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    Kdm1b lysine (K)-specific demethylase 1B [ Mus musculus (house mouse) ]

    Gene ID: 218214, updated on 14-Nov-2024

    Summary

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    Official Symbol
    Kdm1bprovided by MGI
    Official Full Name
    lysine (K)-specific demethylase 1Bprovided by MGI
    Primary source
    MGI:MGI:2145261
    See related
    Ensembl:ENSMUSG00000038080 AllianceGenome:MGI:2145261
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Aof1; 4632428N09Rik
    Summary
    Enables FAD-dependent H3K4me/H3K4me3 demethylase activity; flavin adenine dinucleotide binding activity; and zinc ion binding activity. Involved in genomic imprinting. Acts upstream of or within epigenetic programing of female pronucleus. Located in nucleus. Is expressed in several structures, including alimentary system; genitourinary system; integumental system; nervous system; and sensory organ. Orthologous to human KDM1B (lysine demethylase 1B). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in bladder adult (RPKM 25.1), liver E14 (RPKM 13.2) and 27 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Kdm1b in Genome Data Viewer
    Location:
    13 A5; 13 24.5 cM
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 13 NC_000079.7 (47196849..47238085)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 13 NC_000079.6 (47043373..47085279)

    Chromosome 13 - NC_000079.7Genomic Context describing neighboring genes Neighboring gene NHL repeat containing 1 Neighboring gene NLR family, pyrin domain containing 4B pseudogene Neighboring gene STARR-positive B cell enhancer ABC_E1875 Neighboring gene thiopurine methyltransferase Neighboring gene DEK proto-oncogene Neighboring gene STARR-seq mESC enhancer starr_34433 Neighboring gene predicted gene, 40935 Neighboring gene ring finger protein 144B

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Loss of the Maternal Effect Gene Nlrp2 Alters the Transcriptome of Ovulated Mouse Oocytes and Impacts Expression of Histone Demethylase KDM1B.
      Title: Loss of the Maternal Effect Gene Nlrp2 Alters the Transcriptome of Ovulated Mouse Oocytes and Impacts Expression of Histone Demethylase KDM1B.
    2. Lysine Demethylase 1B Promotes Tear Secretion Disorder in Sjogren's Syndrome by Regulating the PAX6/CLU Axis.
      Title: Lysine Demethylase 1B Promotes Tear Secretion Disorder in Sjogren's Syndrome by Regulating the PAX6/CLU Axis.
    3. reveal a direct role of hypoxia-inducible factor in regulating miRNA biogenesis and consequently activating the miR-215-KDM1B-mediated signaling required for glioma-initiating cells adaptation to hypoxia
      Title: MiR-215 Is Induced Post-transcriptionally via HIF-Drosha Complex and Mediates Glioma-Initiating Cell Adaptation to Hypoxia by Targeting KDM1B.
    4. Data indicate that Myst4, Jmjd2b, Aof1 genes are regulated by H3K9me under hyperinsulinemia/hyperglycemia.
      Title: Histone H3 lysine 4 monomethylation (H3K4me1) and H3 lysine 9 monomethylation (H3K9me1): distribution and their association in regulating gene expression under hyperglycaemic/hyperinsulinemic conditions in 3T3 cells.
    5. AOF1 is the second histone demethylase in the family of flavin-dependent amine oxidases and reveals a demethylase-independent repression function.
      Title: AOF1 is a histone H3K4 demethylase possessing demethylase activity-independent repression function.
    6. oocytes from KDM1B-deficient females showed a substantial increase in H3K4 methylation and failed to set up the DNA methylation marks at four out of seven imprinted genes examined
      Title: KDM1B is a histone H3K4 demethylase required to establish maternal genomic imprints.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (1) 
    • Gene trapped (1) 
    • Targeted (2)  1 citation

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC38211

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables FAD binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables FAD binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables FAD-dependent H3K4me/H3K4me3 demethylase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables FAD-dependent H3K4me/H3K4me3 demethylase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables flavin adenine dinucleotide binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables histone H3K4 demethylase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    NOT enables histone H3K4me/H3K4me2/H3K4me3 demethylase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables histone binding IEA
    Inferred from Electronic Annotation
    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 protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables zinc ion binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables zinc ion binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within epigenetic programing of female pronucleus IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within genomic imprinting IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in genomic imprinting IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in transcription initiation-coupled chromatin remodeling ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in 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 IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of nucleosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    lysine-specific histone demethylase 1B
    Names
    amine oxidase, flavin containing 1
    flavin-containing amine oxidase domain-containing protein 1
    lysine-specific histone demethylase 2
    NP_001389837.1
    NP_001389838.1
    NP_758466.1
    XP_006516976.1
    XP_006516979.1
    XP_006516980.1
    XP_006516982.1
    XP_006516983.1

    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_001402908.1 → NP_001389837.1  lysine-specific histone demethylase 1B isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC096628, AC154171

    2. NM_001402909.1 → NP_001389838.1  lysine-specific histone demethylase 1B isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC096628, AC154171

    3. NM_172262.4 → NP_758466.1  lysine-specific histone demethylase 1B isoform 1

      See identical proteins and their annotated locations for NP_758466.1

      Status: VALIDATED

      Source sequence(s)
      AC096628, AC154171
      Consensus CDS
      CCDS26489.1
      UniProtKB/Swiss-Prot
      Q8C5C4, Q8CEC1, Q8CIG3
      Related
      ENSMUSP00000038373.9, ENSMUST00000037025.16
      Conserved Domains (3) summary
      pfam01593
      Location:405 → 823
      Amino_oxidase; Flavin containing amine oxidoreductase
      pfam04433
      Location:287 → 369
      SWIRM; SWIRM domain
      pfam07496
      Location:138 → 191
      zf-CW; CW-type Zinc Finger

    RNA

    1. NR_175316.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC096628, AC154171

    2. NR_175317.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC096628, AC154171

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000079.7 Reference GRCm39 C57BL/6J

      Range
      47196849..47238085
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006516920.3 → XP_006516983.1  lysine-specific histone demethylase 1B isoform X7

      Conserved Domains (2) summary
      PLN02328
      Location:308 → 724
      PLN02328; lysine-specific histone demethylase 1 homolog
      pfam07496
      Location:138 → 191
      zf-CW; CW-type Zinc Finger

    2. XM_006516913.5 → XP_006516976.1  lysine-specific histone demethylase 1B isoform X1

      Conserved Domains (2) summary
      PLN02328
      Location:315 → 831
      PLN02328; lysine-specific histone demethylase 1 homolog
      pfam07496
      Location:138 → 198
      zf-CW; CW-type Zinc Finger

    3. XM_006516916.5 → XP_006516979.1  lysine-specific histone demethylase 1B isoform X4

      Conserved Domains (2) summary
      PLN02328
      Location:315 → 731
      PLN02328; lysine-specific histone demethylase 1 homolog
      pfam07496
      Location:138 → 198
      zf-CW; CW-type Zinc Finger

    4. XM_006516917.4 → XP_006516980.1  lysine-specific histone demethylase 1B isoform X5

      Conserved Domains (2) summary
      PLN02328
      Location:315 → 730
      PLN02328; lysine-specific histone demethylase 1 homolog
      pfam07496
      Location:138 → 198
      zf-CW; CW-type Zinc Finger

    5. XM_006516919.5 → XP_006516982.1  lysine-specific histone demethylase 1B isoform X6

      Related
      ENSMUST00000128977.3
      Conserved Domains (1) summary
      PLN02328
      Location:5 → 415
      PLN02328; lysine-specific histone demethylase 1 homolog
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8CIG3.1 GenPept UniProtKB/Swiss-Prot:Q8CIG3

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