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Arid4a AT-rich interaction domain 4A [ Mus musculus (house mouse) ]

Gene ID: 238247, updated on 8-Feb-2024

Summary

Official Symbol
Arid4aprovided by MGI
Official Full Name
AT-rich interaction domain 4Aprovided by MGI
Primary source
MGI:MGI:2444354
See related
Ensembl:ENSMUSG00000048118 AllianceGenome:MGI:2444354
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
Rbbp1; A630009N03; A630067N03Rik
Summary
Predicted to enable transcription cis-regulatory region binding activity. Acts upstream of or within several processes, including establishment of Sertoli cell barrier; peptidyl-lysine trimethylation; and regulation of gene expression. Predicted to be located in cytosol; nucleoplasm; and plasma membrane. Predicted to be part of transcription repressor complex. Predicted to be active in nucleus. Used to study acute myeloid leukemia. Orthologous to human ARID4A (AT-rich interaction domain 4A). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in bladder adult (RPKM 3.7), frontal lobe adult (RPKM 3.5) and 28 other tissues See more
Orthologs
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Genomic context

See Arid4a in Genome Data Viewer
Location:
12 C2; 12 29.39 cM
Exon count:
27
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 12 NC_000078.7 (71061314..71146125)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 12 NC_000078.6 (71015081..71099351)

Chromosome 12 - NC_000078.7Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer ABC_E1441 Neighboring gene STARR-positive B cell enhancer ABC_E7144 Neighboring gene STARR-positive B cell enhancer ABC_E1442 Neighboring gene nuclear encoded tRNA lysine 17 (anticodon CTT) Neighboring gene proteasome subunit alpha 3 Neighboring gene RIKEN cDNA 3110056K07 gene Neighboring gene STARR-positive B cell enhancer ABC_E11778 Neighboring gene CapStarr-seq enhancer MGSCv37_chr12:72116322-72116431 Neighboring gene CapStarr-seq enhancer MGSCv37_chr12:72116588-72116697 Neighboring gene STARR-seq mESC enhancer starr_32414 Neighboring gene STARR-positive B cell enhancer ABC_E7145 Neighboring gene STARR-seq mESC enhancer starr_32415 Neighboring gene translocase of outer mitochondrial membrane 20-like Neighboring gene predicted gene, 32906 Neighboring gene translocase of inner mitochondrial membrane 9

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables DNA binding ISO
Inferred from Sequence Orthology
more info
 
enables double-stranded DNA binding IEA
Inferred from Electronic Annotation
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 DNA methylation IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within cell differentiation IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within chromatin organization IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within chromatin organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within erythrocyte development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within establishment of Sertoli cell barrier IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within genomic imprinting IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in negative regulation of DNA-templated transcription ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of cell migration NAS
Non-traceable Author Statement
more info
PubMed 
involved_in negative regulation of stem cell population maintenance NAS
Non-traceable Author Statement
more info
PubMed 
involved_in negative regulation of transcription by RNA polymerase II NAS
Non-traceable Author Statement
more info
PubMed 
involved_in negative regulation of transforming growth factor beta receptor signaling pathway NAS
Non-traceable Author Statement
more info
PubMed 
involved_in positive regulation of stem cell population maintenance NAS
Non-traceable Author Statement
more info
PubMed 
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
 
acts_upstream_of_or_within spermatogenesis IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of transcription by RNA polymerase II IGI
Inferred from Genetic Interaction
more info
PubMed 
Component Evidence Code Pubs
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 NAS
Non-traceable Author Statement
more info
PubMed 
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

Preferred Names
AT-rich interactive domain-containing protein 4A
Names
ARID domain-containing protein 4A
AT rich interactive domain 4A (RBP1-like)
AT rich interactive domain 4A (Rbp1 like)
retinoblastoma-binding protein 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_001081195.1NP_001074664.1  AT-rich interactive domain-containing protein 4A

    See identical proteins and their annotated locations for NP_001074664.1

    Status: VALIDATED

    Source sequence(s)
    AC112794, AC132325
    Consensus CDS
    CCDS36471.1
    UniProtKB/Swiss-Prot
    B2RXT8, B2RY61, F8VPQ2, Q05CI2, Q6PE90
    Related
    ENSMUSP00000035512.6, ENSMUST00000046305.12
    Conserved Domains (4) summary
    smart00333
    Location:58113
    TUDOR; Tudor domain
    cd16882
    Location:312397
    ARID_ARID4A; ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 4A (ARID4A) and similar proteins
    cd18641
    Location:580638
    CBD_RBP1_like; chromo barrel domain of retinoblastoma binding protein 1, and similar proteins
    pfam08169
    Location:170262
    RBB1NT; RBB1NT (NUC162) domain

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000078.7 Reference GRCm39 C57BL/6J

    Range
    71061314..71146125
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_036157396.1XP_036013289.1  AT-rich interactive domain-containing protein 4A isoform X1

    Conserved Domains (5) summary
    cd16882
    Location:312397
    ARID_ARID4A; ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 4A (ARID4A) and similar proteins
    cd18641
    Location:580638
    CBD_RBP1_like; chromo barrel domain of retinoblastoma binding protein 1, and similar proteins
    pfam08169
    Location:170262
    RBB1NT; RBB1NT (NUC162) domain
    cd20459
    Location:461
    Tudor_ARID4A_rpt1; first Tudor domain found in AT-rich interactive domain-containing protein 4A (ARID4A) and similar proteins
    cl02573
    Location:62118
    Tudor_SF; Tudor domain superfamily
  2. XM_036157397.1XP_036013290.1  AT-rich interactive domain-containing protein 4A isoform X1

    Conserved Domains (5) summary
    cd16882
    Location:312397
    ARID_ARID4A; ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 4A (ARID4A) and similar proteins
    cd18641
    Location:580638
    CBD_RBP1_like; chromo barrel domain of retinoblastoma binding protein 1, and similar proteins
    pfam08169
    Location:170262
    RBB1NT; RBB1NT (NUC162) domain
    cd20459
    Location:461
    Tudor_ARID4A_rpt1; first Tudor domain found in AT-rich interactive domain-containing protein 4A (ARID4A) and similar proteins
    cl02573
    Location:62118
    Tudor_SF; Tudor domain superfamily
  3. XM_036157398.1XP_036013291.1  AT-rich interactive domain-containing protein 4A isoform X2

    Conserved Domains (2) summary
    cd18641
    Location:258316
    CBD_RBP1_like; chromo barrel domain of retinoblastoma binding protein 1, and similar proteins
    cl28902
    Location:175
    ARID; ARID/BRIGHT DNA binding domain family
  4. XM_006515834.4XP_006515897.1  AT-rich interactive domain-containing protein 4A isoform X3

    Conserved Domains (2) summary
    cd18641
    Location:258316
    CBD_RBP1_like; chromo barrel domain of retinoblastoma binding protein 1, and similar proteins
    cl28902
    Location:175
    ARID; ARID/BRIGHT DNA binding domain family
  5. XM_036157399.1XP_036013292.1  AT-rich interactive domain-containing protein 4A isoform X4

    Conserved Domains (1) summary
    cl28914
    Location:133
    CD_CSD; CHROMO (CHRromatin Organization Modifier) domains and chromo shadow domains
  6. XM_006515835.2XP_006515898.1  AT-rich interactive domain-containing protein 4A isoform X5

    Conserved Domains (1) summary
    cl28914
    Location:133
    CD_CSD; CHROMO (CHRromatin Organization Modifier) domains and chromo shadow domains

RNA

  1. XR_004937498.1 RNA Sequence