KDM5A, also called ...
311-394 5.18e-06

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: 46.03  E-value: 5.18e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22035679  311 NFLQQLYKFMEDRGTPInKRPVLGYRNLNLFKLFRLVHKLGGFDNIESGAVWKQVYQDLGIPVlNSAAGYNVKCAYKKYL 390
Cdd:cd16873    6 DFLDQLAKFWELQGSTL-KIPVVERKILDLYALSKIVASEGGFEMVTKEKKWSKVGSRMGYLP-GKGTGSLLKSHYERIL 83

                 ....
gi 22035679  391 YGFE 394
Cdd:cd16873   84 YPYE 87
ARID_KDM5B cd16874
ARID/BRIGHT DNA binding domain of lysine-specific demethylase 5B (KDM5B); KDM5B, also called ...
311-393 2.10e-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: 44.16  E-value: 2.10e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22035679  311 NFLQQLYKFMEDRGTPInKRPVLGYRNLNLFKLFRLVHKLGGFDNIESGAVWKQVYQDLGIpVLNSAAGYNVKCAYKKYL 390
Cdd:cd16874    9 NFLDQIAKFWELQGCTL-KIPHVERKILDLFQLNKLVAEEGGFDLVCKERKWTKIATKMGF-APGKAVGSHIRAHYERIL 86

                 ...
gi 22035679  391 YGF 393
Cdd:cd16874   87 YPY 89
Tudor_SF cd04508
Tudor domain superfamily; The Tudor domain is a conserved structural domain, originally ...
63-106 2.13e-05

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: 42.96  E-value: 2.13e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 22035679   63 GAIVEVK-NLDGAYQEAVINKLTDASWYTVVFDDGDEKTLRRSSL 106
Cdd:cd04508    1 GDRVEAKwSDDGQWYPATVVAVNDDGKYTVLFDDGNEEEVSEDDI 45
Tudor_JMJD2_rpt2 cd20392
second Tudor domain found in Jumonji domain-containing protein 2 (JMJD2) family of histone ...
61-112 3.74e-05

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: 42.24  E-value: 3.74e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 22035679   61 KVGAIVEVKNLDGAYQEAVINKLTDASWYTVVFDDGDEKTLRRSSLCLKGER 112
Cdd:cd20392    3 EVGDPVKVKWTDGELYDAKFVGSSIVIMYTVEFEDGSVLTLKREDVYTLDEE 54
PWWP_DNMT3 cd05835
PWWP domain found in the DNA (cytosine-5)-methyltransferase 3 (DNMT3) family; The DNMT3 family ...
191-260 1.29e-03

PWWP domain found in the DNA (cytosine-5)-methyltransferase 3 (DNMT3) family; The DNMT3 family includes DNMT3A and DNMT3B, which are required for genome-wide de novo methylation and is essential for the establishment of DNA methylation patterns during development. DNMT3A, also called DNA methyltransferase HsaIIIA, DNA MTase HsaIIIA, or M.HsaIIIA, modifies DNA in a non-processive manner and also methylates non-CpG sites. It may preferentially methylate DNA linker between 2 nucleosomal cores and is inhibited by histone H1. DNMT3A is recruited to trimethylated 'Lys-36' of histone H3 (H3K36me3) sites. DNMT3B, also called DNA methyltransferase HsaIIIB, DNA MTase HsaIIIB, or M.HsaIIIB, may preferentially methylate nucleosomal DNA within the nucleosome core region. DNMT3B may function as a transcriptional co-repressor by associating with CBX4 and independently of DNA methylation. Members of this family contains a PWWP domain that is responsible for establishing DNA methylation patterns during embryogenesis and gametogenesis. In tumorigenesis, DNA methylation by DNMT3B is known to play a role in the inactivation of tumor suppressor genes. In addition, a point mutation in the PWWP domain of DNMT3B has been identified in patients with ICF (immunodeficiency, centromeric instability, and facial anomalie) syndrome , a rare autosomal recessive disorder characterized by hypomethylation of classical satellite DNA.


Pssm-ID: 438960 [Multi-domain]  Cd Length: 89  Bit Score: 39.17  E-value: 1.29e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 22035679  191 WFPALVV-CPDCSDEIAvKKDNILVRSFKDGKFTSVPRKDVHEITSD-----TAPKPDAVLKQAFEQALEFHKSRT 260
Cdd:cd05835   15 WWPGIVVsHKDCGQKPP-AEGSVWVFWFGDHKVSEVPLDKILPFAEFfnkfyISKNSSKLYKKAVYEALKEAAERS 89
ARID_HMGB9-like cd16872
ARID/BRIGHT DNA binding domain of Arabidopsis thaliana high mobility group B proteins HMGB9, ...
312-394 9.23e-03

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: 36.47  E-value: 9.23e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22035679  312 FLQQLYKFMEDRGTPInKRPVLGYRNLNLFKLFRLVHKLGGFDNIESGAVWKQVYQDLGIPVLNSAAGYNVKCAYKKYLY 391
Cdd:cd16872    5 FWETLRKFHESLGTKF-RIPIVGGKELDLHRLYKEVTSRGGLEKVIKDRKWKEVAAVFNFPPTITNASFVLRKYYLSLLH 83

                 ...
gi 22035679  392 GFE 394
Cdd:cd16872   84 HYE 86
 
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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