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

Gene ID: 55818, updated on 12-May-2016
Official Symbol
KDM3Aprovided by HGNC
Official Full Name
lysine demethylase 3Aprovided by HGNC
Primary source
HGNC:HGNC:20815
See related
Ensembl:ENSG00000115548 HPRD:11054; MIM:611512; Vega:OTTHUMG00000130204
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
This gene encodes a zinc finger protein that contains a jumonji domain and may play a role in hormone-dependent transcriptional activation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2009]
Orthologs
Location:
2p11.2
Exon count:
29
Annotation release Status Assembly Chr Location
107 current GRCh38.p2 (GCF_000001405.28) 2 NC_000002.12 (86440647..86492716)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (86668271..86719839)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene mitochondrial ribosomal protein L35 Neighboring gene receptor accessory protein 1 Neighboring gene uncharacterized LOC105374844 Neighboring gene RNF103-CHMP3 readthrough Neighboring gene charged multivesicular body protein 3 Neighboring gene uncharacterized LOC105374845 Neighboring gene ring finger protein 103

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

  • Chromatin modifying enzymes, organism-specific biosystem (from REACTOME)
    Chromatin modifying enzymes, organism-specific biosystemEukaryotic DNA is associated with histone proteins and organized into a complex nucleoprotein structure called chromatin. This structure decreases the accessibility of DNA but also helps to protect i...
  • Chromatin organization, organism-specific biosystem (from REACTOME)
    Chromatin organization, organism-specific biosystemChromatin organization refers to the composition and conformation of complexes between DNA, protein and RNA. It is determined by processes that result in the specification, formation or maintenance o...
  • Coregulation of Androgen receptor activity, organism-specific biosystem (from Pathway Interaction Database)
    Coregulation of Androgen receptor activity, organism-specific biosystem
    Coregulation of Androgen receptor activity
  • HDMs demethylate histones, organism-specific biosystem (from REACTOME)
    HDMs demethylate histones, organism-specific biosystemHistone lysine demethylases (KDMs) are able to reverse N-methylations of histones and probably other proteins. To date KDMs have been demonstrated to catalyse demethylation of N-epsilon methylated ly...
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Clone Names

  • KIAA0742, DKFZp686A24246, DKFZp686P07111

Gene Ontology Provided by GOA

Function Evidence Code Pubs
androgen receptor binding IDA
Inferred from Direct Assay
more info
PubMed 
core promoter binding IEA
Inferred from Electronic Annotation
more info
 
dioxygenase activity IEA
Inferred from Electronic Annotation
more info
 
histone demethylase activity TAS
Traceable Author Statement
more info
 
iron ion binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
transcription factor activity, sequence-specific DNA binding IEA
Inferred from Electronic Annotation
more info
 
transcription regulatory region sequence-specific DNA binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
androgen receptor signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
formaldehyde biosynthetic process IDA
Inferred from Direct Assay
more info
PubMed 
histone H3-K9 demethylation IDA
Inferred from Direct Assay
more info
PubMed 
histone H3-K9 dimethylation IEA
Inferred from Electronic Annotation
more info
 
hormone-mediated signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
male gonad development IEA
Inferred from Electronic Annotation
more info
 
negative regulation of histone H3-K9 methylation IEA
Inferred from Electronic Annotation
more info
 
oxidation-reduction process IEA
Inferred from Electronic Annotation
more info
 
positive regulation of transcription from RNA polymerase II promoter IEA
Inferred from Electronic Annotation
more info
 
positive regulation of transcription, DNA-templated IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of stem cell population maintenance IEA
Inferred from Electronic Annotation
more info
 
response to hypoxia IEA
Inferred from Electronic Annotation
more info
 
spermatid nucleus elongation IEA
Inferred from Electronic Annotation
more info
 
transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cytoplasm IEA
Inferred from Electronic Annotation
more info
 
membrane IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
Preferred Names
lysine-specific demethylase 3A
Names
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

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
    5502..57070
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001146688.1NP_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
    Q9Y4C1
    Related
    ENSP00000386516, OTTHUMP00000203309, ENST00000409064, OTTHUMT00000329983
    Conserved Domains (2) summary
    smart00558
    Location:10641134
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    cl22893
    Location:11511264
    JmjC; JmjC domain, hydroxylase
  2. NM_018433.5NP_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
    Q9Y4C1
    Related
    ENSP00000323659, ENST00000312912
    Conserved Domains (2) summary
    smart00558
    Location:10641134
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    cl22893
    Location:11511264
    JmjC; JmjC domain, hydroxylase

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 107 details...

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p2 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p2 Primary Assembly

    Range
    86440647..86492716
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011532985.1XP_011531287.1  

    See identical proteins and their annotated locations for XP_011531287.1

    Conserved Domains (2) summary
    smart00558
    Location:10791149
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    cl22893
    Location:11661279
    JmjC; JmjC domain, hydroxylase
  2. XM_011532984.1XP_011531286.1  

    See identical proteins and their annotated locations for XP_011531286.1

    Conserved Domains (2) summary
    smart00558
    Location:10791149
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    cl22893
    Location:11661279
    JmjC; JmjC domain, hydroxylase
  3. XM_011532986.1XP_011531288.1  

    Conserved Domains (2) summary
    smart00558
    Location:794864
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    cl22893
    Location:881994
    JmjC; JmjC domain, hydroxylase
  4. XM_006712051.2XP_006712114.1  

    Conserved Domains (2) summary
    smart00558
    Location:404474
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    cl22893
    Location:491604
    JmjC; JmjC domain, hydroxylase

Alternate CHM1_1.1

Genomic

  1. NC_018913.2 Alternate CHM1_1.1

    Range
    86598317..86649908
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)