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

    Gene ID: 104263, updated on 9-Dec-2024

    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, Dec 2024]
    Expression
    Ubiquitous expression in CNS E11.5 (RPKM 18.6), testis adult (RPKM 15.8) and 25 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See Kdm3a in Genome Data Viewer
    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_000072.7Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer ABC_E10384 Neighboring gene ring finger protein 103 Neighboring gene STARR-positive B cell enhancer ABC_E8110 Neighboring gene charged multivesicular body protein 3 Neighboring gene STARR-seq mESC enhancer starr_16264 Neighboring gene STARR-seq mESC enhancer starr_16265 Neighboring gene STARR-positive B cell enhancer ABC_E3659 Neighboring gene CapStarr-seq enhancer MGSCv37_chr6:71583085-71583314 Neighboring gene STARR-positive B cell enhancer ABC_E9095 Neighboring gene peptidylprolyl isomerase A pseudogene 6_731.1 Neighboring gene predicted gene 44768

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Variation

    Alleles

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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • KIAA0742

    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

    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
    NP_001349129.1
    NP_001349130.1
    NP_766589.1
    XP_030110909.1
    XP_030110910.1
    XP_036021613.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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)

    1. NM_001038695.3NP_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:11531266
      JmjC; JmjC domain, hydroxylase
      smart00558
      Location:10661136
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      pfam07964
      Location:748936
      Red1; Rec10 / Red1
    2. NM_001362200.1NP_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:11531266
      JmjC; JmjC domain, hydroxylase
      smart00558
      Location:10661136
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      pfam07964
      Location:748936
      Red1; Rec10 / Red1
    3. NM_001362201.1NP_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:574644
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      pfam07964
      Location:256444
      Red1; Rec10 / Red1
      cl21464
      Location:661774
      cupin_like; Conserved domain found in cupin and related proteins
    4. NM_173001.3NP_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:11531266
      JmjC; JmjC domain, hydroxylase
      smart00558
      Location:10661136
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      pfam07964
      Location:748936
      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

    1. NC_000072.7 Reference GRCm39 C57BL/6J

      Range
      71565954..71609963 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

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

      Conserved Domains (2) summary
      smart00558
      Location:781851
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      cl40423
      Location:868981
      cupin_RmlC-like; RmlC-like cupin superfamily
    2. XM_030255049.2XP_030110909.1  lysine-specific demethylase 3A isoform X1

      Conserved Domains (2) summary
      smart00558
      Location:781851
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      cl40423
      Location:868981
      cupin_RmlC-like; RmlC-like cupin superfamily
    3. XM_036165720.1XP_036021613.1  lysine-specific demethylase 3A isoform X1

      Conserved Domains (2) summary
      smart00558
      Location:781851
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      cl40423
      Location:868981
      cupin_RmlC-like; RmlC-like cupin superfamily