Human Gene KDM7A (uc003vvm.3)
  Description: Homo sapiens jumonji C domain containing histone demethylase 1 homolog D (S. cerevisiae) (KDM7A), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr7:139,784,546-139,876,741 Size: 92,196 Total Exon Count: 20 Strand: -
Coding Region
   Position: hg19 chr7:139,790,894-139,876,737 Size: 85,844 Coding Exon Count: 20 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:139,784,546-139,876,741)mRNA (may differ from genome)Protein (941 aa)
Gene SorterGenome BrowserOther Species FASTATable SchemaAlphaFoldBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHPRDLynxMGIneXtProtPubMed
ReactomeTreefamUniProtKB

-  Comments and Description Text from UniProtKB
  ID: KDM7_HUMAN
DESCRIPTION: RecName: Full=Lysine-specific demethylase 7; EC=1.14.11.-; AltName: Full=JmjC domain-containing histone demethylation protein 1D;
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.
COFACTOR: Binds 1 Fe(2+) ion per subunit.
BIOPHYSICOCHEMICAL PROPERTIES: Kinetic parameters: KM=1.2 uM for histone H3 H3K9Me2;
SUBCELLULAR LOCATION: Nucleus.
DOMAIN: The PHD-type zinc finger mediates the binding to H3K4me3. Binding to H3K4me3 prevents its access to H3K9me2.
DOMAIN: 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.
SIMILARITY: Belongs to the JHDM1 histone demethylase family. JHDM1D subfamily.
SIMILARITY: Contains 1 JmjC domain.
SIMILARITY: Contains 1 PHD-type zinc finger.
SEQUENCE CAUTION: Sequence=BAD18641.1; Type=Frameshift; Positions=902; Sequence=EAL24032.1; Type=Erroneous gene model prediction;

-  MalaCards Disease Associations
  MalaCards Gene Search: KDM7A
Diseases sorted by gene-association score: bone benign neoplasm (5)

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 11.27 RPKM in Skin - Sun Exposed (Lower leg)
Total median expression: 227.74 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
3' UTR -1658.946348-0.261 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR003347 - JmjC_dom
IPR019786 - Zinc_finger_PHD-type_CS
IPR011011 - Znf_FYVE_PHD
IPR001965 - Znf_PHD
IPR019787 - Znf_PHD-finger
IPR013083 - Znf_RING/FYVE/PHD

Pfam Domains:
PF00628 - PHD-finger
PF02373 - JmjC domain, hydroxylase
PF13621 - Cupin-like domain

SCOP Domains:
51182 - RmlC-like cupins
51197 - Clavaminate synthase-like
57903 - FYVE/PHD zinc finger

Protein Data Bank (PDB) 3-D Structure
MuPIT help
3KV5 - X-ray MuPIT 3KV6 - X-ray MuPIT 3KV9 - X-ray MuPIT 3KVA - X-ray MuPIT 3KVB - X-ray MuPIT 3U78 - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q6ZMT4
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologGenome BrowserNo orthologGenome BrowserNo ortholog
Gene Details   Gene Details 
Gene Sorter   Gene Sorter 
  Ensembl WormBase 
  Protein Sequence Protein Sequence 
  Alignment Alignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005506 iron ion binding
GO:0008270 zinc ion binding
GO:0016491 oxidoreductase activity
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
GO:0032452 histone demethylase activity
GO:0032454 histone demethylase activity (H3-K9 specific)
GO:0035064 methylated histone binding
GO:0035575 histone demethylase activity (H4-K20 specific)
GO:0046872 metal ion binding
GO:0051213 dioxygenase activity
GO:0051864 histone demethylase activity (H3-K36 specific)
GO:0071558 histone demethylase activity (H3-K27 specific)

Biological Process:
GO:0006325 chromatin organization
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0007399 nervous system development
GO:0030901 midbrain development
GO:0033169 histone H3-K9 demethylation
GO:0035574 histone H4-K20 demethylation
GO:0045893 positive regulation of transcription, DNA-templated
GO:0055114 oxidation-reduction process
GO:0070544 histone H3-K36 demethylation
GO:0071557 histone H3-K27 demethylation

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus


-  Descriptions from all associated GenBank mRNAs
  AK131497 - Homo sapiens cDNA FLJ16696 fis, clone TRACH3003832, weakly similar to Mus musculus PHD finger protein 2 (Phf2).
BC127007 - Homo sapiens jumonji C domain containing histone demethylase 1 homolog D (S. cerevisiae), mRNA (cDNA clone IMAGE:40108457), complete cds.
AB528281 - Synthetic construct DNA, clone: pF1KB6016, Homo sapiens JHDM1D gene for jumonji C domain containing histone demethylase 1 homolog D, without stop codon, in Flexi system.
AB051505 - Homo sapiens mRNA for KIAA1718 protein, partial cds.
BX649115 - Homo sapiens mRNA; cDNA DKFZp686M12109 (from clone DKFZp686M12109).
JD354489 - Sequence 335513 from Patent EP1572962.
JD502230 - Sequence 483254 from Patent EP1572962.
AK057208 - Homo sapiens cDNA FLJ32646 fis, clone SYNOV2001262.
BX641017 - Homo sapiens mRNA; cDNA DKFZp686I05109 (from clone DKFZp686I05109).
JD046396 - Sequence 27420 from Patent EP1572962.
JD452974 - Sequence 433998 from Patent EP1572962.
JD498846 - Sequence 479870 from Patent EP1572962.
JD344220 - Sequence 325244 from Patent EP1572962.
JD497970 - Sequence 478994 from Patent EP1572962.
JD491748 - Sequence 472772 from Patent EP1572962.
JD305063 - Sequence 286087 from Patent EP1572962.
JD490407 - Sequence 471431 from Patent EP1572962.
JD563302 - Sequence 544326 from Patent EP1572962.
JD297279 - Sequence 278303 from Patent EP1572962.
JD109726 - Sequence 90750 from Patent EP1572962.
JD486846 - Sequence 467870 from Patent EP1572962.
JD155111 - Sequence 136135 from Patent EP1572962.
JD109908 - Sequence 90932 from Patent EP1572962.
JD320148 - Sequence 301172 from Patent EP1572962.
JD166689 - Sequence 147713 from Patent EP1572962.
JD381339 - Sequence 362363 from Patent EP1572962.
JD521370 - Sequence 502394 from Patent EP1572962.
JD351319 - Sequence 332343 from Patent EP1572962.
JD359184 - Sequence 340208 from Patent EP1572962.
JD285165 - Sequence 266189 from Patent EP1572962.
JD263404 - Sequence 244428 from Patent EP1572962.
JD176068 - Sequence 157092 from Patent EP1572962.
JD559084 - Sequence 540108 from Patent EP1572962.
JD496489 - Sequence 477513 from Patent EP1572962.
JD441048 - Sequence 422072 from Patent EP1572962.
JD248415 - Sequence 229439 from Patent EP1572962.
JD555593 - Sequence 536617 from Patent EP1572962.
JD423435 - Sequence 404459 from Patent EP1572962.
JD566528 - Sequence 547552 from Patent EP1572962.
JD115517 - Sequence 96541 from Patent EP1572962.
JD276591 - Sequence 257615 from Patent EP1572962.
JD201361 - Sequence 182385 from Patent EP1572962.
JD369734 - Sequence 350758 from Patent EP1572962.
JD299198 - Sequence 280222 from Patent EP1572962.
JD316381 - Sequence 297405 from Patent EP1572962.
JD232126 - Sequence 213150 from Patent EP1572962.
JD311205 - Sequence 292229 from Patent EP1572962.
JD102581 - Sequence 83605 from Patent EP1572962.
JD279269 - Sequence 260293 from Patent EP1572962.
JD060939 - Sequence 41963 from Patent EP1572962.
JD243388 - Sequence 224412 from Patent EP1572962.
JD552686 - Sequence 533710 from Patent EP1572962.
JD496457 - Sequence 477481 from Patent EP1572962.
JD560268 - Sequence 541292 from Patent EP1572962.
JD093138 - Sequence 74162 from Patent EP1572962.
JD566542 - Sequence 547566 from Patent EP1572962.
JD291123 - Sequence 272147 from Patent EP1572962.
JD390307 - Sequence 371331 from Patent EP1572962.
JD301400 - Sequence 282424 from Patent EP1572962.
JD038251 - Sequence 19275 from Patent EP1572962.
JD379155 - Sequence 360179 from Patent EP1572962.
JD228907 - Sequence 209931 from Patent EP1572962.
JD113310 - Sequence 94334 from Patent EP1572962.
JD359708 - Sequence 340732 from Patent EP1572962.
JD036711 - Sequence 17735 from Patent EP1572962.
JD554339 - Sequence 535363 from Patent EP1572962.
JD305541 - Sequence 286565 from Patent EP1572962.
JD088578 - Sequence 69602 from Patent EP1572962.
JD428774 - Sequence 409798 from Patent EP1572962.
JD137181 - Sequence 118205 from Patent EP1572962.
JD038039 - Sequence 19063 from Patent EP1572962.
JD340396 - Sequence 321420 from Patent EP1572962.
JD173136 - Sequence 154160 from Patent EP1572962.
JD529609 - Sequence 510633 from Patent EP1572962.
JD226457 - Sequence 207481 from Patent EP1572962.
JD072926 - Sequence 53950 from Patent EP1572962.
JD113670 - Sequence 94694 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q6ZMT4 (Reactome details) participates in the following event(s):

R-HSA-4754187 KDM6A, KDM6B, KDM7A demethylate Me2K28-histone H3
R-HSA-5661121 KDM6A, KDM6B, KDM7A demethylate Me3K28-histone H3
R-HSA-4724284 KDM3A, KDM3B, KDM7A, PHF2:ARID5B, PHF8 demethylate MeK10-histone H3
R-HSA-5661115 KDM3A, KDM3B, KDM7A, PHF2:ARID5B, PHF8 demethylate Me2K10-histone H3
R-HSA-6802927 BRAF and RAF fusion mutant dimers are phosphorylated
R-HSA-6802934 p-BRAF and RAF fusion dimers bind MAP2Ks and MAPKs
R-HSA-6802932 Dissociation of BRAF/RAF fusion complex
R-HSA-6802933 p-BRAF and RAF fusion dimers phosphorylate MAP2Ks
R-HSA-6802935 MAPKs are phosphorylated downstream of BRAF and RAF fusion dimers
R-HSA-3214842 HDMs demethylate histones
R-HSA-6802952 Signaling by BRAF and RAF fusions
R-HSA-3247509 Chromatin modifying enzymes
R-HSA-6802957 Oncogenic MAPK signaling
R-HSA-4839726 Chromatin organization
R-HSA-5663202 Diseases of signal transduction
R-HSA-1643685 Disease

-  Other Names for This Gene
  Alternate Gene Symbols: A4D1S9, C9JJH9, C9JQU2, JHDM1D, KDM7, KDM7_HUMAN, KIAA1718, NM_030647, NP_085150, Q6MZL8, Q6ZMT4, Q9C0E5
UCSC ID: uc003vvm.3
RefSeq Accession: NM_030647
Protein: Q6ZMT4 (aka KDM7_HUMAN)
CCDS: CCDS43658.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_030647.1
exon count: 20CDS single in 3' UTR: no RNA size: 9178
ORF size: 2826CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 5852.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.