Jarid2 jumonji and AT-rich interaction domain containing 2 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Jarid2provided by RGD
Official Full Name: jumonji and AT-rich interaction domain containing 2provided by RGD
Primary source: RGD:1591663
See related: Ensembl:ENSRNOG00000045918 AllianceGenome:RGD:1591663
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable several functions, including histone demethylase activity; ubiquitin binding activity; and ubiquitin modification-dependent histone binding activity. Involved in negative regulation of cardiac muscle cell proliferation and negative regulation of cardiac muscle hypertrophy. Predicted to be located in mitochondrion and nucleoplasm. Predicted to be part of ESC/E(Z) complex. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in autistic disorder. Orthologous to human JARID2 (jumonji and AT-rich interaction domain containing 2). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Adrenal (RPKM 81.4), Kidney (RPKM 80.8) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 17p14

Exon count:: 25

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	17	NC_086035.1 (19983217..20163598, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	17	NC_051352.1 (19777487..19957696, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	17	NC_005116.4 (20183440..20365219, complement)

Chromosome 17 - NC_086035.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

miR-155 inhibition ameliorates TNBS-induced colitis by regulating the Th17 cells differentiation and function and Jarid2/notch1 is closely related with the process.
Title: MiR-155 inhibition ameliorates 2, 4, 6-Trinitrobenzenesulfonic acid (TNBS)-induced experimental colitis in rat via influencing the differentiation of Th17 cells by Jarid2.

Submit: New GeneRIF Correction

General gene information

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Markers

D13Mit179 (e-PCR), detects polymorphism
- UniSTS:126994

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

RH129878 (e-PCR)
- UniSTS:213166

Jarid2 (e-PCR), detects polymorphism
- UniSTS:536529

RH140095 (e-PCR)
- UniSTS:222176

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA binding	ISO Inferred from Sequence Orthology more info
enables chromatin binding	ISO Inferred from Sequence Orthology more info
NOT contributes_to histone H3K27 methyltransferase activity	ISO Inferred from Sequence Orthology more info
contributes_to histone H3K27 methyltransferase activity	ISO Inferred from Sequence Orthology more info
NOT enables histone demethylase activity	IBA Inferred from Biological aspect of Ancestor more info
NOT enables histone demethylase activity	ISO Inferred from Sequence Orthology more info
enables ubiquitin binding	ISO Inferred from Sequence Orthology more info
enables ubiquitin-modified histone reader activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of cardiac muscle cell proliferation	ISO Inferred from Sequence Orthology more info
acts_upstream_of cell population proliferation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cellular response to leukemia inhibitory factor	ISO Inferred from Sequence Orthology more info
involved_in chromatin remodeling	IBA Inferred from Biological aspect of Ancestor more info
involved_in facultative heterochromatin formation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within liver development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of cardiac muscle cell proliferation	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of cardiac muscle cell proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of cardiac muscle cell proliferation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of cardiac muscle hypertrophy	IGI Inferred from Genetic Interaction more info	PubMed
involved_in negative regulation of cardiac muscle hypertrophy	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within protein localization to pericentric heterochromatin	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within random inactivation of X chromosome	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of cell population proliferation	ISO Inferred from Sequence Orthology more info
involved_in regulation of gene expression	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within spleen development	ISO Inferred from Sequence Orthology more info
involved_in stem cell differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within thymus development	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of ESC/E(Z) complex	ISO Inferred from Sequence Orthology more info
part_of chromatin	IBA Inferred from Biological aspect of Ancestor more info
part_of histone methyltransferase complex	ISO Inferred from Sequence Orthology more info
located_in mitochondrion	IEA Inferred from Electronic Annotation more info
located_in mitochondrion	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: protein Jumonji

Names: jumonji, AT rich interactive domain 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_001427247.1 → NP_001414176.1 protein Jumonji

Status: VALIDATED

Source sequence(s)

JAXUCZ010000017

UniProtKB/TrEMBL

A6J730, A6J731, M0RBV7

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086035.1 Reference GRCr8

Range

19983217..20163598 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039096474.2 → XP_038952402.1 protein Jumonji isoform X3

UniProtKB/TrEMBL

A6J730, A6J731, M0RBV7

Conserved Domains (4) summary

smart00545
Location:554 → 595

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

cd16870
Location:618 → 729

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

pfam02373
Location:914 → 1029

JmjC; JmjC domain, hydroxylase

pfam02928
Location:1137 → 1190

zf-C5HC2; C5HC2 zinc finger
XM_017600709.3 → XP_017456198.1 protein Jumonji isoform X3

UniProtKB/TrEMBL

A6J730, A6J731, M0RBV7

Conserved Domains (4) summary

smart00545
Location:554 → 595

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

cd16870
Location:618 → 729

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

pfam02373
Location:914 → 1029

JmjC; JmjC domain, hydroxylase

pfam02928
Location:1137 → 1190

zf-C5HC2; C5HC2 zinc finger
XM_017600710.3 → XP_017456199.1 protein Jumonji isoform X3

UniProtKB/TrEMBL

A6J730, A6J731, M0RBV7

Conserved Domains (4) summary

smart00545
Location:554 → 595

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

cd16870
Location:618 → 729

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

pfam02373
Location:914 → 1029

JmjC; JmjC domain, hydroxylase

pfam02928
Location:1137 → 1190

zf-C5HC2; C5HC2 zinc finger
XM_017600708.3 → XP_017456197.1 protein Jumonji isoform X3

UniProtKB/TrEMBL

A6J730, A6J731, M0RBV7

Conserved Domains (4) summary

smart00545
Location:554 → 595

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

cd16870
Location:618 → 729

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

pfam02373
Location:914 → 1029

JmjC; JmjC domain, hydroxylase

pfam02928
Location:1137 → 1190

zf-C5HC2; C5HC2 zinc finger
XM_063276747.1 → XP_063132817.1 protein Jumonji isoform X4

UniProtKB/TrEMBL

A6J731, A6J732
XM_039096472.2 → XP_038952400.1 protein Jumonji isoform X2

UniProtKB/TrEMBL

A6J731

Conserved Domains (4) summary

smart00545
Location:577 → 618

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

cd16870
Location:641 → 752

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

pfam02373
Location:937 → 1052

JmjC; JmjC domain, hydroxylase

pfam02928
Location:1160 → 1213

zf-C5HC2; C5HC2 zinc finger
XM_017600711.3 → XP_017456200.1 protein Jumonji isoform X4

UniProtKB/TrEMBL

A6J731, A6J732

Conserved Domains (5) summary

smart00501
Location:449 → 540

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

smart00545
Location:382 → 423

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

pfam02373
Location:742 → 857

JmjC; JmjC domain, hydroxylase

pfam02928
Location:965 → 1018

zf-C5HC2; C5HC2 zinc finger

pfam12288
Location:89 → 184

CsoS2_M; Carboxysome shell peptide mid-region
XM_063276746.1 → XP_063132816.1 protein Jumonji isoform X4

UniProtKB/TrEMBL

A6J731, A6J732
XM_017600707.3 → XP_017456196.1 protein Jumonji isoform X1

UniProtKB/TrEMBL

A6J731