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Aliases for KDM3B Gene

Aliases for KDM3B Gene

  • Lysine Demethylase 3B 2 3 5
  • JmjC Domain-Containing Histone Demethylation Protein 2B 3 4
  • Jumonji Domain-Containing Protein 1B 3 4
  • Lysine (K)-Specific Demethylase 3B 2 3
  • Jumonji Domain Containing 1B 2 3
  • Nuclear Protein 5qNCA 3 4
  • C5orf7 3 4
  • JMJD1B 3 4
  • Chromosome 5 Open Reading Frame 7 2
  • Lysine-Specific Demethylase 3B 3
  • EC 1.14.11.- 4
  • EC 1.14.11 61
  • KIAA1082 4
  • JHDM2B 4
  • 5qNCA 3
  • NET22 3

External Ids for KDM3B Gene

Previous HGNC Symbols for KDM3B Gene

  • C5orf7
  • JMJD1B

Previous GeneCards Identifiers for KDM3B Gene

  • GC05P137717
  • GC05P137688
  • GC05P132879

Summaries for KDM3B Gene

GeneCards Summary for KDM3B Gene

KDM3B (Lysine Demethylase 3B) is a Protein Coding gene. Diseases associated with KDM3B include Persistent Hyperplastic Primary Vitreous. Among its related pathways are Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 and Chromatin organization. GO annotations related to this gene include dioxygenase activity. An important paralog of this gene is KDM3A.

UniProtKB/Swiss-Prot for KDM3B Gene

  • Histone demethylase that specifically demethylates Lys-9 of histone H3, thereby playing a central role in histone code. Demethylation of Lys residue generates formaldehyde and succinate. May have tumor suppressor activity.

Gene Wiki entry for KDM3B Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for KDM3B Gene

Genomics for KDM3B Gene

Regulatory Elements for KDM3B Gene

Enhancers for KDM3B 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
GH05G139341 1.2 ENCODE 42 +989.7 989719 2.6 MLX CREB3L1 AGO1 DMAP1 YY1 SLC30A9 ZNF143 ZNF548 SP3 ZNF610 KDM3B PURA RPL7P19 SLC23A1 MZB1 PROB1 MATR3 SNORA74A SIL1 ENSG00000222937
GH05G138335 1.4 ENCODE dbSUPER 30.1 -15.1 -15056 5.0 CREB3L1 AGO1 ZFP64 FEZF1 DMAP1 YBX1 YY1 ZNF143 SP3 NFYC HNRNPA0 CDC23 KDM3B RPL7P19 NME5 SPOCK1 LRRTM2 FAM13B REEP2 CDC25C
GH05G137833 1.8 FANTOM5 Ensembl ENCODE dbSUPER 20 -516.4 -516381 5.9 PKNOX1 FOXA2 SIN3A FEZF1 GATA2 FOS SP3 YY2 TSHZ1 SREBF1 KDM3B CDC23 MYOT FAM13B RNU6-1148P KLHL3 PKD2L2 GC05M137818 NPY6R
GH05G138350 1.4 ENCODE dbSUPER 20.7 +0.7 739 4.7 PKNOX1 ARNT CREB3L1 AGO1 ARID4B SIN3A FEZF1 ZNF2 YY1 SLC30A9 KDM3B CDC23 FAM53C FAM13B BRD8 KIF20A GFRA3 REEP2 GC05P138377
GH05G139292 1.4 ENCODE dbSUPER 20.4 +942.2 942247 3.8 CREB3L1 AGO1 FEZF1 DMAP1 YY1 ZNF143 ZNF263 SP3 ZNF610 ZNF585B KDM3B PURA DNAJC18 LOC101929719 SIL1 GC05P139300
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around KDM3B on UCSC Golden Path with GeneCards custom track

Promoters for KDM3B Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000187478 704 2201 ARNT CREB3L1 AGO1 ARID4B SIN3A FEZF1 ZNF2 YY1 SLC30A9 CBX5

Genomic Location for KDM3B Gene

Chromosome:
5
Start:
138,352,596 bp from pter
End:
138,437,028 bp from pter
Size:
84,433 bases
Orientation:
Plus strand

Genomic View for KDM3B Gene

Genes around KDM3B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
KDM3B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for KDM3B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for KDM3B Gene

Proteins for KDM3B Gene

  • Protein details for KDM3B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q7LBC6-KDM3B_HUMAN
    Recommended name:
    Lysine-specific demethylase 3B
    Protein Accession:
    Q7LBC6
    Secondary Accessions:
    • A6H8X7
    • Q9BVH6
    • Q9BW93
    • Q9BZ52
    • Q9NYF4
    • Q9UPS0

    Protein attributes for KDM3B Gene

    Size:
    1761 amino acids
    Molecular mass:
    191581 Da
    Cofactor:
    Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
    Quaternary structure:
    No Data Available
    Miscellaneous:
    • Its gene is located in the 5q region of the genome which is deleted in del(5q) interstitial deletion, a frequent deletion found in myeloid leukemias and myelodysplasias, suggesting that it may be a good candidate for the del(5q) tumor suppressor gene.
    SequenceCaution:
    • Sequence=BAA83034.2; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for KDM3B Gene

    Alternative splice isoforms for KDM3B Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for KDM3B Gene

Selected DME Specific Peptides for KDM3B Gene

Q7LBC6:
  • GVREMCD
  • CRFFHFRRL
  • DHDPIHDQSWYLD
  • GTTNLHLDVSDA
  • THTNHEDKLQVKN
  • NVMVYVGIP
  • GVLRVEGFL
  • KCRECRL
  • VLKLKDWP
  • GVQGWAIVQFLGD
  • HEPENLMPTQI
  • ECWKQGQP
  • KWGIKANCPC
  • EDFVSPEH
  • YFVRPDLGPKMYNAYGLIT

Post-translational modifications for KDM3B Gene

  • Ubiquitination at isoforms=204, posLast=913913, isoforms=2926, and posLast=12721272
  • Modification sites at PhosphoSitePlus

Other Protein References for KDM3B Gene

Domains & Families for KDM3B Gene

Gene Families for KDM3B Gene

Protein Domains for KDM3B Gene

Suggested Antigen Peptide Sequences for KDM3B Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q7LBC6

UniProtKB/Swiss-Prot:

KDM3B_HUMAN :
  • Leu-Xaa-Xaa-Leu-Leu (LXXLL) motifs are known to mediate the association with nuclear receptors.
  • Belongs to the JHDM2 histone demethylase family.
Domain:
  • Leu-Xaa-Xaa-Leu-Leu (LXXLL) motifs are known to mediate the association with nuclear receptors.
Family:
  • Belongs to the JHDM2 histone demethylase family.
genes like me logo Genes that share domains with KDM3B: view

Function for KDM3B Gene

Molecular function for KDM3B Gene

UniProtKB/Swiss-Prot Function:
Histone demethylase that specifically demethylates Lys-9 of histone H3, thereby playing a central role in histone code. Demethylation of Lys residue generates formaldehyde and succinate. May have tumor suppressor activity.

Enzyme Numbers (IUBMB) for KDM3B Gene

Gene Ontology (GO) - Molecular Function for KDM3B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000976 transcription regulatory region sequence-specific DNA binding IBA --
GO:0016209 antioxidant activity IEA --
GO:0016491 oxidoreductase activity IEA --
GO:0031490 chromatin DNA binding IBA --
GO:0032452 histone demethylase activity TAS --
genes like me logo Genes that share ontologies with KDM3B: view
genes like me logo Genes that share phenotypes with KDM3B: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for KDM3B Gene

Localization for KDM3B Gene

Subcellular locations from UniProtKB/Swiss-Prot for KDM3B 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 KDM3B gene
Compartment Confidence
nucleus 5
golgi apparatus 2
plasma membrane 1
extracellular 1
endoplasmic reticulum 1
cytosol 1
lysosome 1

Gene Ontology (GO) - Cellular Components for KDM3B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000785 chromatin IBA --
GO:0005634 nucleus IEA,IBA --
GO:0005654 nucleoplasm TAS --
genes like me logo Genes that share ontologies with KDM3B: view

Pathways & Interactions for KDM3B Gene

genes like me logo Genes that share pathways with KDM3B: view

Pathways by source for KDM3B Gene

1 Cell Signaling Technology pathway for KDM3B Gene

Gene Ontology (GO) - Biological Process for KDM3B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IBA,IEA --
GO:0016569 covalent chromatin modification IEA --
GO:0033169 histone H3-K9 demethylation IBA --
GO:0055114 oxidation-reduction process IEA --
genes like me logo Genes that share ontologies with KDM3B: view

No data available for SIGNOR curated interactions for KDM3B Gene

Drugs & Compounds for KDM3B Gene

(2) Drugs for KDM3B Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(1) Additional Compounds for KDM3B Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with KDM3B: view

Transcripts for KDM3B Gene

Unigene Clusters for KDM3B Gene

Lysine (K)-specific demethylase 3B:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for KDM3B Gene

ExUns: 1 ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14a · 14b ^ 15 ^ 16a · 16b ^ 17a · 17b ^ 18a · 18b ^ 19a · 19b ^
SP1: - - -
SP2: - - -
SP3:
SP4: -
SP5:
SP6:
SP7:

ExUns: 20a · 20b ^ 21 ^ 22 ^ 23 ^ 24 ^ 25 ^ 26
SP1: -
SP2: -
SP3:
SP4:
SP5:
SP6:
SP7:

Relevant External Links for KDM3B Gene

GeneLoc Exon Structure for
KDM3B
ECgene alternative splicing isoforms for
KDM3B

Expression for KDM3B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for KDM3B Gene

Protein differential expression in normal tissues from HIPED for KDM3B Gene

This gene is overexpressed in Peripheral blood mononuclear cells (9.6), Testis (8.1), CD8 Tcells (7.6), and CD4 Tcells (6.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for KDM3B Gene



Protein tissue co-expression partners for KDM3B Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of KDM3B Gene:

KDM3B

SOURCE GeneReport for Unigene cluster for KDM3B Gene:

Hs.483486

mRNA Expression by UniProt/SwissProt for KDM3B Gene:

Q7LBC6-KDM3B_HUMAN
Tissue specificity: Ubiquitous. Highly expressed in placenta, skeletal muscle, kidney, heart and liver.

Evidence on tissue expression from TISSUES for KDM3B Gene

  • Nervous system(4.6)
  • Bone marrow(4.2)
  • Eye(4.2)
genes like me logo Genes that share expression patterns with KDM3B: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for KDM3B Gene

Orthologs for KDM3B Gene

This gene was present in the common ancestor of animals.

Orthologs for KDM3B Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia KDM3B 34 35
  • 99.75 (n)
dog
(Canis familiaris)
Mammalia KDM3B 34 35
  • 93.68 (n)
cow
(Bos Taurus)
Mammalia KDM3B 34 35
  • 93.42 (n)
rat
(Rattus norvegicus)
Mammalia Kdm3b 34
  • 89.94 (n)
mouse
(Mus musculus)
Mammalia Kdm3b 34 16 35
  • 89.53 (n)
oppossum
(Monodelphis domestica)
Mammalia KDM3B 35
  • 89 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia KDM3B 35
  • 65 (a)
OneToOne
chicken
(Gallus gallus)
Aves KDM3B 34 35
  • 77.32 (n)
lizard
(Anolis carolinensis)
Reptilia KDM3B 35
  • 80 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia kdm3b 34
  • 67.96 (n)
zebrafish
(Danio rerio)
Actinopterygii wu:fe01c10 34
  • 60.25 (n)
IM:7163548 35
  • 52 (a)
OneToOne
wufa12c09 34
fruit fly
(Drosophila melanogaster)
Insecta JHDM2 35
  • 41 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.7055 35
  • 42 (a)
OneToMany
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.509 34
Species where no ortholog for KDM3B 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)
  • 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)
  • 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)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for KDM3B Gene

ENSEMBL:
Gene Tree for KDM3B (if available)
TreeFam:
Gene Tree for KDM3B (if available)

Paralogs for KDM3B Gene

Paralogs for KDM3B Gene

(3) SIMAP similar genes for KDM3B Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with KDM3B: view

Variants for KDM3B Gene

Sequence variations from dbSNP and Humsavar for KDM3B Gene

SNP ID Clin Chr 05 pos Sequence Context AA Info Type
rs1000011653 -- 138,388,938(+) CACCT(G/T)TTTAT intron-variant
rs1000014593 -- 138,359,358(+) GGTTT(C/T)GCCAT intron-variant
rs1000018624 -- 138,388,888(+) CCAAC(A/G)GGAAA intron-variant
rs1000040982 -- 138,394,060(+) AAATT(G/T)CAGCC intron-variant
rs1000073473 -- 138,373,077(+) CTCAC(A/G)CCTTG intron-variant

Structural Variations from Database of Genomic Variants (DGV) for KDM3B Gene

Variant ID Type Subtype PubMed ID
dgv1140e214 CNV gain 21293372
dgv3180n106 CNV deletion 24896259
esv1001610 CNV gain 20482838
esv1005958 CNV insertion 20482838
esv1007306 CNV insertion 20482838
esv1009373 CNV insertion 20482838
esv2664045 CNV deletion 23128226
esv2861124 CNV duplication 24192839
esv3575885 CNV gain 25503493
esv997516 CNV gain 20482838
nsv1033604 CNV gain 25217958
nsv1123986 CNV deletion 24896259

Variation tolerance for KDM3B Gene

Residual Variation Intolerance Score: 1.43% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.97; 68.16% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for KDM3B Gene

Human Gene Mutation Database (HGMD)
KDM3B
SNPedia medical, phenotypic, and genealogical associations of SNPs for
KDM3B

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for KDM3B Gene

Disorders for KDM3B Gene

MalaCards: The human disease database

(1) MalaCards diseases for KDM3B Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
persistent hyperplastic primary vitreous
  • phpv
- elite association - COSMIC cancer census association via MalaCards
Search KDM3B in MalaCards View complete list of genes associated with diseases

Relevant External Links for KDM3B

Genetic Association Database (GAD)
KDM3B
Human Genome Epidemiology (HuGE) Navigator
KDM3B
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
KDM3B
genes like me logo Genes that share disorders with KDM3B: view

No data available for UniProtKB/Swiss-Prot and Genatlas for KDM3B Gene

Publications for KDM3B Gene

  1. Identification and characterization of JMJD2 family genes in silico. (PMID: 15138608) Katoh M. … Katoh M. (Int. J. Oncol. 2004) 2 3 22 64
  2. A novel nuclear protein, 5qNCA (LOC51780) is a candidate for the myeloid leukemia tumor suppressor gene on chromosome 5 band q31. (PMID: 11687974) Hu Z. … Westbrook C.A. (Oncogene 2001) 3 4 22 64
  3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose J.E. … Uhl G.R. (Mol. Med. 2010) 3 46 64
  4. Thirty new loci for age at menarche identified by a meta-analysis of genome-wide association studies. (PMID: 21102462) Elks C.E. … Murray A. (Nat. Genet. 2010) 3 46 64
  5. JHDM2A, a JmjC-containing H3K9 demethylase, facilitates transcription activation by androgen receptor. (PMID: 16603237) Yamane K. … Zhang Y. (Cell 2006) 3 4 64

Products for KDM3B Gene

Sources for KDM3B Gene

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