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    Kdm1b lysine demethylase 1B [ Rattus norvegicus (Norway rat) ]

    Gene ID: 306819, updated on 11-Apr-2024

    Summary

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    Official Symbol
    Kdm1bprovided by RGD
    Official Full Name
    lysine demethylase 1Bprovided by RGD
    Primary source
    RGD:1310701
    See related
    Ensembl:ENSRNOG00000016519 AllianceGenome:RGD:1310701
    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
    Aof1
    Summary
    Predicted to enable several functions, including FAD binding activity; histone H3-di/monomethyl-lysine-4 FAD-dependent demethylase activity; and zinc ion binding activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II; positive regulation of transcription by RNA polymerase II; and regulation of DNA methylation. Predicted to act upstream of or within DNA methylation involved in gamete generation; histone H3-K4 demethylation; and regulation of gene expression by genetic imprinting. Predicted to be located in nucleoplasm. Predicted to be part of nucleosome. Orthologous to human KDM1B (lysine demethylase 1B). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Thymus (RPKM 137.4), Kidney (RPKM 131.9) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Kdm1b in Genome Data Viewer
    Location:
    17p14
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 17 NC_086035.1 (17809232..17850141, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 17 NC_051352.1 (17602961..17643865, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 17 NC_005116.4 (17987972..18028808, complement)

    Chromosome 17 - NC_086035.1Genomic Context describing neighboring genes Neighboring gene ring finger protein 144B Neighboring gene small nucleolar RNA U13 Neighboring gene DEK proto-oncogene Neighboring gene NLR family, pyrin domain containing 4E like, pseudogene 1 Neighboring gene thiopurine S-methyltransferase Neighboring gene NHL repeat containing E3 ubiquitin protein ligase 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. Structure-function analysis reveals a novel mechanism for regulation of histone demethylase LSD2/AOF1/KDM1b. Zhang Q, et al. Cell Res, 2013 Feb. PMID 23266887, Free PMC Article
    2. A novel mammalian flavin-dependent histone demethylase. Karytinos A, et al. J Biol Chem, 2009 Jun 26. PMID 19407342, Free PMC Article
    3. LSD2/KDM1B and its cofactor NPAC/GLYR1 endow a structural and molecular model for regulation of H3K4 demethylation. Fang R, et al. Mol Cell, 2013 Feb 7. PMID 23260659, Free PMC Article
    4. Expression analysis of 6p22 genomic gain in retinoblastoma. Orlic M, et al. Genes Chromosomes Cancer, 2006 Jan. PMID 16180235
    5. KDM1B is a histone H3K4 demethylase required to establish maternal genomic imprints. Ciccone DN, et al. Nature, 2009 Sep 17. PMID 19727073

    See all (7) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables FAD binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables FAD-dependent H3K4me/H3K4me3 demethylase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables chromatin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables flavin adenine dinucleotide binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables flavin adenine dinucleotide binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables histone H3K4 demethylase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    NOT enables histone H3K4me/H3K4me2/H3K4me3 demethylase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables histone binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables oxidoreductase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables transcription factor binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables zinc ion binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    involved_in chromatin remodeling IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within chromatin remodeling ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within epigenetic programing of female pronucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within genomic imprinting ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in transcription initiation-coupled chromatin remodeling ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    part_of chromatin ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of nucleosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    lysine-specific histone demethylase 2
    Names
    amine oxidase (flavin containing) domain 1
    amine oxidase, flavin containing 1
    lysine (K)-specific demethylase 1B
    lysine-specific histone demethylase 1B
    NP_001100813.1
    XP_063132443.1

    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_001107343.1 → NP_001100813.1  lysine-specific histone demethylase 2

      See identical proteins and their annotated locations for NP_001100813.1

      Status: PROVISIONAL

      Source sequence(s)
      CH473977
      UniProtKB/TrEMBL
      A6J705, D3ZP89
      Related
      ENSRNOP00000022244.3, ENSRNOT00000022244.4
      Conserved Domains (2) summary
      PLN02328
      Location:306 → 821
      PLN02328; lysine-specific histone demethylase 1 homolog
      pfam07496
      Location:138 → 191
      zf-CW; CW-type Zinc Finger

    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_086035.1 Reference GRCr8

      Range
      17809232..17850141 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063276373.1 → XP_063132443.1  lysine-specific histone demethylase 2 isoform X1

    RNA

    1. XR_005495273.2 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

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    Chemical Information
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