Human Gene ARID1B (ENST00000350026.10) from GENCODE V43
  Description: Homo sapiens AT-rich interaction domain 1B (ARID1B), transcript variant 1, mRNA. (from RefSeq NM_017519)
RefSeq Summary (NM_017519): This locus encodes an AT-rich DNA interacting domain-containing protein. The encoded protein is a component of the SWI/SNF chromatin remodeling complex and may play a role in cell-cycle activation. The protein encoded by this locus is similar to AT-rich interactive domain-containing protein 1A. These two proteins function as alternative, mutually exclusive ARID-subunits of the SWI/SNF complex. The associated complexes play opposing roles. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2016].
Gencode Transcript: ENST00000350026.10
Gencode Gene: ENSG00000049618.25
Transcript (Including UTRs)
   Position: hg38 chr6:156,777,930-157,209,142 Size: 431,213 Total Exon Count: 19 Strand: +
Coding Region
   Position: hg38 chr6:156,777,930-157,207,891 Size: 429,962 Coding Exon Count: 19 

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 (chr6:156,777,930-157,209,142)mRNA (may differ from genome)Protein (2236 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSCGAPEnsemblEntrez GeneExonPrimerGencode

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=AT-rich interactive domain-containing protein 1B; Short=ARID domain-containing protein 1B; AltName: Full=BRG1-associated factor 250b; Short=BAF250B; AltName: Full=BRG1-binding protein hELD/OSA1; AltName: Full=Osa homolog 2; Short=hOsa2; AltName: Full=p250R;
FUNCTION: Involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). 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). Binds DNA non-specifically.
SUBUNIT: Component of SWI/SNF chromatin remodeling complexes, in some of which it can be mutually exclusive with ARID1A/BAF250A. 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 a SWI/SNF-like EPAFb complex, at least composed of SMARCA4/BRG1/BAF190A, SMARCB1/BAF47, ACTL6A/BAF53A, SMARCE1/BAF57, SMARCD1/BAF60A, SMARCD2/BAF60B, SMARCC1/BAF155, SMARCC2/BAF170, ARID1B/BAF250B, MLLT1/ENL and actin. 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. 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: P51531:SMARCA2; NbExp=3; IntAct=EBI-679921, EBI-679562; P51532:SMARCA4; NbExp=3; IntAct=EBI-679921, EBI-302489;
TISSUE SPECIFICITY: Widely expressed with high levels in heart, skeletal muscle and kidney.
POLYMORPHISM: The poly-Gln region is polymorphic and the number of Gln varies in the population (from 17 to 23).
DISEASE: Defects in ARID1B are the cause of mental retardation autosomal dominant type 12 (MRD12) [MIM:614562]. A disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptative behavior and manifested during the developmental period. MRD12 patients present with moderate to severe psychomotor retardation, and most show evidence of muscular hypotonia. In many patients, expressive speech is more severely affected than receptive function. Additional common findings include short stature, abnormal head shape and low-set, posteriorly rotated, and abnormally shaped ears, downslanting palpebral fissures, a bulbous nasal tip, a thin upper lip, minor teeth anomalies, and brachydactyly or single palmar creases. Autistic features are uncommon.
SIMILARITY: Contains 1 ARID domain.
CAUTION: It is uncertain whether Met-1 or Met-59 is the initiator.
SEQUENCE CAUTION: Sequence=AAL76077.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=AAN70985.1; Type=Frameshift; Positions=857, 863; Sequence=CAA69592.1; Type=Frameshift; Positions=132;

-  Primer design for this transcript

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3

-  MalaCards Disease Associations
  MalaCards Gene Search: ARID1B
Diseases sorted by gene-association score: coffin-siris syndrome 1* (1278), nicolaides-baraitser syndrome* (530), arid1b-related coffin-siris syndrome* (500), hypertrichosis* (424), nail disorder, nonsyndromic congenital, 9* (400), blepharophimosis* (400), blepharophimosis, epicanthus inversus, and ptosis, type 1* (283), trichomegaly* (283), corpus callosum, agenesis of, with facial anomalies and cerebellar ataxia* (231), corpus callosum agenesis* (231), chromosome 6q24-q25 deletion syndrome* (42), muenke syndrome (8), spinocerebellar ataxia 2 (7), ladd syndrome (5), borjeson-forssman-lehmann syndrome (5), intellectual disability (2), autism spectrum disorder (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: 10.94 RPKM in Ovary
Total median expression: 330.87 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
3' UTR -273.601251-0.219 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
2CXY - X-ray MuPIT 2EH9 - X-ray MuPIT

ModBase Predicted Comparative 3D Structure on Q8NFD5
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 BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
Protein SequenceProtein SequenceProtein Sequence   

-  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

Biological Process:
GO:0002931 response to ischemia
GO:0006325 chromatin organization
GO:0006338 chromatin remodeling
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0007270 neuron-neuron synaptic transmission
GO:0007399 nervous system development
GO:0048096 chromatin-mediated maintenance of transcription
GO:0060996 dendritic spine development
GO:0097026 dendritic cell dendrite assembly
GO:1904385 cellular response to angiotensin

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0016514 SWI/SNF complex
GO:0070603 SWI/SNF superfamily-type complex
GO:0071565 nBAF complex

-  Descriptions from all associated GenBank mRNAs
  AB587572 - Synthetic construct DNA, clone: pF1KE1600, Homo sapiens ARID1B gene for AT rich interactive domain 1B, without stop codon, in Flexi system.
AF521671 - Homo sapiens SWI/SNF chromatin remodeling complex subunit OSA2 (OSA2) mRNA, partial cds.
AF253515 - Homo sapiens BAF250b subunit mRNA, complete cds.
AF468300 - Homo sapiens BRG1-binding protein ELD/OSA1 mRNA, complete cds.
AK025945 - Homo sapiens cDNA: FLJ22292 fis, clone HRC04412.
AK074180 - Homo sapiens mRNA for FLJ00253 protein.
AF259792 - Homo sapiens p250R mRNA, complete cds.
AB033061 - Homo sapiens mRNA for KIAA1235 protein, partial cds.
Y08266 - H.sapiens mRNA for DAN15 protein, partial.
JC506671 - Sequence 39 from Patent EP2733220.
JC737783 - Sequence 39 from Patent WO2014075939.
JD458517 - Sequence 439541 from Patent EP1572962.
JD023329 - Sequence 4353 from Patent EP1572962.
AK302356 - Homo sapiens cDNA FLJ57012 complete cds, highly similar to AT-rich interactive domain-containing protein 1B.
AK000921 - Homo sapiens cDNA FLJ10059 fis, clone HEMBA1001405.
JD556917 - Sequence 537941 from Patent EP1572962.
BC009543 - Homo sapiens AT rich interactive domain 1B (SWI1-like), mRNA (cDNA clone IMAGE:3896731), partial cds.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q8NFD5 (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: ARI1B_HUMAN, BAF250B, DAN15, ENST00000350026.1, ENST00000350026.2, ENST00000350026.3, ENST00000350026.4, ENST00000350026.5, ENST00000350026.6, ENST00000350026.7, ENST00000350026.8, ENST00000350026.9, KIAA1235, NM_017519, OSA2, Q5JRD1, Q5VYC4, Q8IZY8, Q8NFD5, Q8TEV0, Q8TF02, Q99491, Q9ULI5, uc003qqp.1, uc003qqp.2, uc003qqp.3, uc003qqp.4, uc003qqp.5
UCSC ID: ENST00000350026.10
RefSeq Accession: NM_017519
Protein: Q8NFD5 (aka ARI1B_HUMAN)
CCDS: CCDS5251.2, CCDS55072.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene ARID1B:
arid1b-dis (ARID1B-Related Disorder)
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.