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

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: mouse all
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Genomic context

Location:: 6p22.3

Exon count:: 23

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (15246069..15522042)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (15119264..15395212)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (15246300..15522273)

Chromosome 6 - NC_000006.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Functional Insight into and Refinement of the Genomic Boundaries of the JARID2-Neurodevelopmental Disorder Episignature.
Title: Functional Insight into and Refinement of the Genomic Boundaries of the JARID2-Neurodevelopmental Disorder Episignature.
JARID2 and EZH2, the eminent epigenetic drivers in human cancer.
Title: JARID2 and EZH2, the eminent epigenetic drivers in human cancer.
Integrated bioinformatics and experimental validation reveal the role of JARID2 in ovarian cancer.
Title: Integrated bioinformatics and experimental validation reveal the role of JARID2 in ovarian cancer.
JARID2 regulates epithelial mesenchymal transition through the PTEN/AKT signalling pathways in ovarian endometriosis.
Title: JARID2 regulates epithelial mesenchymal transition through the PTEN/AKT signalling pathways in ovarian endometriosis.
The LINC00852/miR-29a-3p/JARID2 axis regulates the proliferation and invasion of prostate cancer cell.
Title: The LINC00852/miR-29a-3p/JARID2 axis regulates the proliferation and invasion of prostate cancer cell.
microRNA-206 Suppresses Cholangiocarcinoma Cell Growth and Invasion by Targeting Jumonji AT-Rich Interactive Domain 2.
Title: microRNA-206 Suppresses Cholangiocarcinoma Cell Growth and Invasion by Targeting Jumonji AT-Rich Interactive Domain 2.
LINC01021 maintains tumorigenicity by enhancing N6-methyladenosine reader IMP2 dependent stabilization of MSX1 and JARID2: implication in colorectal cancer.
Title: LINC01021 maintains tumorigenicity by enhancing N6-methyladenosine reader IMP2 dependent stabilization of MSX1 and JARID2: implication in colorectal cancer.
LINC00649 Facilitates the Cellular Process of Bladder Cancer Cells via Signaling Axis miR-16-5p/JARID2.
Title: LINC00649 Facilitates the Cellular Process of Bladder Cancer Cells via Signaling Axis miR-16-5p/JARID2.
Promoting role of circ-Jarid2/miR-129-5p/Celf1 axis in cardiac hypertrophy.
Title: Promoting role of circ-Jarid2/miR-129-5p/Celf1 axis in cardiac hypertrophy.
An RNAi Screening of Clinically Relevant Transcription Factors Regulating Human Adipogenesis and Adipocyte Metabolism.
Title: An RNAi Screening of Clinically Relevant Transcription Factors Regulating Human Adipogenesis and Adipocyte Metabolism.

Submit: New GeneRIF Correction See all GeneRIFs (41)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Developmental delay with variable intellectual disability and dysmorphic facies MedGen: C5774242 OMIM: 620098 GeneReviews: Not available	not available

Copy number response

Description
Copy number response Triplosensitivity No evidence available (Last evaluated 2024-06-11) ClinGen Genome Curation Page Haploinsufficency Some evidence for dosage pathogenicity (Last evaluated 2024-06-11) ClinGen Genome Curation PagePubMed

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 EBI GWAS CatalogPubMed
Genome-wide association analysis of susceptibility and clinical phenotype in multiple sclerosis. EBI GWAS Catalog EBI GWAS CatalogPubMed
Susceptibility loci associated with specific and shared subtypes of lymphoid malignancies. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D6S1349 (e-PCR)
- UniSTS:153600

B346XE1 (e-PCR)
- UniSTS:46872

D6S469 (e-PCR), detects polymorphism
- UniSTS:88863

D6S2005 (e-PCR)
- UniSTS:78893

RH44612 (e-PCR)
- UniSTS:28462

SHGC-58076 (e-PCR)
- UniSTS:10547

D6S289 (e-PCR), detects polymorphism
- UniSTS:78658

RH45453 (e-PCR)
- UniSTS:62531

SHGC-112331 (e-PCR)
- UniSTS:168533

G43636 (e-PCR)
- UniSTS:95064

RH92536 (e-PCR)
- UniSTS:84072

RH121346 (e-PCR)
- UniSTS:138609

STS-N32962 (e-PCR)
- UniSTS:6521

Jarid2 (e-PCR), detects polymorphism
- UniSTS:507004

RH1514 (e-PCR)
- UniSTS:53118

D6S89 (e-PCR)
- UniSTS:147594

D6S339 (e-PCR)
- UniSTS:147597

D6S89 (e-PCR)
- UniSTS:40598

RH37458 (e-PCR)
- UniSTS:50591

SHGC-110030 (e-PCR)
- UniSTS:170159

SHGC-84005 (e-PCR)
- UniSTS:104631

RH37571 (e-PCR)
- UniSTS:43451

SHGC-58184 (e-PCR)
- UniSTS:80576

JARID2_3393 (e-PCR)
- UniSTS:462286

D6S260 (e-PCR)
- UniSTS:82894

RH119279 (e-PCR)
- UniSTS:133841

D6S469 (e-PCR), detects polymorphism
- UniSTS:62932

D6S260 (e-PCR)
- UniSTS:993

SHGC-144924 (e-PCR)
- UniSTS:174328

WI-12425 (e-PCR)
- UniSTS:83452

RH45704 (e-PCR)
- UniSTS:18174

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 demethylase activity	IBA Inferred from Biological aspect of Ancestor more info
NOT enables histone demethylase activity	ISS Inferred from Sequence or Structural Similarity more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables ubiquitin binding	IEA Inferred from Electronic Annotation more info
enables ubiquitin-modified histone reader activity	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
involved_in facultative heterochromatin formation	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 random inactivation of X chromosome	IEA Inferred from Electronic Annotation more info
involved_in regulation of gene expression	IBA Inferred from Biological aspect of Ancestor 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
located_in chromatin	IBA Inferred from Biological aspect of Ancestor 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
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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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)

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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)

NM_001267040.1 → NP_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:451 → 542

BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain

smart00545
Location:384 → 425

JmjN; Small domain found in the jumonji family of transcription factors

pfam02373
Location:744 → 859

JmjC; JmjC domain, hydroxylase

pfam02928
Location:967 → 1020

zf-C5HC2; C5HC2 zinc finger
NM_004973.4 → NP_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

A8K9Z6, B7Z5S5, B7Z8L0, Q5U5L5, Q86X63, Q92833

Related

ENSP00000341280.2, ENST00000341776.7

Conserved Domains (4) summary

smart00545
Location:556 → 597

JmjN; Small domain found in the jumonji family of transcription factors

cd16870
Location:620 → 731

ARID_JARD2; ARID/BRIGHT DNA binding domain of Jumonji/ARID domain-containing protein 2 (JARID2) and similar proteins

pfam02373
Location:916 → 1031

JmjC; JmjC domain, hydroxylase

pfam02928
Location:1139 → 1192

zf-C5HC2; C5HC2 zinc finger

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000006.12 Reference GRCh38.p14 Primary Assembly

Range

15246069..15522042

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011514579.4 → XP_011512881.1 protein Jumonji isoform X1

Conserved Domains (4) summary

smart00501
Location:686 → 777

BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain

smart00545
Location:619 → 660

JmjN; Small domain found in the jumonji family of transcription factors

pfam02373
Location:979 → 1094

JmjC; JmjC domain, hydroxylase

pfam02928
Location:1202 → 1255

zf-C5HC2; C5HC2 zinc finger
XM_017010833.3 → XP_016866322.1 protein Jumonji isoform X2
XM_047418735.1 → XP_047274691.1 protein Jumonji isoform X3
XM_047418736.1 → XP_047274692.1 protein Jumonji isoform X4
XM_047418744.1 → XP_047274700.1 protein Jumonji isoform X10
XM_047418745.1 → XP_047274701.1 protein Jumonji isoform X11
XM_047418746.1 → XP_047274702.1 protein Jumonji isoform X12
XM_047418738.1 → XP_047274694.1 protein Jumonji isoform X5
XM_047418741.1 → XP_047274697.1 protein Jumonji isoform X9
XM_047418737.1 → XP_047274693.1 protein Jumonji isoform X5
XM_047418742.1 → XP_047274698.1 protein Jumonji isoform X9
XM_047418748.1 → XP_047274704.1 protein Jumonji isoform X14
XM_047418743.1 → XP_047274699.1 protein Jumonji isoform X9
XM_017010835.3 → XP_016866324.1 protein Jumonji isoform X9

UniProtKB/Swiss-Prot

Q92833

Conserved Domains (4) summary

smart00501
Location:451 → 542

BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain

smart00545
Location:384 → 425

JmjN; Small domain found in the jumonji family of transcription factors

pfam02373
Location:744 → 859

JmjC; JmjC domain, hydroxylase

pfam02928
Location:967 → 1020

zf-C5HC2; C5HC2 zinc finger
XM_024446424.2 → XP_024302192.1 protein Jumonji isoform X6

Conserved Domains (4) summary

smart00501
Location:600 → 691

BRIGHT; ARID (A/T-rich interaction domain) domain

smart00545
Location:533 → 574

JmjN; Small domain found in the jumonji family of transcription factors

pfam02373
Location:893 → 1008

JmjC; JmjC domain, hydroxylase

pfam02928
Location:1116 → 1169

zf-C5HC2; C5HC2 zinc finger
XM_047418739.1 → XP_047274695.1 protein Jumonji isoform X7
XM_047418740.1 → XP_047274696.1 protein Jumonji isoform X8
XM_024446425.2 → XP_024302193.2 protein Jumonji isoform X13
XM_047418747.1 → XP_047274703.1 protein Jumonji isoform X15