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

Gene ID: 218214, updated on 11-Apr-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 flavin adenine dinucleotide binding activity; histone H3-di/monomethyl-lysine-4 FAD-dependent demethylase activity; and zinc ion binding activity. Involved in regulation of DNA methylation. Acts upstream of or within DNA methylation involved in gamete generation; histone H3-K4 demethylation; and regulation of gene expression by genetic imprinting. 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, Apr 2022]
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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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
  • 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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Related articles in PubMed

  1. Lysine Demethylase 1B Promotes Tear Secretion Disorder in Sjogren's Syndrome by Regulating the PAX6/CLU Axis. Liu S, et al. J Mol Neurosci, 2023 Jan. PMID 36542318
  2. Lysine-specific demethylase-2 is distinctively involved in brown and beige adipogenic differentiation. Takase R, et al. FASEB J, 2019 Apr. PMID 30681884, Free PMC Article
  3. AOF1 is a histone H3K4 demethylase possessing demethylase activity-independent repression function. Yang Z, et al. Cell Res, 2010 Mar. PMID 20101264, Free PMC Article
  4. MiR-215 Is Induced Post-transcriptionally via HIF-Drosha Complex and Mediates Glioma-Initiating Cell Adaptation to Hypoxia by Targeting KDM1B. Hu J, et al. Cancer Cell, 2016 Jan 11. PMID 26766590, Free PMC Article
  5. 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. Gupta J, et al. Biochimie, 2012 Dec. PMID 22951486

See all (26) citations in PubMed

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)
  • Gene trapped (1) 
  • Targeted (2)  1 citation
  • Endonuclease-mediated (1) 

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-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 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 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 ISO
Inferred from Sequence Orthology
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
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 transcription factor binding IBA
Inferred from Biological aspect of Ancestor
more info
  
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 chromatin organization IEA
Inferred from Electronic Annotation
more info
  
involved_in chromatin remodeling IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within chromatin remodeling IDA
Inferred from Direct Assay
more info
 PubMed 
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 
acts_upstream_of_or_within multicellular organism development IEA
Inferred from Electronic Annotation
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 chromosome 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 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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