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

    Gene ID: 282546, updated on 13-Apr-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
    Ensembl: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 transcription factor activity. Predicted to contribute to nucleosome binding activity. Involved in cellular response to angiotensin and response to ischemia. Located in cytoplasm and nucleus. 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, Apr 2022]
    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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    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
    • 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. 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
    2. 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
    3. 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
    4. [Radiotherapy of bone tumors]. Bataini JP, et al. Helv Chir Acta, 1973 Mar. PMID 4633620
    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 IEA
    Inferred from Electronic Annotation
    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
      ENSRNOP00000069438.2, ENSRNOT00000084454.2

    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
      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
      ENSRNOP00000076073.2
      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

      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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