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Arid4a AT-rich interaction domain 4A [ Rattus norvegicus (Norway rat) ]

Gene ID: 314205, updated on 2-Nov-2024

Summary

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Official Symbol
Arid4aprovided by RGD
Official Full Name
AT-rich interaction domain 4Aprovided by RGD
Primary source
RGD:1307442
See related
EnsemblRapid:ENSRNOG00000026239 AllianceGenome:RGD:1307442
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
Summary
Predicted to enable transcription cis-regulatory region binding activity. Predicted to be involved in negative regulation of DNA-templated transcription and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including erythrocyte development; establishment of Sertoli cell barrier; and regulation of gene expression. Predicted to be located in nucleoplasm and plasma membrane. Predicted to be part of transcription repressor complex. Predicted to be active in nucleus. Orthologous to human ARID4A (AT-rich interaction domain 4A). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Biased expression in Thymus (RPKM 119.6), Spleen (RPKM 110.1) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Arid4a in Genome Data Viewer
Location:
6q24
Exon count:
27
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 6 NC_086024.1 (95258429..95335987)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 6 NC_051341.1 (89522459..89593868)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 6 NC_005105.4 (93461713..93532901)

Chromosome 6 - NC_086024.1Genomic Context describing neighboring genes Neighboring gene transfer RNA lysine (anticodon CUU) 9 Neighboring gene proteasome 20S subunit alpha 3 Neighboring gene translocase of outer mitochondrial membrane 20 like Neighboring gene KIAA0586 homolog Neighboring gene translocase of inner mitochondrial membrane 9 Neighboring gene dishevelled-binding antagonist of beta-catenin 1

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. Identification of chromatin remodeling genes Arid4a and Arid4b as leukemia suppressor genes. Wu MY, et al. J Natl Cancer Inst, 2008 Sep 3. PMID 18728284, Free PMC Article
  2. ARID4A and ARID4B regulate male fertility, a functional link to the AR and RB pathways. Wu RC, et al. Proc Natl Acad Sci U S A, 2013 Mar 19. PMID 23487765, Free PMC Article
  3. Deficiency of Rbbp1/Arid4a and Rbbp1l1/Arid4b alters epigenetic modifications and suppresses an imprinting defect in the PWS/AS domain. Wu MY, et al. Genes Dev, 2006 Oct 15. PMID 17043311, Free PMC Article
  4. Identification and characterization of three new components of the mSin3A corepressor complex. Fleischer TC, et al. Mol Cell Biol, 2003 May. PMID 12724404, Free PMC Article
  5. RBP1 recruits the mSIN3-histone deacetylase complex to the pocket of retinoblastoma tumor suppressor family proteins found in limited discrete regions of the nucleus at growth arrest. Lai A, et al. Mol Cell Biol, 2001 Apr. PMID 11283269, Free PMC Article

See all (7) citations in PubMed

GeneRIFs: Gene References Into Functions

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 transcription cis-regulatory region binding IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within chromatin organization ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within erythrocyte development ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within establishment of Sertoli cell barrier ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within genomic imprinting ISO
Inferred from Sequence Orthology
more info
  
involved_in negative regulation of DNA-templated transcription ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
  
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within spermatogenesis ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
located_in nucleoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
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
  
part_of transcription repressor complex ISO
Inferred from Sequence Orthology
more info
  

General protein information

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Preferred Names
AT-rich interactive domain-containing protein 4A
Names
AT rich interactive domain 4A (Rbp1 like)

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_001395713.1 → NP_001382642.1  AT-rich interactive domain-containing protein 4A

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000006
    UniProtKB/TrEMBL
    A0A8I6AQP2
    Related
    ENSRNOP00000029718.5, ENSRNOT00000031595.7
    Conserved Domains (5) summary
    cd18641
    Location:578 → 636
    CBD_RBP1_like; chromo barrel domain of retinoblastoma binding protein 1, and similar proteins
    cl28902
    Location:312 → 397
    ARID; ARID/BRIGHT DNA binding domain family
    pfam08169
    Location:170 → 262
    RBB1NT; RBB1NT (NUC162) domain
    cd20459
    Location:4 → 61
    Tudor_ARID4A_rpt1; first Tudor domain found in AT-rich interactive domain-containing protein 4A (ARID4A) and similar proteins
    cl02573
    Location:62 → 118
    Tudor_SF; Tudor domain superfamily

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_086024.1 Reference GRCr8

    Range
    95258429..95335987
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_039112256.2 → XP_038968184.1  AT-rich interactive domain-containing protein 4A isoform X1

    UniProtKB/TrEMBL
    A0A0G2K094, A0A8I6AQP2
    Related
    ENSRNOP00000071353.2, ENSRNOT00000089473.3
    Conserved Domains (5) summary
    cd18641
    Location:597 → 655
    CBD_RBP1_like; chromo barrel domain of retinoblastoma binding protein 1, and similar proteins
    cl28902
    Location:331 → 416
    ARID; ARID/BRIGHT DNA binding domain family
    pfam08169
    Location:189 → 281
    RBB1NT; RBB1NT (NUC162) domain
    cd20459
    Location:23 → 80
    Tudor_ARID4A_rpt1; first Tudor domain found in AT-rich interactive domain-containing protein 4A (ARID4A) and similar proteins
    cl02573
    Location:81 → 137
    Tudor_SF; Tudor domain superfamily

  2. XM_039112258.2 → XP_038968186.1  AT-rich interactive domain-containing protein 4A isoform X2

    UniProtKB/TrEMBL
    A0A8I6APL4
    Conserved Domains (2) summary
    cd18641
    Location:256 → 314
    CBD_RBP1_like; chromo barrel domain of retinoblastoma binding protein 1, and similar proteins
    cl28902
    Location:1 → 75
    ARID; ARID/BRIGHT DNA binding domain family

  3. XM_039112259.2 → XP_038968187.1  AT-rich interactive domain-containing protein 4A isoform X3

    Conserved Domains (1) summary
    cl28914
    Location:1 → 33
    CD_CSD; CHROMO (CHRromatin Organization Modifier) domains and chromo shadow domains

RNA

  1. XR_010052092.1 RNA Sequence

  2. XR_010052090.1 RNA Sequence

  3. XR_010052094.1 RNA Sequence

  4. XR_010052089.1 RNA Sequence

  5. XR_010052091.1 RNA Sequence

  6. XR_010052093.1 RNA Sequence

  7. XR_010052095.1 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001108029.1: Suppressed sequence

    Description
    NM_001108029.1: 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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