Aliases &
Descriptions
for JMJD6 gene
(According to
1HGNC,
2Entrez Gene,
3UniProtKB/Swiss-Prot,
4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc
, and/or 7Ensembl,
8miRBase)
About This Section
|
| Aliases & Descriptions |
|---|
| jumonji domain containing 61 2 | | Peptide-lysine 5-dioxygenase JMJD62 3 | | Phosphatidylserine receptor1 2 3 | | Histone arginine demethylase JMJD62 3 | | KIAA05851 2 3 | | PTDSR2 3 | | PTDSR11 2 | | PSR2 5 | | Lysyl-hydroxylase JMJD62 3 | | bifunctional arginine demethylase and lysyl-hydroxylase JMJD62 | | Jumonji domain-containing protein 62 3 | | EC 1.14.11.-3 | | JmjC domain-containing protein 62 3 | | Protein PTDSR3 |
Export aliases for JMJD6 gene to outside databasesPrevious GC identifers: GC17M072221 GC17M074708 |
Summaries
for JMJD6 gene(According to Entrez Gene,
Tocris Bioscience,
Wikipedia's
Gene Wiki,
UniProtKB/Swiss-Prot,
and/or
UniProtKB/TrEMBL)
About This Section
|
Entrez Gene summary for JMJD6:
This gene encodes a nuclear protein with a JmjC domain. JmjC domain-containing proteins are predicted to function asprotein hydroxylases or histone demethylases. This protein was first identified as a putative phosphatidylserinereceptor involved in phagocytosis of apoptotic cells; however, subsequent studies have indicated that it does notdirectly function in the clearance of apoptotic cells, and questioned whether it is a true phosphatidylserinereceptor. Multiple transcript variants encoding different isoforms have been found for this gene. (provided by RefSeq)
UniProtKB/Swiss-Prot: JMJD6_HUMAN, Q6NYC1Function: Dioxygenase that can both act as a histone arginine demethylase and a lysyl-hydroxylase. Arginine demethylasewhich demethylates histone H3 at 'Arg-2' (H3R2me) and histone H4 at 'Arg-3' (H4R3me), thereby playing a central rolein histone code. Also acts as a lysyl-hydroxylase that catalyzes 5-hydroxylation on specific lysine residues of targetproteins such as U2AF2/U2AF65 and LUC7L2. Acts as a regulator of RNA splicing by mediating 5-hydroxylation ofU2AF2/U2AF65, affecting the pre-mRNA splicing activity of U2AF2/U2AF65. Required for differentiation of multipleorgans during embryogenesis. Probably acts as a key regulator of hematopoietic differentiation. Seems to be necessaryfor the regulation of macrophage cytokine responses
Gene Wiki entry for JMJD6 |
Genomic Views
for JMJD6 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 JMJD6
Other transcription factors
Search SABiosciences Chromatin IP Primers for JMJD6
Epigenetics:
|  | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays for JMJD6  |
Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track
Entrez Gene cytogenetic band: 17q25 Ensembl cytogenetic band: 17q25.1 HGNC cytogenetic band: 17q25JMJD6 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 GC17M070137: view genomic region
(about GC identifiers)
Start:
|
70,136,605 bp from pter |
End:
|
70,150,592 bp from pter |
Size:
|
13,988 bases |
Orientation:
|
minus strand |
1 alternative location:
| Chr17- 74,708,914-74,722,881 |
RefSeq DNA sequence:- NC_000017.10 NT_010783.15
|
Proteins
for JMJD6 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: JMJD6_HUMAN, Q6NYC1 (See
protein sequence)Recommended Name: Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 Size: 403 amino acids; 46462 Da
Cofactor: Binds 1 Fe(2+) ion per subunit
Subunit: Interacts with LUC7L2, LUC7L3 and U2AF2/U2AF65
Subcellular location: Nucleus
Caution: Was initially thought to constitute the phosphatidylserine receptor, a receptor that mediates recognition ofphosphatidylserine, a specific marker only present at the surface of apoptotic cells. Phosphatidylserine receptorprobably participates in apoptotic cell phagocytosis. This protein was identified using phage display expressing mAb217, an antibody that specifically recognizes phosphatidylserine receptor. However, its nuclear localization and thefact that mAb 217 antibody still recognizes the phosphatidylserine receptor in mice lacking JMJD6, strongly suggestthat it does not constitute the receptor for phosphatidylserine and is not involved in apoptotic cell removal
Sequence caution: Sequence=AAH47003.1; Type=Erroneous initiation; Sequence=BAA25511.1; Type=Erroneous initiation;
PDB structures from  and Proteopedia  :3K2O (3D)
3LD8 (3D)
3LDB (3D)
Secondary accessions: B3KMN8 B4DGX1 Q86VY0 Q8IUM5 Q9Y4E2Alternative splicing: 3 isoforms: Q6NYC1-1 Q6NYC1-2 Q6NYC1-3 Explore the universe of human proteins at neXtProt for JMJD6: NX_Q6NYC1
Post-translational modifications:
View phosphorylation sites using PhosphoSite2
REFSEQ proteins (2 alternative transcripts):
NP_001074930.1 NP_055982.2
ENSEMBL proteins: ENSP00000345857 ENSP00000394085 ENSP00000380750 ENSP00000302916
Human Recombinant Proteins
2 Gene Ontology (GO) cellular component terms (GO ID links to tree view): About this table
JMJD6 for ontologies About GeneDecksing
Antibodies for JMJD6:
Assays for JMJD6: |
Protein
Domains/
Families
for JMJD6 gene(According to InterPro, ProtoNet,
UniProtKB, and/or BLOCKS,
Sets of similar genes according to GeneDecks)
About This Section
|
JMJD6 for domains About GeneDecksing
2 InterPro domains/families:Graphical View of Domain Structure for InterPro Entry Q6NYC1ProtoNet protein and cluster: Q6NYC1 UniProtKB/Swiss-Prot: JMJD6_HUMAN, Q6NYC1Domain: The nuclear localization signal motifs are necessary and sufficient to target it into the nucleusSimilarity: Belongs to the JMJD6 familySimilarity: Contains 1 JmjC domain |
Gene Function
for JMJD6 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: JMJD6_HUMAN, Q6NYC1Function: Dioxygenase that can both act as a histone arginine demethylase and a lysyl-hydroxylase. Arginine demethylasewhich demethylates histone H3 at 'Arg-2' (H3R2me) and histone H4 at 'Arg-3' (H4R3me), thereby playing a central rolein histone code. Also acts as a lysyl-hydroxylase that catalyzes 5-hydroxylation on specific lysine residues of targetproteins such as U2AF2/U2AF65 and LUC7L2. Acts as a regulator of RNA splicing by mediating 5-hydroxylation ofU2AF2/U2AF65, affecting the pre-mRNA splicing activity of U2AF2/U2AF65. Required for differentiation of multipleorgans during embryogenesis. Probably acts as a key regulator of hematopoietic differentiation. Seems to be necessaryfor the regulation of macrophage cytokine responsesInduction: Up-regulated upon cytokine treatment, but not upon TNF treatmentEnzyme Number (IUBMB): EC 1.14.11.-
5/9 Gene Ontology (GO) molecular function terms (GO ID links to tree view) (see all 9): | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0004872 | receptor activity |
IEA | -- | | GO:0005515 | protein binding |
IPI | 19574390 | | 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 |
About this table
JMJD6 for ontologies About GeneDecksing
Animal Models: 15/17 MGI mutant phenotypes (inferred from 6 alleles ) (MGI details for Jmjd6) (see all 17):
JMJD6 for phenotypes About GeneDecksing
|
Pathways & Interactions
for JMJD6 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
|
JMJD6 for pathways About GeneDecksing
1  Sigma-Aldrich "Your Favorite Gene" (powered by Ingenuity) Pathway for JMJD6
SABiosciences Custom Pathway-Focused PCR Arrays for JMJD6
Sigma-Aldrich "Your Favorite Gene" (powered by Ingenuity) Molecular Interaction Network for JMJD6
Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for JMJD6
5/23 Gene Ontology (GO) biological process terms (GO ID links to tree view) (see all 23): About this table
JMJD6 for ontologies About GeneDecksing
|
Drugs & Compounds
for JMJD6 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
|
JMJD6 for compounds About GeneDecksing
 Browse Tocris compounds for JMJD6
4  Novoseek chemical compound relationships for JMJD6 gene
About this table
|
Transcripts
for JMJD6 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 JMJD6 gene (2 alternative transcripts): NM_001081461.1 NM_015167.2 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): BX417653 AA351360 BE466065 AI827036 CD673337 AI419157 AI565339 CR602714 BU732500 CR609667 AB073711 CR600929 CA420455 CK904897 BQ671919 CA436956 BM792988 BQ716899 BE275732 BM827225 BQ028416 BU727487 BM788992 AA262167 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
4 Ensembl transcripts including schematic representations, and UCSC links where relevant: ENST00000344991 ENST00000445478(uc002jsn.1) ENST00000397625 ENST00000303996(uc002jso.2 uc010dgz.2)
|
Expression
for JMJD6 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
| JMJD6 expression in normal and diseased human tissues
1 / 2 10 probe-sets matching JMJD6 gene
Affymetrix
probe-set |
Array |
GeneAnnot data |
GeneNote data |
GeneTide data |
| # genes |
Sensitivity |
Specificity |
Correlation |
Length |
Gb_Accession |
Consensus |
Uniqueness |
Score |
Rank |
| 35851_g_at2
|
U95-A |
1 |
0.94 |
1.00 |
0.76 |
0.89 |
-- |
-- |
-- |
-- |
-- |
| 35850_at2
|
U95-A |
1 |
0.81 |
1.00 |
0.83 |
1.17 |
-- |
-- |
-- |
-- |
-- |
| 35849_at2
|
U95-A |
1 |
0.62 |
1.00 |
0.14 |
0.96 |
-- |
-- |
-- |
-- |
-- |
| 212723_at2
|
U133-A |
1 |
1.00 |
1.00 |
-- |
-- |
-- |
-- |
-- |
-- |
-- |
| 212722_s_at2
|
U133-A |
1 |
1.00 |
1.00 |
-- |
-- |
-- |
-- |
-- |
-- |
-- |
| 215233_at2
|
U133-A |
1 |
0.46 |
1.00 |
-- |
-- |
-- |
-- |
-- |
-- |
-- |
| 212723_at2
|
U133Plus2 |
1 |
1.00 |
1.00 |
-- |
-- |
-- |
-- |
-- |
-- |
-- |
| 212722_s_at2
|
U133Plus2 |
1 |
1.00 |
1.00 |
-- |
-- |
-- |
-- |
-- |
-- |
-- |
| 1552629_a_at2
|
U133Plus2 |
1 |
0.55 |
1.00 |
-- |
-- |
-- |
-- |
-- |
-- |
-- |
| 215233_at2
|
U133Plus2 |
1 |
0.46 |
1.00 |
-- |
-- |
-- |
-- |
-- |
-- |
-- |
About this table
JMJD6 for expression About GeneDecksing
Data from
Genenote
(Publications) and GNF BioGPS
About these images
About these images
CGAP SAGE TAG: GTGGGAAACG
SOURCE GeneReport for Unigene cluster: Hs.514505
UniProtKB/Swiss-Prot: JMJD6_HUMAN, Q6NYC1Tissue specificity: Highly expressed in the heart, skeletal muscle and kidney. Expressed at moderate or low level inbrain, placenta, lung, liver, pancreas, spleen, thymus, prostate, testis and ovary. Up-regulated in many patients withchronic pancreatitis. Expressed in nursing thymic epithelial cells
SABiosciences Custom PCR Arrays for JMJD6
|
Orthologs
for JMJD6 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 JMJD6 gene from 5/15 species (see all 15)
About this table Species with no ortholog for JMJD6
ENSEMBL Gene Tree for JMJD6 (if available) |
Paralogs
for JMJD6 gene(Paralogs according to 1HomoloGene
and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
About This Section
| Paralogs for JMJD6 gene
- JMJD42
JMJD6 for paralogs About GeneDecksing
|
Genomic Variants
for JMJD6 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 17 pos | Sequence | Recs | AA
Chg | Type | More | Recs | Allele
freq | Pop | Total
sample | More |
|---|
About this tableHapMap Linkage Disequilibrium images for JMJD6 (up to first 250kb)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 1 variation for JMJD6
1 CNV: 73037 | | QIAGEN SeqTarget long-range PCR primers for resequencing JMJD6 |
|
Disorders & Mutations
for JMJD6 gene
(in which this Gene is Involved, According to
OMIM, UniProtKB,
Novoseek, PharmGKB,
Genatlas, GeneTests,
Blood group antigen gene mutations by BGMUT,
LSDB, HGMD, GAD,
HuGE Navigator,
and/or TGDB.)
About This Section
|
JMJD6 for disorders About GeneDecksing
OMIM: 604914
1 Novoseek disease relationship for JMJD6 gene
| Disease |
-log (P-Val) |
Hits |
PubMed IDs for Articles with Shared Sentences (# sentences) |
| inflammation |
37 |
2 |
11877474 (2) |
About this table
Export disorders and mutations for JMJD6 gene to outside databases
|
Medical News
for JMJD6 gene(Possibly Related Articles in
Doctor's Guide)
About This Section
| -- |
Publications
for JMJD6 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
|
10/63 PubMed articles for JMJD6 gene, integrated from 7 sources (see all 63):
(articles sorted by number of sources associating them with JMJD6)- Phosphatidylserine receptor in chronic pancreatitis: evidence for a macrophage independent role. (PubMed id 15622002)1, 2, 7 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, 2, 7 Cao W.M.... Ishida T. (2004)
- Elastase-mediated phosphatidylserine receptor cleavage impairs apoptotic cell clearance in cystic fibrosis and bronchiectasis. (PubMed id 11877474)1, 3, 7 Vandivier R.W....Henson P.M. (2002)
- Jmjd6 catalyses lysyl-hydroxylation of U2AF65, a protein associated with RNA splicing. (PubMed id 19574390)1, 2 Webby C.J....Boettger A. (2009)
- JMJD6 is a histone arginine demethylase. (PubMed id 17947579)1, 2 Chang B.... Bruick R.K. (2007)
- Nuclear localization of the phosphatidylserine receptor protein via multiple nuclear localization signals. (PubMed id 14729065)1, 2 Cui P.... Pei D. (2004)
- Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
- The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 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)1, 2 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, 7 Hong J.R....Wu J.L. (2004)
|
External Searches for JMJD6 gene
(in PubMed,
OMIM, and NCBI Bookshelf)
About This Section
|
|
Genome Databases showing JMJD6 gene
(According to
Entrez Gene,
HGNC,
AceView,
euGenes,
Ensembl,
miRBase,
ECgene,
Kegg,
and/or
H-InvDB)
About This Section
|
|
Other Databases showing JMJD6 gene
(According to HUGE)
About This Section
| |
Specialized Databases showing JMJD6 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 JMJD6 gene:
Search GeneIP for patents involving JMJD6
GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search
|
Products
for JMJD6 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 JMJD6 |
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