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Aliases & Descriptions for JMJD6
(According to
1 HGNC ,
2 Entrez Gene ,
3 UniProtKB/Swiss-Prot ,
4 UniProtKB/TrEMBL , 5 OMIM , 6 GeneLoc
, and/or 7 Ensembl ,
8 miRBase )About This Section
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Aliases EC 1.14.11.- 3 KIAA0585 1 , 2 , 3 PSR 2 , 5 PTDSR 2 , 3 PTDSR1 1 , 2
Descriptions JmjC domain-containing protein 6 3 Jumonji domain-containing protein 6 3 Phosphatidylserine receptor 1 , 2 , 3 Protein PTDSR 3 jumonji domain containing 6 2
Search outside databases for aliases for JMJD6 gene
Summaries for JMJD6 (According to Entrez Gene ,
Wikipedia's
Gene Wiki ,
UniProtKB/Swiss-Prot ,
and/or
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EntrezGene summary for JMJD6 : This gene encodes a nuclear protein with a JmjC domain. JmjC domain-containing proteins arepredicted to function as protein hydroxylases or histone demethylases. This protein was firstidentified as a putative phosphatidylserine receptor involved in phagocytosis of apoptotic cells;however, subsequent studies have indicated that it does not directly function in the clearance ofapoptotic cells, and questioned whether it is a true phosphatidylserine receptor. Multipletranscript variants encoding different isoforms have been found for this gene. [provided byRefSeq] UniProtKB/Swiss-Prot: JMJD6_HUMAN, Q6NYC1 Function : Arginine demethylase which demethylates histone H3 at 'Arg-2' (H3R2me) and histone H4 at'Arg-3' (H4R3me). Required for differentiation of multiple organs during embryogenesis. Probablyacts as a key regulator of hematopoietic differentiation. Seems to be necessary for the regulationof macrophage cytokine responses
Gene Wiki entry for JMJD6
Genomic Location for JMJD6
(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
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Genomic View : UCSC Golden Path with GeneCards custom track Entrez Gene cytogenetic band: 17q25 Ensembl cytogenetic band: 17q25.2 HGNC cytogenetic band: 17q25 JMJD6 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 17 GeneLoc Exon Structure
GeneLoc location for GC17M072221:
(about GC identifiers )
Start:
72,220,509 bp from pter
End:
72,234,476 bp from pter
Size:
13,968 bases
Orientation:
minus strand
RefSeq DNA sequence: NC_000017.9 NT_010641.15 Proteins for JMJD6
(According to
1 UniProtKB ,
and/or Ensembl ,
Phosphorylation sites according to 2 Phosphosite ,
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: JMJD6_HUMAN, Q6NYC1 (See
protein sequence )Recommended Name: Histone arginine demethylase JMJD6 Size : 403 amino acids; 46462 Da
Subcellular location : Nucleus
Caution : Was initially thought to constitute the phosphatidylserine receptor, a receptor thatmediates recognition of phosphatidylserine, a specific marker only present at the surface ofapoptotic cells. Phosphatidylserine receptor probably participates in apoptotic cell phagocytosis.This protein was identified using phage display expressing mAb 217, an antibody that specificallyrecognizes phosphatidylserine receptor. However, its nuclear localization and the fact that mAb217 antibody still recognizes the phosphatidylserine receptor in mice lacking JMJD6, stronglysuggest that it does not constitute the receptor for phosphatidylserine and is not involved inapoptotic cell removal
Secondary accessions : Q86VY0 Q8IUM5 Q9Y4E2Alternative splicing : 3 isoforms : Q6NYC1-1 Q6NYC1-2 Q6NYC1-3
Post-translational modifications:
View phosphorylation sites using PhosphoSite 2
REFSEQ proteins (2 alternative transcripts):
NP_001074930.1 NP_055982.2 ENSEMBL proteins: ENSP00000345857 ENSP00000302916 ENSP00000380750 Human Recombinant Proteins               OriGene Purified Recombinant Human Protein: JMJD6 2 Gene Ontology (GO) cellular component terms (links to tree view) :
About this table Antibodies for JMJD6: Assays for JMJD6:
Protein
Domains/ Families for JMJD6(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 Q6NYC1 ProtoNet protein and cluster: Q6NYC1
UniProtKB/Swiss-Prot: JMJD6_HUMAN, Q6NYC1 Domain : The nuclear localization signal motifs are necessary and sufficient to target it into thenucleus Similarity : Belongs to the PTDSR familySimilarity : Contains 1 JmjC domain
Gene Function for JMJD6
(According to MGI Jun 06 2009, UniProtKB ,
IUBMB ,and/or Genatlas ,
shRNA from
OriGene ,
Sigma-Aldrich , RNAi from
Sigma-Aldrich ,
RNAi Products ,
Clones , and
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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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               OriGene 29mer shRNA kit in GFP-retroviral vectors (see all 2 ): NM_015167 Applied Biosystems Silencer ® siRNAs for JMJD6 Sigma-Aldrich siRNA for JMJD6 Sigma-Aldrich shRNA for JMJD6 Explore Sigma-Aldrich super-pooled esiRNAs                OriGene GFP tagged cDNA clones in CMV expression vector (see all 2 ): NM_001081461                                  Myc/DDK tagged cDNA clones in CMV expression vector (see all 2 ): NM_001081461                                  untagged cDNA clones in CMV expression vector (see all 3 ): NM_001081461  Primers: Browse
Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers               OriGene genome-wide validated SYBR primer pairs: NM_001081461 UniProtKB/Swiss-Prot: JMJD6_HUMAN, Q6NYC1 Function : Arginine demethylase which demethylates histone H3 at 'Arg-2' (H3R2me) and histone H4 at'Arg-3' (H4R3me). Required for differentiation of multiple organs during embryogenesis. Probablyacts as a key regulator of hematopoietic differentiation. Seems to be necessary for the regulationof macrophage cytokine responses Induction : Up-regulated upon cytokine treatment, but not upon TNF-alpha treatmentEnzyme Number (IUBMB): EC 1.14.11.-
15/17 MGI mutant phenotypes (inferred from 6 alleles ) (MGI details for Jmjd6) (see all 17
):5/6 Gene Ontology (GO) molecular function terms (links to tree view) (see all 6
):
GO ID Qualified GO term Evidence PubMed IDs GO:0004872 receptor activity
IEA -- 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 -- GO:0033746 histone demethylase activity (H3-R2 specific)
IDA 17947579 GO:0033749 histone demethylase activity (H4-R3 specific)
IDA 17947579
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Pathways & Interactions for JMJD6
(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 1 UniProtKB ,
2 MINT , and/or
3 STRING ,
with links to IntAct and
Ensembl ,
Ontologies according to Gene Ontology Consortium 01 Apr 2009 via
Entrez Gene .)
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1 Sigma-Aldrich "Your Favorite Gene" Pathway for JMJD6 (Your Favorite Gene powered by Ingenuity) 2 Interacting proteins for JMJD6 (ENSP00000302916 3 ) via UniProtKB, MINT, and/or STRING About this table 5/16 Gene Ontology (GO) biological process terms (links to tree view) (see all 16
):
GO ID Qualified GO term Evidence PubMed IDs GO:0001568 blood vessel development
IEA -- GO:0001822 kidney development
IEA -- GO:0006915 apoptosis
IEA -- GO:0007166 cell surface receptor linked signal transduction
IEA -- GO:0007275 multicellular organismal development
IEA --
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Drugs & Compounds for JMJD6 (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 Tocris compounds for JMJD6 3 Novoseek chemical compound relationships for JMJD6 gene
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Transcripts for JMJD6(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
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               OriGene 29mer shRNA kit in GFP-retroviral vectors (see all 2 ): NM_015167 Sigma-Aldrich siRNA for JMJD6 Sigma-Aldrich shRNA for JMJD6 Explore Sigma-Aldrich super-pooled esiRNAs
Applied Biosystems Silencer ® siRNAs: NM_001081461 NM_015167
REFSEQ mRNAs for JMJD6 gene (2 alternative transcripts): NM_001081461.1 NM_015167.2
Applied Biosystems TaqMan ® Gene Expression Assays: NM_001081461 NM_015167
               OriGene GFP tagged cDNA clones in CMV expression vector (see all 2 ): NM_001081461                                  Myc/DDK tagged cDNA clones in CMV expression vector (see all 2 ): NM_001081461                                  untagged cDNA clones in CMV expression vector (see all 3 ): NM_001081461  
Additional cDNA sequence: AB011157.1 AB073711.1 AK021780.1 AK294816.1 AK314541.1 BC016837.1 BC047003.1 BC066654.1 CR594304.1 CR597139.1 CR598927.1 CR600929.1 CR601337.1 CR602714.1 CR609667.1 CR613854.1 EF527406.1 EF527407.1
15 DOTS entries : DT.100701748 DT.95298523 DT.100812905 DT.316217 DT.100812903 DT.120924927 DT.91824600 DT.203158 DT.95298519 DT.100812912 DT.100812901 DT.100812900 DT.100812909 DT.120925009 DT.95298521
24/263 AceView cDNA sequences (see all 263
):BM687017 BM916892 AB011157 CR609667 BC016837 AI253789 AI682172 AI926454 AI026025 CR594304 BP375107 BQ669508 CR601337 BQ639908 BI910055 CB529456 BQ223112 BI759425 AI078362 BQ672747 CD673337 BQ426076 BQ002475 BQ668503
Unigene Cluster for JMJD6: Jumonji domain containing 6 Hs.514505 [show with all ESTs ] Unigene Representative Sequence: NM_001081461 GeneLoc Exon Structure 2 Alternative Splicing Database (ASD) splice patterns (SP) for JMJD6 ExUns: 1 ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7 SP1 :           -         SP2 :                  
About this scheme ECgene alternative splicing isoforms for JMJD6 3 Ensembl transcripts including schematic representations : ENST00000344991
ENST00000303996
ENST00000397625
Expression for JMJD6
(Experimental results according to
1 GeneNote
and GNF BioGPS ,
probe sets-to-genes annotations according to
2 GeneAnnot ,
3 GeneTide ,
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
)
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JMJD6 expression in normal and diseased human tissues Applied Biosystems TaqMan ® Gene Expression Assays for JMJD6 1 / 2
10 probe-sets matching JMJD6 gene Data from
(Publications) and GNF BioGPS About these images About these images CGAP SAGE TAG: GTGGGAAACGSOURCE GeneReport for Unigene cluster: Hs.514505 UniProtKB/Swiss-Prot: JMJD6_HUMAN, Q6NYC1 Tissue specificity : Highly expressed in the heart, skeletal muscle and kidney. Expressed atmoderate or low level in brain, placenta, lung, liver, pancreas, spleen, thymus, prostate, testisand ovary. Up-regulated in many patients with chronic pancreatitis. Expressed in nursing thymicepithelial cells
Orthologs for JMJD6
(Orthologs according to
1,2 HomoloGene (2 older version, for species not in 1 newer version),
3 euGenes ,
4 SGD
and/or
5 MGI Jun 06 2009,
with possible further links to
Flybase
and/or
WormBase ,
Gene Trees according to Ensembl )
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Orthologs for JMJD6 gene from 5/15 species (see all 15
)
About this table Species with no ortholog for JMJD6 ENSEMBL Gene Tree for JMJD6 Paralogs for JMJD6 (Paralogs according to 1 HomoloGene and 2 Ensembl , Pseudogenes according to 3 Pseudogene.org )About This Section
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Paralogs for JMJD6 gene JMJD4 2
SNPs/Variants for JMJD6 (According to the
1 NCBI SNP Database ,
2 Ensembl ,
3 PupaSUITE , and
UniProtKB ,
Linkage Disequilibrium by HapMap ,
Genotyping Reagents from
Applied Biosystems )
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HapMap Linkage Disequilibrium images for JMJD6 (up to first 250kb)
Disorders & Mutations for JMJD6
(in which this Gene is Involved, According to
OMIM, UniProtKB ,
Novoseek , PharmGKB ,
Genatlas , GeneTests ,
Blood group antigen gene mutations by BGMUT ,
HGMD, GAD ,
HuGE Navigator ,
BCGD ,
and/or TGDB .)
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OMIM: 604914 1 Novoseek disease relationship for JMJD6 gene
Disease
Score
Articles
PubMed IDs for Articles with Shared Sentences (# sentences)
inflammation
38.84
2
11877474 (2)
About this table
Medical News for JMJD6 (Possibly Related Articles in
Doctor's Guide )
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--
Publications for JMJD6 (in
PubMed .
Associations of this gene to articles via
1 Novoseek ,
2 HGNC ,
3 Entrez Gene ,
4 UniProtKB/Swiss-Prot ,
5 UniProtKB/TrEMBL ,
6 GAD , and/or
7 PharmGKB )
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10/58 PubMed articles for JMJD6 gene (see all 58
): Phosphatidylserine receptor in chronic pancreatitis: evidence for a macrophage independent role. (PubMed id 15622002) 1, 3, 4 Koeninger J.... Friess H. (2005) Phosphatidylserine receptor cooperates with high-density lipoprotein receptor in recognition of apoptotic cells by thymic nurse cells. (PubMed id 15072554) 1, 3, 4 Cao W.M.... Ishida T. (2004) Elastase-mediated phosphatidylserine receptor cleavage impairs apoptotic cell clearance in cystic fibrosis and bronchiectasis. (PubMed id 11877474) 1, 2, 3 Vandivier R.W....Henson P.M. (2002) JMJD6 is a histone arginine demethylase. (PubMed id 17947579) 3, 4 Chang B.... Bruick R.K. (2007) Nuclear localization of the phosphatidylserine receptor protein via multiple nuclear localization signals. (PubMed id 14729065) 3, 4 Cui P.... Pei D. (2004) The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334) 3, 4 Gerhard D.S....Malek J. (2004) Prediction of the coding sequences of unidentified human genes. IX. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro. (PubMed id 9628581) 3, 4 Nagase T....Ohara O. (1998) Phosphatidylserine receptor is required for the engulfment of dead apoptotic cells and for normal embryonic development in zebrafish. (PubMed id 15469976) 1, 3 Hong J.R....Wu J.L. (2004) Cell corpse engulfment mediated by C. elegans phosphatidylserine receptor through CED-5 and CED-12. (PubMed id 14645848) 1, 3 Wang X....Xue D. (2003) The phosphatidylserine receptor from Hydra is a nuclear protein with potential Fe(II) dependent oxygenase activity. (PubMed id 15193161) 1, 3 Cikala M....Bottger A. (2004)
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Genome Databases showing JMJD6
(According to
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HGNC ,
AceView ,
euGenes ,
Ensembl ,
miRBase ,
ECgene ,
and/or
H-InvDB )
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Other Databases showing JMJD6
(According to HUGE )
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Specialized Databases showing JMJD6 (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
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-- Services for JMJD6 (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 )About This Section
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