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Category Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21

GIFtS
-

JHDM1D Gene

protein-coding GIFtS: 45
GCID: GC07M139784

jumonji C domain containing histone demethylase 1 homolog...

Explore 3 diseases affiliated with
JHDM1D via

MalaCards

our new
Human Malady Compendium

(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc, ⁷Ensembl, ⁸DME, ⁹miRBase, and/or ¹⁰fRNAdb)
About This Section

Aliases
Jumonji C Domain Containing Histone Demethylase 1 Homolog D (S. Cerevisiae)¹ ²		Jumonji C Domain-Containing Histone Demethylase 1 Homolog D²
KIAA1718¹ ³		Lysine-Specific Demethylase 7²
JmjC Domain-Containing Histone Demethylation Protein 1D² ³		EC 1.14.11.-³
KDM7A²		KDM7³
Histone Lysine Demethylase JHDM1D²

External Ids:	HGNC: 22224¹	Entrez Gene: 80853²	Ensembl: ENSG00000006459⁷	UniProtKB: Q6ZMT4³

Export aliases for JHDM1D gene to outside databases

Previous GC identifers: GC07M139432 GC07M134078

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

UniProtKB/Swiss-Prot: KDM7_HUMAN, Q6ZMT4

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

(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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section

RefSeq DNA sequence:

NC_000007.13 NC_018918.1 NT_007914.15 NT_079596.2

Regulatory elements:

SABiosciences Regulatory transcription factor binding sites in the JHDM1D gene promoter:
Pax-6
Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids

Search SABiosciences Chromatin IP Primers for JHDM1D

Epigenetics:

QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat JHDM1D

Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 7q34 Ensembl cytogenetic band: 7q34 HGNC cytogenetic band: 7q34

JHDM1D Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
JHDM1D gene location

GeneLoc information about chromosome 7 GeneLoc Exon Structure

GeneLoc location for GC07M139784: view genomic region (about GC identifiers)

Start:	139,784,546 bp from pter	End:	139,876,835 bp from pter
Size:	92,290 bases	Orientation:	minus strand

1 alternative location:

Chr7-,CRA_TCAG 139,113,396-139,205,589

(According to ¹UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to ²PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
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 model

prediction;

6 PDB 3D structures from and Proteopedia for JHDM1D:

3KV5 (3D)

3KV6 (3D)

3KV9 (3D)

3KVA (3D)

3KVB (3D)

3U78 (3D)

Secondary accessions: A4D1S9 C9JJH9 C9JQU2 Q6MZL8 Q9C0E5

Alternative splicing: 2 isoforms: Q6ZMT4-1 Q6ZMT4-2 (May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay. No experimental confirmation available)

Explore the universe of human proteins at neXtProt for JHDM1D: NX_Q6ZMT4

Post-translational modifications:

View modification sites using PhosphoSitePlus²

View neXtProt modification sites for NX_Q6ZMT4

JHDM1D Protein expression data from MOPED and PaxDb: About this image

REFSEQ proteins: NP_085150.1

ENSEMBL proteins:

ENSP00000380692 ENSP00000420143 ENSP00000006967

Human Recombinant Protein Products:

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	Uscn Proteins for JHDM1D

Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005634	nucleus	IDA	--
GO:0005730	NOT nucleolus	IDA	--

JHDM1D for ontologies About GeneDecksing

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	Uscn ELISAs and CLIAs for JHDM1D

(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section

JHDM1D for domains About GeneDecksing

5/6 InterPro domains/families (see all 6):

IPR003347 JmjC_dom

IPR019786 Zinc_finger_PHD-type_CS

IPR001965 Znf_PHD

IPR013083 Znf_RING/FYVE/PHD

IPR011011 Znf_FYVE_PHD

Graphical View of Domain Structure for InterPro Entry Q6ZMT4

ProtoNet protein and cluster: Q6ZMT4

1 Blocks protein family: IPB003347 Transcription factor jumonji

UniProtKB/Swiss-Prot: KDM7_HUMAN, Q6ZMT4

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

(According to ¹UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or ²DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
About This Section

Function Summary:

UniProtKB/Swiss-Prot: KDM7_HUMAN, Q6ZMT4

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

Biophysicochemical properties: Kinetic parameters: KM=1.2 uM for histone H3 H3K9Me2;

Enzyme Number (IUBMB): EC 1.14.11.-¹

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In Situ Assay
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Gene Ontology (GO): 5/9 molecular function terms (GO ID links to tree view) (see all 9): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005506	iron ion binding	TAS	--
GO:0008270	zinc ion binding	IDA	--
GO:0016702	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen	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	--
GO:0032454	histone demethylase activity (H3-K9 specific)	IDA	--

JHDM1D for ontologies About GeneDecksing

2 GenomeRNAi human phenotypes for JHDM1D:

Decreased Tat-dependent transc

Increased S DNA content

Animal Models:
1 MGI mutant phenotype (inferred from 1 allele) (MGI details for Jhdm1d):

skeleton

JHDM1D for phenotypes About GeneDecksing

(Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to ¹UniProtKB, ²MINT, ³I2D, and/or ⁴STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
About This Section

Interactions:

Search SABiosciences Gene Network Central^TM Interacting Genes and Proteins Networks for JHDM1D

Gene Ontology (GO): 5/7 biological process terms (GO ID links to tree view) (see all 7): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0006351	transcription, DNA-dependent	IEA	--
GO:0030901	midbrain development	ISS	--
GO:0033169	histone H3-K9 demethylation	IDA	--
GO:0035574	histone H4-K20 demethylation	IDA	--
GO:0045893	positive regulation of transcription, DNA-dependent	IEA	--

JHDM1D for ontologies About GeneDecksing

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section

Browse Small Molecules at EMD Millipore

Browse drugs & compounds from Enzo Life Sciences

Browse Tocris compounds for JHDM1D
Search CenterWatch for drugs/clinical trials and news about JHDM1D / KDM7

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
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Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section

REFSEQ mRNAs for JHDM1D gene:

NM_030647.1

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

4 Ensembl transcripts including schematic representations, and UCSC links where relevant:

ENST00000397560(uc010lng.3 uc003vvm.3) ENST00000472616 ENST00000478996

ENST00000006967

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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:

AI671992 AI813397 AI672783 AI002118 BX106614 BF806223 AI143364 AW972132

BQ317991 BF825492

GeneLoc Exon Structure

2 Alternative Splicing Database (ASD) splice patterns (SP) for JHDM1D About this scheme

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

ECgene alternative splicing isoforms for JHDM1D

(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

JHDM1D expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: TGTGTCCTTT

About this image
See JHDM1D Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for JHDM1D

SOURCE GeneReport for Unigene cluster: Hs.308710

SABiosciences Custom PCR Arrays for JHDM1D

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In Situ
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(Orthologs according to ^1,2HomoloGene (²older version, for species not in ¹newer version), ³euGenes, ⁴SGD , ⁵MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or ⁶Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
About This Section

This gene was present in the common ancestor of animals.

Orthologs for JHDM1D gene from 5/17 species (see all 17) About this table

Organism	Taxonomic classification	Gene	Description	Human Similarity	Orthology Type	Details
chicken (Gallus gallus)	Aves	JHDM1D¹	jumonji C domain containing histone demethylase 1 homolog more	79.21(n) 80.73(a)		418110 XM_416344.3 XP_416344.3
lizard (Anolis carolinensis)	Reptilia	JHDM1D⁶	--	69(a)	1 ↔ 1	5(15251925-15309297)
zebrafish (Danio rerio)	Actinopterygii	jhdm1db¹	jumonji C domain containing histone demethylase 1 homolog more	63.07(n) 62.95(a)		503902 NM_001202419.1 NP_001189348.1
honey bee (Apis mellifera)	Insecta	--	--	34(a)	1 → many	Group2.1(237930-242703)
worm (Caenorhabditis elegans)	Secernentea	jmjd-1.1⁶ jmjd-1.2⁶ (see all 3)	Lysine-specific demethylase 7 homolog (see all 3)	27(a) 18(a) (see all 3)	many ↔ many many ↔ many (see all 3)	II(11806504-11808766) IV(4660983-4665200)

ENSEMBL Gene Tree for JHDM1D (if available)
TreeFam Gene Tree for JHDM1D (if available)

(Paralogs according to ¹HomoloGene,
²Ensembl, and ³SIMAP, Pseudogenes according to ⁴Pseudogene.org Build 68)
About This Section

Paralogs for JHDM1D gene

PHF2² PHF8² KDM2A² KDM2B² FBXL19²

3 SIMAP similar genes for JHDM1D using alignment to 4 protein entries: KDM7_HUMAN (see all proteins):

PHF8 FBXL10 PHF2

JHDM1D for paralogs About GeneDecksing

(SNPs/Variants according to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section

SNP ID	Valid	Clinical significance	Chr 7 pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
rs113945142^1,2		--	139784086(+)	`CCTCAC/TGGAGT`	1	--	ds500¹		3		CSA WA	121
rs182307852^1,2		--	139784162(+)	`TTTGTC/GTCTCA`	1	--	ds500¹		0	--	--	--	--
rs143362447^1,2		--	139784230(+)	`AAACAC/GTGCCT`	1	--	ds500¹		0	--	--	--	--
rs59618522^1,2	C,F,	--	139784261(+)	`AAATAT/CTTGTG`	1	--	ds500¹		12		NA WA CSA EA	374
rs77215786^1,2		--	139784305(+)	`ATGTTC/TATTAG`	1	--	ds500¹		1		WA	118
rs150506969^1,2		--	139784326(+)	`ACATCC/TGTTTC`	1	--	ds500¹		0	--	--	--	--
rs139479284^1,2		--	139784327(+)	`CATCCA/GTTTCT`	1	--	ds500¹		0	--	--	--	--
rs185541175^1,2		--	139784384(+)	`TCTTTA/GAGCAA`	1	--	ds500¹		0	--	--	--	--
rs191242939^1,2		--	139784423(+)	`AAATAA/GGACAA`	1	--	ds500¹		0	--	--	--	--
rs183551994^1,2		--	139784440(+)	`TTCACA/GTTGAA`	1	--	ds500¹		0	--	--	--	--

HapMap Linkage Disequilibrium report for JHDM1D (139784546 - 139876835 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 2 variations for JHDM1D
2 CNVs: 64962 100148

SABiosciences Cancer Mutation PCR Assays

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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
About This Section

JHDM1D for disorders About GeneDecksing

3 diseases for JHDM1D: About MalaCards

cleft lip/palate cleft lip neuronitis

Human Genome Epidemiology (HuGE) Navigator: JHDM1D (1 document)

Export disorders for JHDM1D gene to outside databases

(in PubMed. Associations of this gene to articles via ¹Entrez Gene, ²UniProtKB/Swiss-Prot, ³HGNC, ⁴GAD, ⁵PharmGKB, ⁶HMDB, ⁷DrugBank, ⁸UniProtKB/TrEMBL, ⁹ Novoseek, and/or ¹⁰fRNAdb)
About This Section

PubMed articles for JHDM1D gene, integrated from 9 sources (see all 12):
(articles sorted by number of sources associating them with JHDM1D)

Utopia: connect your pdf to the dynamic
world of online information

Enzymatic and structural insights for substrate specificity of a family of jumonji histone lysine demethylases. (PubMed id 20023638)^{1, 2, 3} Horton J.R.... Cheng X. (2010)
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)
Increased expression of histone demethylase JHDM1D und er nutrient starvation suppresses tumor growth via down-regulating angiogenesis. (PubMed id 22143793)¹ Osawa T....Shibuya M. (2011)
Histone H4K20/H3K9 demethylase PHF8 regulates zebrafish brain and craniofacial development. (PubMed id 20622853)² Qi H.H....Shi Y. (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)

(in PubMed, OMIM, and NCBI Bookshelf)
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(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 80853	HGNC: 22224	AceView: KIAA1718.1	Ensembl:ENSG00000006459	euGenes: HUgn80853
ECgene: JHDM1D	H-InvDB: JHDM1D

(According to HUGE)
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HUGE: KIAA1718

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section

Name	Description
PharmGKB entry for JHDM1D	Pharmacogenomics, SNPs, Pathways

Intellectual Property for JHDM1D gene
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Patent Information for JHDM1D gene:
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GeneCards and IP:
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JHDM1D Gene

jumonji C domain containing histone demethylase 1 homolog...

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JHDM1D Gene

jumonji C domain containing histone demethylase 1 homolog...

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