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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
  • 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 Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins.. Gene Ontology (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

Additional gene information 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

GeneHancer (GH) Regulatory Elements for KDM3B Gene

Promoters and enhancers for KDM3B 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
GH05J138350 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 696.5 +0.7 739 4.7 PKNOX1 FOXA2 ARNT ARID4B SIN3A FEZF1 ZNF2 IRF4 YY1 SLC30A9 KDM3B CDC23 BRD8 HNRNPA0 FAM53C RPL7P19 FAM13B KIF20A GFRA3 REEP2
GH05J138463 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 47 +112.7 112653 4.1 CLOCK IRF4 YY1 E2F8 ZNF143 SP3 SSRP1 ZNF610 ZNF585B GLIS1 EGR1 HNRNPA0 CDC23 BRD8 KDM3B RPL7P19 ETF1 FAM13B FAM53C REEP2
GH05J138335 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 49 -15.1 -15056 5 CLOCK ZFP64 FEZF1 DMAP1 YBX1 IRF4 YY1 ZNF213 E2F8 ZNF143 CDC25C FAM53C HNRNPA0 KDM3B CDC23 RPL7P19 REEP2 MATR3 BRD8 NME5
GH05J139270 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE 39.1 +922.5 922451 8.2 CLOCK MLX FEZF1 DMAP1 IRF4 YY1 ZNF143 SP3 MEF2D ZNF610 MATR3 SNORA74D SNHG4 ENSG00000280987 KDM3B RPL7P19 SLC23A1 DNAJC18 ETF1 LOC105379194
GH05J139341 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 43.8 +989.7 989719 2.6 MLX DMAP1 YY1 SLC30A9 ZNF213 E2F8 ZNF143 ZNF548 SP3 ZNF610 PAIP2 PURA KDM3B RPL7P19 ENSG00000232174 SLC23A1 MZB1 PROB1 MATR3 SNORA74A
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around KDM3B on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the KDM3B gene promoter:
  • NF-kappaB1
  • NF-kappaB
  • STAT3
  • ATF-2
  • STAT5A

Genomic Locations for KDM3B Gene

Genomic Locations for KDM3B Gene
chr5:138,352,596-138,437,028
(GRCh38/hg38)
Size:
84,433 bases
Orientation:
Plus strand
chr5:137,688,285-137,772,717
(GRCh37/hg19)
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

Post-translational modifications for KDM3B Gene

  • Ubiquitination at Lys1272, isoforms=2926, Lys913, and Lys204
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for KDM3B Gene

Domains & Families for KDM3B Gene

Gene Families for KDM3B Gene

HGNC:
Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins
  • Predicted secreted proteins

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.
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

Phenotypes From GWAS Catalog 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

Clone 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

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for KDM3B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000785 chromatin IBA --
GO:0005634 nucleus 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 KEGG pathway 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 IEA --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IBA --
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:

Clone 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, 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

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 33
  • 99.75 (n)
OneToOne
dog
(Canis familiaris)
Mammalia KDM3B 34 33
  • 93.68 (n)
OneToOne
cow
(Bos Taurus)
Mammalia KDM3B 34 33
  • 93.42 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Kdm3b 33
  • 89.94 (n)
mouse
(Mus musculus)
Mammalia Kdm3b 16 34 33
  • 89.53 (n)
oppossum
(Monodelphis domestica)
Mammalia KDM3B 34
  • 89 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia KDM3B 34
  • 65 (a)
OneToOne
chicken
(Gallus gallus)
Aves KDM3B 34 33
  • 77.32 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia KDM3B 34
  • 80 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia kdm3b 33
  • 67.96 (n)
zebrafish
(Danio rerio)
Actinopterygii wu:fe01c10 33
  • 60.25 (n)
IM:7163548 34
  • 52 (a)
OneToOne
wufa12c09 33
fruit fly
(Drosophila melanogaster)
Insecta JHDM2 34
  • 41 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.7055 34
  • 42 (a)
OneToMany
Cin.509 33
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.509 33
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)
Aminode:
Evolutionary constrained regions (ECRs) for KDM3B: view image

Paralogs for KDM3B Gene

Paralogs for KDM3B Gene

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

  • KDM3B_HUMAN
  • F5H275_HUMAN
  • H0Y946_HUMAN
  • H0Y9V5_HUMAN
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 Variation AA Info Type
rs1000011653 -- 138,388,938(+) T/G intron_variant
rs1000014593 -- 138,359,358(+) C/T genic_upstream_transcript_variant, intron_variant
rs1000018624 -- 138,388,888(+) A/G intron_variant
rs1000040982 -- 138,394,060(+) T/G intron_variant
rs1000073473 -- 138,373,077(+) G/A genic_upstream_transcript_variant, 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)

Additional Variant Information for KDM3B Gene

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

SNP Genotyping and Copy Number Assay Products

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: HGMD and DISEASES

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

Additional Disease Information for KDM3B

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
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 (International journal of oncology 2004) 2 3 22 58
  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 CA (Oncogene 2001) 3 4 22 58
  3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58
  4. Thirty new loci for age at menarche identified by a meta-analysis of genome-wide association studies. (PMID: 21102462) Elks CE … Murray A (Nature genetics 2010) 3 44 58
  5. JHDM2A, a JmjC-containing H3K9 demethylase, facilitates transcription activation by androgen receptor. (PMID: 16603237) Yamane K … Zhang Y (Cell 2006) 3 4 58

Products for KDM3B Gene

Sources for KDM3B Gene

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