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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 Metabolism of proteins and Chromatin organization. Gene Ontology (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.

Additional gene information for KDM1B Gene

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

GeneHancer (GH) Regulatory Elements for KDM1B Gene

Promoters and enhancers for KDM1B Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH06J018152 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 652.3 -0.8 -759 4.2 HDGF FOXA2 PKNOX1 SMAD1 ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2 TPMT KDM1B NHLRC1 RNF144B
GH06J018400 Enhancer 1.4 FANTOM5 Ensembl ENCODE dbSUPER 11.2 +245.8 245813 1.7 PKNOX1 JUN BMI1 BATF KLF5 IRF4 SCRT2 ATF7 ETV6 BCLAF1 PIR43810 RNF144B KDM1B DEK KIF13A PIR42478
GH06J018386 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 4.3 +233.4 233427 5.5 PKNOX1 FOXA2 ARID4B SIN3A DMAP1 ZNF2 YY1 SP3 SP5 ZHX2 RNF144B RNU6-263P DEK IMPDH1P9 KDM1B KIF13A PIR43810
GH06J018327 Promoter/Enhancer 1.9 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 4.6 +174.0 173962 4.3 TEAD4 JUNB OSR2 HIC1 SP1 CTBP1 PRDM6 GATA3 ZNF629 SCRT2 RNF144B DEK KDM1B KIF13A PIR61433 PIR39754 GC06P018364
GH06J017701 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 2.4 -450.7 -450656 6.4 MLX ZFP64 DMAP1 IRF4 YY1 ZNF213 E2F8 ZNF143 SP3 NFYC NUP153 LOC105374952 RNU6-190P FAM8A1 KDM1B
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around KDM1B on UCSC Golden Path with GeneCards custom track

Genomic Locations for KDM1B Gene

Genomic Locations for KDM1B Gene
chr6:18,155,329-18,223,854
(GRCh38/hg38)
Size:
68,526 bases
Orientation:
Plus strand
chr6:18,155,560-18,224,084
(GRCh37/hg19)
Size:
68,525 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 Lys649 and Lys378
  • Modification sites at PhosphoSitePlus

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

Enzyme Numbers (IUBMB) for KDM1B Gene

Phenotypes From GWAS Catalog 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
genes like me logo Genes that share phenotypes with KDM1B: view

Animal Model Products

  • Taconic Biosciences Mouse Models for KDM1B

miRNA for KDM1B Gene

Clone 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

Subcellular locations from the

Human Protein Atlas (HPA)

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:0006325 chromatin organization IEA --
GO:0006349 regulation of gene expression by genetic imprinting ISS,IEA 19727073
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0007275 multicellular organism development 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: 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
genes like me logo Genes that share compounds with KDM1B: view

Transcripts for KDM1B Gene

mRNA/cDNA for KDM1B Gene

Unigene Clusters for KDM1B Gene

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

Clone 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, 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

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 33
  • 99.66 (n)
OneToOne
cow
(Bos Taurus)
Mammalia KDM1B 34
  • 69 (a)
OneToOne
dog
(Canis familiaris)
Mammalia KDM1B 34
  • 68 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Kdm1b 34
  • 64 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia KDM1B 34
  • 60 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia KDM1B 34
  • 50 (a)
OneToOne
chicken
(Gallus gallus)
Aves KDM1B 34
  • 62 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia KDM1B 34
  • 59 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii si:dkey-7o6.3 34
  • 22 (a)
ManyToMany
worm
(Caenorhabditis elegans)
Secernentea amx-1 34
  • 26 (a)
OneToMany
lsd-1 34
  • 17 (a)
OneToMany
spr-5 34
  • 17 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for KDM1B: view image

Paralogs for KDM1B Gene

Paralogs for KDM1B Gene

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

  • KDM1B_HUMAN
  • F2Z2A7_HUMAN
  • H0Y6H0_HUMAN
  • J3KPL2_HUMAN
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 Variation AA Info Type
rs141028204 uncertain-significance, Thiopurine methyltransferase deficiency 18,155,054(+) G/A upstream_transcript_variant
rs543585967 uncertain-significance, Thiopurine methyltransferase deficiency 18,155,126(+) C/ upstream_transcript_variant
rs886061267 uncertain-significance, Thiopurine methyltransferase deficiency 18,155,022(+) A/G upstream_transcript_variant
rs1000017171 -- 18,168,710(+) T/A intron_variant
rs1000036179 -- 18,224,186(+) T/C downstream_transcript_variant

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)

Additional Variant Information for KDM1B Gene

Human Gene Mutation Database (HGMD)
KDM1B
SNPedia medical, phenotypic, and genealogical associations of SNPs for
KDM1B

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for KDM1B Gene

Disorders for KDM1B Gene

Additional Disease Information for 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 (The Journal of biological chemistry 2009) 2 3 22 58
  2. LSD2/KDM1B and its cofactor NPAC/GLYR1 endow a structural and molecular model for regulation of H3K4 demethylation. (PMID: 23260659) Fang R … Shi YG (Molecular cell 2013) 3 4 58
  3. Structure-function analysis reveals a novel mechanism for regulation of histone demethylase LSD2/AOF1/KDM1b. (PMID: 23266887) Zhang Q … Wong J (Cell research 2013) 3 4 58
  4. KDM1B is a histone H3K4 demethylase required to establish maternal genomic imprints. (PMID: 19727073) Ciccone DN … Chen T (Nature 2009) 2 3 58
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58

Products for KDM1B Gene

Sources for KDM1B Gene

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