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

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 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

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_000079.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.

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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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AI482520 (e-PCR)
- UniSTS:160294

Aof1 (e-PCR), detects polymorphism
- UniSTS:506729

NoName (e-PCR)
- UniSTS:237009

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

EC 1.14.99.66

NP_001389838.1

EC 1.14.99.66

NP_758466.1

EC 1.14.99.66

XP_006516976.1

EC 1.14.99.66

XP_006516979.1

EC 1.14.99.66

XP_006516980.1

EC 1.14.99.66

XP_006516982.1

EC 1.14.99.66

XP_006516983.1

EC 1.14.99.66

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)

NM_001402908.1 → NP_001389837.1 lysine-specific histone demethylase 1B isoform 2

Status: VALIDATED

Source sequence(s)

AC096628, AC154171
NM_001402909.1 → NP_001389838.1 lysine-specific histone demethylase 1B isoform 3

Status: VALIDATED

Source sequence(s)

AC096628, AC154171
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

NR_175316.1 RNA Sequence

Status: VALIDATED

Source sequence(s)

AC096628, AC154171
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

NC_000079.7 Reference GRCm39 C57BL/6J

Range

47196849..47238085

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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
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
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