Kdm3a lysine demethylase 3A [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Kdm3aprovided by RGD
Official Full Name: lysine demethylase 3Aprovided by RGD
Primary source: RGD:708351
See related: EnsemblRapid:ENSRNOG00000007814 AllianceGenome:RGD:708351
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
Also known as: Jmjd1; Jmjd1a
Summary: Predicted to enable several functions, including histone H3K9me/H3K9me2 demethylase activity; iron ion binding activity; and nuclear androgen receptor binding activity. Involved in male gonad development; positive regulation of gene expression; and response to hypoxia. Predicted to be located in chromatin; cytoplasm; and nucleus. Predicted to be part of histone deacetylase complex. Human ortholog(s) of this gene implicated in cervical cancer and colon cancer. Orthologous to human KDM3A (lysine demethylase 3A). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Thymus (RPKM 184.7), Testes (RPKM 139.3) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 4q32

Exon count:: 29

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	4	NC_086022.1 (105189208..105233526, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	4	NC_051339.1 (103630907..103675073, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	4	NC_005103.4 (99503160..99547315, complement)

Chromosome 4 - NC_086022.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages 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?

Lysine demethylase KDM3A alleviates hyperoxia-induced bronchopulmonary dysplasia in mice by promoting ETS1 expression.
Title: Lysine demethylase KDM3A alleviates hyperoxia-induced bronchopulmonary dysplasia in mice by promoting ETS1 expression.
The histone demthylase KDM3A protects the myocardium from ischemia/reperfusion injury via promotion of ETS1 expression.
Title: The histone demthylase KDM3A protects the myocardium from ischemia/reperfusion injury via promotion of ETS1 expression.
Down-regulated microRNA-199a-3p enhances osteogenic differentiation of bone marrow mesenchymal stem cells by targeting Kdm3a in ovariectomized rats.
Title: Down-regulated microRNA-199a-3p enhances osteogenic differentiation of bone marrow mesenchymal stem cells by targeting Kdm3a in ovariectomized rats.
KDM3A inhibition modulates macrophage polarization to aggravate post-MI injuries and accelerates adverse ventricular remodeling via an IRF4 signaling pathway.
Title: KDM3A inhibition modulates macrophage polarization to aggravate post-MI injuries and accelerates adverse ventricular remodeling via an IRF4 signaling pathway.
KDM3A inhibition may exert numerous protective effects on high insulinstimulated vascular smooth muscle cell.
Title: KDM3A inhibition attenuates high concentration insulin‑induced vascular smooth muscle cell injury by suppressing MAPK/NF‑κB pathways.
In the present report, hypoxia is shown to activate a HIF-KDM3A-MMP12 signaling cascade that promotes trophoblast invasion and trophoblast-directed uterine spiral artery remodeling.
Title: HIF-KDM3A-MMP12 regulatory circuit ensures trophoblast plasticity and placental adaptations to hypoxia.
Histone demethylase KDM3a promotes vascular neointimal hyperplasia in diabetic rats via AGTR1 and ROCK2 signaling pathways.
Title: Histone demethylase KDM3a, a novel regulator of vascular smooth muscle cells, controls vascular neointimal hyperplasia in diabetic rats.
Despite these differences in rats, genetic knockout of Kdm3a in mice resulted in no dramatic effect on immune system development and activation or EAE susceptibility and severity
Title: A silent exonic SNP in kdm3a affects nucleic acids structure but does not regulate experimental autoimmune encephalomyelitis.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH141531 (e-PCR)
- UniSTS:223525

AU049619 (e-PCR)
- UniSTS:146065

AU046560 (e-PCR)
- UniSTS:111333

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables chromatin DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables chromatin binding	IEA Inferred from Electronic Annotation more info
enables chromatin binding	ISO Inferred from Sequence Orthology more info
enables histone H3K9 demethylase activity	IBA Inferred from Biological aspect of Ancestor more info
enables histone H3K9 demethylase activity	IEA Inferred from Electronic Annotation more info
enables histone H3K9 demethylase activity	ISO Inferred from Sequence Orthology more info
enables histone H3K9me/H3K9me2 demethylase activity	IEA Inferred from Electronic Annotation more info
enables histone H3K9me/H3K9me2 demethylase activity	ISO Inferred from Sequence Orthology more info
enables iron ion binding	IEA Inferred from Electronic Annotation more info
enables iron ion binding	ISO Inferred from Sequence Orthology more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables nuclear androgen receptor binding	IEA Inferred from Electronic Annotation more info
enables nuclear androgen receptor binding	ISO Inferred from Sequence Orthology more info
enables transcription coregulator activity	IBA Inferred from Biological aspect of Ancestor more info
enables transcription coregulator activity	IEA Inferred from Electronic Annotation more info
enables transcription coregulator activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in androgen receptor signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in androgen receptor signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in cellular response to leukemia inhibitory factor	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cellular response to leukemia inhibitory factor	ISO Inferred from Sequence Orthology more info
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in demethylation	IEA Inferred from Electronic Annotation more info
involved_in formaldehyde biosynthetic process	IEA Inferred from Electronic Annotation more info
involved_in formaldehyde biosynthetic process	ISO Inferred from Sequence Orthology more info
involved_in hormone-mediated signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in male gonad development	IEP Inferred from Expression Pattern more info	PubMed
involved_in positive regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cold-induced thermogenesis	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cold-induced thermogenesis	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in positive regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in regulation of stem cell differentiation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of stem cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in regulation of stem cell population maintenance	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of stem cell population maintenance	ISO Inferred from Sequence Orthology more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in response to hypoxia	IEP Inferred from Expression Pattern more info	PubMed
involved_in spermatid nucleus elongation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within spermatid nucleus elongation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within spermatogenesis	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in chromatin	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
part_of histone deacetylase complex	IBA Inferred from Biological aspect of Ancestor more info
part_of histone deacetylase complex	IEA Inferred from Electronic Annotation more info
located_in male germ cell nucleus	IEA Inferred from Electronic Annotation more info
located_in male germ cell nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: lysine-specific demethylase 3A

Names: [histone H3]-dimethyl-L-lysine(9) demethylase 3A; jmjC domain-containing histone demethylation protein 2A; jumonji domain containing 1A; jumonji domain-containing protein 1A; lysine (K)-specific demethylase 3A; probable zinc finger protein; testis-specific gene A protein; zinc finger protein TSGA

NP_001376169.1

EC 1.14.11.65

NP_786940.2

EC 1.14.11.65

XP_006236699.1

EC 1.14.11.65

XP_038963496.1

EC 1.14.11.65

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_001389240.1 → NP_001376169.1 lysine-specific demethylase 3A isoform 1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000004

UniProtKB/TrEMBL

A0A0G2K220, A6IA85, D3ZLJ9

Related

ENSRNOP00000041218.5, ENSRNOT00000045279.7

Conserved Domains (2) summary

smart00558
Location:1066 → 1136

JmjC; A domain family that is part of the cupin metalloenzyme superfamily

pfam02373
Location:1153 → 1266

JmjC; JmjC domain, hydroxylase
NM_175764.3 → NP_786940.2 lysine-specific demethylase 3A isoform 2

Status: VALIDATED

Source sequence(s)

JAXUCZ010000004

UniProtKB/TrEMBL

A0A0G2K220

Related

ENSRNOP00000110251.1, ENSRNOT00000130688.1

Conserved Domains (2) summary

smart00558
Location:952 → 1022

JmjC; A domain family that is part of the cupin metalloenzyme superfamily

pfam02373
Location:1039 → 1152

JmjC; JmjC domain, hydroxylase

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_086022.1 Reference GRCr8

Range

105189208..105233526 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006236637.5 → XP_006236699.1 lysine-specific demethylase 3A isoform X1

See identical proteins and their annotated locations for XP_006236699.1

UniProtKB/TrEMBL

A0A0G2K220, A6IA85, D3ZLJ9

Conserved Domains (2) summary

smart00558
Location:1066 → 1136

JmjC; A domain family that is part of the cupin metalloenzyme superfamily

pfam02373
Location:1153 → 1266

JmjC; JmjC domain, hydroxylase
XM_039107568.2 → XP_038963496.1 lysine-specific demethylase 3A isoform X2

UniProtKB/TrEMBL

A0A0G2K220

Conserved Domains (2) summary

smart00558
Location:781 → 851

JmjC; A domain family that is part of the cupin metalloenzyme superfamily

pfam02373
Location:868 → 981

JmjC; JmjC domain, hydroxylase