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

Gene ID: 104263, updated on 5-Jan-2023

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 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; histone modification; and spermatid nucleus elongation. Located in cytoplasm and nucleus. Is expressed in 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, Apr 2022]
Expression
Ubiquitous expression in CNS E11.5 (RPKM 18.6), testis adult (RPKM 15.8) and 25 other tissues See more
Orthologs
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Genomic context

See Kdm3a in Genome Data Viewer
Location:
6; 6 C1
Exon count:
30
Annotation release Status Assembly Chr Location
109 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 ring finger protein 103 Neighboring gene charged multivesicular body protein 3 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

Homology

Clone Names

  • KIAA0742

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables chromatin DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables chromatin binding IDA
Inferred from Direct Assay
more info
PubMed 
enables dioxygenase activity IEA
Inferred from Electronic Annotation
more info
 
enables histone H3K9 demethylase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 ISO
Inferred from Sequence Orthology
more info
 
enables iron ion binding ISO
Inferred from Sequence Orthology
more info
 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
 
enables nuclear androgen receptor binding ISO
Inferred from Sequence Orthology
more info
 
enables oxidoreductase activity IEA
Inferred from Electronic Annotation
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
PubMed 
enables transcription coregulator activity IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
involved_in androgen receptor signaling pathway ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within cell differentiation IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within cellular response to leukemia inhibitory factor IEP
Inferred from Expression Pattern
more info
PubMed 
acts_upstream_of_or_within chromatin organization IEA
Inferred from Electronic Annotation
more info
 
involved_in formaldehyde biosynthetic process ISO
Inferred from Sequence Orthology
more info
 
involved_in histone H3-K9 demethylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
PubMed 
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
is_active_in chromatin IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
PubMed 
located_in male germ cell nucleus IDA
Inferred from Direct Assay
more info
PubMed 
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
    Q6PCM1, 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
    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
    Q6PCM1, 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: Mus musculus Annotation Release 109 details...Open this link in a new tab

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