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ARID4A AT-rich interaction domain 4A [ Homo sapiens (human) ]

Gene ID: 5926, updated on 13-Feb-2019

Summary

Official Symbol
ARID4Aprovided by HGNC
Official Full Name
AT-rich interaction domain 4Aprovided by HGNC
Primary source
HGNC:HGNC:9885
See related
Ensembl:ENSG00000032219 MIM:180201
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
RBP1; RBBP1; RBP-1; RBBP-1
Summary
The protein encoded by this gene is a ubiquitously expressed nuclear protein. It binds directly, with several other proteins, to retinoblastoma protein (pRB) which regulates cell proliferation. pRB represses transcription by recruiting the encoded protein. This protein, in turn, serves as a bridging molecule to recruit HDACs and, in addition, provides a second HDAC-independent repression function. The encoded protein possesses transcriptional repression activity. Multiple alternatively spliced transcripts have been observed for this gene, although not all transcript variants have been fully described. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in bone marrow (RPKM 9.9), lymph node (RPKM 6.1) and 25 other tissues See more
Orthologs

Genomic context

See ARID4A in Genome Data Viewer
Location:
14q23.1
Exon count:
28
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 14 NC_000014.9 (58298385..58373733)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (58765103..58840713)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene PSMA3 antisense RNA 1 Neighboring gene long intergenic non-protein coding RNA 216 Neighboring gene RNA, U6 small nuclear 341, pseudogene Neighboring gene uncharacterized LOC105370522 Neighboring gene translocase of outer mitochondrial membrane 20 like Neighboring gene translocase of inner mitochondrial membrane 9 Neighboring gene KIAA0586 Neighboring gene heat shock factor binding protein 1 pseudogene 1

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Pathways from BioSystems

  • Chromatin modifying enzymes, organism-specific biosystem (from REACTOME)
    Chromatin modifying enzymes, organism-specific biosystemEukaryotic DNA is associated with histone proteins and organized into a complex nucleoprotein structure called chromatin. This structure decreases the accessibility of DNA but also helps to protect i...
  • Chromatin organization, organism-specific biosystem (from REACTOME)
    Chromatin organization, organism-specific biosystemChromatin organization refers to the composition and conformation of complexes between DNA, protein and RNA. It is determined by processes that result in the specification, formation or maintenance o...
  • HDACs deacetylate histones, organism-specific biosystem (from REACTOME)
    HDACs deacetylate histones, organism-specific biosystemLysine deacetylases (KDACs), historically referred to as histone deacetylases (HDACs), are divided into the Rpd3/Hda1 metal-dependent 'classical HDAC family' (de Ruijter et al. 2003, Verdin et al. 2...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
 
transcription regulatory region DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
erythrocyte development IEA
Inferred from Electronic Annotation
more info
 
establishment of Sertoli cell barrier IEA
Inferred from Electronic Annotation
more info
 
histone H3-K4 trimethylation IEA
Inferred from Electronic Annotation
more info
 
histone H3-K9 trimethylation IEA
Inferred from Electronic Annotation
more info
 
histone H4-K20 trimethylation IEA
Inferred from Electronic Annotation
more info
 
negative regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
regulation of gene expression by genetic imprinting IEA
Inferred from Electronic Annotation
more info
 
regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
spermatogenesis IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cytosol IDA
Inferred from Direct Assay
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
plasma membrane IDA
Inferred from Direct Assay
more info
 
transcriptional repressor complex IDA
Inferred from Direct Assay
more info
PubMed 

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)
retinoblastoma-binding protein 1

NCBI Reference Sequences (RefSeq)

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.

Genomic

  1. NG_052999.1 RefSeqGene

    Range
    5120..80349
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_002892.3NP_002883.3  AT-rich interactive domain-containing protein 4A isoform I

    See identical proteins and their annotated locations for NP_002883.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the full length isoform.
    Source sequence(s)
    AL139021, BC026230, BX279740, DB218466, S57153
    Consensus CDS
    CCDS9732.1
    UniProtKB/Swiss-Prot
    P29374
    UniProtKB/TrEMBL
    A0A024R657, Q05CG0
    Related
    ENSP00000347602.3, ENST00000355431.7
    Conserved Domains (4) summary
    smart00501
    Location:312401
    BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
    smart00333
    Location:58113
    TUDOR; Tudor domain
    pfam08169
    Location:171261
    RBB1NT; RBB1NT (NUC162) domain
    pfam11717
    Location:575629
    Tudor-knot; RNA binding activity-knot of a chromodomain
  2. NM_023000.2NP_075376.2  AT-rich interactive domain-containing protein 4A isoform II

    See identical proteins and their annotated locations for NP_075376.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks 162 bp in the coding region, as compared to variant 1, but maintains the same reading frame. The encoded protein lacks 54 internal codons and is thought to lack phosphorylation sites.
    Source sequence(s)
    AL139021, BC026230, BX279740, DB218466, S57160
    Consensus CDS
    CCDS45114.1
    UniProtKB/Swiss-Prot
    P29374
    UniProtKB/TrEMBL
    A0A024R6A2, Q05CG0
    Related
    ENSP00000378597.3, ENST00000395168.7
    Conserved Domains (4) summary
    smart00501
    Location:312401
    BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
    smart00333
    Location:58113
    TUDOR; Tudor domain
    pfam08169
    Location:171261
    RBB1NT; RBB1NT (NUC162) domain
    pfam11717
    Location:575629
    Tudor-knot; RNA binding activity-knot of a chromodomain
  3. NM_023001.2NP_075377.2  AT-rich interactive domain-containing protein 4A isoform III

    See identical proteins and their annotated locations for NP_075377.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks 207 bp in the coding region, as compared to variant 1, but maintains the same reading frame. The encoded protein lacks 69 internal codons and is thought to lack phosphorylation sites.
    Source sequence(s)
    AL139021, BC026230, BX279740, DB218466, S57162
    Consensus CDS
    CCDS9733.1
    UniProtKB/Swiss-Prot
    P29374
    UniProtKB/TrEMBL
    A0A024R680, Q05CG0
    Related
    ENSP00000344556.3, ENST00000348476.7
    Conserved Domains (4) summary
    smart00501
    Location:312401
    BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
    smart00333
    Location:58113
    TUDOR; Tudor domain
    pfam08169
    Location:171261
    RBB1NT; RBB1NT (NUC162) domain
    pfam11717
    Location:575629
    Tudor-knot; RNA binding activity-knot of a chromodomain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000014.9 Reference GRCh38.p12 Primary Assembly

    Range
    58298385..58373733
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017021560.1XP_016877049.1  AT-rich interactive domain-containing protein 4A isoform X1

  2. XM_017021563.1XP_016877052.1  AT-rich interactive domain-containing protein 4A isoform X4

  3. XM_005267964.2XP_005268021.1  AT-rich interactive domain-containing protein 4A isoform X2

    See identical proteins and their annotated locations for XP_005268021.1

    Conserved Domains (4) summary
    smart00501
    Location:312401
    BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
    smart00333
    Location:58113
    TUDOR; Tudor domain
    pfam08169
    Location:171261
    RBB1NT; RBB1NT (NUC162) domain
    pfam11717
    Location:575629
    Tudor-knot; RNA binding activity-knot of a chromodomain
  4. XM_005267965.2XP_005268022.1  AT-rich interactive domain-containing protein 4A isoform X5

    Conserved Domains (4) summary
    smart00501
    Location:312401
    BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
    smart00333
    Location:58113
    TUDOR; Tudor domain
    pfam08169
    Location:171261
    RBB1NT; RBB1NT (NUC162) domain
    pfam11717
    Location:575629
    Tudor-knot; RNA binding activity-knot of a chromodomain
  5. XM_017021562.1XP_016877051.1  AT-rich interactive domain-containing protein 4A isoform X3

  6. XM_017021561.1XP_016877050.1  AT-rich interactive domain-containing protein 4A isoform X1

  7. XM_017021564.1XP_016877053.1  AT-rich interactive domain-containing protein 4A isoform X6

  8. XM_017021565.1XP_016877054.1  AT-rich interactive domain-containing protein 4A isoform X7

    Related
    ENSP00000416053.2, ENST00000417477.2
  9. XM_024449684.1XP_024305452.1  AT-rich interactive domain-containing protein 4A isoform X9

    Conserved Domains (1) summary
    pfam11717
    Location:660
    Tudor-knot; RNA binding activity-knot of a chromodomain
  10. XM_024449683.1XP_024305451.1  AT-rich interactive domain-containing protein 4A isoform X8

    Conserved Domains (1) summary
    pfam11717
    Location:660
    Tudor-knot; RNA binding activity-knot of a chromodomain

RNA

  1. XR_001750495.1 RNA Sequence

  2. XR_001750496.1 RNA Sequence

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