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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292438 575 SEEDFLKDVMQFLLQRGHTRlvpqgglaeFPDAVLNAKRLDLYNLYKEVVSRGGFYVGNGINWKGQVFSKMSNHTvtnKM 654
Cdd:cd16100     1 EREEFLEQLRAFLESRGTPL---------LKPPTIGGKPLDLYKLYRAVVSRGGYEKVTEKKLWKEVARKLGLPT---SS 68

                          90
                  ....*....|....*....
gi 1002292438 655 TGVGNTLKRHYETYLLEYE 673
Cdd:cd16100    69 TSAAQALKRIYEKYLLPFE 87

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292438 575 SEEDFLKDVMQFLLQRGHTRlvpqgglaeFPDAVLNAKRLDLYNLYKEVVSRGGFYVGNGINWKGQVFSKMSNHTvtnKM 654
Cdd:cd16100     1 EREEFLEQLRAFLESRGTPL---------LKPPTIGGKPLDLYKLYRAVVSRGGYEKVTEKKLWKEVARKLGLPT---SS 68

                          90
                  ....*....|....*....
gi 1002292438 655 TGVGNTLKRHYETYLLEYE 673
Cdd:cd16100    69 TSAAQALKRIYEKYLLPFE 87

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292438  576 EEDFLKDVMQFLLQRGHTRLVPQgglaefpdaVLNAKRLDLYNLYKEVVSRGGF-YVGNGINWKgQVFSKMSnhtVTNKM 654
Cdd:smart01014   3 RELFLDRLRKFMEKRGTPLDKIP---------VIGGKPLDLYRLYRAVQKRGGFdKVTKKKKWK-QVARELG---IPPSA 69

                           90
                   ....*....|....*....
gi 1002292438  655 TGVGNTLKRHYETYLLEYE 673
Cdd:smart01014  70 TSAGTSLRKHYEKYLLPYE 88

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1002292438 684 CLLCHSS-APGDWVNCGLCGEWAHFGCdrrqgLGTFKDYAKTDGLEYICPHCS 735
Cdd:pfam00628   2 CAVCGKSdDGGELVQCDGCDDWFHLAC-----LGPPLDPAEIPSGEWLCPECK 49

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292438 575 SEEDFLKDVMQFLLQRGHTRlvpqgglaeFPDAVLNAKRLDLYNLYKEVVSRGGFYVGNGINWKGQVFSKMSNHTvtnKM 654
Cdd:cd16100     1 EREEFLEQLRAFLESRGTPL---------LKPPTIGGKPLDLYKLYRAVVSRGGYEKVTEKKLWKEVARKLGLPT---SS 68

                          90
                  ....*....|....*....
gi 1002292438 655 TGVGNTLKRHYETYLLEYE 673
Cdd:cd16100    69 TSAAQALKRIYEKYLLPFE 87

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292438  576 EEDFLKDVMQFLLQRGHTRLVPQgglaefpdaVLNAKRLDLYNLYKEVVSRGGF-YVGNGINWKgQVFSKMSnhtVTNKM 654
Cdd:smart01014   3 RELFLDRLRKFMEKRGTPLDKIP---------VIGGKPLDLYRLYRAVQKRGGFdKVTKKKKWK-QVARELG---IPPSA 69

                           90
                   ....*....|....*....
gi 1002292438  655 TGVGNTLKRHYETYLLEYE 673
Cdd:smart01014  70 TSAGTSLRKHYEKYLLPYE 88

PHD finger found in Transcription factor 19 (TCF-19), Lysine-specific demethylase KDM5A and KDM5B, and other similar proteins; TCF-19 was identified as a putative trans-activating factor with expression beginning at the late G1-S boundary in dividing cells. It functions as a novel islet factor necessary for proliferation and survival in the INS-1 beta cell line. It plays an important role in susceptibility to both Type 1 Diabetes Mellitus (T1DM) and Type 2 Diabetes Mellitus (T2DM); it has been suggested that it may positively impact beta cell mass under conditions of beta cell stress and increased insulin demand. 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 interaction 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. This family also includes Caenorhabditis elegans Lysine-specific demethylase 7 homolog (ceKDM7A). ceKDM7A (also termed JmjC domain-containing protein 1.2, PHD finger protein 8 homolog, or PHF8 homolog) is a plant homeodomain (PHD)- and JmjC domain-containing protein that functions as a histone demethylase specific for H3K9me2 and H3K27me2. The binding of the PHD finger to H3K4me3 guides H3K9me2- and H3K27me2-specific demethylation by its catalytic JmjC domain in a trans-histone regulation mechanism. In addition, this family includes plant protein OBERON 1 and OBERON 2, Alfin1-like (AL) proteins, histone acetyltransferases (HATs) HAC, and AT-rich interactive domain-containing protein 4 (ARID4).

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1002292438 683 CCLLCHSSApGDWVNCGLCGEWAHFGCDRRQGlgtfkdYAKTDGLEYICPHC 734
Cdd:cd15517     5 CNLETAAVD-ELWVQCDGCDKWFHQFCLGLSN------ERYADEDKFKCPNC 49

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292438 578 DFLKDVMQFLLQRGHTRLVPqgglaefpdaVLNAKRLDLYNLYKEVVSRGGFYVGNginwKGQVFSKMSNHTVTNKMTGV 657
Cdd:cd16873     6 DFLDQLAKFWELQGSTLKIP----------VVERKILDLYALSKIVASEGGFEMVT----KEKKWSKVGSRMGYLPGKGT 71

                          90
                  ....*....|....*..
gi 1002292438 658 GNTLKRHYETYLLEYEL 674
Cdd:cd16873    72 GSLLKSHYERILYPYEL 88

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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1002292438 608 VLNAKRLDLYNLYKEVVSRGGF-YVGNGINWkGQVFSKMsnHTVTNKmtGVGNTLKRHYETYLLEYE 673
Cdd:cd16864    26 NVERKALDLFTLHKIVQEEGGFeEVTKERKW-SKVARRL--GYPPGK--GVGSLLRGHYERILYPYD 87

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292438 578 DFLKDVMQFLLQRGHtrlvpqgGLAEFPdaVLNAKRLDLYNLYKEVVSRGGFY-VGNGINWKgQVFSKMsnhtvtnkmtG 656
Cdd:cd16865     5 PFLDRLLRFMEERGS-------PITNCP--QISKQPLDLFRLYVTVKERGGVAeVTKNKKWK-EICTEL----------N 64

                          90       100
                  ....*....|....*....|...
gi 1002292438 657 VGN------TLKRHYETYLLEYE 673
Cdd:cd16865    65 IGAsssaafTLRKNYIKYLLAYE 87

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292438 577 EDFLKDVMQFLLQRGhtrlVPqggLAEFPdaVLNAKRLDLYNLYKEVVSRGGFY-VGNGINWKgQVFSKMSNHTVTnkmT 655
Cdd:cd16868     3 ENFLEQLYKFMEDRG----TP---INKPP--VLGYKDLDLFKLYKLVQELGGMErVSQGAKWR-SIYQQLGIPVLN---S 69

                          90
                  ....*....|....*...
gi 1002292438 656 GVGNTLKRHYETYLLEYE 673
Cdd:cd16868    70 AASHNIKQAYKKYLYAFE 87

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292438 577 EDFLKDVMQFLLQRGhtrlVPqggLAEFPdaVLNAKRLDLYNLYKEVVSRGGFY-VGNGINWkgQVFSKMSNhtVTNKMT 655
Cdd:cd16881    21 KEFLDDLFSFMQKRG----TP---VNRIP--IMAKQVLDLYELYNLVVARGGLVeVINKKLW--REITKGLH--LPSSIT 87

                          90
                  ....*....|....*...
gi 1002292438 656 GVGNTLKRHYETYLLEYE 673
Cdd:cd16881    88 SAAFTLRTQYMKYLYPYE 105