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JHDM1D Gene

protein-coding GIFtS: 43

GC07M139432

jumonji C domain containing histone demethylase 1 homolog D (S. cerevisiae)
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database

(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc , and/or ⁷Ensembl, ⁸miRBase)
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Aliases
KIAA1718 ^¹, ², ³

Descriptions
jumonji C domain containing histone demethylase 1 homolog D ^²
jumonji C domain containing histone demethylase 1 homolog D (S. cerevisiae) ^²
jumonji C domain-containing histone demethylase 1 homolog D ^²

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

Search outside databases for aliases for JHDM1D gene

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

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 36),
and/or miRBase,
Genomic Views according to UCSC and Ensembl, Transcription factor binding sites according to SABiosciences)
About This Section

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)

GeneLoc gene densities for chromosome 7 GeneLoc Exon Structure

GeneLoc location for GC07M139432: (about GC identifiers)

Start:	139,431,015 bp from pter
End:	139,523,210 bp from pter
Size:	92,196 bases
Orientation:	minus strand

1 alternative location:

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

RefSeq DNA sequence:

NC_000007.12 NT_007914.14 NT_079596.2

(According to ¹UniProtKB, and/or Ensembl, Phosphorylation sites according to ²Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Enzo Life Sciences, Abnova, OriGene and/or, Abcam,
Biochemical Assays by Invitrogen, Millipore, R&D Systems, Cell Signaling Technology, and/or Enzo Life Sciences, Ontologies according to Gene Ontology Consortium 01 Apr 2009 and Entrez Gene, Antibodies by Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Cell Signaling Technology, Abcam, Abnova, and/or Novus Biologicals)
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UniProtKB/Swiss-Prot: JHD1D_HUMAN, Q6ZMT4 (See protein sequence)

Recommended Name: JmjC domain-containing histone demethylation protein 1D

Size: 941 amino acids; 106557 Da

Sequence caution: Sequence=BAD18641.1; Type=Frameshift; Positions=902;

Secondary accessions: Q6MZL8 Q9C0E5

Alternative splicing: 2 isoforms: Q6ZMT4-1 Q6ZMT4-2

REFSEQ proteins: NP_085150.1

ENSEMBL proteins:

ENSP00000380692 ENSP00000006967

Human Recombinant Proteins

	Browse Drug Discovery Central at Invitrogen for human recombinant proteins
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	Recombinant Proteins from Abcam (JHDM1D)
	Browse Abnova for Human Recombinant Proteins

Browse Origene for full length recombinant human proteins expressed in human HEK293 cells

Antibodies for JHDM1D:

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	Sigma-Aldrich Antibodies for JHDM1D
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Assays for JHDM1D:

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(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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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: JHD1D_HUMAN, Q6ZMT4

Similarity: Belongs to the JHDM1 histone demethylase family

Similarity: Contains 1 JmjC domain

Similarity: Contains 1 PHD-type zinc finger

(According to MGI Jun 06 2009, UniProtKB, IUBMB,and/or Genatlas,
shRNA from OriGene, Sigma-Aldrich, RNAi from Sigma-Aldrich,
RNAi Products, Clones, and Q-PCR Products from Invitrogen, Millipore, OriGene, and/or Abnova, siRNAs from Applied Biosystems, SYBR primers from OriGene, Cell-based Assays from Millipore, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
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Inhib. RNA:		Invitrogen RNAi Products for gene knock-down (JHDM1D)
		Browse for Gene Knock-down Tools from Millipore
		Browse Abnova for Chimera RNAi Products

OriGene 29mer shRNA kit in GFP-retroviral vectors (see all 2): NM_030647

Applied Biosystems Silencer® siRNAs for JHDM1D

Sigma-Aldrich siRNA and siRNA Panels for JHDM1D

Browse shRNA at Sigma-Aldrich

Explore Sigma-Aldrich super-pooled esiRNAs

Clones:		Browse Clone Ranger at Invitrogen for clones
		Browse Clones for the Expression of Recombinant Proteins Available from Millipore

OriGene GFP tagged cDNA clone in CMV expression vector: NM_030647
Myc/DDK tagged cDNA clone in CMV expression vector: NM_030647
untagged cDNA clones in CMV expression vector (see all 2): NM_030647

Primers:

Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers

OriGene genome-wide validated SYBR primer pairs: NM_030647

3 Gene Ontology (GO) molecular function terms (links to tree view):

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005515	protein binding	IEA	--
GO:0008270	zinc ion binding	IEA	--
GO:0046872	metal ion binding	IEA	--

About this table

(Pathways according to Invitrogen (maps by GeneGo), Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB,
Sets of similar genes according to GeneDecks, Proteins Network according to SABiosciences, Interactions according to ¹UniProtKB, ²MINT, and/or ³STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
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(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)
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Browse drugs & compounds from Enzo Life Sciences

Browse Small Molecules at Sigma-Aldrich

Browse Tocris compounds for JHDM1D

(GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 219 Homo sapiens; Jun 2 2009) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView,
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 Invitrogen, Millipore, and/or Abnova,
siRNAs from Applied Biosystems, Sigma-Aldrich,
shRNA from Sigma-Aldrich, OriGene,
Tagged/untagged cDNA clones from OriGene,
Expression Assays from Applied Biosystems)
About This Section

Inhib. RNA:		Invitrogen RNAi Products for gene knock-down (JHDM1D)
		Browse for Gene Knock-down Tools from Millipore
		Browse Abnova for Chimera RNAi Products

OriGene 29mer shRNA kit in GFP-retroviral vectors (see all 2): NM_030647

Sigma-Aldrich siRNA and siRNA Panels for JHDM1D

Browse shRNA at Sigma-Aldrich

Explore Sigma-Aldrich super-pooled esiRNAs

Applied Biosystems Silencer® siRNAs:

NM_030647

REFSEQ mRNAs for JHDM1D gene:

NM_030647.1

Applied Biosystems TaqMan ® Gene Expression Assays:

NM_030647

              OriGene GFP tagged cDNA clone in CMV expression vector: NM_030647
                                 Myc/DDK tagged cDNA clone in CMV expression vector: NM_030647
                                 untagged cDNA clones in CMV expression vector (see all 2): NM_030647

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 AI143364 BF806223 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

2 Ensembl transcripts including schematic representations:

ENST00000397560 ENST00000006967

(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 219 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
Expression Assays from Applied Biosystems )
About This Section

JHDM1D expression in normal and diseased human tissues

Applied Biosystems TaqMan ® Gene Expression Assays for JHDM1D

¹ / ²

7 probe-sets matching JHDM1D gene

Affymetrix probe-set	Array	# genes	Sensitivity	Specificity	Correlation	Length	Gb_Accession	Consensus	Uniqueness	Score	Rank
Affymetrix probe-set	Array	GeneAnnot data			GeneNote data		GeneTide data
78471_at²	U95-E	1	1.00	1.00	0.38	1.68	--	--	--	--	--
54435_r_at²	U95-C	1	1.00	1.00	0.83	0.37	--	--	--	--	--
32910_at²	U95-A	1	1.00	1.00	-0.18	0.28	--	--	--	--	--
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

Data from

(Publications) and GNF BioGPS
About these images
About these images

CGAP SAGE TAG: TGTGTCCTTT

SOURCE GeneReport for Unigene cluster: Hs.308710

(Orthologs according to ^1,2HomoloGene (²older version, for species not in ¹newer version), ³euGenes, ⁴SGD and/or ⁵MGI Jun 06 2009, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
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Orthologs for JHDM1D gene from 5/6 species (see all 6 )

Organism	Gene	Locus	Description	Human Similarity	NCBI accessions
dog (Canis familiaris)	LOC482769¹	--	similar to PHD finger protein 8	93.54(n) 94.18(a)	482769 XM_539885.2 XP_539885.2
chimpanzee (Pan troglodytes)	LOC472532¹	--	KIAA1718 protein	99.47(n) 99.57(a)	472532 XM_527907.2 XP_527907.2
cow (Bos taurus)	LOC521504¹	--	similar to jumonji C domain containing histone demethylase more	93.42(n) 93.16(a)	521504 XM_599768.3 XP_599768.3
mouse (Mus musculus)	Jhdm1d^{1, 5}	6⁵	jumonji C domain-containing histone demethylase 1 homolog more^{1, 5}	90.69(n)¹ 90.09(a)¹	338523¹ NM_001033430.2¹ NP_001028602.1¹ AA546623⁵ AK035529⁵ (see all 20)
chicken (Gallus gallus)	JHDM1D¹	--	jumonji C domain-containing histone demethylase 1 homolog more	79.52(n) 81(a)	418110 XM_416344.2 XP_416344.2

About this table Species with no ortholog for JHDM1D

ENSEMBL Gene Tree for JHDM1D

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

Paralogs for JHDM1D gene

PHF2² PHF8²

(According to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Genotyping Reagents from Applied Biosystems)
About This Section

10/501 NCBI SNPs in JHDM1D are shown (see all 501 )
(Click for Applied Biosystems TaqMan ® Genotyping Assay) (see all 91)

AB	SNP ID	Valid	Chr 7 pos	Sequence	Recs	AA Chg	Type	More	Recs	Allele freq	Pop	Total sample	More
AB	Genomic Data				Transcription Data				Allele Frequencies
				--	--	--		--	--				--
	rs6950119^1,2	A,C,F,H	139443900(+)	`CACACG/TTGTAA`	1	R/S	mis¹ ese³		12		EA NA EU WA	1050
	rs11972958^1,2	A,C,F,H	139432655(+)	`TCTCAG/ATTAAA`	1	--	ut3¹		7		NA EU EA WA	562
--	rs1062854^1,2	C,F,H	139432611(-)	`GTTCTC/TCCCTT`	1	--	ut3¹		5		MN EU EA WA	604
--	rs10984^1,2	A,C,F	139431493(+)	`ACCCCC/AAACAA`	1	--	ut3¹		3		MN EA	1767
	rs11762010^1,2	C,H	139437357(+)	`CAGCAG/ACTCTG`	1	--	ut3¹ ese³		4		EU EA WA	416
--	rs6967957^1,2	A,C	139524653(+)	`tgctgC/Tgatct`	1	--	ng3¹		0	--	--	--	--
--	rs2072163^1,2	C,H	139448254(-)	`GGAGGT/GCCTCA`	1	G/V	mis¹ ese³		4		EU EA WA	402
	rs6949738^1,2	H	139473762(+)	`TGTTAG/TGATTC`	1	P/H	mis¹ ese³		4		EU EA WA	418
--	rs5020212^1,2	H	139465454(+)	`AAGATC/ATGGTG`	1	Y/D	mis¹ ese³		4		EU EA WA	406
--	rs194213^1,2	F	139524789(-)	`aacatG/Agtgaa`	1	--	ng3¹		1		MN	184

About this table

HapMap Linkage Disequilibrium images for JHDM1D (up to first 250kb)

(in which this Gene is Involved, According to OMIM, UniProtKB, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, HGMD, GAD, HuGE Navigator, BCGD, and/or TGDB.)
About This Section

(Possibly Related Articles in Doctor's Guide)
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(in PubMed. Associations of this gene to articles via ¹Novoseek, ²HGNC, ³Entrez Gene, ⁴UniProtKB/Swiss-Prot, ⁵UniProtKB/TrEMBL, ⁶GAD, and/or ⁷PharmGKB)
About This Section

4 PubMed articles for JHDM1D gene:

Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)^{3, 4} 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)^{3, 4} Nagase T....Ohara O. (2000)
The full-ORF clone resource of the German cDNA Consortium. (PubMed id 17974005)⁴ Bechtel S....Schupp I. (2007)
Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)³ Strausberg R.L....Marra M.A. (2002)

(in PubMed, OMIM, and NCBI Bookshelf)
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		AND	OR
Aliases
Free Text

Query String		PubMed OMIM NCBI Bookshelf
	(Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, 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 ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
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Licensable Technologies for JHDM1D
(Available from WIS Yeda, Salk, Tufts)

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(Reagents available from Applied Biosystems, Antibodies and assays by Cell Signaling Technology, Abcam, Novus Biologicals,
Sigma-Aldrich, R&D Systems, Millipore, Abnova, and/or Invitrogen, Clones available from OriGene,and/or Invitrogen, Drugs and/or compounds by Sigma-Aldrich,
Enzo Life Sciences, and/or Tocris Bioscience)
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Products for JHDM1D:

TaqMan ® Gene Expression Assays

TaqMan ® Genotyping Assays

Free SNP selection tool

Invitrogen iPath Pathways	Invitrogen BLOCK-iT™ RNAi
Invitrogen Antibodies	Invitrogen Assays
Invitrogen Clones	Invitrogen Q-PCR Products
Invitrogen Human Recombinant Kinases	Invitrogen Custom Antibody and Peptide Service
Invitrogen Proteins / Assays / Screening Services	Search Invitrogen catalog for JHDM1D-related products

	Millipore Custom Antibody & Bulk Services
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JHDM1D Gene

protein-coding GIFtS: 43

Aliases &
Descriptions
for JHDM1D

Summaries
for JHDM1D

Genomic Location
for JHDM1D

Proteins
for JHDM1D

Protein Domains/
Families
for JHDM1D

Gene Function
for JHDM1D

Pathways & Interactions
for JHDM1D

Drugs & Compounds
for JHDM1D

Transcripts
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Expression
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Orthologs
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Paralogs
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Genome Databases showing JHDM1D

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Gene Index: 3 5 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

JHDM1D Gene

protein-coding GIFtS: 43

Aliases & Descriptionsfor JHDM1D

Summariesfor JHDM1D

Genomic Locationfor JHDM1D

Proteinsfor JHDM1D

Protein Domains/Familiesfor JHDM1D

Gene Functionfor JHDM1D

Pathways & Interactionsfor JHDM1D

Drugs & Compoundsfor JHDM1D

Transcriptsfor JHDM1D

Expression for JHDM1D

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SNPs/Variantsfor JHDM1D

Disorders & Mutationsfor JHDM1D

Medical Newsfor JHDM1D

Publicationsfor JHDM1D

Search for JHDM1D

Genome Databases showing JHDM1D

Other Databases showing JHDM1D

Specialized Databases showing JHDM1D

Licensable Technologiesfor JHDM1D

Servicesfor JHDM1D

Gene Index: 3 5 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

Aliases &
Descriptions
for JHDM1D

Summaries
for JHDM1D

Genomic Location
for JHDM1D

Proteins
for JHDM1D

Protein Domains/
Families
for JHDM1D

Gene Function
for JHDM1D

Pathways & Interactions
for JHDM1D

Drugs & Compounds
for JHDM1D

Transcripts
for JHDM1D

Expression
for JHDM1D

Orthologs
for JHDM1D

Paralogs
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SNPs/Variants
for JHDM1D

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for JHDM1D

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Licensable Technologies
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