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ARID1B AT-rich interaction domain 1B [ Homo sapiens (human) ]

Gene ID: 57492, updated on 3-Mar-2019

Summary

Official Symbol
ARID1Bprovided by HGNC
Official Full Name
AT-rich interaction domain 1Bprovided by HGNC
Primary source
HGNC:HGNC:18040
See related
Ensembl:ENSG00000049618 MIM:614556
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CSS1; OSA2; 6A3-5; DAN15; MRD12; P250R; BRIGHT; BAF250B; ELD/OSA1
Summary
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]
Expression
Ubiquitous expression in thyroid (RPKM 7.6), skin (RPKM 7.3) and 25 other tissues See more
Orthologs

Genomic context

See ARID1B in Genome Data Viewer
Location:
6q25.3
Exon count:
24
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 6 NC_000006.12 (156777847..157210779)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (157098980..157531913)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378073 Neighboring gene nuclear-encoded mitochondrial tRNA-Val (TAC) 1-1 Neighboring gene microRNA 4466 Neighboring gene uncharacterized LOC105378075 Neighboring gene lactate dehydrogenase A like 6F, pseudogene Neighboring gene transmembrane protein 242

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Coffin-Siris syndrome 1
MedGen: C3281201 OMIM: 135900 GeneReviews: Coffin-Siris Syndrome
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2012-09-06)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated (2012-09-06)

ClinGen Genome Curation PagePubMed

NHGRI GWAS Catalog

Description
APOE and BCHE as modulators of cerebral amyloid deposition: a florbetapir PET genome-wide association study.
NHGRI GWA Catalog
Genome-wide association study identifies five loci associated with susceptibility to pancreatic cancer in Chinese populations.
NHGRI GWA Catalog
Genome-wide association study of sensory disturbances in the inferior alveolar nerve after bilateral sagittal split ramus osteotomy.
NHGRI GWA Catalog
Meta-analysis of genome-wide association studies identifies six new Loci for serum calcium concentrations.
NHGRI GWA Catalog

Pathways from BioSystems

  • Chromatin modifying enzymes, organism-specific biosystem (from REACTOME)
    Chromatin modifying enzymes, organism-specific biosystemEukaryotic DNA is associated with histone proteins and organized into a complex nucleoprotein structure called chromatin. This structure decreases the accessibility of DNA but also helps to protect i...
  • Chromatin organization, organism-specific biosystem (from REACTOME)
    Chromatin organization, organism-specific biosystemChromatin organization refers to the composition and conformation of complexes between DNA, protein and RNA. It is determined by processes that result in the specification, formation or maintenance o...
  • RMTs methylate histone arginines, organism-specific biosystem (from REACTOME)
    RMTs methylate histone arginines, organism-specific biosystemArginine methylation is a common post-translational modification; around 2% of arginine residues are methylated in rat liver nuclei (Boffa et al. 1977). Arginine can be methylated in 3 different ways...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA1235

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA binding IEA
Inferred from Electronic Annotation
more info
 
DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
transcription coactivator activity NAS
Non-traceable Author Statement
more info
PubMed 
Process Evidence Code Pubs
chromatin remodeling IEA
Inferred from Electronic Annotation
more info
 
chromatin-mediated maintenance of transcription NAS
Non-traceable Author Statement
more info
PubMed 
nervous system development IEA
Inferred from Electronic Annotation
more info
 
regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
SWI/SNF complex IDA
Inferred from Direct Assay
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
 
nBAF complex IEA
Inferred from Electronic Annotation
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
plasma membrane IDA
Inferred from Direct Assay
more info
 

General protein information

Preferred Names
AT-rich interactive domain-containing protein 1B
Names
ARID domain-containing protein 1B
AT rich interactive domain 1B (SWI1-like)
BRG1-associated factor 250b
BRG1-binding protein ELD/OSA1
ELD (eyelid)/OSA protein

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_032093.2 RefSeqGene

    Range
    4926..437850
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001346813.1NP_001333742.1  AT-rich interactive domain-containing protein 1B isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) represents the longest transcript and encodes the longest isoform (3).
    Source sequence(s)
    AL049820, AL162578, AL355297, AL591545
    Consensus CDS
    CCDS87459.1
    UniProtKB/Swiss-Prot
    Q8NFD5
    Related
    ENSP00000490491.1, ENST00000636930.1
  2. NM_001363725.1NP_001350654.1  AT-rich interactive domain-containing protein 1B isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and coding sequence compared to variant 3. The resulting isoform (4) is shorter at the N-terminus compared to isoform 3.
    Source sequence(s)
    AL049820, AL591545
    Consensus CDS
    CCDS87460.1
    Conserved Domains (3) summary
    smart00501
    Location:357448
    BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
    pfam09606
    Location:470850
    Med15; ARC105 or Med15 subunit of Mediator complex non-fungal
    pfam12031
    Location:12301485
    BAF250_C; SWI/SNF-like complex subunit BAF250/Osa
  3. NM_017519.2NP_059989.2  AT-rich interactive domain-containing protein 1B isoform 1

    See identical proteins and their annotated locations for NP_059989.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) lacks an alternate in-frame exon compared to variant 3. The resulting isoform (1) has the same N- and C-termini but is shorter compared to isoform 3.
    Source sequence(s)
    AF521671, AL355297, AL591545, BU733862, Y08266
    Consensus CDS
    CCDS5251.2
    UniProtKB/Swiss-Prot
    Q8NFD5
    Related
    ENSP00000055163.7, ENST00000350026.10
    Conserved Domains (3) summary
    smart00501
    Location:10541145
    BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
    pfam12031
    Location:19272182
    DUF3518; Domain of unknown function (DUF3518)
    cl02310
    Location:698764
    Glyco_hydro_81; Glycosyl hydrolase family 81
  4. NM_020732.3NP_065783.3  AT-rich interactive domain-containing protein 1B isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains an alternate in-frame exon and lacks another alternate in-frame exon compared to variant 3. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 3.
    Source sequence(s)
    AF468300, AF521671, AL355297, AL591545, BU733862, Y08266
    Consensus CDS
    CCDS55072.1
    UniProtKB/Swiss-Prot
    Q8NFD5
    Related
    ENSP00000498155.1, ENST00000647938.1
    Conserved Domains (3) summary
    smart00501
    Location:10671158
    BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
    pfam12031
    Location:19402195
    DUF3518; Domain of unknown function (DUF3518)
    cl02310
    Location:711777
    Glyco_hydro_81; Glycosyl hydrolase family 81

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p12 Primary Assembly

    Range
    156777847..157210779
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011535984.2XP_011534286.2  AT-rich interactive domain-containing protein 1B isoform X1

  2. XM_017011103.2XP_016866592.1  AT-rich interactive domain-containing protein 1B isoform X2

  3. XM_017011105.2XP_016866594.1  AT-rich interactive domain-containing protein 1B isoform X4

  4. XM_017011107.2XP_016866596.1  AT-rich interactive domain-containing protein 1B isoform X6

  5. XM_017011104.1XP_016866593.1  AT-rich interactive domain-containing protein 1B isoform X3

  6. XM_017011106.2XP_016866595.1  AT-rich interactive domain-containing protein 1B isoform X5

  7. XM_017011109.2XP_016866598.1  AT-rich interactive domain-containing protein 1B isoform X7

    UniProtKB/TrEMBL
    A0A1B0GVK1
    Related
    ENSP00000490550.1, ENST00000637904.1
    Conserved Domains (3) summary
    smart00501
    Location:357448
    BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
    pfam09606
    Location:470850
    Med15; ARC105 or Med15 subunit of Mediator complex non-fungal
    pfam12031
    Location:12301485
    BAF250_C; SWI/SNF-like complex subunit BAF250/Osa
  8. XM_011535988.3XP_011534290.1  AT-rich interactive domain-containing protein 1B isoform X8

    Related
    ENSP00000490385.1, ENST00000635957.1
    Conserved Domains (4) summary
    smart00501
    Location:154245
    BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
    pfam09606
    Location:277711
    Med15; ARC105 or Med15 subunit of Mediator complex non-fungal
    pfam03353
    Location:588666
    Lin-8; Ras-mediated vulval-induction antagonizt
    pfam12031
    Location:10271282
    DUF3518; Domain of unknown function (DUF3518)

RNA

  1. XR_002956289.1 RNA Sequence

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