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ARID5A AT-rich interaction domain 5A [ Homo sapiens (human) ]

Gene ID: 10865, updated on 11-Sep-2019

Summary

Official Symbol
ARID5Aprovided by HGNC
Official Full Name
AT-rich interaction domain 5Aprovided by HGNC
Primary source
HGNC:HGNC:17361
See related
Ensembl:ENSG00000196843 MIM:611583
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
MRF1; MRF-1; RP11-363D14
Summary
Members of the ARID protein family, including ARID5A, have diverse functions but all appear to play important roles in development, tissue-specific gene expression, and regulation of cell growth (Patsialou et al., 2005 [PubMed 15640446]).[supplied by OMIM, Mar 2008]
Expression
Ubiquitous expression in bone marrow (RPKM 12.1), appendix (RPKM 8.5) and 24 other tissues See more
Orthologs

Genomic context

See ARID5A in Genome Data Viewer
Location:
2q11.2
Exon count:
9
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 2 NC_000002.12 (96536752..96552638)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (97202464..97218375)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene neuralized E3 ubiquitin protein ligase 3 Neighboring gene uncharacterized LOC105373496 Neighboring gene KAT8 regulatory NSL complex subunit 3 Neighboring gene fer-1 like family member 5

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 Functions

What's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Genome-wide association study of theta band event-related oscillations identifies serotonin receptor gene HTR7 influencing risk of alcohol dependence.
NHGRI GWA Catalog

HIV-1 interactions

Replication interactions

Interaction Pubs
Knockdown of AT rich interactive domain 5A (ARID5A) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

Go to the HIV-1, Human Interaction Database

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 TAS
Traceable Author Statement
more info
PubMed 
DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
 
DNA-binding transcription repressor activity, RNA polymerase II-specific IC
Inferred by Curator
more info
 
RNA binding IEA
Inferred from Electronic Annotation
more info
 
androgen receptor binding IDA
Inferred from Direct Assay
more info
PubMed 
estrogen receptor binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
retinoid X receptor binding IDA
Inferred from Direct Assay
more info
PubMed 
sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
thyroid hormone receptor binding IDA
Inferred from Direct Assay
more info
PubMed 
transcription corepressor activity IDA
Inferred from Direct Assay
more info
PubMed 
transcription factor binding IDA
Inferred from Direct Assay
more info
PubMed 
transcription regulatory region DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
cellular response to estrogen stimulus IDA
Inferred from Direct Assay
more info
PubMed 
innate immune response IEA
Inferred from Electronic Annotation
more info
 
negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of transcription, DNA-templated TAS
Traceable Author Statement
more info
PubMed 
regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
nucleolus IDA
Inferred from Direct Assay
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
 

General protein information

Preferred Names
AT-rich interactive domain-containing protein 5A
Names
ARID domain-containing protein 5A
AT rich interactive domain 5A (MRF1-like)
RFVG5814
modulator recognition factor 1
modulator recognition factor I

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.

mRNA and Protein(s)

  1. NM_001319085.2NP_001306014.1  AT-rich interactive domain-containing protein 5A isoform a

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (a).
    Source sequence(s)
    BC067301, BX396215, HY002073
    Conserved Domains (1) summary
    smart00501
    Location:61202
    BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
  2. NM_001319087.2NP_001306016.1  AT-rich interactive domain-containing protein 5A isoform b

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice junction compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is 1 aa shorter compared to isoform a.
    Source sequence(s)
    BC067301, CR981009, HY002073
    Conserved Domains (1) summary
    smart00501
    Location:61201
    BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
  3. NM_001319092.1NP_001306021.1  AT-rich interactive domain-containing protein 5A isoform d

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and coding sequence and uses an alternate in-frame splice junction compared to variant 1. The resulting isoform (d) is shorter at the N-terminus and lacks an alternate internal segment compared to isoform a.
    Source sequence(s)
    AC013270, AI085152, BC047390
    Consensus CDS
    CCDS82484.1
    UniProtKB/Swiss-Prot
    Q03989
    Related
    ENSP00000400785.1, ENST00000454558.2
    Conserved Domains (1) summary
    smart00501
    Location:180
    BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
  4. NM_001319093.2NP_001306022.1  AT-rich interactive domain-containing protein 5A isoform e

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) uses two alternate splice junctions and lacks an alternate exon compared to variant 1. The resulting isoform (e) is shorter at the N-terminus compared to isoform a. Variants 5, 6, and 7 all encode the same isoform (e).
    Source sequence(s)
    AC013270, BC067301, HY076710
  5. NM_001319094.2NP_001306023.1  AT-rich interactive domain-containing protein 5A isoform e

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) uses two alternate splice junctions compared to variant 1. The resulting isoform (e) is shorter at the N-terminus compared to isoform a. Variants 5, 6, and 7 all encode the same isoform (e).
    Source sequence(s)
    BC067301, BM556343, HY002073
  6. NM_001319096.2NP_001306025.1  AT-rich interactive domain-containing protein 5A isoform e

    Status: VALIDATED

    Description
    Transcript Variant: This variant (7) uses lacks an alternate exon compared to variant 1. The resulting isoform (e) is shorter at the N-terminus compared to isoform a. Variants 5, 6, and 7 all encode the same isoform (e).
    Source sequence(s)
    AI085152, BX648918
  7. NM_212481.3NP_997646.1  AT-rich interactive domain-containing protein 5A isoform c

    See identical proteins and their annotated locations for NP_997646.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternate in-frame splice junction compared to variant 1. The resulting isoform (c) has the same N- and C-termini but is shorter compared to isoform a.
    Source sequence(s)
    AI085152, HY002073, M62324
    Consensus CDS
    CCDS33251.1
    UniProtKB/Swiss-Prot
    Q03989
    Related
    ENSP00000350078.3, ENST00000357485.8
    Conserved Domains (1) summary
    smart00501
    Location:61148
    BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p13 Primary Assembly

    Range
    96536752..96552638
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017003184.1XP_016858673.1  AT-rich interactive domain-containing protein 5A isoform X3

    Conserved Domains (2) summary
    cl02633
    Location:5296
    ARID; ARID/BRIGHT DNA binding domain
    cl26464
    Location:26334
    Atrophin-1; Atrophin-1 family
  2. XM_017003183.1XP_016858672.1  AT-rich interactive domain-containing protein 5A isoform X1

  3. XM_024452563.1XP_024308331.1  AT-rich interactive domain-containing protein 5A isoform X3

    Conserved Domains (2) summary
    cl02633
    Location:5296
    ARID; ARID/BRIGHT DNA binding domain
    cl26464
    Location:26334
    Atrophin-1; Atrophin-1 family
  4. XM_024452564.1XP_024308332.1  AT-rich interactive domain-containing protein 5A isoform X3

    Conserved Domains (2) summary
    cl02633
    Location:5296
    ARID; ARID/BRIGHT DNA binding domain
    cl26464
    Location:26334
    Atrophin-1; Atrophin-1 family
  5. XM_011510499.2XP_011508801.1  AT-rich interactive domain-containing protein 5A isoform X2

    See identical proteins and their annotated locations for XP_011508801.1

    Conserved Domains (1) summary
    smart00501
    Location:71158
    BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_006673.2: Suppressed sequence

    Description
    NM_006673.2: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
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