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

Gene ID: 55818, updated on 14-Nov-2024

Summary

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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, Nov 2024]
Expression
Ubiquitous expression in testis (RPKM 32.2), bone marrow (RPKM 27.1) and 25 other tissues See more
Orthologs
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Genomic context

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See KDM3A in Genome Data Viewer
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_000002.12Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 10968 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:86457835-86458493 Neighboring gene Sharpr-MPRA regulatory region 10790 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11711 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:86487052-86487642 Neighboring gene receptor accessory protein 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:86551277-86551778 Neighboring gene U8 small nucleolar RNA Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:86667563-86668106 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16160 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11712 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11713 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16161 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:86708929-86710128 Neighboring gene MPRA-validated peak3779 silencer Neighboring gene RNF103-CHMP3 readthrough Neighboring gene RNA, U6 small nuclear 640, pseudogene Neighboring gene charged multivesicular body protein 3 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_59439 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16162 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16163 Neighboring gene Sharpr-MPRA regulatory region 1991 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16164 Neighboring gene CHMP3 and RNF103 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11714 Neighboring gene ring finger protein 103

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Lysine-specific demethylase KDM3A regulates ovarian cancer stemness and chemoresistance. Ramadoss S, et al. Oncogene, 2017 Mar. PMID 27694900, Free PMC Article
  2. KDM3A histone demethylase functions as an essential factor for activation of JAK2-STAT3 signaling pathway. Kim H, et al. Proc Natl Acad Sci U S A, 2018 Nov 13. PMID 30377265, Free PMC Article
  3. Identification of Two Novel Mutations in KDM3A Regulatory Gene in Iranian Infertile Males. Hojati Z, et al. Iran Biomed J, 2019 May. PMID 30053768, Free PMC Article
  4. Histone demethylase JMJD1A promotes alternative splicing of AR variant 7 (AR-V7) in prostate cancer cells. Fan L, et al. Proc Natl Acad Sci U S A, 2018 May 15. PMID 29712835, Free PMC Article
  5. Ascorbate antagonizes nickel ion to regulate JMJD1A expression in kidney cancer cells. Guo X, et al. Acta Biochim Biophys Sin (Shanghai), 2012 Apr. PMID 22318714

See all (125) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. Histone demethylase JMJD1A in cancer progression and therapeutic resistance.
    Title: Histone demethylase JMJD1A in cancer progression and therapeutic resistance.
  8. 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.
  9. 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.
  10. 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)

Pathways from PubChem

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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

Homology

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 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
NP_060903.2
XP_006712114.1
XP_047301057.1
XP_047301058.1
XP_047301059.1
XP_047301060.1
XP_047301061.1
XP_054198968.1
XP_054198969.1
XP_054198970.1
XP_054198971.1
XP_054198972.1
XP_054198973.1

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

  1. NG_047167.1 RefSeqGene

    Range
    5725..57070
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. 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

  2. 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

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    86437044..86492716
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    UniProtKB/Swiss-Prot
    D6W5M3, Q53S72, Q68D47, Q68UT9, Q6N050, Q8IY08, Q9Y4C1

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

    UniProtKB/Swiss-Prot
    D6W5M3, Q53S72, Q68D47, Q68UT9, Q6N050, Q8IY08, Q9Y4C1

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

    UniProtKB/Swiss-Prot
    D6W5M3, Q53S72, Q68D47, Q68UT9, Q6N050, Q8IY08, Q9Y4C1

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

    UniProtKB/Swiss-Prot
    D6W5M3, Q53S72, Q68D47, Q68UT9, Q6N050, Q8IY08, Q9Y4C1

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

  6. 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

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    86439057..86494729
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054342994.1 → XP_054198969.1  lysine-specific demethylase 3A isoform X1

    UniProtKB/Swiss-Prot
    D6W5M3, Q53S72, Q68D47, Q68UT9, Q6N050, Q8IY08, Q9Y4C1

  2. XM_054342993.1 → XP_054198968.1  lysine-specific demethylase 3A isoform X1

    UniProtKB/Swiss-Prot
    D6W5M3, Q53S72, Q68D47, Q68UT9, Q6N050, Q8IY08, Q9Y4C1

  3. XM_054342996.1 → XP_054198971.1  lysine-specific demethylase 3A isoform X1

    UniProtKB/Swiss-Prot
    D6W5M3, Q53S72, Q68D47, Q68UT9, Q6N050, Q8IY08, Q9Y4C1

  4. XM_054342995.1 → XP_054198970.1  lysine-specific demethylase 3A isoform X1

    UniProtKB/Swiss-Prot
    D6W5M3, Q53S72, Q68D47, Q68UT9, Q6N050, Q8IY08, Q9Y4C1

  5. XM_054342997.1 → XP_054198972.1  lysine-specific demethylase 3A isoform X2

  6. XM_054342998.1 → XP_054198973.1  lysine-specific demethylase 3A isoform X3

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9Y4C1.4 GenPept UniProtKB/Swiss-Prot:Q9Y4C1

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