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    KDM1B lysine (K)-specific demethylase 1B [ Homo sapiens ]

    Gene ID: 221656, updated on 11-May-2012
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    Summary

    Official Symbol
    KDM1Bprovided by HGNC
    Official Full Name
    lysine (K)-specific demethylase 1Bprovided by HGNC
    Primary source
    HGNC:21577
    Locus tag
    RP1-298J15.1
    See related
    Ensembl:ENSG00000165097; HPRD:18524; MIM:613081; Vega:OTTHUMG00000014316
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    AOF1; LSD2; C6orf193; bA204B7.3; dJ298J15.2; FLJ33898; FLJ34109; FLJ43328; DKFZp686I0412
    Summary
    Flavin-dependent histone demethylases, such as KDM1B, regulate histone lysine methylation, an epigenetic mark that regulates gene expression and chromatin function (Karytinos et al., 2009 [PubMed 19407342]).[supplied by OMIM, Oct 2009]
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    Genomic context

    Location :
    6p22.3
    Sequence :
    Chromosome: 6; NC_000006.11 (18155619..18224084)
    See KDM1B in Epigenomics, MapViewer

    Chromosome 6 - NC_000006.11Genomic Context describing neighboring genes Neighboring gene NHL repeat containing 1 Neighboring gene thiopurine S-methyltransferase Neighboring gene DEK oncogene Neighboring gene DEAD (Asp-Glu-Ala-Asp) box polypeptide 18 pseudogene 3

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    Genomic regions, transcripts, and products

    Go to nucleotideGraphics FASTA GenBank

    Go to reference sequence details
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    Bibliography

    Related articles in PubMed

    1. Systematic and quantitative assessment of the ubiquitin-modified proteome. Kim W, et al. Mol Cell, 2011 Oct 21. PMID 21906983.
    2. A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. Wagner SA, et al. Mol Cell Proteomics, 2011 Oct. PMID 21890473.
    3. Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level. Danielsen JM, et al. Mol Cell Proteomics, 2011 Mar. PMID 21139048.
    4. The ubiquitin carboxyl hydrolase BAP1 forms a ternary complex with YY1 and HCF-1 and is a critical regulator of gene expression. Yu H, et al. Mol Cell Biol, 2010 Nov. PMID 20805357.
    5. Human LSD2/KDM1b/AOF1 regulates gene transcription by modulating intragenic H3K4me2 methylation. Fang R, et al. Mol Cell, 2010 Jul 30. PMID 20670891.

    See all (15) citations in PubMed

    GeneRIFs: Gene References Into Functions What's a GeneRIF?

    1. Human LSD2/KDM1b/AOF1 regulates gene transcription by modulating intragenic H3K4me2 methylation.
      Title: Human LSD2/KDM1b/AOF1 regulates gene transcription by modulating intragenic H3K4me2 methylation.
    Submit: New GeneRIF Correction
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    Phenotypes

    Review eQTL and phenotype association data in this region using PheGenI

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    Interactions

    Products Interactant Other Gene Complex Source Pubs Description
    BioGRID:128743 BioGRID:113911 BAP1    BioGRID  PubMed Affinity Capture-MS; Co-purification 
    BioGRID:128743 BioGRID:107343 CCNT1    BioGRID  PubMed Affinity Capture-MS; Affinity Capture-Western 
    BioGRID:128743 BioGRID:116123 EHMT2    BioGRID  PubMed Affinity Capture-MS; Affinity Capture-Western 
    BioGRID:128743 BioGRID:116625 PAXIP1    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:128743 BioGRID:113871 SMC1A    BioGRID  PubMed Affinity Capture-Western 
    BioGRID:128743 BioGRID:113164 UBC    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:128743 BioGRID:116272 WDR5    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:128743 BioGRID:120250 WHSC1L1    BioGRID  PubMed Affinity Capture-MS; Affinity Capture-Western 
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    General gene information

    Markers

    Genotypes

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    flavin adenine dinucleotide binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    histone demethylase activity (H3-dimethyl-K4 specific) IEA
    Inferred from Electronic Annotation
    more info
    		  
    histone demethylase activity (H3-dimethyl-K4 specific) ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    histone demethylase activity (H3-monomethyl-K4 specific) IEA
    Inferred from Electronic Annotation
    more info
    		  
    histone demethylase activity (H3-monomethyl-K4 specific) ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    oxidoreductase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    DNA methylation involved in gamete generation IEA
    Inferred from Electronic Annotation
    more info
    		  
    chromatin modification IEA
    Inferred from Electronic Annotation
    more info
    		  
    histone H3-K4 demethylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    histone H3-K4 demethylation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    multicellular organismal development IEA
    Inferred from Electronic Annotation
    more info
    		  
    regulation of DNA methylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    regulation of DNA methylation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    regulation of gene expression by genetic imprinting IEA
    Inferred from Electronic Annotation
    more info
    		  
    regulation of gene expression by genetic imprinting ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    regulation of transcription, DNA-dependent IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  
    nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
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    General protein information

    Preferred Names
    lysine-specific histone demethylase 1B
    Names
    lysine-specific histone demethylase 1B
    amine oxidase, flavin containing 1
    lysine-specific histone demethylase 2
    amine oxidase (flavin containing) domain 1
    flavin-containing amine oxidase domain-containing protein 1
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    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.

    mRNA and Protein(s)

    1. NM_153042.3 → NP_694587.3  lysine-specific histone demethylase 1B

      Status: VALIDATED

      Source sequence(s)
      AA332652, AJ420481, AK125318, AL031774, DA099422
      Consensus CDS
      CCDS34343.1
      UniProtKB/TrEMBL
      A2A2C6
      UniProtKB/Swiss-Prot
      Q8NB78
      Related
      ENSP00000297792, OTTHUMP00000179124, ENST00000297792, OTTHUMT00000277080
      Conserved Domains (3) summary
      pfam01593
      Location:267 – 322
      Blast Score: 161
      Amino_oxidase; Flavin containing amine oxidoreductase
      pfam07496
      Location:137 – 192
      Blast Score: 132
      zf-CW; CW-type Zinc Finger
      cl09931
      Location:336 – 587
      Blast Score: 303
      NADB_Rossmann; Rossmann-fold NAD(P)(+)-binding proteins

    RefSeqs of Annotated Genomes: Build 37.3

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

    Reference GRCh37.p5 Primary Assembly

    Genomic

    1. NC_000006.11 Reference GRCh37.p5 Primary Assembly

      Range
      18155619..18224084
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate HuRef

    Genomic

    1. AC_000138.1 Alternate HuRef

      Range
      18099960..18168421
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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    Related Sequences

    Nucleotide Protein
    Heading Accession and Version
    genomic AL031774.1 CAM28215.1
      CAM28216.1
      CAM28217.1
    genomic AL031774.1 CAM28215.1
      CAM28216.1
      CAM28217.1
    genomic AL589723.7 CAM14159.1
    genomic CH471087.1 EAW55400.1
      EAW55401.1
    mRNA AA332652.1 None
    mRNA AJ420481.1 None
    mRNA AK091217.1 BAC03612.1
    mRNA AK125318.1 BAC86124.1
    mRNA BC113093.1 AAI13094.1
    mRNA CR627410.1 CAH10499.1
    mRNA DA099422.1 None
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q08EI0 GenPept UniProtKB/TrEMBL:Q08EI0
    Q8NB78.3 GenPept UniProtKB/Swiss-Prot:Q8NB78
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    Additional Links

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials
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