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KDM7A Gene(Protein Coding)

Lysine Demethylase 7A

GCID:
GC07M140084
GIFtS:
40
Genes Participants
UDN Logo

Aliases for KDM7A Gene

Aliases for KDM7A Gene

  • Lysine Demethylase 7A 2 3 5
  • JmjC Domain-Containing Histone Demethylation Protein 1D 3 4
  • Lysine (K)-Specific Demethylase 7A 2 3
  • 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
  • Histone Lysine Demethylase JHDM1D 3
  • Lysine-Specific Demethylase 7A 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 Oncogenic MAPK signaling and HIV Life Cycle. Gene Ontology (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 PHF8.

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.

Additional gene information for KDM7A Gene

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

Genomics for KDM7A Gene

Products:

  1. Regulatory Element

GeneHancer (GH) Regulatory Elements for KDM7A Gene

Promoters and enhancers for KDM7A 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
GH07I140174 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 559.3 +0.5 548 3.4 FEZF1 DMAP1 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 ZFP41 GLIS1 KDM7A GC07P140176 JHDM1D-AS1 UBN2 SLC37A3 PARP12 TBXAS1 ENSG00000251728 GC07M140095
GH07I140229 Enhancer 1.8 FANTOM5 Ensembl ENCODE dbSUPER 23.9 -54.8 -54802 5.7 PKNOX1 FOXA2 MLX ZFP64 ARID4B SIN3A FEZF1 DMAP1 IRF4 SLC30A9 KDM7A RNU6-797P JHDM1D-AS1 TBXAS1 RAB19 GC07P140221 RNU1-58P
GH07I140252 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 16.8 -76.1 -76069 2.2 FOXA2 MLX ARID4B ZNF48 ETS1 ATF7 RUNX3 SP5 REST MIER2 KDM7A RNU6-797P TBXAS1 RNU1-58P ENSG00000270512
GH07I140313 Enhancer 1.3 FANTOM5 Ensembl ENCODE 15.8 -138.6 -138629 3.7 FOXA2 RAD21 YY1 FOS RXRA CEBPB REST ELF1 ZNF217 SP1 KDM7A RNU6-797P TBXAS1 LOC105375534 RNA5SP247 SLC37A3
GH07I140317 Enhancer 1.1 FANTOM5 ENCODE 16.2 -140.8 -140759 0.2 HDAC1 PKNOX1 ARNT TCF12 GATA2 EGR1 ETV6 CREM NCOA1 NFIC KDM7A RNU6-797P TBXAS1 LOC105375534 RNA5SP247 SLC37A3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around KDM7A on UCSC Golden Path with GeneCards custom track

Genomic Locations for KDM7A Gene

Genomic Locations for KDM7A Gene
chr7:140,084,746-140,177,035
(GRCh38/hg38)
Size:
92,290 bases
Orientation:
Minus strand
chr7:139,784,546-139,876,835
(GRCh37/hg19)

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 Structure • Gene Density

RefSeq DNA sequence for KDM7A Gene

Proteins for KDM7A Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • 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

Protein Expression for KDM7A Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for KDM7A Gene

No Post-translational modifications

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

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

Protein Domains for KDM7A Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for KDM7A Gene

GenScript: Design optimal peptide antigens:

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.
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.
Family:
  • Belongs to the JHDM1 histone demethylase family. JHDM1D subfamily.
genes like me logo Genes that share domains with KDM7A: view

Function for KDM7A Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

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

Phenotypes From GWAS Catalog for KDM7A Gene

Gene Ontology (GO) - Molecular Function for KDM7A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005506 iron ion binding TAS 20194436
GO:0008270 zinc ion binding IDA 20023638
GO:0016491 oxidoreductase activity IEA --
GO:0016706 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 IDA 20023638
GO:0032452 histone demethylase activity TAS --
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

Inhibitory RNA Products

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

Nucleus.

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 KDM7A gene
Compartment Confidence
nucleus 5
extracellular 2
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for KDM7A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,IC 20023638
GO:0005654 nucleoplasm TAS --
GO:0005730 nucleolus IDA --
genes like me logo Genes that share ontologies with KDM7A: view

Pathways & Interactions for KDM7A Gene

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

Pathways by source 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:0006355 regulation of transcription, DNA-templated IEA --
GO:0007399 nervous system development IEA --
GO:0016569 covalent chromatin modification IEA --
GO:0030901 midbrain development ISS --
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

Products:

  1. Drug

(2) Drugs for KDM7A Gene - From: ApexBio and DGIdb

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
TC-E 5002 Pharma 0
Daminozide Pharma KDM2A inhibitor 7

(1) ApexBio Compounds for KDM7A Gene

Compound Action Cas Number
TC-E 5002 1453071-47-0
genes like me logo Genes that share compounds with KDM7A: view

Drug Products

Transcripts for KDM7A Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for KDM7A Gene

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

Inhibitory RNA Products

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

Products:

  1. Primer

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for KDM7A Gene

mRNA expression in normal human tissues for KDM7A Gene
mRNA expression by GTEx for KDM7A GenemRNA expression by BioGPS 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



NURSA nuclear receptor signaling pathways regulating expression of KDM7A Gene:

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

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer 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 34
  • 100 (a)
 OneToOne
JHDM1D 33
  • 99.72 (n)
dog
(Canis familiaris)
 Mammalia KDM7A 34
  • 94 (a)
 OneToOne
JHDM1D 33
  • 93.55 (n)
cow
(Bos Taurus)
 Mammalia JHDM1D 33
  • 93.46 (n)
KDM7A 34
  • 93 (a)
 OneToOne
mouse
(Mus musculus)
 Mammalia Kdm7a 33 16
  • 90.84 (n)
Jhdm1d 34
  • 90 (a)
 OneToOne
rat
(Rattus norvegicus)
 Mammalia Jhdm1d 33
  • 90.66 (n)
oppossum
(Monodelphis domestica)
 Mammalia KDM7A 34
  • 86 (a)
 OneToOne
platypus
(Ornithorhynchus anatinus)
 Mammalia KDM7A 34
  • 79 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves KDM7A 34
  • 80 (a)
 OneToOne
JHDM1D 33
  • 79.13 (n)
lizard
(Anolis carolinensis)
 Reptilia KDM7A 34
  • 70 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia kdm7a 33
  • 68.41 (n)
zebrafish
(Danio rerio)
 Actinopterygii kdm7ab 33 34
  • 63.21 (n)
kdm7aa 34
  • 54 (a)
 OneToMany
worm
(Caenorhabditis elegans)
 Secernentea jmjd-1.1 34
  • 27 (a)
 ManyToMany
jmjd-1.2 34
  • 19 (a)
 ManyToMany
baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes JHD1 34
  • 27 (a)
 OneToMany
Species where no ortholog for KDM7A 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)
  • 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 Variation AA Info Type
rs1000094529 -- 140,097,799(-) C/T intron_variant
rs1000119989 -- 140,152,854(-) G/A genic_upstream_transcript_variant, intron_variant
rs1000135774 -- 140,093,179(-) G/C intron_variant
rs1000170033 -- 140,171,475(-) TATATTTATATTTATATTTATAT/TATATTTATATTTATATTTATATTTATAT genic_upstream_transcript_variant, intron_variant
rs1000174506 -- 140,135,932(-) G/A genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for KDM7A Gene

Variant ID Type Subtype PubMed ID
dgv11623n54 CNV loss 21841781
dgv11624n54 CNV gain 21841781
dgv11625n54 CNV gain 21841781
dgv11626n54 CNV loss 21841781
dgv3678n106 CNV deletion 24896259
esv2622729 CNV deletion 19546169
esv2735212 CNV deletion 23290073
esv29440 CNV loss 19812545
nsv477579 CNV novel sequence insertion 20440878
nsv608478 CNV loss 21841781
nsv608479 CNV loss 21841781
nsv608480 CNV gain+loss 21841781
nsv608481 CNV gain 21841781
nsv608482 CNV loss 21841781
nsv608486 CNV loss 21841781
nsv608487 CNV gain+loss 21841781
nsv608496 CNV loss 21841781
nsv966894 CNV duplication 23825009

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)

Additional Variant Information for KDM7A Gene

Human Gene Mutation Database (HGMD)
KDM7A
SNPedia medical, phenotypic, and genealogical associations of SNPs for
KDM7A

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for KDM7A Gene

Disorders for KDM7A Gene

MalaCards: The human disease database

(2) MalaCards diseases for KDM7A Gene - From: HGMD and 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

Additional Disease Information for KDM7A

ATLAS of Genetics and Cytogenetics in Oncology and Haematology
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 JR … Cheng X (Nature structural & molecular biology 2010) 2 3 4 58
  2. Dual-specificity histone demethylase KIAA1718 (KDM7A) regulates neural differentiation through FGF4. (PMID: 20084082) Huang C … Chen CD (Cell research 2010) 2 3 58
  3. KDM7 is a dual demethylase for histone H3 Lys 9 and Lys 27 and functions in brain development. (PMID: 20194436) Tsukada Y … Nakayama KI (Genes & development 2010) 3 4 58
  4. Histone H4K20/H3K9 demethylase PHF8 regulates zebrafish brain and craniofacial development. (PMID: 20622853) Qi HH … Shi Y (Nature 2010) 3 4 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 KDM7A Gene

Sources for KDM7A Gene

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