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JARID2 jumonji and AT-rich interaction domain containing 2 [ Homo sapiens (human) ]

Gene ID: 3720, updated on 1-Jun-2020

Summary

Official Symbol
JARID2provided by HGNC
Official Full Name
jumonji and AT-rich interaction domain containing 2provided by HGNC
Primary source
HGNC:HGNC:6196
See related
Ensembl:ENSG00000008083 MIM:601594
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
JMJ
Summary
This gene encodes a Jumonji- and AT-rich interaction domain (ARID)-domain-containing protein. The encoded protein is a DNA-binding protein that functions as a transcriptional repressor. This protein interacts with the Polycomb repressive complex 2 (PRC2) which plays an essential role in regulating gene expression during embryonic development. This protein facilitates the recruitment of the PRC2 complex to target genes. Alternate splicing results in multiple transcript variants. Mutations in this gene are associated with chronic myeloid malignancies. [provided by RefSeq, May 2012]
Expression
Broad expression in bone marrow (RPKM 19.2), testis (RPKM 12.2) and 23 other tissues See more
Orthologs

Genomic context

See JARID2 in Genome Data Viewer
Location:
6p22.3
Exon count:
23
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 6 NC_000006.12 (15245975..15522042)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (15246206..15522273)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene RNA, 7SL, cytoplasmic 332, pseudogene Neighboring gene uncharacterized LOC105374946 Neighboring gene nonconserved acetylation island sequence 83 enhancer Neighboring gene JARID2 antisense RNA 1 Neighboring gene RNA, U6 small nuclear 522, pseudogene Neighboring gene RNA, U6 small nuclear 645, pseudogene Neighboring gene uncharacterized LOC105374947 Neighboring gene dystrobrevin binding protein 1 Neighboring gene uncharacterized LOC102724520

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

Copy number response

Description
Copy number response
Haploinsufficency

No evidence available (Last evaluated (2013-11-07)

ClinGen Genome Curation Page
Triplosensitivity

No evidence available (Last evaluated (2013-11-07)

ClinGen Genome Curation Page

NHGRI GWAS Catalog

Description
Genetic variants and environmental factors associated with hormonal markers of ovarian reserve in Caucasian and African American women.
NHGRI GWA Catalog
Genome-wide association analysis of susceptibility and clinical phenotype in multiple sclerosis.
NHGRI GWA Catalog
Susceptibility loci associated with specific and shared subtypes of lymphoid malignancies.
NHGRI GWA Catalog

Pathways from PubChem

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 transcription repressor activity, RNA polymerase II-specific IEA
Inferred from Electronic Annotation
more info
 
RNA polymerase II regulatory region sequence-specific DNA binding IEA
Inferred from Electronic Annotation
more info
 
chromatin binding ISS
Inferred from Sequence or Structural Similarity
more info
 
histone demethylase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
NOT histone demethylase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
NOT histone demethylase activity (H3-trimethyl-K4 specific) IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
transcription factor binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
cellular response to leukemia inhibitory factor IEA
Inferred from Electronic Annotation
more info
 
central nervous system development TAS
Traceable Author Statement
more info
PubMed 
chromatin remodeling IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone H3-K4 demethylation, trimethyl-H3-K4-specific IEA
Inferred from Electronic Annotation
more info
 
liver development IEA
Inferred from Electronic Annotation
more info
 
negative regulation of cardiac muscle cell proliferation IEA
Inferred from Electronic Annotation
more info
 
negative regulation of cardiac muscle hypertrophy IEA
Inferred from Electronic Annotation
more info
 
negative regulation of gene expression, epigenetic TAS
Traceable Author Statement
more info
 
negative regulation of histone methylation ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
negative regulation of transcription, DNA-templated ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of histone H3-K9 methylation ISS
Inferred from Sequence or Structural Similarity
more info
 
spleen development IEA
Inferred from Electronic Annotation
more info
 
stem cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
thymus development IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
colocalizes_with ESC/E(Z) complex IDA
Inferred from Direct Assay
more info
PubMed 
histone methyltransferase complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone methyltransferase complex ISS
Inferred from Sequence or Structural Similarity
more info
 
mitochondrion 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 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
protein Jumonji
Names
jumonji homolog
jumonji, AT rich interactive domain 2
jumonji-like protein
jumonji/ARID domain-containing protein 2

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_001267040.1NP_001253969.1  protein Jumonji isoform 2

    See identical proteins and their annotated locations for NP_001253969.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and initiates translation at a downstream AUG, compared to variant 1. The resulting isoform (2) has a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AK303610, AL021938, AL136162, CA435807
    Consensus CDS
    CCDS58996.1
    UniProtKB/Swiss-Prot
    Q92833
    Related
    ENSP00000380478.3, ENST00000397311.4
    Conserved Domains (4) summary
    smart00501
    Location:451542
    BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
    smart00545
    Location:384425
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:744859
    JmjC; JmjC domain, hydroxylase
    pfam02928
    Location:9671020
    zf-C5HC2; C5HC2 zinc finger
  2. NM_004973.4NP_004964.2  protein Jumonji isoform 1

    See identical proteins and their annotated locations for NP_004964.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AK292861, AL021938, AL136162, CA435807
    Consensus CDS
    CCDS4533.1
    UniProtKB/Swiss-Prot
    Q92833
    Related
    ENSP00000341280.2, ENST00000341776.7
    Conserved Domains (4) summary
    smart00501
    Location:623714
    BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
    smart00545
    Location:556597
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:9161031
    JmjC; JmjC domain, hydroxylase
    pfam02928
    Location:11391192
    zf-C5HC2; C5HC2 zinc finger

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_000006.12 Reference GRCh38.p13 Primary Assembly

    Range
    15245975..15522042
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011514579.3XP_011512881.1  protein Jumonji isoform X1

    Conserved Domains (4) summary
    smart00501
    Location:686777
    BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
    smart00545
    Location:619660
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:9791094
    JmjC; JmjC domain, hydroxylase
    pfam02928
    Location:12021255
    zf-C5HC2; C5HC2 zinc finger
  2. XM_017010833.2XP_016866322.1  protein Jumonji isoform X2

  3. XM_017010834.2XP_016866323.1  protein Jumonji isoform X4

    UniProtKB/Swiss-Prot
    Q92833
    Conserved Domains (4) summary
    smart00501
    Location:451542
    BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
    smart00545
    Location:384425
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:744859
    JmjC; JmjC domain, hydroxylase
    pfam02928
    Location:9671020
    zf-C5HC2; C5HC2 zinc finger
  4. XM_017010835.2XP_016866324.1  protein Jumonji isoform X4

    UniProtKB/Swiss-Prot
    Q92833
    Conserved Domains (4) summary
    smart00501
    Location:451542
    BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
    smart00545
    Location:384425
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:744859
    JmjC; JmjC domain, hydroxylase
    pfam02928
    Location:9671020
    zf-C5HC2; C5HC2 zinc finger
  5. XM_024446424.1XP_024302192.1  protein Jumonji isoform X3

    Conserved Domains (4) summary
    smart00501
    Location:600691
    BRIGHT; ARID (A/T-rich interaction domain) domain
    smart00545
    Location:533574
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:8931008
    JmjC; JmjC domain, hydroxylase
    pfam02928
    Location:11161169
    zf-C5HC2; C5HC2 zinc finger
  6. XM_024446425.1XP_024302193.1  protein Jumonji isoform X5

    Conserved Domains (3) summary
    smart00501
    Location:451542
    BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
    smart00545
    Location:384425
    JmjN; Small domain found in the jumonji family of transcription factors
    cl21464
    Location:744786
    cupin_like; Conserved domain found in cupin and related proteins
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