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Aliases for KDM7A Gene

Aliases for KDM7A Gene

  • Lysine Demethylase 7A 2 3
  • Lysine (K)-Specific Demethylase 7A 2 3 5
  • JmjC Domain-Containing Histone Demethylation Protein 1D 3 4
  • Lysine-Specific Demethylase 7 3 4
  • JHDM1D 3 4
  • Jumonji C Domain Containing Histone Demethylase 1 Homolog D (S. Cerevisiae) 2
  • Jumonji C Domain Containing Histone Demethylase 1 Homolog D 3
  • Jumonji C Domain-Containing Histone Demethylase 1 Homolog D 3
  • Histone Lysine Demethylase JHDM1D 3
  • EC 1.14.11.- 4
  • KIAA1718 4
  • KDM7 4

External Ids for KDM7A Gene

Previous HGNC Symbols for KDM7A Gene

  • JHDM1D

Previous GeneCards Identifiers for KDM7A Gene

  • GC07M139785

Summaries for KDM7A Gene

GeneCards Summary for KDM7A Gene

KDM7A (Lysine Demethylase 7A) is a Protein Coding gene. Diseases associated with KDM7A include bone benign neoplasm and connective tissue benign neoplasm. Among its related pathways are Chromatin organization and Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3. GO annotations related to this gene include iron ion binding and oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors. An important paralog of this gene is KDM2B.

UniProtKB/Swiss-Prot for KDM7A Gene

  • Histone demethylase required for brain development. Specifically demethylates dimethylated Lys-9 and Lys-27 (H3K9me2 and H3K27me2, respectively) of histone H3 and monomethylated histone H4 Lys-20 residue (H4K20Me1), thereby playing a central role in histone code. Specifically binds trimethylated Lys-4 of histone H3 (H3K4me3), affecting histone demethylase specificity: in presence of H3K4me3, it has no demethylase activity toward H3K9me2, while it has high activity toward H3K27me2. Demethylates H3K9me2 in absence of H3K4me3. Has activity toward H4K20Me1 only when nucleosome is used as a substrate and when not histone octamer is used as substrate.

No data available for Entrez Gene Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for KDM7A Gene

Genomics for KDM7A Gene

Regulatory Elements for KDM7A Gene

Enhancers for KDM7A 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 KDM7A on UCSC Golden Path with GeneCards custom track

Promoters for KDM7A Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around KDM7A on UCSC Golden Path with GeneCards custom track

Genomic Location for KDM7A Gene

Chromosome:
7
Start:
140,084,746 bp from pter
End:
140,177,035 bp from pter
Size:
92,290 bases
Orientation:
Minus strand

Genomic View for KDM7A Gene

Genes around KDM7A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
KDM7A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for KDM7A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for KDM7A Gene

Proteins for KDM7A Gene

  • Protein details for KDM7A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q6ZMT4-KDM7A_HUMAN
    Recommended name:
    Lysine-specific demethylase 7A
    Protein Accession:
    Q6ZMT4
    Secondary Accessions:
    • A4D1S9
    • C9JJH9
    • C9JQU2
    • Q6MZL8
    • Q9C0E5

    Protein attributes for KDM7A Gene

    Size:
    941 amino acids
    Molecular mass:
    106557 Da
    Cofactor:
    Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAD18641.1; Type=Frameshift; Positions=902; Evidence={ECO:0000305}; Sequence=EAL24032.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for KDM7A Gene

    Alternative splice isoforms for KDM7A Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for KDM7A Gene

Proteomics data for KDM7A Gene at MOPED

Post-translational modifications for KDM7A Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for KDM7A Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for KDM7A Gene

Domains & Families for KDM7A Gene

Gene Families for KDM7A Gene

Suggested Antigen Peptide Sequences for KDM7A Gene

Graphical View of Domain Structure for InterPro Entry

Q6ZMT4

UniProtKB/Swiss-Prot:

KDM7A_HUMAN :
  • The PHD-type zinc finger mediates the binding to H3K4me3. Binding to H3K4me3 prevents its access to H3K9me2.
  • Belongs to the JHDM1 histone demethylase family. JHDM1D subfamily.
  • Contains 1 PHD-type zinc finger.
Domain:
  • The PHD-type zinc finger mediates the binding to H3K4me3. Binding to H3K4me3 prevents its access to H3K9me2.
  • The linker region is a critical determinant of demethylase specificity. It prevents the active site of JmjC to reach the target H3K9me2 when the PHD-type zinc finger binds to H3K4me3, while it favors selectivity toward H3K27me2.
  • Contains 1 JmjC domain.
Family:
  • Belongs to the JHDM1 histone demethylase family. JHDM1D subfamily.
Similarity:
  • Contains 1 PHD-type zinc finger.
genes like me logo Genes that share domains with KDM7A: view

Function for KDM7A Gene

Molecular function for KDM7A Gene

UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=1.2 uM for histone H3 H3K9Me2 {ECO:0000269 PubMed:20023638};
UniProtKB/Swiss-Prot Function:
Histone demethylase required for brain development. Specifically demethylates dimethylated Lys-9 and Lys-27 (H3K9me2 and H3K27me2, respectively) of histone H3 and monomethylated histone H4 Lys-20 residue (H4K20Me1), thereby playing a central role in histone code. Specifically binds trimethylated Lys-4 of histone H3 (H3K4me3), affecting histone demethylase specificity: in presence of H3K4me3, it has no demethylase activity toward H3K9me2, while it has high activity toward H3K27me2. Demethylates H3K9me2 in absence of H3K4me3. Has activity toward H4K20Me1 only when nucleosome is used as a substrate and when not histone octamer is used as substrate.

Enzyme Numbers (IUBMB) for KDM7A Gene

Gene Ontology (GO) - Molecular Function for KDM7A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IEA --
GO:0035064 methylated histone binding IDA 20023638
GO:0071558 histone demethylase activity (H3-K27 specific) IEA,IDA 20023638
genes like me logo Genes that share ontologies with KDM7A: view
genes like me logo Genes that share phenotypes with KDM7A: view

Animal Models for KDM7A Gene

MGI Knock Outs for KDM7A:

Animal Model Products

miRNA for KDM7A Gene

miRTarBase miRNAs that target KDM7A

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for KDM7A Gene

Localization for KDM7A Gene

Subcellular locations from UniProtKB/Swiss-Prot for KDM7A Gene

No data available for Subcellular locations from COMPARTMENTS and Gene Ontology (GO) - Cellular Components for KDM7A Gene

Pathways & Interactions for KDM7A Gene

genes like me logo Genes that share pathways with KDM7A: view

Pathways by source for KDM7A Gene

Interacting Proteins for KDM7A Gene

Gene Ontology (GO) - Biological Process for KDM7A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0035574 histone H4-K20 demethylation IDA 20622853
GO:0055114 oxidation-reduction process IEA --
GO:0070544 histone H3-K36 demethylation IDA 20622853
genes like me logo Genes that share ontologies with KDM7A: view

No data available for SIGNOR curated interactions for KDM7A Gene

Drugs & Compounds for KDM7A Gene

No Compound Related Data Available

Transcripts for KDM7A Gene

mRNA/cDNA for KDM7A Gene

(3) REFSEQ mRNAs :
(10) Selected AceView cDNA sequences:
(3) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Alternative Splicing Database (ASD) splice patterns (SP) for KDM7A Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15
SP1: -
SP2:

Relevant External Links for KDM7A Gene

GeneLoc Exon Structure for
KDM7A
ECgene alternative splicing isoforms for
KDM7A

Expression for KDM7A Gene

mRNA expression in normal human tissues for KDM7A Gene

mRNA differential expression in normal tissues according to GTEx for KDM7A Gene

This gene is overexpressed in Muscle - Skeletal (x4.3).

Protein differential expression in normal tissues from HIPED for KDM7A Gene

This gene is overexpressed in Vitreous humor (25.9), Stomach (19.4), Breast (11.5), and Lung (7.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for KDM7A Gene



genes like me logo Genes that share expression patterns with KDM7A: view

Primer Products

In Situ Assay Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA Expression by UniProt/SwissProt and Protein tissue co-expression partners for KDM7A Gene

Orthologs for KDM7A Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for KDM7A Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia KDM7A 36
  • 100 (a)
OneToOne
JHDM1D 35
  • 99.72 (n)
  • 99.68 (a)
platypus
(Ornithorhynchus anatinus)
Mammalia KDM7A 36
  • 79 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Jhdm1d 36
  • 90 (a)
OneToOne
Kdm7a 16
Kdm7a 35
  • 90.84 (n)
  • 90.24 (a)
oppossum
(Monodelphis domestica)
Mammalia KDM7A 36
  • 86 (a)
OneToOne
dog
(Canis familiaris)
Mammalia KDM7A 36
  • 94 (a)
OneToOne
JHDM1D 35
  • 93.55 (n)
  • 93.99 (a)
cow
(Bos Taurus)
Mammalia KDM7A 36
  • 93 (a)
OneToOne
JHDM1D 35
  • 93.46 (n)
  • 93.27 (a)
rat
(Rattus norvegicus)
Mammalia Jhdm1d 35
  • 90.66 (n)
  • 90.5 (a)
chicken
(Gallus gallus)
Aves KDM7A 36
  • 80 (a)
OneToOne
JHDM1D 35
  • 79.13 (n)
  • 80.57 (a)
lizard
(Anolis carolinensis)
Reptilia KDM7A 36
  • 70 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia kdm7a 35
  • 68.41 (n)
  • 71.33 (a)
zebrafish
(Danio rerio)
Actinopterygii kdm7ab 36
  • 56 (a)
OneToMany
kdm7aa 36
  • 54 (a)
OneToMany
kdm7ab 35
  • 63.21 (n)
  • 63.75 (a)
worm
(Caenorhabditis elegans)
Secernentea jmjd-1.2 36
  • 19 (a)
ManyToMany
jmjd-1.1 36
  • 27 (a)
ManyToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes JHD1 36
  • 27 (a)
OneToMany
Species with no ortholog for KDM7A:
  • 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)
  • 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)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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)

Evolution for KDM7A Gene

ENSEMBL:
Gene Tree for KDM7A (if available)
TreeFam:
Gene Tree for KDM7A (if available)

Paralogs for KDM7A Gene

Paralogs for KDM7A Gene

(2) SIMAP similar genes for KDM7A Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with KDM7A: view

Variants for KDM7A Gene

Sequence variations from dbSNP and Humsavar for KDM7A Gene

SNP ID Clin Chr 07 pos Sequence Context AA Info Type
VAR_049652 -
rs6950119 - 140,097,631(+) CACAC(A/G/T)TGTAA reference, missense
rs886645 -- 140,148,644(-) AAAAC(G/T)ATTAA intron-variant
rs987018 -- 140,170,996(-) CCTCC(C/T)GTTTC intron-variant
rs998975 -- 140,102,929(+) tccag(A/C)ggcaa intron-variant

Variation tolerance for KDM7A Gene

Residual Variation Intolerance Score: 16.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.56; 44.54% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for KDM7A Gene

HapMap Linkage Disequilibrium report
KDM7A
Human Gene Mutation Database (HGMD)
KDM7A

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for KDM7A Gene

Disorders for KDM7A Gene

MalaCards: The human disease database

(2) MalaCards diseases for KDM7A Gene - From: DISEASES

Disorder Aliases PubMed IDs
bone benign neoplasm
connective tissue benign neoplasm
  • neoplasm of soft tissue
- elite association - COSMIC cancer census association via MalaCards
Search KDM7A in MalaCards View complete list of genes associated with diseases

Relevant External Links for KDM7A

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
KDM7A
genes like me logo Genes that share disorders with KDM7A: view

No data available for UniProtKB/Swiss-Prot and Genatlas for KDM7A Gene

Publications for KDM7A Gene

  1. Enzymatic and structural insights for substrate specificity of a family of jumonji histone lysine demethylases. (PMID: 20023638) Horton J.R. … Cheng X. (Nat. Struct. Mol. Biol. 2010) 2 3 4 67
  2. Dual-specificity histone demethylase KIAA1718 (KDM7A) regulates neural differentiation through FGF4. (PMID: 20084082) Huang C. … Chen C.D. (Cell Res. 2010) 2 3
  3. Histone Modifier Genes Alter Conotruncal Heart Phenotypes in 22q11.2 Deletion Syndrome. (PMID: 26608785) Guo T. … Morrow B.E. (Am. J. Hum. Genet. 2015) 3
  4. Increased expression of histone demethylase JHDM1D under nutrient starvation suppresses tumor growth via down-regulating angiogenesis. (PMID: 22143793) Osawa T. … Shibuya M. (Proc. Natl. Acad. Sci. U.S.A. 2011) 3
  5. KDM7 is a dual demethylase for histone H3 Lys 9 and Lys 27 and functions in brain development. (PMID: 20194436) Tsukada Y. … Nakayama K.I. (Genes Dev. 2010) 3

Products for KDM7A Gene

Sources for KDM7A Gene

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