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

    Gene ID: 84159, updated on 7-Jul-2019

    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
    109.20190607 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 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 FunctionsWhat'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

    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...
    • FTO Obesity Variant Mechanism, organism-specific biosystem (from WikiPathways)
      FTO Obesity Variant Mechanism, organism-specific biosystemMechanism underlying the association of FTO locus variants and obesity. The wild type T allele at rs1421085 in the FTO locus comprises a protein-DNA binding motif for ARID5B that represses the transc...
    • HDMs demethylate histones, organism-specific biosystem (from REACTOME)
      HDMs demethylate histones, organism-specific biosystemHistone lysine demethylases (KDMs) are able to reverse N-methylations of histones and probably other proteins. To date KDMs have been demonstrated to catalyse demethylation of N-epsilon methylated ly...
    • Mesodermal Commitment Pathway, organism-specific biosystem (from WikiPathways)
      Mesodermal Commitment Pathway, organism-specific biosystemModel depicting mesodermal specification based on the literature and highly enriched gene expression profiles via comparison across dozens of independent induced and embryonic pluripotent stem cell l...
    • Pathways Affected in Adenoid Cystic Carcinoma, organism-specific biosystem (from WikiPathways)
      Pathways Affected in Adenoid Cystic Carcinoma, organism-specific biosystemProtein pathways altered by mutations in adenoid cystic carcinoma. Pathways include epigentic modification, DNA damage checkpoint signals, MYB/MYC signalling pathway, FGF/IGF/PI3K signalling, and not...

    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
      5001..200695
      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 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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