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Aliases for KDM1B Gene

Aliases for KDM1B Gene

  • Lysine Demethylase 1B 2 3
  • Lysine (K)-Specific Demethylase 1B 2 3 5
  • Flavin-Containing Amine Oxidase Domain-Containing Protein 1 3 4
  • Amine Oxidase (Flavin Containing) Domain 1 2 3
  • Lysine-Specific Histone Demethylase 2 3 4
  • Amine Oxidase, Flavin Containing 1 2 3
  • C6orf193 3 4
  • AOF1 3 4
  • LSD2 3 4
  • Chromosome 6 Open Reading Frame 193 2
  • DJ298J15.2 3
  • EC 1.-.-.- 4
  • BA204B7.3 3

External Ids for KDM1B Gene

Previous HGNC Symbols for KDM1B Gene

  • C6orf193
  • AOF1

Previous GeneCards Identifiers for KDM1B Gene

  • GC06P018266

Summaries for KDM1B Gene

Entrez Gene Summary for KDM1B Gene

  • Flavin-dependent histone demethylases, such as KDM1B, regulate histone lysine methylation, an epigenetic mark that regulates gene expression and chromatin function (Karytinos et al., 2009 [PubMed 19407342]).[supplied by OMIM, Oct 2009]

GeneCards Summary for KDM1B Gene

KDM1B (Lysine Demethylase 1B) is a Protein Coding gene. Among its related pathways are Chromatin organization and Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3. GO annotations related to this gene include oxidoreductase activity and histone demethylase activity (H3-dimethyl-K4 specific). An important paralog of this gene is SMOX.

UniProtKB/Swiss-Prot for KDM1B Gene

  • Histone demethylase that demethylates Lys-4 of histone H3, a specific tag for epigenetic transcriptional activation, thereby acting as a corepressor. Required for de novo DNA methylation of a subset of imprinted genes during oogenesis. Acts by oxidizing the substrate by FAD to generate the corresponding imine that is subsequently hydrolyzed. Demethylates both mono- and di-methylated Lys-4 of histone H3. Has no effect on tri-methylated Lys-4, mono-, di- or tri-methylated Lys-9, mono-, di- or tri-methylated Lys-27, mono-, di- or tri-methylated Lys-36 of histone H3, or on mono-, di- or tri-methylated Lys-20 of histone H4 (By similarity).

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for KDM1B Gene

Genomics for KDM1B Gene

Regulatory Elements for KDM1B Gene

Enhancers for KDM1B Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around KDM1B on UCSC Golden Path with GeneCards custom track

Promoters for KDM1B Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around KDM1B on UCSC Golden Path with GeneCards custom track

Genomic Location for KDM1B Gene

Chromosome:
6
Start:
18,155,329 bp from pter
End:
18,223,854 bp from pter
Size:
68,526 bases
Orientation:
Plus strand

Genomic View for KDM1B Gene

Genes around KDM1B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
KDM1B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for KDM1B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for KDM1B Gene

Proteins for KDM1B Gene

  • Protein details for KDM1B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8NB78-KDM1B_HUMAN
    Recommended name:
    Lysine-specific histone demethylase 1B
    Protein Accession:
    Q8NB78
    Secondary Accessions:
    • A2A2C5
    • A2A2C6
    • Q5TGV3
    • Q6AI15
    • Q6ZUU4
    • Q8N258
    • Q96EL7

    Protein attributes for KDM1B Gene

    Size:
    822 amino acids
    Molecular mass:
    92098 Da
    Cofactor:
    Name=FAD; Xref=ChEBI:CHEBI:57692;
    Quaternary structure:
    • Does not form a complex with RCOR1/CoREST.
    SequenceCaution:
    • Sequence=BAC03663.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for KDM1B Gene

    Alternative splice isoforms for KDM1B Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for KDM1B Gene

Proteomics data for KDM1B Gene at MOPED

Post-translational modifications for KDM1B Gene

  • Ubiquitination at Lys 378 and Lys 649
  • Modification sites at PhosphoSitePlus

Other Protein References for KDM1B Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

No data available for DME Specific Peptides for KDM1B Gene

Domains & Families for KDM1B Gene

Gene Families for KDM1B Gene

Protein Domains for KDM1B Gene

Graphical View of Domain Structure for InterPro Entry

Q8NB78

UniProtKB/Swiss-Prot:

KDM1B_HUMAN :
  • The SWIRM domain may act as an anchor site for a histone tail.
  • Belongs to the flavin monoamine oxidase family.
  • Contains 1 CW-type zinc finger.
Domain:
  • The SWIRM domain may act as an anchor site for a histone tail.
  • Contains 1 SWIRM domain.
Family:
  • Belongs to the flavin monoamine oxidase family.
Similarity:
  • Contains 1 CW-type zinc finger.
genes like me logo Genes that share domains with KDM1B: view

Function for KDM1B Gene

Molecular function for KDM1B Gene

UniProtKB/Swiss-Prot Function:
Histone demethylase that demethylates Lys-4 of histone H3, a specific tag for epigenetic transcriptional activation, thereby acting as a corepressor. Required for de novo DNA methylation of a subset of imprinted genes during oogenesis. Acts by oxidizing the substrate by FAD to generate the corresponding imine that is subsequently hydrolyzed. Demethylates both mono- and di-methylated Lys-4 of histone H3. Has no effect on tri-methylated Lys-4, mono-, di- or tri-methylated Lys-9, mono-, di- or tri-methylated Lys-27, mono-, di- or tri-methylated Lys-36 of histone H3, or on mono-, di- or tri-methylated Lys-20 of histone H4 (By similarity).

Enzyme Numbers (IUBMB) for KDM1B Gene

Gene Ontology (GO) - Molecular Function for KDM1B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
genes like me logo Genes that share ontologies with KDM1B: view

Phenotypes for KDM1B Gene

genes like me logo Genes that share phenotypes with KDM1B: view

Animal Model Products

  • Taconic Biosciences Mouse Models for KDM1B

CRISPR Products

miRNA for KDM1B Gene

miRTarBase miRNAs that target KDM1B

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for KDM1B Gene

Localization for KDM1B Gene

Subcellular locations from UniProtKB/Swiss-Prot for KDM1B Gene

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for KDM1B Gene COMPARTMENTS Subcellular localization image for KDM1B gene
Compartment Confidence
nucleus 5
cytosol 2

No data available for Gene Ontology (GO) - Cellular Components for KDM1B Gene

Pathways & Interactions for KDM1B Gene

genes like me logo Genes that share pathways with KDM1B: view

Pathways by source for KDM1B Gene

Gene Ontology (GO) - Biological Process for KDM1B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007275 multicellular organism development IEA --
GO:0034720 histone H3-K4 demethylation IEA,ISS 19727073
GO:0044030 regulation of DNA methylation IEA,ISS 19727073
genes like me logo Genes that share ontologies with KDM1B: view

No data available for SIGNOR curated interactions for KDM1B Gene

Drugs & Compounds for KDM1B Gene

(5) Drugs for KDM1B Gene - From: ApexBio and HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
FAD Approved Pharma 0
IOX 1 Pharma Histone demethylase inhibitor; cell permeable 0
ML324 Pharma JMJD2 demethylase inhibitor, potent and cell-permeable 0
SP2509 Pharma Demethylase 1 (LSD1) antagonist, novel Lysine-specific 0
Tranylcypromine hydrochloride Pharma Irreversible inhibitor of LSD1; also inhibits MAO 0

(4) ApexBio Compounds for KDM1B Gene

Compound Action Cas Number
IOX 1 5852-78-8
ML324 JMJD2 demethylase inhibitor, potent and cell-permeable 1222800-79-4
SP2509 Demethylase 1 (LSD1) antagonist, novel Lysine-specific 1423715-09-6
Tranylcypromine hydrochloride 1986-47-6
genes like me logo Genes that share compounds with KDM1B: view

Transcripts for KDM1B Gene

Unigene Clusters for KDM1B Gene

Lysine (K)-specific demethylase 1B:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for KDM1B Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8a · 8b ^ 9a · 9b ^ 10 ^ 11 ^ 12a · 12b ^ 13 ^ 14 ^ 15 ^ 16a · 16b
SP1: - -
SP2: - - - - - - - -
SP3:
SP4:
SP5: -
SP6:

Relevant External Links for KDM1B Gene

GeneLoc Exon Structure for
KDM1B
ECgene alternative splicing isoforms for
KDM1B

Expression for KDM1B Gene

mRNA expression in normal human tissues for KDM1B Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for KDM1B Gene

This gene is overexpressed in Retina (14.7), Placenta (12.5), Fetal Brain (11.6), Fetal ovary (6.7), and Stomach (6.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for KDM1B Gene



SOURCE GeneReport for Unigene cluster for KDM1B Gene Hs.709336

genes like me logo Genes that share expression patterns with KDM1B: view

Primer Products

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Protein tissue co-expression partners for KDM1B Gene

Orthologs for KDM1B Gene

This gene was present in the common ancestor of animals.

Orthologs for KDM1B Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia KDM1B 35
  • 99.66 (n)
  • 99.83 (a)
KDM1B 36
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia KDM1B 36
  • 69 (a)
OneToOne
dog
(Canis familiaris)
Mammalia KDM1B 36
  • 68 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia KDM1B 36
  • 60 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Kdm1b 36
  • 64 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia KDM1B 36
  • 50 (a)
OneToOne
chicken
(Gallus gallus)
Aves KDM1B 36
  • 62 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia KDM1B 36
  • 59 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii si:dkey-7o6.3 36
  • 22 (a)
ManyToMany
worm
(Caenorhabditis elegans)
Secernentea amx-1 36
  • 26 (a)
OneToMany
lsd-1 36
  • 17 (a)
OneToMany
spr-5 36
  • 17 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 54 (a)
OneToOne
Species with no ortholog for KDM1B:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for KDM1B Gene

ENSEMBL:
Gene Tree for KDM1B (if available)
TreeFam:
Gene Tree for KDM1B (if available)

Paralogs for KDM1B Gene

Paralogs for KDM1B Gene

(2) SIMAP similar genes for KDM1B Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with KDM1B: view

Variants for KDM1B Gene

Sequence variations from dbSNP and Humsavar for KDM1B Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type
rs1011620 -- 18,171,246(-) TTTCT(C/T)CTCCT intron-variant
rs1207042 -- 18,189,009(-) GTCAG(A/G)AGTTC intron-variant
rs1207043 -- 18,188,972(-) ACCCC(A/G)TCTCT intron-variant
rs1207044 -- 18,188,932(-) GTAGC(A/G)TGCGC intron-variant
rs1207045 -- 18,188,839(-) GCCAC(C/T)GCACT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for KDM1B Gene

Variant ID Type Subtype PubMed ID
nsv883460 CNV Gain 21882294

Variation tolerance for KDM1B Gene

Residual Variation Intolerance Score: 25.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.16; 61.61% of all genes are more intolerant (likely to be disease-causing)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Relevant External Links for KDM1B Gene

Disorders for KDM1B Gene

Relevant External Links for KDM1B

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
KDM1B

No disorders were found for KDM1B Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for KDM1B Gene

Publications for KDM1B Gene

  1. A novel mammalian flavin-dependent histone demethylase. (PMID: 19407342) Karytinos A. … Mattevi A. (J. Biol. Chem. 2009) 2 3 23 67
  2. KDM1B is a histone H3K4 demethylase required to establish maternal genomic imprints. (PMID: 19727073) Ciccone D.N. … Chen T. (Nature 2009) 2 3
  3. Proximity biotinylation and affinity purification are complementary approaches for the interactome mapping of chromatin-associated protein complexes. (PMID: 25281560) Lambert J.P. … Gingras A.C. (J Proteomics 2015) 3
  4. Proteomic analyses reveal distinct chromatin-associated and soluble transcription factor complexes. (PMID: 25609649) Li X. … Chen J. (Mol. Syst. Biol. 2015) 3
  5. Lysine-specific demethylase 2 suppresses lipid influx and metabolism in hepatic cells. (PMID: 25624347) Nagaoka K. … Nakao M. (Mol. Cell. Biol. 2015) 3

Products for KDM1B Gene

Sources for KDM1B Gene

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