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    Kdm1a lysine demethylase 1A [ Rattus norvegicus (Norway rat) ]

    Gene ID: 500569, updated on 9-Dec-2024

    Summary

    Official Symbol
    Kdm1aprovided by RGD
    Official Full Name
    lysine demethylase 1Aprovided by RGD
    Primary source
    RGD:1562975
    See related
    EnsemblRapid:ENSRNOG00000022372 AllianceGenome:RGD:1562975
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Aof2; Kdm1; RGD1562975
    Summary
    Enables chromatin binding activity. Involved in several processes, including cellular response to cAMP; nervous system development; and positive regulation of cell size. Located in chromatin. Biomarker of breast cancer; diabetic retinopathy; schizophrenia; and transient cerebral ischemia. Orthologous to human KDM1A (lysine demethylase 1A). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Thymus (RPKM 190.0), Brain (RPKM 146.9) and 9 other tissues See more
    Orthologs
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    Genomic context

    See Kdm1a in Genome Data Viewer
    Location:
    5q36
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 5 NC_086023.1 (154066436..154121913, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 5 NC_051340.1 (148782976..148838319, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 5 NC_005104.4 (154909003..154965171, complement)

    Chromosome 5 - NC_086023.1Genomic Context describing neighboring genes Neighboring gene 5-hydroxytryptamine receptor 1D Neighboring gene aminoacyl tRNA synthase complex-interacting multifunctional protein 1-like Neighboring gene leucine zipper protein 1 Neighboring gene uncharacterized LOC120103012 Neighboring gene testis expressed 46 Neighboring gene lactamase beta like 1

    Genomic regions, transcripts, and products

    Expression

    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Interactions

    General gene information

    Gene Ontology Provided by RGD

    Items 1 - 25 of 29
    Function Evidence Code Pubs
    enables DNA-binding transcription factor binding  
    enables FAD-dependent H3K4me/H3K4me3 demethylase activity  
    enables FAD-dependent H3K4me/H3K4me3 demethylase activity  
    enables MRF binding  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding  
    enables RNA polymerase II-specific DNA-binding transcription factor binding  
    enables chromatin binding  
    enables chromatin binding PubMed 
    enables chromatin binding  
    enables demethylase activity  
    enables enzyme binding  
    enables flavin adenine dinucleotide binding  
    enables flavin adenine dinucleotide binding  
    enables histone H3K4 demethylase activity  
    enables histone H3K9 demethylase activity  
    enables histone H3K9me2/H3K9me3 demethylase activity  
    enables histone demethylase activity  
    enables identical protein binding  
    enables lncRNA binding  
    enables nuclear androgen receptor binding  
    enables nuclear receptor coactivator activity  
    enables oxidoreductase activity  
    enables p53 binding  
    enables promoter-specific chromatin binding  
    enables protein binding PubMed 
    NOT enables telomeric DNA binding  
    enables telomeric repeat-containing RNA binding  
    enables transcription coactivator activity  
    enables transcription corepressor activity  
    Items 1 - 25 of 29
    Items 1 - 25 of 46
    Process Evidence Code Pubs
    acts_upstream_of_or_within DNA repair-dependent chromatin remodeling  
    acts_upstream_of_or_within cell differentiation  
    acts_upstream_of_or_within cellular response to UV  
    involved_in cellular response to cAMP PubMed 
    acts_upstream_of_or_within cellular response to gamma radiation  
    involved_in cerebral cortex development PubMed 
    involved_in epigenetic regulation of gene expression  
    involved_in granulocyte differentiation  
    involved_in guanine metabolic process PubMed 
    involved_in muscle cell development  
    involved_in negative regulation of DNA damage response, signal transduction by p53 class mediator  
    involved_in negative regulation of DNA-binding transcription factor activity  
    involved_in negative regulation of DNA-templated transcription  
    involved_in negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator  
    acts_upstream_of_or_within negative regulation of neurogenesis  
    acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II  
    involved_in negative regulation of transcription by RNA polymerase II  
    involved_in negative regulation of transcription initiation-coupled chromatin remodeling  
    involved_in neuron maturation PubMed 
    acts_upstream_of_or_within neuron projection extension  
    acts_upstream_of_or_within pituitary gland development  
    involved_in positive regulation of cell size PubMed 
    involved_in positive regulation of cold-induced thermogenesis  
    involved_in positive regulation of cold-induced thermogenesis PubMed 
    involved_in positive regulation of epithelial to mesenchymal transition  
    involved_in positive regulation of erythrocyte differentiation  
    involved_in positive regulation of megakaryocyte differentiation  
    involved_in positive regulation of neural precursor cell proliferation  
    involved_in positive regulation of neuroblast proliferation  
    involved_in positive regulation of neuron projection development PubMed 
    acts_upstream_of_or_within positive regulation of protein ubiquitination  
    involved_in positive regulation of stem cell proliferation  
    involved_in positive regulation of transcription by RNA polymerase II PubMed 
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II  
    involved_in positive regulation of transcription by RNA polymerase II  
    involved_in protein demethylation  
    involved_in protein modification process PubMed 
    involved_in protein modification process PubMed 
    acts_upstream_of_or_within regulation of double-strand break repair via homologous recombination  
    acts_upstream_of_or_within regulation of neurogenesis  
    involved_in regulation of primitive erythrocyte differentiation  
    acts_upstream_of_or_within regulation of protein localization  
    involved_in regulation of transcription by RNA polymerase II  
    involved_in response to fungicide PubMed 
    involved_in response to organic cyclic compound PubMed 
    acts_upstream_of transcription by RNA polymerase II  
    Items 1 - 25 of 46
    Component Evidence Code Pubs
    part_of DNA repair complex  
    located_in chromatin  
    located_in chromatin PubMed 
    is_active_in chromatin  
    located_in chromatin  
    located_in chromosome, telomeric region  
    located_in nucleoplasm  
    located_in nucleoplasm  
    is_active_in nucleus  
    is_active_in nucleus  
    located_in nucleus  
    part_of protein-containing complex  

    General protein information

    Preferred Names
    lysine-specific histone demethylase 1A
    Names
    amine oxidase (flavin containing) domain 2
    lysine (K)-specific demethylase 1
    lysine (K)-specific demethylase 1A
    neuroprotective protein 3
    NP_001123570.1
    XP_038966552.1

    NCBI Reference Sequences (RefSeq)

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    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_001130098.1NP_001123570.1  lysine-specific histone demethylase 1A

      See identical proteins and their annotated locations for NP_001123570.1

      Status: PROVISIONAL

      Source sequence(s)
      EF688598
      UniProtKB/TrEMBL
      A6ITB7, B3STT9, F1MA31
      Related
      ENSRNOP00000052846.5, ENSRNOT00000055992.6
      Conserved Domains (2) summary
      PLN02328
      Location:203845
      PLN02328; lysine-specific histone demethylase 1 homolog
      PHA03378
      Location:3898
      PHA03378; EBNA-3B; Provisional

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086023.1 Reference GRCr8

      Range
      154066436..154121913 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039110624.2XP_038966552.1  lysine-specific histone demethylase 1A isoform X1

      UniProtKB/TrEMBL
      A0A8I6G2K8, A6ITB7
      Related
      ENSRNOP00000078937.2, ENSRNOT00000115653.2
      Conserved Domains (2) summary
      PLN02328
      Location:183825
      PLN02328; lysine-specific histone demethylase 1 homolog
      PHA03378
      Location:3898
      PHA03378; EBNA-3B; Provisional
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