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Arid1b AT-rich interaction domain 1B [ Rattus norvegicus (Norway rat) ]

Gene ID: 282546, updated on 28-Oct-2024

Summary

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Official Symbol
Arid1bprovided by RGD
Official Full Name
AT-rich interaction domain 1Bprovided by RGD
Primary source
RGD:708504
See related
EnsemblRapid:ENSRNOG00000017030 AllianceGenome:RGD:708504
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as
6A3-5; Smcf1; smcf-1
Summary
Predicted to enable DNA binding activity. Predicted to contribute to nucleosome binding activity. Involved in cellular response to angiotensin and response to ischemia. Predicted to be located in several cellular components, including cytosol; nucleus; and synapse. Predicted to be part of SWI/SNF complex and nBAF complex. Predicted to be active in nucleoplasm. Used to study ischemia. Biomarker of hypertension and ischemia. Human ortholog(s) of this gene implicated in Coffin-Siris syndrome; Coffin-Siris syndrome 1; intellectual disability; lung non-small cell carcinoma; and neuroblastoma. Orthologous to human ARID1B (AT-rich interaction domain 1B). [provided by Alliance of Genome Resources, Oct 2024]
Expression
Biased expression in Adrenal (RPKM 141.7), Kidney (RPKM 111.0) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Arid1b in Genome Data Viewer
Location:
1q11
Exon count:
21
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 1 NC_086019.1 (47973199..48328793)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 1 NC_051336.1 (45567991..45923644)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 1 NC_005100.4 (45923119..46232301)

Chromosome 1 - NC_086019.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102548472 Neighboring gene uncharacterized LOC134484862 Neighboring gene transmembrane protein 242 Neighboring gene lactate dehydrogenase A-like 6B Neighboring gene uncharacterized LOC120099115

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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Related articles in PubMed

  1. [Radiotherapy of bone tumors]. Bataini JP, et al. Helv Chir Acta, 1973 Mar. PMID 4633620
  2. 6A3-5/Osa2 is an early activated gene implicated in the control of vascular smooth muscle cell functions. Garin G, et al. J Biomed Biotechnol, 2006. PMID 17489020, Free PMC Article
  3. Expanding the phenotypic spectrum of ARID1B-mediated disorders and identification of altered cell-cycle dynamics due to ARID1B haploinsufficiency. Sim JC, et al. Orphanet J Rare Dis, 2014 Mar 27. PMID 24674232, Free PMC Article
  4. The molecular mechanism of the transcriptional activator SWI regulating gene ARID1B affecting swallowing dysfunction after stroke in rats. Li X, et al. Pharmazie, 2021 Oct 1. PMID 34620277
  5. Haploinsufficiency of ARID1B, a member of the SWI/SNF-a chromatin-remodeling complex, is a frequent cause of intellectual disability. Hoyer J, et al. Am J Hum Genet, 2012 Mar 9. PMID 22405089, Free PMC Article

See all (18) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The molecular mechanism of the transcriptional activator SWI regulating gene ARID1B affecting swallowing dysfunction after stroke in rats.
    Title: The molecular mechanism of the transcriptional activator SWI regulating gene ARID1B affecting swallowing dysfunction after stroke in rats.
  2. 6A3-5 expression is associated with alpha-smooth muscle cell actin in mesangial cells, arteriolar smooth muscle cells, and interstitial myofibroblasts. could potentially be a novel early vascular marker of acute and chronic renal ischemic stress
    Title: Ischemia induces early expression of a new transcription factor (6A3-5) in kidney vascular smooth muscle cells: studies in rat and human renal pathology.
Submit: New GeneRIF Correction

General gene information

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Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables DNA binding ISO
Inferred from Sequence Orthology
more info
  
enables DNA-binding transcription factor activity TAS
Traceable Author Statement
more info
 PubMed 
contributes_to nucleosome binding IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in cellular response to angiotensin IEP
Inferred from Expression Pattern
more info
 PubMed 
involved_in chromatin remodeling IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within dendritic cell dendrite assembly ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within dendritic spine development ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within neuron-neuron synaptic transmission ISO
Inferred from Sequence Orthology
more info
  
involved_in positive regulation of DNA-templated transcription IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in response to ischemia IEP
Inferred from Expression Pattern
more info
 PubMed 
Component Evidence Code Pubs
part_of SWI/SNF complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of SWI/SNF complex ISO
Inferred from Sequence Orthology
more info
  
part_of brahma complex IEA
Inferred from Electronic Annotation
more info
  
located_in cytosol IEA
Inferred from Electronic Annotation
more info
  
located_in cytosol ISO
Inferred from Sequence Orthology
more info
  
part_of nBAF complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of nBAF complex ISO
Inferred from Sequence Orthology
more info
  
is_active_in nucleoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
  
located_in nucleus ISO
Inferred from Sequence Orthology
more info
  
located_in plasma membrane IEA
Inferred from Electronic Annotation
more info
  
located_in plasma membrane ISO
Inferred from Sequence Orthology
more info
  
located_in synapse ISO
Inferred from Sequence Orthology
more info
  

General protein information

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Preferred Names
AT-rich interactive domain-containing protein 1B
Names
AT rich interactive domain 1B (Swi1 like)
transcription factor 1

NCBI Reference Sequences (RefSeq)

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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.

mRNA and Protein(s)

  1. NM_001419802.1 → NP_001406731.1  AT-rich interactive domain-containing protein 1B

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000001
    UniProtKB/TrEMBL
    A0A0G2JVD3
    Related
    ENSRNOP00000110916.1, ENSRNOT00000161412.1

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

  1. NC_086019.1 Reference GRCr8

    Range
    47973199..48328793
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_039099697.2 → XP_038955625.1  AT-rich interactive domain-containing protein 1B isoform X4

    UniProtKB/TrEMBL
    F1LNP1
    Related
    ENSRNOP00000022939.7, ENSRNOT00000022939.9
    Conserved Domains (4) summary
    PHA03247
    Location:126 → 391
    PHA03247; large tegument protein UL36; Provisional
    pfam09606
    Location:703 → 1080
    Med15; ARC105 or Med15 subunit of Mediator complex non-fungal
    cd16877
    Location:590 → 682
    ARID_ARID1B; ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 1B (ARID1B) and similar proteins
    pfam12031
    Location:1473 → 1728
    BAF250_C; SWI/SNF-like complex subunit BAF250/Osa

  2. XM_039099688.2 → XP_038955616.1  AT-rich interactive domain-containing protein 1B isoform X1

    Conserved Domains (4) summary
    PHA03247
    Location:719 → 984
    PHA03247; large tegument protein UL36; Provisional
    pfam09606
    Location:1296 → 1672
    Med15; ARC105 or Med15 subunit of Mediator complex non-fungal
    cd16877
    Location:1183 → 1275
    ARID_ARID1B; ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 1B (ARID1B) and similar proteins
    pfam12031
    Location:2065 → 2320
    BAF250_C; SWI/SNF-like complex subunit BAF250/Osa

  3. XM_039099696.2 → XP_038955624.1  AT-rich interactive domain-containing protein 1B isoform X3

    Related
    ENSRNOP00000076073.3, ENSRNOT00000092976.3
    Conserved Domains (4) summary
    PHA03247
    Location:575 → 924
    PHA03247; large tegument protein UL36; Provisional
    pfam09606
    Location:1236 → 1613
    Med15; ARC105 or Med15 subunit of Mediator complex non-fungal
    cd16877
    Location:1123 → 1215
    ARID_ARID1B; ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 1B (ARID1B) and similar proteins
    pfam12031
    Location:2006 → 2261
    BAF250_C; SWI/SNF-like complex subunit BAF250/Osa

  4. XM_039099692.2 → XP_038955620.1  AT-rich interactive domain-containing protein 1B isoform X2

    Related
    ENSRNOP00000109702.1, ENSRNOT00000126261.1
    Conserved Domains (4) summary
    PHA03247
    Location:575 → 945
    PHA03247; large tegument protein UL36; Provisional
    pfam09606
    Location:1259 → 1636
    Med15; ARC105 or Med15 subunit of Mediator complex non-fungal
    cd16877
    Location:1146 → 1238
    ARID_ARID1B; ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 1B (ARID1B) and similar proteins
    pfam12031
    Location:2029 → 2284
    BAF250_C; SWI/SNF-like complex subunit BAF250/Osa

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_172157.1: Suppressed sequence

    Description
    NM_172157.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.
Nucleotide Protein Strain
Heading Accession and Version

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