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Aliases for KDM1B Gene

Aliases for KDM1B Gene

  • Lysine 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
  • Lysine (K)-Specific Demethylase 1B 2 3
  • C6orf193 3 4
  • AOF1 3 4
  • LSD2 3 4
  • Lysine-Specific Histone Demethylase 1B 3
  • 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 Deubiquitination and Metabolism of proteins. GO annotations related to this gene include oxidoreductase activity and histone demethylase activity (H3-dimethyl-K4 specific). An important paralog of this gene is KDM1A.

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.

No data available for CIViC summary , 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 Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH06G018400 1.7 FANTOM5 Ensembl ENCODE dbSUPER 11.2 +245.8 245814 1.7 PKNOX1 TBL1XR1 JUN BMI1 YY1 GATA2 CBX5 POLR2A EED SCRT2 RNF144B KDM1B DEK KIF13A PIR43810 PIR42478
GH06G018327 1.6 FANTOM5 Ensembl ENCODE dbSUPER 4.6 +174.0 173963 4.3 BHLHE40 JUNB OSR2 HIC1 PRDM6 SCRT2 ZNF629 IKZF1 KLF9 ETV6 RNF144B DEK KDM1B KIF13A PIR61433 GC06P018364 PIR39754
GH06G018386 1.7 FANTOM5 ENCODE dbSUPER 4.2 +233.4 233427 5.5 FOXA2 PKNOX1 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF263 SP3 SP5 RNF144B RNU6-263P DEK IMPDH1P9 KDM1B KIF13A PIR43810
GH06G017927 2.1 VISTA FANTOM5 Ensembl ENCODE dbSUPER 2.6 -224.1 -224113 7.2 FOXA2 PKNOX1 MLX ARID4B YY1 SP5 SMARCB1 ZNF592 KAT8 MEF2D KIF13A NHLRC1 LOC105374952 RNF144B KDM1B RPS12P12 GC06P017893
GH06G018179 0.8 Ensembl dbSUPER 6.4 +24.4 24359 1.4 MAFF ZNF316 MAFG EMSY MAFK TPMT KDM1B DEK
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

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
ENSR00000194242 -29 2201 HDGF PKNOX1 CREB3L1 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF766

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;
    Cofactor:
    Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
    Quaternary structure:
    • Does not form a complex with RCOR1/CoREST (By similarity). Interacts with its cofactor GLYR1 at nucleosomes; this interaction stimulates H3K4me1 and H3K4me2 demethylation (PubMed:23260659).
    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

Post-translational modifications for KDM1B Gene

  • Ubiquitination at posLast=378378 and isoforms=2, 4649
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for KDM1B Gene

Domains & Families for KDM1B Gene

Gene Families 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.
Domain:
  • The SWIRM domain may act as an anchor site for a histone tail.
Family:
  • Belongs to the flavin monoamine oxidase family.
genes like me logo Genes that share domains with KDM1B: view

Function for KDM1B Gene

Molecular function for KDM1B Gene

UniProtKB/Swiss-Prot EnzymeRegulation:
Histone H3K4me1 and H3K4me2 demethylase activity is enhanced by GLYR1.
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.

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 --
GO:0005515 protein binding IPI 23260659
GO:0008270 zinc ion binding IDA 23260659
GO:0016491 oxidoreductase activity IEA --
GO:0032452 histone demethylase activity TAS --
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

Inhibitory RNA Products

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
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for KDM1B gene
Compartment Confidence
nucleus 5
cytosol 2

Gene Ontology (GO) - Cellular Components for KDM1B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000786 nucleosome IDA 23260659
GO:0005634 nucleus ISS 19727073
GO:0005654 nucleoplasm TAS --
genes like me logo Genes that share ontologies with KDM1B: view

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:0006349 regulation of gene expression by genetic imprinting ISS 19727073
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0007275 multicellular organism development IEA --
GO:0016569 covalent chromatin modification IEA --
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 0
ML324 Pharma JMJD2 demethylase inhibitor, potent and cell-permeable 0
SP2509 Pharma Demethylase 1 (LSD1) antagonist, novel Lysine-specific 0
Tranylcypromine hydrochloride Pharma 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

Drug Products

Transcripts for KDM1B Gene

Unigene Clusters for KDM1B Gene

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

CRISPR Products

Inhibitory RNA Products

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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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, MaxQB, and MOPED for KDM1B Gene



NURSA nuclear receptor signaling pathways regulating expression of KDM1B Gene:

KDM1B

SOURCE GeneReport for Unigene cluster for KDM1B Gene:

Hs.709336

Evidence on tissue expression from TISSUES for KDM1B Gene

  • Liver(4.2)
  • Nervous system(4.2)
genes like me logo Genes that share expression patterns with KDM1B: view

Primer Products

No data available for mRNA differential expression in normal tissues , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer 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 34 35
  • 99.66 (n)
cow
(Bos Taurus)
Mammalia KDM1B 35
  • 69 (a)
OneToOne
dog
(Canis familiaris)
Mammalia KDM1B 35
  • 68 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Kdm1b 35
  • 64 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia KDM1B 35
  • 60 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia KDM1B 35
  • 50 (a)
OneToOne
chicken
(Gallus gallus)
Aves KDM1B 35
  • 62 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia KDM1B 35
  • 59 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii si:dkey-7o6.3 35
  • 22 (a)
ManyToMany
worm
(Caenorhabditis elegans)
Secernentea amx-1 35
  • 26 (a)
OneToMany
lsd-1 35
  • 17 (a)
OneToMany
spr-5 35
  • 17 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 54 (a)
OneToOne
Species where no ortholog for KDM1B was found in the sources mined by GeneCards:
  • 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
rs141028204 Uncertain significance 18,155,054(+) TGCCG(A/G)CCATT upstream-variant-2KB, utr-variant-5-prime
rs543585967 Uncertain significance 18,155,126(+) CTCCG(-/C)GCCCC upstream-variant-2KB, utr-variant-5-prime
rs886061267 Uncertain significance 18,155,022(-) CTCAC(C/T)CGGGC intron-variant, upstream-variant-2KB
rs1000017171 -- 18,168,710(+) TCCTG(A/T)CTGTA intron-variant
rs1000036179 -- 18,224,186(+) TGATT(C/T)AGATT nc-transcript-variant, downstream-variant-500B, utr-variant-3-prime

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

Variant ID Type Subtype PubMed ID
nsv1034755 CNV loss 25217958
nsv1114783 CNV deletion 24896259
nsv601050 CNV gain 21841781

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)

Relevant External Links for KDM1B Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
KDM1B

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot 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 22 64
  2. LSD2/KDM1B and its cofactor NPAC/GLYR1 endow a structural and molecular model for regulation of H3K4 demethylation. (PMID: 23260659) Fang R. … Shi Y.G. (Mol. Cell 2013) 3 4 64
  3. Structure-function analysis reveals a novel mechanism for regulation of histone demethylase LSD2/AOF1/KDM1b. (PMID: 23266887) Zhang Q. … Wong J. (Cell Res. 2013) 3 4 64
  4. KDM1B is a histone H3K4 demethylase required to establish maternal genomic imprints. (PMID: 19727073) Ciccone D.N. … Chen T. (Nature 2009) 2 3 64
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64

Products for KDM1B Gene

Sources for KDM1B Gene

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