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Aliases for KDM3B Gene

Aliases for KDM3B Gene

  • Lysine Demethylase 3B 2 3
  • Lysine (K)-Specific Demethylase 3B 2 3 5
  • JmjC Domain-Containing Histone Demethylation Protein 2B 3 4
  • Jumonji Domain-Containing Protein 1B 3 4
  • Jumonji Domain Containing 1B 2 3
  • Nuclear Protein 5qNCA 3 4
  • C5orf7 3 4
  • JMJD1B 3 4
  • Chromosome 5 Open Reading Frame 7 2
  • EC 1.14.11.- 4
  • EC 1.14.11 63
  • 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 Chromatin organization and Chromatin Regulation / Acetylation. GO annotations related to this gene include dioxygenase activity. An important paralog of this gene is HR.

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 , 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 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 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

ENSRs around KDM3B on UCSC Golden Path with GeneCards custom track

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

Proteomics data for KDM3B Gene at MOPED

Post-translational modifications for KDM3B Gene

  • Ubiquitination at Lys 204, Lys 913, Lys 926, and Lys 1272
  • Modification sites at PhosphoSitePlus

Other Protein References for KDM3B Gene

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for KDM3B (JMJD1B)

Domains & Families for KDM3B Gene

Gene Families for KDM3B Gene

Protein Domains for KDM3B Gene

InterPro:
Blocks:
ProtoNet:

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.
  • Contains 1 JmjC domain.
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:0051213 dioxygenase activity IEA --
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

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
Jensen Localization Image for KDM3B Gene COMPARTMENTS Subcellular localization image for KDM3B gene
Compartment Confidence
nucleus 5
golgi apparatus 2
cytosol 1
endoplasmic reticulum 1
extracellular 1
lysosome 1
plasma membrane 1
vacuole 1

No data available for Gene Ontology (GO) - Cellular Components for KDM3B Gene

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:0006325 chromatin organization TAS --
GO:0006351 transcription, DNA-templated IEA --
GO:0055114 oxidation-reduction process IEA --
GO:0072718 response to cisplatin 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:

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 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, MOPED, and MaxQB for KDM3B Gene



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.
genes like me logo Genes that share expression patterns with KDM3B: view

Protein tissue co-expression partners for KDM3B Gene

- Elite partner

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues 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
cow
(Bos Taurus)
Mammalia KDM3B 35
  • 93.42 (n)
  • 96.3 (a)
KDM3B 36
  • 97 (a)
OneToOne
dog
(Canis familiaris)
Mammalia KDM3B 35
  • 93.68 (n)
  • 96.98 (a)
KDM3B 36
  • 97 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Kdm3b 35
  • 89.53 (n)
  • 93.36 (a)
Kdm3b 16
Kdm3b 36
  • 94 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia KDM3B 35
  • 99.75 (n)
  • 99.83 (a)
KDM3B 36
  • 100 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Kdm3b 35
  • 89.94 (n)
  • 93.64 (a)
oppossum
(Monodelphis domestica)
Mammalia KDM3B 36
  • 89 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia KDM3B 36
  • 65 (a)
OneToOne
chicken
(Gallus gallus)
Aves KDM3B 35
  • 77.32 (n)
  • 84.46 (a)
KDM3B 36
  • 84 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia KDM3B 36
  • 80 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia kdm3b 35
  • 67.96 (n)
  • 71.25 (a)
zebrafish
(Danio rerio)
Actinopterygii wu:fe01c10 35
  • 60.25 (n)
  • 60.02 (a)
wufa12c09 35
IM:7163548 36
  • 52 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta JHDM2 36
  • 41 (a)
OneToMany
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.509 35
sea squirt
(Ciona savignyi)
Ascidiacea CSA.7055 36
  • 42 (a)
OneToMany
Species with no ortholog for KDM3B:
  • 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
rs6865472 - 138,381,576(+) ATTCA(A/G)CGCCT reference, missense
rs7706614 - 138,419,119(+) AAATA(A/G)CAATA reference, missense
rs740077 -- 138,424,394(-) AGGTA(G/T)CTGTG intron-variant
rs11334 -- 138,436,607(+) GGTGT(C/G)TTCCC utr-variant-3-prime
rs757647 -- 138,371,626(-) AGACA(C/T)TTGCT intron-variant

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

Variant ID Type Subtype PubMed ID
esv2664045 CNV Deletion 23128226
esv1005958 CNV Insertion 20482838
esv1001610 CNV Gain 20482838
esv997516 CNV Gain 20482838
esv1009373 CNV Insertion 20482838
esv1007306 CNV Insertion 20482838

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

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

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. 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 23 67
  2. Identification and characterization of JMJD2 family genes in silico. (PMID: 15138608) Katoh M. … Katoh M. (Int. J. Oncol. 2004) 2 3 23
  3. Temporal proteomics of NGF-TrkA signaling identifies an inhibitory role for the E3 ligase Cbl-b in neuroblastoma cell differentiation. (PMID: 25921289) Emdal K.B. … Olsen J.V. (Sci Signal 2015) 3
  4. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin E.L. … Gygi S.P. (Cell 2015) 3
  5. A human interactome in three quantitative dimensions organized by stoichiometries and abundances. (PMID: 26496610) Hein M.Y. … Mann M. (Cell 2015) 3

Products for KDM3B Gene

Sources for KDM3B Gene

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