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Arid4b AT-rich interaction domain 4B [ Rattus norvegicus (Norway rat) ]

Gene ID: 84481, updated on 2-Nov-2024

Summary

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Symbol
Arid4bprovided by RGD
Full Name
AT-rich interaction domain 4Bprovided by RGD
Primary source
RGD:619919
See related
EnsemblRapid:ENSRNOG00000016391 AllianceGenome:RGD:619919
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
Bcaa
Summary
Predicted to enable transcription cis-regulatory region binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within establishment of Sertoli cell barrier; regulation of gene expression; and spermatogenesis. Predicted to be located in cytosol; mitochondrion; and nucleoplasm. Predicted to be active in nucleus. Orthologous to human ARID4B (AT-rich interaction domain 4B). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Biased expression in Thymus (RPKM 158.9), Adrenal (RPKM 130.5) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Arid4b in Genome Data Viewer
Location:
17q12.1
Exon count:
26
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 17 NC_086035.1 (55833908..55958382, complement)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 17 NC_051352.1 (51138419..51262894, complement)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 17 NC_005116.4 (53831353..53955897, complement)

Chromosome 17 - NC_086035.1Genomic Context describing neighboring genes Neighboring gene HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1 Neighboring gene 40S ribosomal protein S19 pseudogene Neighboring gene Y-box-binding protein 1-like Neighboring gene geranylgeranyl diphosphate synthase 1 Neighboring gene tubulin folding cofactor E Neighboring gene beta-1,3-N-acetylgalactosaminyltransferase 2

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. Characterization of BRCAA1 and its novel antigen epitope identification. Cui D, et al. Cancer Epidemiol Biomarkers Prev, 2004 Jul. PMID 15247124
  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. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

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 IEA
Inferred from Electronic Annotation
more info
  
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
  
involved_in establishment of Sertoli cell barrier IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within establishment of Sertoli cell barrier ISO
Inferred from Sequence Orthology
more info
  
involved_in genomic imprinting IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within genomic imprinting ISO
Inferred from Sequence Orthology
more info
  
involved_in positive regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
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
  
involved_in spermatogenesis IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within spermatogenesis ISO
Inferred from Sequence Orthology
more info
  
involved_in transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
located_in cytosol ISO
Inferred from Sequence Orthology
more info
  
located_in mitochondrion ISO
Inferred from Sequence Orthology
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 IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
AT-rich interactive domain-containing protein 4B
Names
180 kDa Sin3-associated polypeptide
ARID domain-containing protein 4B
AT rich interactive domain 4B (Rbp1 like)
AT-rich interactive domain-containing protein 4B-like
histone deacetylase complex subunit SAP180
retinoblastoma-binding protein 1-like 1
retinoblastoma-binding protein 1-related protein
sin3-associated polypeptide p180

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_001414215.1 → NP_001401144.1  AT-rich interactive domain-containing protein 4B isoform 1

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000017
    UniProtKB/TrEMBL
    A0A0G2JVS0

  2. NM_053421.3 → NP_445873.2  AT-rich interactive domain-containing protein 4B isoform 2

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000017
    UniProtKB/Swiss-Prot
    Q9JKB5
    UniProtKB/TrEMBL
    A6K9C7, F1LMH4, F1LYA4
    Related
    ENSRNOP00000010836.7, ENSRNOT00000010836.8
    Conserved Domains (5) summary
    PTZ00121
    Location:450 → 763
    PTZ00121; MAEBL; Provisional
    cd16883
    Location:308 → 399
    ARID_ARID4B; ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 4B (ARID4B) and similar proteins
    pfam08169
    Location:168 → 263
    RBB1NT; RBB1NT (NUC162) domain
    cd20460
    Location:1 → 61
    Tudor_ARID4B_rpt1; first Tudor domain found in AT-rich interactive domain-containing protein 4B (ARID4B) and similar proteins
    cd20462
    Location:62 → 118
    Tudor_ARID4B_rpt2; second Tudor domain found in AT-rich interactive domain-containing protein 4B (ARID4B) and similar proteins

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_086035.1 Reference GRCr8

    Range
    55833908..55958382 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_008771766.4 → XP_008769988.1  AT-rich interactive domain-containing protein 4B isoform X4

    UniProtKB/Swiss-Prot
    Q9JKB5
    Conserved Domains (3) summary
    smart00333
    Location:58 → 113
    TUDOR; Tudor domain
    smart01014
    Location:311 → 394
    ARID; ARID/BRIGHT DNA binding domain
    pfam08169
    Location:169 → 262
    RBB1NT; RBB1NT (NUC162) domain

  2. XM_063276774.1 → XP_063132844.1  AT-rich interactive domain-containing protein 4B isoform X3

  3. XM_008771765.4 → XP_008769987.1  AT-rich interactive domain-containing protein 4B isoform X2

    UniProtKB/Swiss-Prot
    Q9JKB5
    Conserved Domains (3) summary
    smart00333
    Location:58 → 113
    TUDOR; Tudor domain
    smart01014
    Location:311 → 394
    ARID; ARID/BRIGHT DNA binding domain
    pfam08169
    Location:169 → 262
    RBB1NT; RBB1NT (NUC162) domain

  4. XM_008771764.4 → XP_008769986.1  AT-rich interactive domain-containing protein 4B isoform X1

    UniProtKB/Swiss-Prot
    Q9JKB5
    Related
    ENSRNOP00000069593.3, ENSRNOT00000078643.3
    Conserved Domains (4) summary
    smart00333
    Location:58 → 113
    TUDOR; Tudor domain
    smart01014
    Location:311 → 394
    ARID; ARID/BRIGHT DNA binding domain
    pfam08169
    Location:169 → 262
    RBB1NT; RBB1NT (NUC162) domain
    pfam11717
    Location:571 → 624
    Tudor-knot; RNA binding activity-knot of a chromodomain

  5. XM_039096118.2 → XP_038952046.1  AT-rich interactive domain-containing protein 4B isoform X5

    Conserved Domains (2) summary
    cl28902
    Location:1 → 80
    ARID; ARID/BRIGHT DNA binding domain family
    cl28914
    Location:254 → 311
    CD_CSD; CHROMO (CHRromatin Organization Modifier) domains and chromo shadow domains

RNA

  1. XR_361039.5 RNA Sequence

Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9JKB5.1 GenPept UniProtKB/Swiss-Prot:Q9JKB5

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