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KDM1A lysine demethylase 1A [ Homo sapiens (human) ]

Gene ID: 23028, updated on 11-Oct-2020

Summary

Official Symbol
KDM1Aprovided by HGNC
Official Full Name
lysine demethylase 1Aprovided by HGNC
Primary source
HGNC:HGNC:29079
See related
Ensembl:ENSG00000004487 MIM:609132
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
AOF2; CPRF; KDM1; LSD1; BHC110
Summary
This gene encodes a nuclear protein containing a SWIRM domain, a FAD-binding motif, and an amine oxidase domain. This protein is a component of several histone deacetylase complexes, though it silences genes by functioning as a histone demethylase. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2009]
Expression
Broad expression in testis (RPKM 45.8), endometrium (RPKM 15.8) and 25 other tissues See more
Orthologs

Genomic context

See KDM1A in Genome Data Viewer
Location:
1p36.12
Exon count:
21
Annotation release Status Assembly Chr Location
109.20200815 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (23019443..23083691)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (23345937..23410184)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene lactamase beta like 1 Neighboring gene testis expressed 46 Neighboring gene microRNA 3115 Neighboring gene leucine zipper protein 1 Neighboring gene RNA, U6 small nuclear 514, pseudogene Neighboring gene RNA, U6 small nuclear 135, pseudogene

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?

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Tat tat LSD1/KDM1 demethylates HIV-1 Tat at position K51 in vitro and in cells PubMed
tat LSD1 interacts with CTIP2 and co-localizes with HIV-1 Tat. LSD1 is required for CTIP2 recruitment at the HIV-1 proximal promoter to repress HIV-1 replication and transcription PubMed
tat LSD1/KDM1 and CoREST proteins are recruited to the HIV-1 LTR in response to HIV-1 Tat and formation of the LSD1/KDM1/CoREST complex functions as a co-activator of HIV-1 transcription PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA0601

Gene Ontology Provided by GOA

Function Evidence Code Pubs
MRF binding IDA
Inferred from Direct Assay
more info
PubMed 
RNA polymerase II transcription factor binding ISS
Inferred from Sequence or Structural Similarity
more info
 
androgen receptor binding IDA
Inferred from Direct Assay
more info
PubMed 
chromatin binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
chromatin binding IDA
Inferred from Direct Assay
more info
PubMed 
demethylase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
enzyme binding IPI
Inferred from Physical Interaction
more info
PubMed 
flavin adenine dinucleotide binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
flavin adenine dinucleotide binding IDA
Inferred from Direct Assay
more info
PubMed 
histone demethylase activity EXP
Inferred from Experiment
more info
PubMed 
histone demethylase activity IDA
Inferred from Direct Assay
more info
PubMed 
histone demethylase activity (H3-K4 specific) IDA
Inferred from Direct Assay
more info
PubMed 
histone demethylase activity (H3-K9 specific) IDA
Inferred from Direct Assay
more info
PubMed 
histone demethylase activity (H3-K9 specific) TAS
Traceable Author Statement
more info
 
histone demethylase activity (H3-dimethyl-K4 specific) IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone demethylase activity (H3-dimethyl-K4 specific) IDA
Inferred from Direct Assay
more info
PubMed 
nuclear receptor transcription coactivator activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
oxidoreductase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
oxidoreductase activity IDA
Inferred from Direct Assay
more info
PubMed 
p53 binding IPI
Inferred from Physical Interaction
more info
PubMed 
promoter-specific chromatin binding ISS
Inferred from Sequence or Structural Similarity
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
NOT telomeric DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
telomeric repeat-containing RNA binding IDA
Inferred from Direct Assay
more info
PubMed 
transcription factor binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
transcription factor binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
alternative mRNA splicing, via spliceosome IEA
Inferred from Electronic Annotation
more info
 
blood coagulation TAS
Traceable Author Statement
more info
 
cellular response to UV IDA
Inferred from Direct Assay
more info
PubMed 
cellular response to cAMP IEA
Inferred from Electronic Annotation
more info
 
cellular response to gamma radiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
cerebral cortex development IEA
Inferred from Electronic Annotation
more info
 
guanine metabolic process IEA
Inferred from Electronic Annotation
more info
 
histone H3-K4 demethylation IDA
Inferred from Direct Assay
more info
PubMed 
histone H3-K9 demethylation IDA
Inferred from Direct Assay
more info
PubMed 
muscle cell development ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
negative regulation of DNA binding IC
Inferred by Curator
more info
PubMed 
negative regulation of DNA damage response, signal transduction by p53 class mediator IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of DNA-binding transcription factor activity IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of DNA-binding transcription factor activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of histone H3-K4 methylation ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of histone H3-K9 methylation ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of protein binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of transcription by RNA polymerase II ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
neuron maturation IEA
Inferred from Electronic Annotation
more info
 
oxidation-reduction process IEA
Inferred from Electronic Annotation
more info
 
positive regulation of DNA-binding transcription factor activity IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of cell size IEA
Inferred from Electronic Annotation
more info
 
positive regulation of chromatin binding 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 histone ubiquitination IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of neural precursor cell proliferation ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of neuroblast proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of neuron projection development IEA
Inferred from Electronic Annotation
more info
 
positive regulation of stem cell proliferation ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
protein demethylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of cellular protein localization IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of double-strand break repair via homologous recombination IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
response to fungicide IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
DNA repair complex IDA
Inferred from Direct Assay
more info
PubMed 
nuclear chromatin IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nuclear chromatin IDA
Inferred from Direct Assay
more info
PubMed 
nuclear chromatin ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
nuclear chromosome, telomeric region IDA
Inferred from Direct Assay
more info
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 
protein-containing complex IDA
Inferred from Direct Assay
more info
PubMed 
transcription factor complex ISS
Inferred from Sequence or Structural Similarity
more info
 

General protein information

Preferred Names
lysine-specific histone demethylase 1A
Names
BRAF35-HDAC complex protein BHC110
FAD-binding protein BRAF35-HDAC complex, 110 kDa subunit
[histone H3]-dimethyl-L-lysine(4) FAD-dependent demethylase 1A
amine oxidase (flavin containing) domain 2
flavin-containing amine oxidase domain-containing protein 2
lysine (K)-specific demethylase 1A
lysine-specific histone demethylase 1
NP_001009999.1
NP_001350583.1
NP_055828.2
XP_005245843.1
XP_006710536.1
XP_006710537.1
XP_016856205.1
XP_016856206.1

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_047129.1 RefSeqGene

    Range
    5026..69247
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001009999.3NP_001009999.1  lysine-specific histone demethylase 1A isoform a

    See identical proteins and their annotated locations for NP_001009999.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
    Source sequence(s)
    BC025362, BC040194, BC048134, BG717076
    Consensus CDS
    CCDS53278.1
    UniProtKB/Swiss-Prot
    O60341
    Related
    ENSP00000383042.4, ENST00000400181.8
    Conserved Domains (4) summary
    pfam01593
    Location:308849
    Amino_oxidase; Flavin containing amine oxidoreductase
    pfam04433
    Location:197284
    SWIRM; SWIRM domain
    pfam13450
    Location:303361
    NAD_binding_8; NAD(P)-binding Rossmann-like domain
    cl21568
    Location:391495
    SurA_N_3; SurA N-terminal domain
  2. NM_001363654.2NP_001350583.1  lysine-specific histone demethylase 1A isoform c

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks two alternate in-frame exons and uses an alternate in-frame splice for a 3' exon, compared to variant 1. The encoded protein (isoform c) is shorter than isoform a.
    Source sequence(s)
    AL031428
    Consensus CDS
    CCDS85939.1
    Related
    ENSP00000473297.2, ENST00000465864.2
    Conserved Domains (2) summary
    cl27535
    Location:183831
    Amino_oxidase; Flavin containing amine oxidoreductase
    cl27975
    Location:2398
    EBV-NA3; Epstein-Barr virus nuclear antigen 3 (EBNA-3)
  3. NM_015013.4NP_055828.2  lysine-specific histone demethylase 1A isoform b

    See identical proteins and their annotated locations for NP_055828.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks two alternate in-frame exons, compared to variant 1. The encoded protein (isoform b) is shorter than isoform a.
    Source sequence(s)
    AB011173, BC025362, BG717076
    Consensus CDS
    CCDS30627.1
    UniProtKB/Swiss-Prot
    O60341
    Related
    ENSP00000349049.3, ENST00000356634.7
    Conserved Domains (2) summary
    cl27535
    Location:183825
    Amino_oxidase; Flavin containing amine oxidoreductase
    cl27975
    Location:2398
    EBV-NA3; Epstein-Barr virus nuclear antigen 3 (EBNA-3)

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20200815

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    23019443..23083691
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006710474.3XP_006710537.1  lysine-specific histone demethylase 1A isoform X1

    Conserved Domains (5) summary
    pfam01593
    Location:308851
    Amino_oxidase; Flavin containing amine oxidoreductase
    pfam04433
    Location:197284
    SWIRM; SWIRM domain
    pfam13450
    Location:303361
    NAD_binding_8; NAD(P)-binding Rossmann-like domain
    cl17182
    Location:441549
    NAT_SF; N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate
    cl21568
    Location:395491
    SurA_N_3; SurA N-terminal domain
  2. XM_017000716.1XP_016856205.1  lysine-specific histone demethylase 1A isoform X5

  3. XM_005245786.2XP_005245843.1  lysine-specific histone demethylase 1A isoform X2

    See identical proteins and their annotated locations for XP_005245843.1

    Conserved Domains (4) summary
    pfam01593
    Location:308845
    Amino_oxidase; Flavin containing amine oxidoreductase
    pfam04433
    Location:197284
    SWIRM; SWIRM domain
    pfam13450
    Location:303361
    NAD_binding_8; NAD(P)-binding Rossmann-like domain
    cl21568
    Location:395491
    SurA_N_3; SurA N-terminal domain
  4. XM_017000717.1XP_016856206.1  lysine-specific histone demethylase 1A isoform X6

  5. XM_006710473.3XP_006710536.1  lysine-specific histone demethylase 1A isoform X4

    Conserved Domains (4) summary
    smart00150
    Location:430532
    SPEC; Spectrin repeats
    pfam01593
    Location:308809
    Amino_oxidase; Flavin containing amine oxidoreductase
    pfam04433
    Location:197284
    SWIRM; SWIRM domain
    pfam13450
    Location:303361
    NAD_binding_8; NAD(P)-binding Rossmann-like domain
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