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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
    mouse all
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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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    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

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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