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

Gene ID: 55818, updated on 21-Oct-2019

Summary

Official Symbol
KDM3Aprovided by HGNC
Official Full Name
lysine demethylase 3Aprovided by HGNC
Primary source
HGNC:HGNC:20815
See related
Ensembl:ENSG00000115548 MIM:611512
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]
Expression
Ubiquitous expression in testis (RPKM 32.2), bone marrow (RPKM 27.1) and 25 other tissues See more
Orthologs

Genomic context

See KDM3A in Genome Data Viewer
Location:
2p11.2
Exon count:
28
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 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 Sharpr-MPRA regulatory region 10968 Neighboring gene mitochondrial ribosomal protein L35 Neighboring gene receptor accessory protein 1 Neighboring gene RNF103-CHMP3 readthrough Neighboring gene RNA, U6 small nuclear 640, pseudogene Neighboring gene charged multivesicular body protein 3 Neighboring gene uncharacterized LOC105374845 Neighboring gene Sharpr-MPRA regulatory region 1991

Genomic regions, transcripts, and products

Expression

  • Project title: 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pathways from BioSystems

  • 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...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA0742, DKFZp686A24246, DKFZp686P07111

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA-binding transcription factor activity IEA
Inferred from Electronic Annotation
more info
 
RNA polymerase II core promoter sequence-specific DNA binding IEA
Inferred from Electronic Annotation
more info
 
androgen receptor binding IDA
Inferred from Direct Assay
more info
PubMed 
chromatin DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
dioxygenase activity IEA
Inferred from Electronic Annotation
more info
 
histone demethylase activity (H3-K9 specific) IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone demethylase activity (H3-K9 specific) IMP
Inferred from Mutant Phenotype
more info
PubMed 
iron ion binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
transcription regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
androgen receptor signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
cellular response to leukemia inhibitory factor IEA
Inferred from Electronic Annotation
more info
 
formaldehyde biosynthetic process IDA
Inferred from Direct Assay
more info
PubMed 
histone H3-K9 demethylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone H3-K9 demethylation IDA
Inferred from Direct Assay
more info
PubMed 
histone H3-K9 demethylation IMP
Inferred from Mutant Phenotype
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 
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 cold-induced thermogenesis ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
positive regulation of transcription by RNA polymerase II 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 differentiation IEA
Inferred from Electronic Annotation
more info
 
regulation of stem cell population maintenance IEA
Inferred from Electronic Annotation
more info
 
spermatid nucleus elongation IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
chromatin IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytoplasm IEA
Inferred from Electronic Annotation
more info
 
membrane HDA PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

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

NCBI Reference Sequences (RefSeq)

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_001146688.1NP_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
    ENSP00000386516.1, ENST00000409064.5
    Conserved Domains (2) summary
    smart00558
    Location:10641134
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    cl21464
    Location:11511264
    cupin_like; Conserved domain found in cupin and related proteins
  2. NM_018433.6NP_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
    ENSP00000323659.5, ENST00000312912.10
    Conserved Domains (2) summary
    smart00558
    Location:10641134
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    cl21464
    Location:11511264
    cupin_like; Conserved domain found in cupin and related proteins

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20190905

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p13 Primary Assembly

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

mRNA and Protein(s)

  1. XM_024452995.1XP_024308763.1  lysine-specific demethylase 3A isoform X1

    Conserved Domains (3) summary
    smart00558
    Location:10641134
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    pfam07964
    Location:748936
    Red1; Rec10 / Red1
    cl21464
    Location:11511258
    cupin_like; Conserved domain found in cupin and related proteins
  2. XM_024452994.1XP_024308762.1  lysine-specific demethylase 3A isoform X1

    Conserved Domains (3) summary
    smart00558
    Location:10641134
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    pfam07964
    Location:748936
    Red1; Rec10 / Red1
    cl21464
    Location:11511258
    cupin_like; Conserved domain found in cupin and related proteins
  3. XM_017004494.1XP_016859983.1  lysine-specific demethylase 3A isoform X3

  4. XM_006712051.4XP_006712114.1  lysine-specific demethylase 3A isoform X5

    Conserved Domains (2) summary
    smart00558
    Location:404474
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    cl21464
    Location:491604
    cupin_like; Conserved domain found in cupin and related proteins
  5. XM_024452996.1XP_024308764.1  lysine-specific demethylase 3A isoform X2

    Conserved Domains (3) summary
    smart00558
    Location:779849
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    pfam07964
    Location:463651
    Red1; Rec10 / Red1
    cl21464
    Location:866973
    cupin_like; Conserved domain found in cupin and related proteins
  6. XM_024452997.1XP_024308765.1  lysine-specific demethylase 3A isoform X4

    Conserved Domains (3) summary
    smart00558
    Location:404474
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    pfam07964
    Location:88276
    Red1; Rec10 / Red1
    cl21464
    Location:491598
    cupin_like; Conserved domain found in cupin and related proteins
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