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ARID5B AT-rich interaction domain 5B [ Homo sapiens (human) ]

Gene ID: 84159, updated on 13-Mar-2020

Summary

Official Symbol
ARID5Bprovided by HGNC
Official Full Name
AT-rich interaction domain 5Bprovided by HGNC
Primary source
HGNC:HGNC:17362
See related
Ensembl:ENSG00000150347 MIM:608538
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
MRF2; DESRT; MRF-2
Summary
This gene encodes a member of the AT-rich interaction domain (ARID) family of DNA binding proteins. The encoded protein forms a histone H3K9Me2 demethylase complex with PHD finger protein 2 and regulates the transcription of target genes involved in adipogenesis and liver development. This gene also plays a role in cell growth and differentiation of B-lymphocyte progenitors, and single nucleotide polymorphisms in this gene are associated with acute lymphoblastic leukemia. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Sep 2011]
Expression
Ubiquitous expression in gall bladder (RPKM 21.6), fat (RPKM 15.6) and 24 other tissues See more
Orthologs

Genomic context

See ARID5B in Genome Data Viewer
Location:
10q21.2
Exon count:
12
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 10 NC_000010.11 (61901254..62096944)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (63661013..63856707)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene ciliary associated calcium binding coiled-coil 1 Neighboring gene CRISPRi-validated cis-regulatory element chr10.1925 Neighboring gene long intergenic non-protein coding RNA 2625 Neighboring gene uncharacterized LOC105378326 Neighboring gene rhotekin 2 Neighboring gene long intergenic non-protein coding RNA 2621

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
Confirmation of Childhood Acute Lymphoblastic Leukemia Variants, ARID5B and IKZF1, and Interaction with Parental Environmental Exposures.
NHGRI GWA Catalog
Discovery and fine mapping of serum protein loci through transethnic meta-analysis.
NHGRI GWA Catalog
Genetics of rheumatoid arthritis contributes to biology and drug discovery.
NHGRI GWA Catalog
Genome-wide association analyses identify multiple loci associated with central corneal thickness and keratoconus.
NHGRI GWA Catalog
Genome-wide association study identifies eight loci associated with blood pressure.
NHGRI GWA Catalog
Genome-wide association study supports the role of the immunological system and of the neurodevelopmental processes in response to haloperidol treatment.
NHGRI GWA Catalog
Germline genomic variants associated with childhood acute lymphoblastic leukemia.
NHGRI GWA Catalog
Identification of germline susceptibility loci in ETV6-RUNX1-rearranged childhood acute lymphoblastic leukemia.
NHGRI GWA Catalog
Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers.
NHGRI GWA Catalog
Loci on 7p12.2, 10q21.2 and 14q11.2 are associated with risk of childhood acute lymphoblastic leukemia.
NHGRI GWA Catalog
Meta-analysis followed by replication identifies loci in or near CDKN1B, TET3, CD80, DRAM1, and ARID5B as associated with systemic lupus erythematosus in Asians.
NHGRI GWA Catalog
Meta-analysis identifies nine new loci associated with rheumatoid arthritis in the Japanese population.
NHGRI GWA Catalog
Novel susceptibility variants at 10p12.31-12.2 for childhood acute lymphoblastic leukemia in ethnically diverse populations.
NHGRI GWA Catalog
Variation at 10p12.2 and 10p14 influences risk of childhood B-cell acute lymphoblastic leukemia and phenotype.
NHGRI GWA Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ21150, FLJ41888

Gene Ontology Provided by GOA

Process Evidence Code Pubs
adipose tissue development ISS
Inferred from Sequence or Structural Similarity
more info
 
adrenal gland development IEA
Inferred from Electronic Annotation
more info
 
cell development IEA
Inferred from Electronic Annotation
more info
 
cellular response to leukemia inhibitory factor IEA
Inferred from Electronic Annotation
more info
 
face morphogenesis IEA
Inferred from Electronic Annotation
more info
 
fat cell differentiation IEA
Inferred from Electronic Annotation
more info
 
fat pad development IEA
Inferred from Electronic Annotation
more info
 
female gonad development IEA
Inferred from Electronic Annotation
more info
 
fibroblast migration IEA
Inferred from Electronic Annotation
more info
 
kidney development IEA
Inferred from Electronic Annotation
more info
 
liver development TAS
Traceable Author Statement
more info
PubMed 
male gonad development IEA
Inferred from Electronic Annotation
more info
 
multicellular organism growth IEA
Inferred from Electronic Annotation
more info
 
muscle organ morphogenesis 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 
nitrogen compound metabolic process IEA
Inferred from Electronic Annotation
more info
 
platelet-derived growth factor receptor signaling pathway IEA
Inferred from Electronic Annotation
more info
 
positive regulation of DNA-binding transcription factor activity IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of nucleic acid-templated transcription IEA
Inferred from Electronic Annotation
more info
 
post-embryonic development IEA
Inferred from Electronic Annotation
more info
 
regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
roof of mouth development IEA
Inferred from Electronic Annotation
more info
 
skeletal system morphogenesis IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
AT-rich interactive domain-containing protein 5B
Names
ARID domain-containing protein 5B
AT-rich interactive domain 5B (MRF1-like)
MRF1-like protein
modulator recognition factor 2 (MRF2)

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_030027.1 RefSeqGene

    Range
    5446..200691
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001244638.2NP_001231567.1  AT-rich interactive domain-containing protein 5B isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AI149153, BC015120, BC036831, BX352258, BX472565, BX537690, M73837
    Consensus CDS
    CCDS58082.1
    UniProtKB/Swiss-Prot
    Q14865
    Related
    ENSP00000308862.5, ENST00000309334.5
    Conserved Domains (1) summary
    smart00501
    Location:76168
    BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
  2. NM_032199.3NP_115575.1  AT-rich interactive domain-containing protein 5B isoform 1

    See identical proteins and their annotated locations for NP_115575.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AL671972, BC056680, DB014195, M73837
    Consensus CDS
    CCDS31208.1
    UniProtKB/Swiss-Prot
    Q14865
    Related
    ENSP00000279873.7, ENST00000279873.12
    Conserved Domains (2) summary
    smart00501
    Location:319411
    BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
    cl02608
    Location:34108
    BAH; BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). BAH domains have first been described as domains found in the polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure of Chromatin). They also occur in ...

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000010.11 Reference GRCh38.p13 Primary Assembly

    Range
    61901254..62096944
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011540262.1XP_011538564.1  AT-rich interactive domain-containing protein 5B isoform X1

    Conserved Domains (2) summary
    smart00501
    Location:242334
    BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
    cl02608
    Location:34108
    BAH; BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). BAH domains have first been described as domains found in the polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure of Chromatin). They also occur in ...
  2. XM_024448230.1XP_024303998.1  AT-rich interactive domain-containing protein 5B isoform X2

    Conserved Domains (2) summary
    smart00501
    Location:130222
    BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
    cl26511
    Location:221347
    Neuromodulin_N; Gap junction protein N-terminal region
  3. XM_024448231.1XP_024303999.1  AT-rich interactive domain-containing protein 5B isoform X3

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