Aliases &
Descriptions
for JHDM1D gene
(According to
1HGNC,
2Entrez Gene,
3UniProtKB/Swiss-Prot,
4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc
, and/or 7Ensembl,
8miRBase)
About This Section
|
| Aliases & Descriptions |
|---|
| jumonji C domain containing histone demethylase 1 homolog D (S. cerevisiae)1 2 | | jumonji C domain-containing histone demethylase 1 homolog D2 | | KIAA17181 2 3 | | lysine-specific demethylase 72 | | JmjC domain-containing histone demethylation protein 1D2 3 | | KDM73 | | KDM7A2 | | EC 1.14.11.-3 | | histone lysine demethylase JHDM1D2 | | |
Export aliases for JHDM1D gene to outside databasesPrevious GC identifers: GC07M139432 GC07M139784 |
Summaries
for JHDM1D gene(According to Entrez Gene,
Tocris Bioscience,
Wikipedia's
Gene Wiki,
UniProtKB/Swiss-Prot,
and/or
UniProtKB/TrEMBL)
About This Section
|
UniProtKB/Swiss-Prot: KDM7_HUMAN, Q6ZMT4Function: 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 H4K20Me1only when nucleosome is used as a substrate and when not histone octamer is used as substrate
|
Genomic Views
for JHDM1D gene
(According to
GeneLoc and/or
HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to
UCSC (hg19) and
Ensembl (release 60),
Regulatory elements and Epigenetics data according to
Qiagen and/or
SABiosciences)
About This Section
|
Regulatory elements:
 Search SABiosciences Regulatory transcription factor binding sites for JHDM1D
Other transcription factors
Search SABiosciences Chromatin IP Primers for JHDM1D
Epigenetics:
|  | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays  |
Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track
Entrez Gene cytogenetic band: 7q34 Ensembl cytogenetic band: 7q34 HGNC cytogenetic band: 7q34JHDM1D Gene in genomic location: bands according to Ensembl, locations according to
 (and/or Entrez Gene and/or Ensembl if different)
GeneLoc gene densities for chromosome 7 GeneLoc Exon Structure GeneLoc location for GC07M134078: view genomic region
(about GC identifiers)
Start:
|
134,078,435 bp from pter |
End:
|
134,132,804 bp from pter |
Size:
|
54,370 bases |
Orientation:
|
minus strand |
1 alternative location:
| Chr7- 139,784,546-139,876,835 |
RefSeq DNA sequence:- NC_000007.13 NT_007914.15 NT_079596.2
|
Proteins
for JHDM1D gene
(According to
1UniProtKB,
neXtProt,
and/or Ensembl,
Phosphorylation sites according to 2Phosphosite,
RefSeq according to NCBI,
PDB rendering according to OCA and/or Proteopedia,
Recombinant Proteins
from
Millipore,
Sigma-Aldrich,
R&D Systems,
GenScript,
Enzo Life Sciences,
OriGene,
Novus Biologicals,
Sino Biological, and/or
ProSpec,
Biochemical Assays by
Millipore,
Sigma-Aldrich,
R&D Systems,
OriGene,
GenScript,
Cell Signaling Technology,
Enzo Life Sciences, and/or
Uscn,
Ontologies according to Gene
Ontology Consortium 01 Dec 2010 and
Entrez Gene,
Antibodies by
Millipore,
Sigma-Aldrich,
R&D Systems,
GenScript,
Cell Signaling Technology,
OriGene,
Novus Biologicals, and/or
Epitomics)
About This Section
|
UniProtKB/Swiss-Prot: KDM7_HUMAN, Q6ZMT4 (See
protein sequence)Recommended Name: Lysine-specific demethylase 7 Size: 941 amino acids; 106557 Da
Cofactor: Binds 1 Fe(2+) ion per subunit
Subcellular location: Nucleus
Sequence caution: Sequence=BAD18641.1; Type=Frameshift; Positions=902; Sequence=EAL24032.1; Type=Erroneous gene modelprediction;
PDB structures from  and Proteopedia  :3KV5 (3D)
3KV6 (3D)
3KV9 (3D)
3KVA (3D)
3KVB (3D)
Secondary accessions: A4D1S9 C9JJH9 C9JQU2 Q6MZL8 Q9C0E5Alternative splicing: 2 isoforms: Q6ZMT4-1 Q6ZMT4-2 Explore the universe of human proteins at neXtProt for JHDM1D: NX_Q6ZMT4
REFSEQ proteins: NP_085150.1
ENSEMBL proteins: ENSP00000006967 ENSP00000380692 ENSP00000420143
Human Recombinant Proteins
2 Gene Ontology (GO) cellular component terms (GO ID links to tree view): About this table
JHDM1D for ontologies About GeneDecksing
Antibodies for JHDM1D:
Assays for JHDM1D: |
Protein
Domains/
Families
for JHDM1D gene(According to InterPro, ProtoNet,
UniProtKB, and/or BLOCKS,
Sets of similar genes according to GeneDecks)
About This Section
|
JHDM1D for domains About GeneDecksing
5/7 InterPro domains/families (see all 7):Graphical View of Domain Structure for InterPro Entry Q6ZMT4ProtoNet protein and cluster: Q6ZMT4 1 Blocks protein family: IPB003347 Transcription factor jumonji
UniProtKB/Swiss-Prot: KDM7_HUMAN, Q6ZMT4Domain: The PHD-type zinc finger mediates the binding to H3K4me3. Binding to H3K4me3 prevents its access to H3K9me2Domain: The linker region is a critical determinant of demethylase specificity. It prevents the active site of JmjC toreach the target H3K9me2 when the PHD-type zinc finger binds to H3K4me3, while it favors selectivity toward H3K27me2Similarity: Belongs to the JHDM1 histone demethylase family. JHDM1D subfamilySimilarity: Contains 1 JmjC domainSimilarity: Contains 1 PHD-type zinc finger |
Gene Function
for JHDM1D gene
(According to UniProtKB,
IUBMB,and/or
Genatlas, Animal models from MGI Dec 24 2010,
shRNA from
OriGene,
Sigma-Aldrich,
RNAi from
Millipore,
siRNAs from
Sigma-Aldrich,
OriGene,
Qiagen,
Super-pooled esiRNAs from Sigma-Aldrich,
microRNA from Sigma-Aldrich,
Qiagen,
SABiosciences,
Clones from Millipore,
Sigma-Aldrich,
OriGene,
GenScript,
Sino Biological,
Cell Lines from GenScript,
Ontologies according to Gene Ontology Consortium 01 Dec 2010 via
Entrez Gene.)
About This Section
|
UniProtKB/Swiss-Prot: KDM7_HUMAN, Q6ZMT4Function: 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 H4K20Me1only when nucleosome is used as a substrate and when not histone octamer is used as substrateBiophysicochemical properties: Kinetic parameters: KM=1.2 uM for histone H3 H3K9Me2;Enzyme Number (IUBMB): EC 1.14.11.-
5/12 Gene Ontology (GO) molecular function terms (GO ID links to tree view) (see all 12): | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0005506 | iron ion binding |
TAS | -- | | GO:0005515 | protein binding |
IEA | -- | | GO:0008270 | zinc ion binding |
IDA | -- | | GO:0016491 | oxidoreductase activity |
IEA | -- | | GO:0016702 | oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen |
IEA | -- |
About this table
JHDM1D for ontologies About GeneDecksing
|
Pathways & Interactions
for JHDM1D gene
(Pathways according to
Millipore,
Cell Signaling Technology,
Sigma-Aldrich,
KEGG
and/or UniProtKB,
Sets of similar genes according to GeneDecks,
PCR Arrays from
SABiosciences,
Proteins Network according to
SABiosciences,
Sigma-Aldrich,
Interactions according to 1UniProtKB,
2MINT, and/or
3STRING,
with links to IntAct and
Ensembl,
Ontologies according to Gene Ontology Consortium 01 Dec 2010 via
Entrez Gene).
About This Section
|
SABiosciences Custom Pathway-Focused PCR Arrays for JHDM1D
Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for JHDM1D
5/10 Gene Ontology (GO) biological process terms (GO ID links to tree view) (see all 10): About this table
JHDM1D for ontologies About GeneDecksing
|
Drugs & Compounds
for JHDM1D gene(Chemical Compounds according to UniProtKB, Enzo Life Sciences,
Sigma-Aldrich, Tocris Bioscience, and/or
Novoseek and Drugs according to
Enzo Life Sciences and/or
PharmGKB)
About This Section
|
 Browse Tocris compounds for JHDM1D
|
Transcripts
for JHDM1D gene(GenBank/EMBL/DDBJ Accessions according to
Unigene
(Build 228 Homo sapiens; Dec 8 2010) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or
AceView,
transcript ids from Ensembl
with links to UCSC,
non coding RNAs according to
RNAdb,
ESTs according to GeneTide,
exon structure from GeneLoc,
alternative splicing isoforms according to ASD and/or
ECgene,
RNAi Products from
Millipore,
siRNAs from
Sigma-Aldrich,
OriGene,
Qiagen,
Super-pooled esiRNAs from Sigma-Aldrich,
shRNA from
Sigma-Aldrich,
OriGene,
microRNA from Sigma-Aldrich,
Qiagen,
SABiosciences,
Tagged/untagged cDNA clones from
OriGene,
Sigma-Aldrich,
GenScript,
Primers from
OriGene and/or
SABiosciences)
About This Section
|
REFSEQ mRNAs for JHDM1D gene: NM_030647.1 Additional cDNA sequence: AB051505.1 AK057208.1 AK131497.1 BC127006.1 BC127007.1 BX641017.1 BX649115.1 6 DOTS entries: DT.213389 DT.95168311 DT.99965433 DT.40221597 DT.91983211 DT.95168309 10 AceView cDNA sequences: AI813397 AI671992 AI672783 AI002118 BX106614 BF806223 AI143364 AW972132 BQ317991 BF825492 Unigene Cluster for JHDM1D: Jumonji C domain containing histone demethylase 1 homolog D (S. cerevisiae) Hs.308710 [show with all ESTs]Unigene Representative Sequence: NM_030647
GeneLoc Exon Structure
2 Alternative Splicing Database (ASD) splice patterns (SP) for JHDM1D
| ExUns: | 1 | ^ | 2 | ^ | 3 | ^ | 4 | ^ | 5 | ^ | 6 | ^ | 7 | ^ | 8 | ^ | 9 | ^ | 10 | ^ | 11 | ^ | 12 | ^ | 13 | ^ | 14 | ^ | 15 |
|---|
|
| SP1: | | | | | | | | | | | | | | | | | | | | | | | | | - | | | | | | |
| SP2: | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
About this scheme
ECgene alternative splicing isoforms for JHDM1D
4 Ensembl transcripts including schematic representations, and UCSC links where relevant: ENST00000478996 ENST00000006967 ENST00000397560(uc010lng.2 uc003vvm.2)
ENST00000472616
|
Expression
for JHDM1D gene
(Experimental results according to
1GeneNote
and GNF BioGPS,
probe sets-to-genes annotations according to
2GeneAnnot ,
3GeneTide ,
Sets of similar genes according to GeneDecks,
Electronic Northern calculations according to data from
UniGene (Build 228 Homo sapiens),
SAGE tags according to
CGAP,
plus additional links to
SOURCE, and/or
GNF
BioGPS, and/or
EXPOLDB, and/or
UniProtKB,
Primers from
OriGene and/or
SABiosciences
)
About This Section
| JHDM1D expression in normal and diseased human tissues
1 / 2 7 probe-sets matching JHDM1D gene
Affymetrix
probe-set |
Array |
GeneAnnot data |
GeneNote data |
GeneTide data |
| # genes |
Sensitivity |
Specificity |
Correlation |
Length |
Gb_Accession |
Consensus |
Uniqueness |
Score |
Rank |
| 78471_at2
|
U95-E |
1 |
1.00 |
1.00 |
0.38 |
1.68 |
-- |
-- |
-- |
-- |
-- |
| 32910_at2
|
U95-A |
1 |
1.00 |
1.00 |
-0.18 |
0.28 |
-- |
-- |
-- |
-- |
-- |
| 54435_r_at2
|
U95-C |
1 |
0.69 |
1.00 |
0.83 |
0.37 |
-- |
-- |
-- |
-- |
-- |
| 225142_at2
|
U133-B |
1 |
1.00 |
1.00 |
-- |
-- |
-- |
-- |
-- |
-- |
-- |
| 221778_at2
|
U133-A |
1 |
1.00 |
1.00 |
-- |
-- |
-- |
-- |
-- |
-- |
-- |
| 225142_at2
|
U133Plus2 |
1 |
1.00 |
1.00 |
-- |
-- |
-- |
-- |
-- |
-- |
-- |
| 221778_at2
|
U133Plus2 |
1 |
1.00 |
1.00 |
-- |
-- |
-- |
-- |
-- |
-- |
-- |
About this table
JHDM1D for expression About GeneDecksing
Data from
Genenote
(Publications) and GNF BioGPS
About these images
About these images
CGAP SAGE TAG: TGTGTCCTTT
SOURCE GeneReport for Unigene cluster: Hs.308710
SABiosciences Custom PCR Arrays for JHDM1D
|
Orthologs
for JHDM1D gene
(Orthologs according to
1,2HomoloGene (2older version, for species not in 1newer version),
3euGenes,
4SGD
and/or
5MGI Dec 24 2010,
with possible further links to
Flybase
and/or
WormBase,
Gene Trees according to Ensembl)
About This Section
|
Orthologs for JHDM1D gene from 5/6 species (see all 6)
About this table Species with no ortholog for JHDM1D
ENSEMBL Gene Tree for JHDM1D (if available) |
Paralogs
for JHDM1D gene(Paralogs according to 1HomoloGene
and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
About This Section
| Paralogs for JHDM1D gene
- PHF22 PHF82 KDM2A2 KDM2B2 FBXL192
JHDM1D for paralogs About GeneDecksing
|
Genomic Variants
for JHDM1D gene(SNPs according to the
1NCBI SNP Database,
2Ensembl,
3PupaSUITE, and
UniProtKB,
Linkage Disequilibrium by HapMap,
Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Resequencing Primers from Qiagen)
About This Section
|
| Genomic Data | Transcription Related Data | Allele Frequencies | | SNP ID | Valid | Chr 7 pos | Sequence | Recs | AA
Chg | Type | More | Recs | Allele
freq | Pop | Total
sample | More |
|---|
About this tableHapMap Linkage Disequilibrium images for JHDM1D (up to first 250kb)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 2 variations for JHDM1D
2 CNVs: 64962 100148 |
Disorders & Mutations
for JHDM1D gene
(in which this Gene is Involved, According to
OMIM, UniProtKB,
PharmGKB,
Genatlas, GeneTests,
Blood group antigen gene mutations by BGMUT,
LSDB, HGMD, GAD,
HuGE Navigator,
and/or TGDB.)
About This Section
| -- |
Medical News
for JHDM1D gene(Possibly Related Articles in
Doctor's Guide)
About This Section
| -- |
Publications
for JHDM1D gene (in
PubMed.
Associations of this gene to articles via
1Entrez Gene,
2UniProtKB/Swiss-Prot,
3HGNC,
4GAD,
5PharmGKB,
6UniProtKB/TrEMBL, and/or
7Novoseek)
About This Section
|
10/11 PubMed articles for JHDM1D gene, integrated from 7 sources (see all 11):
(articles sorted by number of sources associating them with JHDM1D)- Dual-specificity histone demethylase KIAA1718 (KDM7A) regulates neural differentiation through FGF4. (PubMed id 20084082)1, 3 Huang C....Chen C.D. (2010)
- Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
- Prediction of the coding sequences of unidentified human genes. XIX. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PubMed id 11214970)1, 2 Nagase T.... Ohara O. (2000)
- Histone H4K20/H3K9 demethylase PHF8 regulates zebrafish brain and craniofacial development. (PubMed id 20622853)2 Qi H.H....Shi Y. (2010)
- Enzymatic and structural insights for substrate specificity of a family of jumonji histone lysine demethylases. (PubMed id 20023638)2 Horton J.R.... Cheng X. (2010)
- KDM7 is a dual demethylase for histone H3 Lys 9 and L ys 27 and functions in brain development. (PubMed id 20194436)2 Tsukada Y....Nakayama K.I. (2010)
- Toward a confocal subcellular atlas of the human proteome. (PubMed id 18029348)1 Barbe L....Andersson-Svahn H. (2008)
- The full-ORF clone resource of the German cDNA consortium. (PubMed id 17974005)2 Bechtel S.... Schupp I. (2007)
- Human chromosome 7: DNA sequence and biology. (PubMed id 12690205)2 Scherer S.W.... Tsui L.-C. (2003)
- The DNA sequence of human chromosome 7. (PubMed id 12853948)2 Hillier L.W.... Wilson R.K. (2003)
|
External Searches for JHDM1D gene
(in PubMed,
OMIM, and NCBI Bookshelf)
About This Section
|
|
Genome Databases showing JHDM1D gene
(According to
Entrez Gene,
HGNC,
AceView,
euGenes,
Ensembl,
miRBase,
ECgene,
Kegg,
and/or
H-InvDB)
About This Section
|
|
Other Databases showing JHDM1D gene
(According to HUGE)
About This Section
| |
Specialized Databases showing JHDM1D gene(According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section
|
|
About This Section
| Patent Information for JHDM1D gene:
Search GeneIP for patents involving JHDM1D
GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search
|
Products
for JHDM1D gene(Antibodies, recombinant proteins, and assays by Millipore, Sigma-Aldrich, R&D Systems, Qiagen, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Epitomics, ProSpec, Uscn,
Clones available from Millipore, Sigma-Aldrich, OriGene, GenScript, Sino Biological, PCR Arrays from SABiosciences, Drugs and/or compounds by Sigma-Aldrich, Tocris Bioscience, and/or
Enzo Life Sciences)
About This Section
|
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| |  | Search Tocris compounds for JHDM1D |
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