Human Gene ARID1A (ENST00000324856.13) from GENCODE V43
  Description: Homo sapiens AT-rich interaction domain 1A (ARID1A), transcript variant 1, mRNA. (from RefSeq NM_006015)
RefSeq Summary (NM_006015): This gene encodes a member of the SWI/SNF family, whose members have helicase and ATPase activities and are thought to regulate transcription of certain genes by altering the chromatin structure around those genes. The encoded protein is part of the large ATP-dependent chromatin remodeling complex SNF/SWI, which is required for transcriptional activation of genes normally repressed by chromatin. It possesses at least two conserved domains that could be important for its function. First, it has a DNA-binding domain that can specifically bind an AT-rich DNA sequence known to be recognized by a SNF/SWI complex at the beta-globin locus. Second, the C-terminus of the protein can stimulate glucocorticoid receptor-dependent transcriptional activation. It is thought that the protein encoded by this gene confers specificity to the SNF/SWI complex and may recruit the complex to its targets through either protein-DNA or protein-protein interactions. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008].
Gencode Transcript: ENST00000324856.13
Gencode Gene: ENSG00000117713.21
Transcript (Including UTRs)
   Position: hg38 chr1:26,696,015-26,782,104 Size: 86,090 Total Exon Count: 20 Strand: +
Coding Region
   Position: hg38 chr1:26,696,404-26,780,756 Size: 84,353 Coding Exon Count: 20 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesGeneReviewsMethods
Data last updated at UCSC: 2023-02-17 13:02:02

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr1:26,696,015-26,782,104)mRNA (may differ from genome)Protein (2285 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=AT-rich interactive domain-containing protein 1A; Short=ARID domain-containing protein 1A; AltName: Full=B120; AltName: Full=BRG1-associated factor 250; Short=BAF250; AltName: Full=BRG1-associated factor 250a; Short=BAF250A; AltName: Full=Osa homolog 1; Short=hOSA1; AltName: Full=SWI-like protein; AltName: Full=SWI/SNF complex protein p270; AltName: Full=SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin subfamily F member 1; AltName: Full=hELD;
FUNCTION: Involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). Binds DNA non-specifically. Also involved in vitamin D- coupled transcription regulation via its association with the WINAC complex, a chromatin-remodeling complex recruited by vitamin D receptor (VDR), which is required for the ligand-bound VDR- mediated transrepression of the CYP27B1 gene. Belongs to the neural progenitors-specific chromatin remodeling complex (npBAF complex) and the neuron-specific chromatin remodeling complex (nBAF complex). During neural development a switch from a stem/progenitor to a post-mitotic chromatin remodeling mechanism occurs as neurons exit the cell cycle and become committed to their adult state. The transition from proliferating neural stem/progenitor cells to post-mitotic neurons requires a switch in subunit composition of the npBAF and nBAF complexes. As neural progenitors exit mitosis and differentiate into neurons, npBAF complexes which contain ACTL6A/BAF53A and PHF10/BAF45A, are exchanged for homologous alternative ACTL6B/BAF53B and DPF1/BAF45B or DPF3/BAF45C subunits in neuron-specific complexes (nBAF). The npBAF complex is essential for the self-renewal/proliferative capacity of the multipotent neural stem cells. The nBAF complex along with CREST plays a role regulating the activity of genes essential for dendrite growth (By similarity).
SUBUNIT: Component of SWI/SNF chromatin remodeling complexes, in some of which it can be mutually exclusive with ARID1B/BAF250B. Component of the BAF (SWI/SNF-A) complex, which includes at least actin (ACTB), ARID1A, ARID1B/BAF250, SMARCA2, SMARCA4/BRG1/BAF190A, ACTL6A/BAF53, ACTL6B/BAF53B, SMARCE1/BAF57, SMARCC1/BAF155, SMARCC2/BAF170, SMARCB1/SNF5/INI1, and one or more of SMARCD1/BAF60A, SMARCD2/BAF60B, or SMARCD3/BAF60C. In muscle cells, the BAF complex also contains DPF3. Component of the SWI/SNF-B (PBAF) complex, at least composed of SMARCA4/BRG1/BAF190A, SMARCB1/BAF47, ACTL6A/BAF53A or ACTL6B/BAF53B, SMARCE1/BAF57, SMARCD1/BAF60A, SMARCD2/BAF60B, perhaps SMARCD3/BAF60C, SMARCC1/BAF155, SMARCC2/BAF170, PB1/BAF180, ARID2/BAF200, ARID1A/BAF250A or ARID1B/BAF250B and actin. Component of the SWI/SNF Brm complex, at least composed of SMARCA2/BRM/BAF190B, SMARCB1/BAF47, ACTL6A/BAF53A or ACTL6B/BAF53B, SMARCE1/BAF57, BAF60 (one or more of SMARCD1/BAF60A, SMARCD2/BAF60B, or SMARCD3/BAF60C), SMARCC1/BAF155, SMARCC2/BAF170, ARID1A/BAF250A, SIN3A, HDAC1, HDAC2, and RBAP4. Component of the SWI/SNF complex Brg1(I), at least composed of SMARCA4/BRG1/BAF190A, SMARCB1/BAF47, ACTL6A/BAF53A or ACTL6B/BAF53B, SMARCE1/BAF57, BAF60 (one or more of SMARCD1/BAF60A, SMARCD2/BAF60B, or SMARCD3/BAF60C), SMARCC1/BAF155, SMARCC2/BAF170, ARID1A/BAF250A, SIN3A, and probably HDAC2 and RBAP4. Component of the SWI/SNF Brg1(II), at least composed of SMARCA4/BRG1/BAF190A, SMARCB1/BAF47, ACTL6A/BAF53A or ACTL6B/BAF53B, SMARCE1/BAF57, SMARCC1/BAF155, SMARCC2/BAF170, ARID1A/BAF250A and probably HDAC2 and RBAP4. Component of a SWI/SNF-like EPAFa complex, at least composed of SMARCA4/BRG1/BAF190A, SMARCB1/BAF47, ACTL6A/BAF53A, SMARCE1/BAF57, SMARCD1/BAF60A, SMARCC1/BAF155, SMARCC2/BAF170, BAF250A and MLLT1/ENL. Component of a SWI/SNF-like complex containing ARID1A/BAF250A and ARID1B/BAF250B. Interacts through its C- terminus with SMARCA2/BRM/BAF190B and SMARCA4/BRG1/BAF190A. Component of the WINAC complex, at least composed of SMARCA2, SMARCA4, SMARCB1, SMARCC1, SMARCC2, SMARCD1, SMARCE1, ACTL6A, BAZ1B/WSTF, ARID1A, SUPT16H, CHAF1A and TOP2B. Interacts with SMARCC1/BAF155. Component of neural progenitors-specific chromatin remodeling complex (npBAF complex) composed of at least, ARID1A/BAF250A or ARID1B/BAF250B, SMARCD1/BAF60A, SMARCD3/BAF60C, SMARCA2/BRM/BAF190B, SMARCA4/BRG1/BAF190A, SMARCB1/BAF47, SMARCC1/BAF155, SMARCE1/BAF57, SMARCC2/BAF170, PHF10/BAF45A, ACTL6A/BAF53A and actin. Component of neuron-specific chromatin remodeling complex (nBAF complex) composed of at least, ARID1A/BAF250A or ARID1B/BAF250B, SMARCD1/BAF60A, SMARCD3/BAF60C, SMARCA2/BRM/BAF190B, SMARCA4/BRG1/BAF190A, SMARCB1/BAF47, SMARCC1/BAF155, SMARCE1/BAF57, SMARCC2/BAF170, DPF1/BAF45B, DPF3/BAF45C, ACTL6B/BAF53B and actin (By similarity).
INTERACTION: Q14526:HIC1; NbExp=2; IntAct=EBI-637887, EBI-2507362; P51531:SMARCA2; NbExp=3; IntAct=EBI-637887, EBI-679562; P51532:SMARCA4; NbExp=11; IntAct=EBI-637887, EBI-302489;
TISSUE SPECIFICITY: Highly expressed in spleen, thymus, prostate, testis, ovary, small intestine, colon, and PBL, and at a much lower level in heart, brain, placenta, lung, liver, skeletal muscle, kidney, and pancreas.
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
DISEASE: Defects in ARID1A are the cause of mental retardation autosomal dominant type 14 (MRD14) [MIM:614607]. A disease characterized by multiple congenital anomalies and mental retardation. Mental retardation is defined by significantly below average general intellectual functioning associated with impairments in adaptative behavior and manifested during the developmental period. MRD14 patients manifest developmental delay, abnormal corpus callosum, absent/hypoplastic fifth finger/toenails, sparse scalp hair, long eyelashes, and a coarse facial appearance with wide mouth, thick lips, and abnormal ears.
SIMILARITY: Contains 1 ARID domain.
SEQUENCE CAUTION: Sequence=AAF75765.1; Type=Frameshift; Positions=374; Sequence=AAG33967.1; Type=Frameshift; Positions=872, 885; Sequence=BAA23269.1; Type=Frameshift; Positions=Several; Sequence=BAA83073.1; Type=Erroneous gene model prediction; Sequence=BAA83073.1; Type=Frameshift; Positions=Several;

-  Primer design for this transcript

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-  MalaCards Disease Associations
  MalaCards Gene Search: ARID1A
Diseases sorted by gene-association score: coffin-siris syndrome 2* (919), arid1a-related coffin-siris syndrome* (500), coffin-siris syndrome 1* (183), ovarian clear cell carcinoma (27), ovarian clear cell adenocarcinoma (24), clear cell adenofibroma (16), endometrioid ovary carcinoma (16), intraventricular meningioma (11), malignant ovarian surface epithelial-stromal neoplasm (10), ovary epithelial cancer (10), ovary adenocarcinoma (9), clear cell adenocarcinoma (8), hypertrichosis (6), ectrodactyly, ectodermal dysplasia, and cleft lip/palate syndrome 3 (6), intrahepatic cholangiocarcinoma (6), adenofibroma (6), endometriosis of ovary (4), borjeson-forssman-lehmann syndrome (4), female reproductive organ cancer (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 22.12 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 603.53 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -217.90389-0.560 Picture PostScript Text
3' UTR -319.801348-0.237 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR011989 - ARM-like
IPR021906 - DUF3518

Pfam Domains:
PF01388 - ARID/BRIGHT DNA binding domain
PF12031 - SWI/SNF-like complex subunit BAF250/Osa

Protein Data Bank (PDB) 3-D Structure
MuPIT help

ModBase Predicted Comparative 3D Structure on O14497
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologGenome BrowserNo ortholog
Gene Details     
Gene Sorter     
MGIRGD  WormBase 
Protein SequenceProtein Sequence  Protein Sequence 
AlignmentAlignment  Alignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0003677 DNA binding
GO:0003713 transcription coactivator activity
GO:0005515 protein binding
GO:0016922 ligand-dependent nuclear receptor binding
GO:0031491 nucleosome binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0001704 formation of primary germ layer
GO:0001843 neural tube closure
GO:0003205 cardiac chamber development
GO:0003408 optic cup formation involved in camera-type eye development
GO:0006325 chromatin organization
GO:0006337 nucleosome disassembly
GO:0006338 chromatin remodeling
GO:0006344 maintenance of chromatin silencing
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0007369 gastrulation
GO:0007399 nervous system development
GO:0007566 embryo implantation
GO:0019827 stem cell population maintenance
GO:0030520 intracellular estrogen receptor signaling pathway
GO:0030521 androgen receptor signaling pathway
GO:0030900 forebrain development
GO:0042766 nucleosome mobilization
GO:0042921 glucocorticoid receptor signaling pathway
GO:0043044 ATP-dependent chromatin remodeling
GO:0045893 positive regulation of transcription, DNA-templated
GO:0048096 chromatin-mediated maintenance of transcription
GO:0055007 cardiac muscle cell differentiation
GO:0060674 placenta blood vessel development
GO:0071277 cellular response to calcium ion
GO:1901998 toxin transport

Cellular Component:
GO:0000790 nuclear chromatin
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0016514 SWI/SNF complex
GO:0070603 SWI/SNF superfamily-type complex
GO:0071564 npBAF complex
GO:0071565 nBAF complex

-  Descriptions from all associated GenBank mRNAs
  AF231056 - Homo sapiens BRG1-Associated Factor 250a (BAF250a) mRNA, complete cds.
AF521670 - Homo sapiens SWI/SNF chromatin remodeling complex subunit OSA1 (OSA1) mRNA, partial cds.
LP955724 - Sequence 6 from Patent WO2017214373.
AF219114 - Homo sapiens chromatin remodelling factor p250 mRNA, partial cds.
AB210022 - Homo sapiens mRNA for ARID1A variant protein, partial cds, clone: ha02793.
AB051293 - Homo sapiens mRNA for SWI related protein, complete cds.
AF265208 - Homo sapiens SWI-SNF complex protein p270 mRNA, partial cds.
AB384378 - Synthetic construct DNA, clone: pF1KSDB0043, Homo sapiens ARID1A gene for AT-rich interactive domain-containing protein 1A, complete cds, without stop codon, in Flexi system.
AB001895 - Homo sapiens mRNA for B120, complete cds.
AF268913 - Homo sapiens OSA1 nuclear protein mRNA, complete cds.
JD310570 - Sequence 291594 from Patent EP1572962.
JD459169 - Sequence 440193 from Patent EP1572962.
JD226589 - Sequence 207613 from Patent EP1572962.
JD406337 - Sequence 387361 from Patent EP1572962.
JD458434 - Sequence 439458 from Patent EP1572962.
JD215419 - Sequence 196443 from Patent EP1572962.
JD204161 - Sequence 185185 from Patent EP1572962.
JD485323 - Sequence 466347 from Patent EP1572962.
JD076696 - Sequence 57720 from Patent EP1572962.
AK223275 - Homo sapiens mRNA for AT rich interactive domain 1A (SWI- like) isoform a variant, clone: STM08271.
AK027655 - Homo sapiens cDNA FLJ14749 fis, clone NT2RP3002876, weakly similar to Drosophila melanogaster eyelid (eld) mRNA.
AK074940 - Homo sapiens cDNA FLJ90459 fis, clone NT2RP3001754.
AK308363 - Homo sapiens cDNA, FLJ98311.
AK027442 - Homo sapiens cDNA FLJ14536 fis, clone NT2RM2001105, weakly similar to Drosophila melanogaster eyelid (eld) mRNA.
JD155350 - Sequence 136374 from Patent EP1572962.
JD510888 - Sequence 491912 from Patent EP1572962.
JD362422 - Sequence 343446 from Patent EP1572962.
JD518204 - Sequence 499228 from Patent EP1572962.
AK027467 - Homo sapiens cDNA FLJ14561 fis, clone NT2RM2002091, weakly similar to Drosophila melanogaster eyelid (eld) mRNA.
JD502489 - Sequence 483513 from Patent EP1572962.
JD404133 - Sequence 385157 from Patent EP1572962.
JD217823 - Sequence 198847 from Patent EP1572962.
JD381825 - Sequence 362849 from Patent EP1572962.
JD531168 - Sequence 512192 from Patent EP1572962.
JD319843 - Sequence 300867 from Patent EP1572962.
JD132247 - Sequence 113271 from Patent EP1572962.
JD327927 - Sequence 308951 from Patent EP1572962.
JD280350 - Sequence 261374 from Patent EP1572962.
JD054098 - Sequence 35122 from Patent EP1572962.
JD389167 - Sequence 370191 from Patent EP1572962.
JD277695 - Sequence 258719 from Patent EP1572962.
JD310830 - Sequence 291854 from Patent EP1572962.
JD553075 - Sequence 534099 from Patent EP1572962.
JD087373 - Sequence 68397 from Patent EP1572962.
JD387996 - Sequence 369020 from Patent EP1572962.
JD391493 - Sequence 372517 from Patent EP1572962.
BC112895 - Homo sapiens AT rich interactive domain 1A (SWI-like), mRNA (cDNA clone IMAGE:4802284), partial cds.
JD069088 - Sequence 50112 from Patent EP1572962.
AF217506 - Homo sapiens uncharacterized bone marrow protein BM029 mRNA, complete cds.
JD365661 - Sequence 346685 from Patent EP1572962.
JD424169 - Sequence 405193 from Patent EP1572962.
JD374986 - Sequence 356010 from Patent EP1572962.
JD095299 - Sequence 76323 from Patent EP1572962.
JD458268 - Sequence 439292 from Patent EP1572962.
JD186296 - Sequence 167320 from Patent EP1572962.
JD406905 - Sequence 387929 from Patent EP1572962.
JD279759 - Sequence 260783 from Patent EP1572962.
JD174874 - Sequence 155898 from Patent EP1572962.
JD457873 - Sequence 438897 from Patent EP1572962.
JD085678 - Sequence 66702 from Patent EP1572962.
JD428663 - Sequence 409687 from Patent EP1572962.
JD259292 - Sequence 240316 from Patent EP1572962.
JD163303 - Sequence 144327 from Patent EP1572962.
JD288899 - Sequence 269923 from Patent EP1572962.
JD413490 - Sequence 394514 from Patent EP1572962.
JD403517 - Sequence 384541 from Patent EP1572962.
JD253521 - Sequence 234545 from Patent EP1572962.
JD304297 - Sequence 285321 from Patent EP1572962.
JD529999 - Sequence 511023 from Patent EP1572962.
JD234990 - Sequence 216014 from Patent EP1572962.
JD316772 - Sequence 297796 from Patent EP1572962.
JD214121 - Sequence 195145 from Patent EP1572962.
JD323654 - Sequence 304678 from Patent EP1572962.
JD487701 - Sequence 468725 from Patent EP1572962.
JD166522 - Sequence 147546 from Patent EP1572962.
JD510823 - Sequence 491847 from Patent EP1572962.
JD302538 - Sequence 283562 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_vdrPathway - Control of Gene Expression by Vitamin D Receptor
h_hSWI-SNFpathway - Chromatin Remodeling by hSWI/SNF ATP-dependent Complexes

Reactome (by CSHL, EBI, and GO)

Protein O14497 (Reactome details) participates in the following event(s):

R-HSA-3215448 SWI/SNF chromatin remodelling complex enhances MEP50:PRMT5 methyltransferase activity
R-HSA-8938217 RUNX1 binds the SWI/SNF complex
R-HSA-3214858 RMTs methylate histone arginines
R-HSA-8939243 RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known
R-HSA-3247509 Chromatin modifying enzymes
R-HSA-8878171 Transcriptional regulation by RUNX1
R-HSA-4839726 Chromatin organization
R-HSA-212436 Generic Transcription Pathway
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: ARI1A_HUMAN, BAF250, BAF250A, C1orf4, D3DPL1, ENST00000324856.1, ENST00000324856.10, ENST00000324856.11, ENST00000324856.12, ENST00000324856.2, ENST00000324856.3, ENST00000324856.4, ENST00000324856.5, ENST00000324856.6, ENST00000324856.7, ENST00000324856.8, ENST00000324856.9, NM_006015, O14497, OSA1, Q53FK9, Q5T0W1, Q5T0W2, Q5T0W3, Q8NFD6, Q96T89, Q9BY33, Q9HBJ5, Q9UPZ1, SMARCF1, uc001bmv.1, uc001bmv.2, uc001bmv.3, uc001bmv.4
UCSC ID: ENST00000324856.13
RefSeq Accession: NM_006015
Protein: O14497 (aka ARI1A_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene ARID1A:
cdh-ov (Congenital Diaphragmatic Hernia Overview)
coffin-siris (Coffin-Siris Syndrome)

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.