KDM3A lysine demethylase 3A [Homo sapiens (human)] - Gene

Summary

Official Symbol: KDM3Aprovided by HGNC
Official Full Name: lysine demethylase 3Aprovided by HGNC
Primary source: HGNC:HGNC:20815
See related: Ensembl:ENSG00000115548 MIM:611512; AllianceGenome:HGNC:20815
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: TSGA; JMJD1; JHDM2A; JHMD2A; JMJD1A
Summary: Enables histone H3K9me/H3K9me2 demethylase activity; iron ion binding activity; and nuclear androgen receptor binding activity. Involved in androgen receptor signaling pathway; formaldehyde biosynthetic process; and positive regulation of DNA-templated transcription. Located in nucleoplasm. Implicated in cervical cancer and colon cancer. Biomarker of Ewing sarcoma; hepatocellular carcinoma; nasopharynx carcinoma; and prostate cancer. [provided by Alliance of Genome Resources, Dec 2024]
Expression: Ubiquitous expression in testis (RPKM 32.2), bone marrow (RPKM 27.1) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 2p11.2

Exon count:: 30

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (86437044..86492716)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (86439057..86494729)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (86668494..86719839)

Chromosome 2 - NC_000002.12 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: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Impact of Hypoxia and the Levels of Transcription Factor HIF-1alpha and JMJD1A on Epithelial-Mesenchymal Transition in Head and Neck Squamous Cell Carcinoma Cell Lines.
Title: Impact of Hypoxia and the Levels of Transcription Factor HIF-1α and JMJD1A on Epithelial-Mesenchymal Transition in Head and Neck Squamous Cell Carcinoma Cell Lines.
Knockout of KDM3A in MDA-MB-231 breast cancer cells inhibits tumor malignancy and promotes apoptosis.
Title: Knockout of KDM3A in MDA-MB-231 breast cancer cells inhibits tumor malignancy and promotes apoptosis.
KDM3A promotes oral squamous cell carcinoma cell proliferation and invasion via H3K9me2 demethylation-activated DCLK1.
Title: KDM3A promotes oral squamous cell carcinoma cell proliferation and invasion via H3K9me2 demethylation-activated DCLK1.
Histone demethylase JHDM2A participates in the repair of arsenic-induced DNA damage in L-02 cells by regulating DDB2.
Title: Histone demethylase JHDM2A participates in the repair of arsenic-induced DNA damage in L-02 cells by regulating DDB2.
Downregulation of miR-335 exhibited an oncogenic effect via promoting KDM3A/YAP1 networks in clear cell renal cell carcinoma.
Title: Downregulation of miR-335 exhibited an oncogenic effect via promoting KDM3A/YAP1 networks in clear cell renal cell carcinoma.
Spermatozoa retrieval in azoospermia and expression profile of JMJD1A, TNP2, and PRM2 in a subset of the Karachi population.
Title: Spermatozoa retrieval in azoospermia and expression profile of JMJD1A, TNP2, and PRM2 in a subset of the Karachi population.
Histone demethylase JMJD1A in cancer progression and therapeutic resistance.
Title: Histone demethylase JMJD1A in cancer progression and therapeutic resistance.
Overexpression of let-7d explains down-regulated KDM3A and ENO2 in the pathogenesis of preeclampsia.
Title: Overexpression of let-7d explains down-regulated KDM3A and ENO2 in the pathogenesis of preeclampsia.
HIF-1alpha/JMJD1A signaling regulates inflammation and oxidative stress following hyperglycemia and hypoxia-induced vascular cell injury.
Title: HIF-1α/JMJD1A signaling regulates inflammation and oxidative stress following hyperglycemia and hypoxia-induced vascular cell injury.
KDM3A regulates alternative splicing of cell-cycle genes following DNA damage.
Title: KDM3A regulates alternative splicing of cell-cycle genes following DNA damage.

Submit: New GeneRIF Correction See all GeneRIFs (78)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

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

RH92486 (e-PCR)
- UniSTS:91200

RH77990 (e-PCR)
- UniSTS:22339

RH69600 (e-PCR)
- UniSTS:4197

Clone Names

KIAA0742, DKFZp686A24246, DKFZp686P07111

Gene Ontology Provided by GOA

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 histone H3K9 demethylase activity	IBA Inferred from Biological aspect of Ancestor more info
enables histone H3K9 demethylase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables histone H3K9me/H3K9me2 demethylase activity	IDA Inferred from Direct Assay more info	PubMed
enables iron ion binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables nuclear androgen receptor binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables transcription coregulator activity	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in androgen receptor signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in cellular response to leukemia inhibitory factor	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in formaldehyde biosynthetic process	IDA Inferred from Direct Assay more info	PubMed
involved_in hormone-mediated signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of DNA-templated transcription	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of cold-induced thermogenesis	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in regulation of stem cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in regulation of stem cell population maintenance	IEA Inferred from Electronic Annotation more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in spermatid nucleus elongation	IEA Inferred from Electronic Annotation 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
part_of histone deacetylase complex	IBA Inferred from Biological aspect of Ancestor more info
located_in male germ cell nucleus	IEA Inferred from Electronic Annotation more info
located_in membrane	HDA more info	PubMed
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

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 C domain-containing histone demethylase 2A; jumonji domain-containing protein 1A; lysine (K)-specific demethylase 3A; testis-specific protein A

NP_001140160.1

EC 1.14.11.65

NP_060903.2

EC 1.14.11.65

XP_006712114.1

EC 1.14.11.65

XP_047301057.1

EC 1.14.11.65

XP_047301058.1

EC 1.14.11.65

XP_047301059.1

EC 1.14.11.65

XP_047301060.1

EC 1.14.11.65

XP_047301061.1

EC 1.14.11.65

XP_054198968.1

EC 1.14.11.65

XP_054198969.1

EC 1.14.11.65

XP_054198970.1

EC 1.14.11.65

XP_054198971.1

EC 1.14.11.65

XP_054198972.1

EC 1.14.11.65

XP_054198973.1

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.

Genomic

NG_047167.1 RefSeqGene

Range

5725..57070

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001146688.2 → NP_001140160.1 lysine-specific demethylase 3A

See identical proteins and their annotated locations for NP_001140160.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Both variants 1 and 2 encode the same protein.

Source sequence(s)

AB018285, BX647271, BX648841

Consensus CDS

CCDS1990.1

UniProtKB/Swiss-Prot

D6W5M3, Q53S72, Q68D47, Q68UT9, Q6N050, Q8IY08, Q9Y4C1

UniProtKB/TrEMBL

B4E2H5

Related

ENSP00000386516.1, ENST00000409064.5

Conserved Domains (2) summary

smart00558
Location:1064 → 1134

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

cl21464
Location:1151 → 1264

cupin_like; Conserved domain found in cupin and related proteins
NM_018433.6 → NP_060903.2 lysine-specific demethylase 3A

See identical proteins and their annotated locations for NP_060903.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript. Both variants 1 and 2 encode the same protein.

Source sequence(s)

AB018285, BX647271, BX648841, DB087171

Consensus CDS

CCDS1990.1

UniProtKB/Swiss-Prot

D6W5M3, Q53S72, Q68D47, Q68UT9, Q6N050, Q8IY08, Q9Y4C1

UniProtKB/TrEMBL

B4E2H5

Related

ENSP00000323659.5, ENST00000312912.10

Conserved Domains (2) summary

smart00558
Location:1064 → 1134

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

cl21464
Location:1151 → 1264

cupin_like; Conserved domain found in cupin and related proteins

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_000002.12 Reference GRCh38.p14 Primary Assembly

Range

86437044..86492716

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047445102.1 → XP_047301058.1 lysine-specific demethylase 3A isoform X1

UniProtKB/Swiss-Prot

D6W5M3, Q53S72, Q68D47, Q68UT9, Q6N050, Q8IY08, Q9Y4C1

UniProtKB/TrEMBL

B4E2H5
XM_047445101.1 → XP_047301057.1 lysine-specific demethylase 3A isoform X1

UniProtKB/Swiss-Prot

D6W5M3, Q53S72, Q68D47, Q68UT9, Q6N050, Q8IY08, Q9Y4C1

UniProtKB/TrEMBL

B4E2H5
XM_047445104.1 → XP_047301060.1 lysine-specific demethylase 3A isoform X1

UniProtKB/Swiss-Prot

D6W5M3, Q53S72, Q68D47, Q68UT9, Q6N050, Q8IY08, Q9Y4C1

UniProtKB/TrEMBL

B4E2H5
XM_047445103.1 → XP_047301059.1 lysine-specific demethylase 3A isoform X1

UniProtKB/Swiss-Prot

D6W5M3, Q53S72, Q68D47, Q68UT9, Q6N050, Q8IY08, Q9Y4C1

UniProtKB/TrEMBL

B4E2H5
XM_047445105.1 → XP_047301061.1 lysine-specific demethylase 3A isoform X2

UniProtKB/TrEMBL

B4E2H5
XM_006712051.5 → XP_006712114.1 lysine-specific demethylase 3A isoform X3

Conserved Domains (2) summary

smart00558
Location:404 → 474

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

cl21464
Location:491 → 604

cupin_like; Conserved domain found in cupin and related proteins