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

Gene ID: 3720, updated on 12-Nov-2022

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; AllianceGenome:HGNC:6196
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; DIDDF
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
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Genomic context

See JARID2 in Genome Data Viewer
Location:
6p22.3
Exon count:
23
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (15246069..15522042)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (15119264..15395212)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (15246300..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 Sharpr-MPRA regulatory region 4383 Neighboring gene RNA, U6 small nuclear 522, pseudogene Neighboring gene RNA, U6 small nuclear 645, pseudogene Neighboring gene Sharpr-MPRA regulatory region 1760 Neighboring gene uncharacterized LOC105374947 Neighboring gene uncharacterized LOC124901267 Neighboring gene Sharpr-MPRA regulatory region 14615 Neighboring gene dystrobrevin binding protein 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 Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
DEVELOPMENTAL DELAY WITH VARIABLE INTELLECTUAL DISABILITY AND DYSMORPHIC FACIES
MedGen: CN322372 OMIM: 620098 GeneReviews: Not available
not available

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

EBI GWAS Catalog

Description
Genetic variants and environmental factors associated with hormonal markers of ovarian reserve in Caucasian and African American women.
EBI GWAS Catalog
Genome-wide association analysis of susceptibility and clinical phenotype in multiple sclerosis.
EBI GWAS Catalog
Susceptibility loci associated with specific and shared subtypes of lymphoid malignancies.
EBI GWAS 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
enables DNA binding IEA
Inferred from Electronic Annotation
more info
 
enables chromatin binding ISS
Inferred from Sequence or Structural Similarity
more info
 
contributes_to histone H3K27 methyltransferase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
NOT enables histone H3K4me/H3K4me2/H3K4me3 demethylase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables histone demethylase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
NOT enables histone demethylase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
enables ubiquitin binding IEA
Inferred from Electronic Annotation
more info
 
enables ubiquitin modification-dependent histone binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
involved_in cardiac muscle cell proliferation IEA
Inferred from Electronic Annotation
more info
 
involved_in cellular response to leukemia inhibitory factor IEA
Inferred from Electronic Annotation
more info
 
involved_in central nervous system development TAS
Traceable Author Statement
more info
PubMed 
involved_in chromatin remodeling IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in dosage compensation by inactivation of X chromosome IEA
Inferred from Electronic Annotation
more info
 
involved_in facultative heterochromatin formation IEA
Inferred from Electronic Annotation
more info
 
involved_in histone modification IEA
Inferred from Electronic Annotation
more info
 
involved_in liver development IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of cardiac muscle cell proliferation IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of cardiac muscle hypertrophy IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
involved_in protein localization to pericentric heterochromatin IEA
Inferred from Electronic Annotation
more info
 
involved_in spleen development IEA
Inferred from Electronic Annotation
more info
 
involved_in stem cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in thymus development IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
part_of ESC/E(Z) complex IEA
Inferred from Electronic Annotation
more info
 
part_of histone methyltransferase complex ISS
Inferred from Sequence or Structural Similarity
more info
 
located_in mitochondrion IDA
Inferred from Direct Assay
more info
 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 
located_in nucleoplasm TAS
Traceable Author Statement
more info
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in 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)

NEW Try the new Transcript table

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
    Q86X63, Q92833
    Related
    ENSP00000341280.2, ENST00000341776.7
    Conserved Domains (4) summary
    smart00545
    Location:556597
    JmjN; Small domain found in the jumonji family of transcription factors
    cd16870
    Location:620731
    ARID_JARD2; ARID/BRIGHT DNA binding domain of Jumonji/ARID domain-containing protein 2 (JARID2) and similar proteins
    pfam02373
    Location:9161031
    JmjC; JmjC domain, hydroxylase
    pfam02928
    Location:11391192
    zf-C5HC2; C5HC2 zinc finger

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    15246069..15522042
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011514579.4XP_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_017010833.3XP_016866322.1  protein Jumonji isoform X2

  3. XM_047418735.1XP_047274691.1  protein Jumonji isoform X3

  4. XM_047418736.1XP_047274692.1  protein Jumonji isoform X4

  5. XM_047418744.1XP_047274700.1  protein Jumonji isoform X10

  6. XM_047418745.1XP_047274701.1  protein Jumonji isoform X11

  7. XM_047418746.1XP_047274702.1  protein Jumonji isoform X12

  8. XM_047418738.1XP_047274694.1  protein Jumonji isoform X5

  9. XM_047418741.1XP_047274697.1  protein Jumonji isoform X9

  10. XM_047418737.1XP_047274693.1  protein Jumonji isoform X5

  11. XM_047418742.1XP_047274698.1  protein Jumonji isoform X9

  12. XM_047418748.1XP_047274704.1  protein Jumonji isoform X15

  13. XM_047418743.1XP_047274699.1  protein Jumonji isoform X9

  14. XM_017010835.3XP_016866324.1  protein Jumonji isoform X9

    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
  15. XM_024446424.2XP_024302192.1  protein Jumonji isoform X6

    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
  16. XM_047418739.1XP_047274695.1  protein Jumonji isoform X7

  17. XM_047418740.1XP_047274696.1  protein Jumonji isoform X8

  18. XM_024446425.2XP_024302193.2  protein Jumonji isoform X13

  19. XM_047418747.1XP_047274703.1  protein Jumonji isoform X14

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    15119264..15395212
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)