Kdm3a lysine (K)-specific demethylase 3A [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Kdm3aprovided by MGI
Official Full Name: lysine (K)-specific demethylase 3Aprovided by MGI
Primary source: MGI:MGI:98847
See related: Ensembl:ENSMUSG00000053470 AllianceGenome:MGI:98847
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: TGSA; Tsga; Jmjd1; KDM2A; JHDM2a; Jmjd1a; 1700105C21Rik; C230043E16Rik
Summary: Enables chromatin binding activity; histone H3K9 demethylase activity; and transcription coregulator activity. Involved in positive regulation of cold-induced thermogenesis. Acts upstream of or within several processes, including cellular response to leukemia inhibitory factor; positive regulation of transcription by RNA polymerase II; and spermatid nucleus elongation. Located in cytoplasm and male germ cell nucleus. Is expressed in several structures, including cerebral cortex; extraembryonic ectoderm; ovary; and pituitary gland. Used to study obesity. 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: Ubiquitous expression in CNS E11.5 (RPKM 18.6), testis adult (RPKM 15.8) and 25 other tissues See more
Orthologs: human all
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Genomic context

Location:: 6 C1; 6 32.18 cM

Exon count:: 30

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	6	NC_000072.7 (71565954..71609963, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	6	NC_000072.6 (71588970..71632990, complement)

Chromosome 6 - NC_000072.7 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: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Histone Demethylase KDM3 (JMJD1) in Transcriptional Regulation and Cancer Progression.
Title: Histone Demethylase KDM3 (JMJD1) in Transcriptional Regulation and Cancer Progression.
LncRNA HOX transcript antisense RNA mitigates cardiac function injury in chronic heart failure via regulating microRNA-30a-5p to target KDM3A.
Title: LncRNA HOX transcript antisense RNA mitigates cardiac function injury in chronic heart failure via regulating microRNA-30a-5p to target KDM3A.
MiR-216a-5p alleviates chronic constriction injury-induced neuropathic pain in rats by targeting KDM3A and inactivating Wnt/beta-catenin signaling pathway.
Title: MiR-216a-5p alleviates chronic constriction injury-induced neuropathic pain in rats by targeting KDM3A and inactivating Wnt/β-catenin signaling pathway.
MicroRNA-194 acts as a suppressor during abdominal aortic aneurysm via inhibition of KDM3A-mediated BNIP3.
Title: MicroRNA-194 acts as a suppressor during abdominal aortic aneurysm via inhibition of KDM3A-mediated BNIP3.
H3K9 Demethylases JMJD1A and JMJD1B Control Prospermatogonia to Spermatogonia Transition in Mouse Germline.
Title: H3K9 Demethylases JMJD1A and JMJD1B Control Prospermatogonia to Spermatogonia Transition in Mouse Germline.
JMJD1A Represses the Development of Cardiomyocyte Hypertrophy by Regulating the Expression of Catalase.
Title: JMJD1A Represses the Development of Cardiomyocyte Hypertrophy by Regulating the Expression of Catalase.
Lysine-specific demethylase 3A is important for autophagic occurrence.
Title: Lysine-specific demethylase 3A is important for autophagic occurrence.
JMJD1 A is a co-activator of EPO expression
Title: Histone H3K9 demethylase JMJD1A is a co-activator of erythropoietin expression under hypoxia.
JMJD1A and JMJD1B, in combination, ensure early embryogenesis and embryonic stem cell viability by establishing the correct Histone 3 lysine 9 methylated epigenome.
Title: Combined Loss of JMJD1A and JMJD1B Reveals Critical Roles for H3K9 Demethylation in the Maintenance of Embryonic Stem Cells and Early Embryogenesis.
JMJD1A mediates two major signaling pathways, namely, beta-adrenergic receptor and peroxisome proliferator-activated receptor-gamma (PPARgamma) activation, via PRDM16-PPARgamma-P-JMJD1A complex for beige adipogenesis.
Title: Histone demethylase JMJD1A coordinates acute and chronic adaptation to cold stress via thermogenic phospho-switch.

Submit: New GeneRIF Correction See all GeneRIFs (27)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (4)
Gene trapped (3) 1 citation
Targeted (7) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

NoName (e-PCR)
- UniSTS:224291

RH125286 (e-PCR)
- UniSTS:162108

T25656 (e-PCR)
- UniSTS:125633

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables FAD-dependent histone H3K9me/H3K9me2 demethylase activity	IEA Inferred from Electronic Annotation more info
enables chromatin DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables histone H3K9 demethylase activity	IBA Inferred from Biological aspect of Ancestor more info
enables histone H3K9 demethylase activity	IDA Inferred from Direct Assay more info	PubMed
enables histone H3K9 demethylase activity	IMP Inferred from Mutant Phenotype more info	PubMed
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 nuclear androgen receptor binding	IEA Inferred from Electronic Annotation more info
enables nuclear androgen receptor binding	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables transcription coregulator activity	IBA Inferred from Biological aspect of Ancestor more info
enables transcription coregulator activity	IDA Inferred from Direct Assay more info	PubMed

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
acts_upstream_of_or_within cellular response to leukemia inhibitory factor	IEP Inferred from Expression Pattern more info	PubMed
involved_in chromatin remodeling	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 positive regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cold-induced thermogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of gene expression	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of stem cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of stem cell population maintenance	IGI Inferred from Genetic Interaction more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within spermatid nucleus elongation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within spermatogenesis	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in chromatin	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
part_of histone deacetylase complex	IBA Inferred from Biological aspect of Ancestor more info
located_in male germ cell nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
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 protein 1A; testis specific gene A

NP_001033784.2

EC 1.14.11.65

NP_001349129.1

EC 1.14.11.65

NP_001349130.1

EC 1.14.11.65

NP_766589.1

EC 1.14.11.65

XP_030110909.1

EC 1.14.11.65

XP_030110910.1

EC 1.14.11.65

XP_036021613.1

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_001038695.3 → NP_001033784.2 lysine-specific demethylase 3A isoform a

See identical proteins and their annotated locations for NP_001033784.2

Status: VALIDATED

Description

Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2, and 3 all encode the same isoform (a).

Source sequence(s)

AK007123, AK129204, CB519830

Consensus CDS

CCDS20233.1

UniProtKB/Swiss-Prot

Q2MJQ6, Q3TKW8, Q3UML3, Q6PCM1, Q6ZQ57, Q8K2J6, Q8K2K4, Q8R350

Related

ENSMUSP00000065716.5, ENSMUST00000065509.11

Conserved Domains (3) summary

pfam02373
Location:1153 → 1266

JmjC; JmjC domain, hydroxylase

smart00558
Location:1066 → 1136

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

pfam07964
Location:748 → 936

Red1; Rec10 / Red1
NM_001362200.1 → NP_001349129.1 lysine-specific demethylase 3A isoform a

Status: VALIDATED

Description

Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2, and 3 all encode the same isoform (a).

Source sequence(s)

AC118686

Consensus CDS

CCDS20233.1

UniProtKB/Swiss-Prot

Q2MJQ6, Q3TKW8, Q3UML3, Q6PCM1, Q6ZQ57, Q8K2J6, Q8K2K4, Q8R350

Related

ENSMUSP00000145959.2, ENSMUST00000207023.2

Conserved Domains (3) summary

pfam02373
Location:1153 → 1266

JmjC; JmjC domain, hydroxylase

smart00558
Location:1066 → 1136

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

pfam07964
Location:748 → 936

Red1; Rec10 / Red1
NM_001362201.1 → NP_001349130.1 lysine-specific demethylase 3A isoform b

Status: VALIDATED

Description

Transcript Variant: This variant (4) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (b) has a shorter and distinct N-terminus compared to isoform 1.

Source sequence(s)

AC118686, AK166797, KJ461739

UniProtKB/TrEMBL

A0A023ULC4

Conserved Domains (3) summary

smart00558
Location:574 → 644

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

pfam07964
Location:256 → 444

Red1; Rec10 / Red1

cl21464
Location:661 → 774

cupin_like; Conserved domain found in cupin and related proteins
NM_173001.3 → NP_766589.1 lysine-specific demethylase 3A isoform a

See identical proteins and their annotated locations for NP_766589.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a). Variants 1, 2, and 3 all encode the same isoform (a).

Source sequence(s)

AC118686, AK007123, BC059264

Consensus CDS

CCDS20233.1

UniProtKB/Swiss-Prot

Q2MJQ6, Q3TKW8, Q3UML3, Q6PCM1, Q6ZQ57, Q8K2J6, Q8K2K4, Q8R350

Related

ENSMUSP00000128789.2, ENSMUST00000167220.4

Conserved Domains (3) summary

pfam02373
Location:1153 → 1266

JmjC; JmjC domain, hydroxylase

smart00558
Location:1066 → 1136

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

pfam07964
Location:748 → 936

Red1; Rec10 / Red1

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000072.7 Reference GRCm39 C57BL/6J

Range

71565954..71609963 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_030255050.2 → XP_030110910.1 lysine-specific demethylase 3A isoform X1

Conserved Domains (2) summary

smart00558
Location:781 → 851

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

cl40423
Location:868 → 981

cupin_RmlC-like; RmlC-like cupin superfamily
XM_030255049.2 → XP_030110909.1 lysine-specific demethylase 3A isoform X1

Conserved Domains (2) summary

smart00558
Location:781 → 851

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

cl40423
Location:868 → 981

cupin_RmlC-like; RmlC-like cupin superfamily
XM_036165720.1 → XP_036021613.1 lysine-specific demethylase 3A isoform X1

Conserved Domains (2) summary

smart00558
Location:781 → 851

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

cl40423
Location:868 → 981

cupin_RmlC-like; RmlC-like cupin superfamily