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

Gene ID: 218214, updated on 12-May-2024

Summary

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
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Genomic context

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

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

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
 
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

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

    Status: VALIDATED

    Source sequence(s)
    AC096628, AC154171
  2. NM_001402909.1NP_001389838.1  lysine-specific histone demethylase 1B isoform 3

    Status: VALIDATED

    Source sequence(s)
    AC096628, AC154171
  3. NM_172262.4NP_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:405823
    Amino_oxidase; Flavin containing amine oxidoreductase
    pfam04433
    Location:287369
    SWIRM; SWIRM domain
    pfam07496
    Location:138191
    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_006516920.3XP_006516983.1  lysine-specific histone demethylase 1B isoform X7

    Conserved Domains (2) summary
    PLN02328
    Location:308724
    PLN02328; lysine-specific histone demethylase 1 homolog
    pfam07496
    Location:138191
    zf-CW; CW-type Zinc Finger
  2. XM_006516913.5XP_006516976.1  lysine-specific histone demethylase 1B isoform X1

    Conserved Domains (2) summary
    PLN02328
    Location:315831
    PLN02328; lysine-specific histone demethylase 1 homolog
    pfam07496
    Location:138198
    zf-CW; CW-type Zinc Finger
  3. XM_006516916.5XP_006516979.1  lysine-specific histone demethylase 1B isoform X4

    Conserved Domains (2) summary
    PLN02328
    Location:315731
    PLN02328; lysine-specific histone demethylase 1 homolog
    pfam07496
    Location:138198
    zf-CW; CW-type Zinc Finger
  4. XM_006516917.4XP_006516980.1  lysine-specific histone demethylase 1B isoform X5

    Conserved Domains (2) summary
    PLN02328
    Location:315730
    PLN02328; lysine-specific histone demethylase 1 homolog
    pfam07496
    Location:138198
    zf-CW; CW-type Zinc Finger
  5. XM_006516919.5XP_006516982.1  lysine-specific histone demethylase 1B isoform X6

    Related
    ENSMUST00000128977.3
    Conserved Domains (1) summary
    PLN02328
    Location:5415
    PLN02328; lysine-specific histone demethylase 1 homolog