Free for academic non-profit institutions. Other users need a Commercial license

Aliases for JMJD6 Gene

Aliases for JMJD6 Gene

  • Jumonji Domain Containing 6 2 3
  • Phosphatidylserine Receptor 2 3 4
  • Jumonji Domain-Containing Protein 6 3 4
  • Histone Arginine Demethylase JMJD6 3 4
  • Peptide-Lysine 5-Dioxygenase JMJD6 3 4
  • JmjC Domain-Containing Protein 6 3 4
  • Lysyl-Hydroxylase JMJD6 3 4
  • PTDSR 3 4
  • PSR 3 6
  • Bifunctional Arginine Demethylase And Lysyl-Hydroxylase JMJD6 3
  • Protein PTDSR 4
  • EC 1.14.11.- 4
  • EC 1.14.11 64
  • KIAA0585 4
  • PTDSR1 3

External Ids for JMJD6 Gene

Previous Symbols for JMJD6 Gene

  • PTDSR

Summaries for JMJD6 Gene

Entrez Gene Summary for JMJD6 Gene

  • This gene encodes a nuclear protein with a JmjC domain. JmjC domain-containing proteins are predicted to function as protein hydroxylases or histone demethylases. This protein was first identified 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 of apoptotic cells, and questioned whether it is a true phosphatidylserine receptor. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

GeneCards Summary for JMJD6 Gene

JMJD6 (Jumonji Domain Containing 6) is a Protein Coding gene. Diseases associated with JMJD6 include chorioretinal scar and intramuscular hemangioma. GO annotations related to this gene include RNA binding and receptor activity. An important paralog of this gene is JMJD4.

UniProtKB/Swiss-Prot for JMJD6 Gene

  • Dioxygenase that can both act as a histone arginine demethylase and a lysyl-hydroxylase. Acts as a lysyl-hydroxylase that catalyzes 5-hydroxylation on specific lysine residues of target proteins such as U2AF2/U2AF65 and LUC7L2. Acts as a regulator of RNA splicing by mediating 5-hydroxylation of U2AF2/U2AF65, affecting the pre-mRNA splicing activity of U2AF2/U2AF65. In addition to peptidyl-lysine 5-dioxygenase activity, may act as an RNA hydroxylase, as suggested by its ability to bind single strand RNA. Also acts as an arginine demethylase which demethylates histone H3 at Arg-2 (H3R2me) and histone H4 at Arg-3 (H4R3me), thereby playing a role in histone code. However, histone arginine demethylation may not constitute the primary activity in vivo. Has no histone lysine demethylase activity. Required for differentiation of multiple organs during embryogenesis. Acts as a key regulator of hematopoietic differentiation: required for angiogenic sprouting by regulating the pre-mRNA splicing activity of U2AF2/U2AF65. Seems to be necessary for the regulation of macrophage cytokine responses.

Gene Wiki entry for JMJD6 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for JMJD6 Gene

Genomics for JMJD6 Gene

Genomic Location for JMJD6 Gene

Start:
76,712,832 bp from pter
End:
76,726,799 bp from pter
Size:
13,968 bases
Orientation:
Minus strand

Genomic View for JMJD6 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for JMJD6 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for JMJD6 Gene

Regulatory Elements for JMJD6 Gene

Proteins for JMJD6 Gene

  • Protein details for JMJD6 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q6NYC1-JMJD6_HUMAN
    Recommended name:
    Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6
    Protein Accession:
    Q6NYC1
    Secondary Accessions:
    • B3KMN8
    • B4DGX1
    • Q86VY0
    • Q8IUM5
    • Q9Y4E2

    Protein attributes for JMJD6 Gene

    Size:
    403 amino acids
    Molecular mass:
    46462 Da
    Cofactor:
    Name=Fe(2+); Xref=ChEBI:CHEBI:29033; Note=Binds 1 Fe(2+) ion per subunit.;
    Quaternary structure:
    • Interacts with LUC7L2, LUC7L3 and U2AF2/U2AF65. Interacts with BRD4. Interacts with LIAT1 (By similarity).
    SequenceCaution:
    • Sequence=AAH47003.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305}; Sequence=BAA25511.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for JMJD6 Gene

    Alternative splice isoforms for JMJD6 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for JMJD6 Gene

Proteomics data for JMJD6 Gene at MOPED

Post-translational modifications for JMJD6 Gene

  • Modification sites at PhosphoSitePlus
  • Ubiquitination at Lys167 and Lys204

Other Protein References for JMJD6 Gene

Domains for JMJD6 Gene

Protein Domains for JMJD6 Gene

InterPro:
ProtoNet:

UniProtKB/Swiss-Prot:

JMJD6_HUMAN
Domain:
  • The nuclear localization signal motifs are necessary and sufficient to target it into the nucleus:
    • Q6NYC1
  • Contains 1 JmjC domain.:
    • Q6NYC1
Family:
  • Belongs to the JMJD6 family.:
    • Q6NYC1
genes like me logo Genes that share domains with JMJD6: view

No data available for Gene Families for JMJD6 Gene

Function for JMJD6 Gene

Molecular function for JMJD6 Gene

UniProtKB/Swiss-Prot BiophysicochemicalProperties: Kinetic parameters: KM=39 uM for 2-oxoglutarate {ECO:0000269 PubMed:20684070};
UniProtKB/Swiss-Prot Function: Dioxygenase that can both act as a histone arginine demethylase and a lysyl-hydroxylase. Acts as a lysyl-hydroxylase that catalyzes 5-hydroxylation on specific lysine residues of target proteins such as U2AF2/U2AF65 and LUC7L2. Acts as a regulator of RNA splicing by mediating 5-hydroxylation of U2AF2/U2AF65, affecting the pre-mRNA splicing activity of U2AF2/U2AF65. In addition to peptidyl-lysine 5-dioxygenase activity, may act as an RNA hydroxylase, as suggested by its ability to bind single strand RNA. Also acts as an arginine demethylase which demethylates histone H3 at Arg-2 (H3R2me) and histone H4 at Arg-3 (H4R3me), thereby playing a role in histone code. However, histone arginine demethylation may not constitute the primary activity in vivo. Has no histone lysine demethylase activity. Required for differentiation of multiple organs during embryogenesis. Acts as a key regulator of hematopoietic differentiation: required for angiogenic sprouting by regulating the pre-mRNA splicing activity of U2AF2/U2AF65. Seems to be necessary for the regulation of macrophage cytokine responses.
UniProtKB/Swiss-Prot Induction: Up-regulated upon cytokine treatment, but not upon TNF treatment.

Enzyme Numbers (IUBMB) for JMJD6 Gene

Gene Ontology (GO) - Molecular Function for JMJD6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding TAS 21060799
GO:0003727 single-stranded RNA binding IDA 20679243
GO:0004872 receptor activity IEA --
GO:0005506 iron ion binding IDA 20679243
GO:0005515 protein binding IPI 19574390
genes like me logo Genes that share ontologies with JMJD6: view
genes like me logo Genes that share phenotypes with JMJD6: view

Animal Models for JMJD6 Gene

MGI Knock Outs for JMJD6:

miRNA for JMJD6 Gene

miRTarBase miRNAs that target JMJD6

No data available for Transcription Factor Targeting and HOMER Transcription for JMJD6 Gene

Localization for JMJD6 Gene

Subcellular locations from UniProtKB/Swiss-Prot for JMJD6 Gene

Nucleus, nucleoplasm. Nucleus, nucleolus. Note=Mainly found throughout the nucleoplasm outside of regions containing heterochromatic DNA, with some localization in nucleolus. During mitosis, excluded from the nucleus and reappears in the telophase of the cell cycle.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for JMJD6 Gene COMPARTMENTS Subcellular localization image for JMJD6 gene
Compartment Confidence
nucleus 5
extracellular 2
plasma membrane 2

Gene Ontology (GO) - Cellular Components for JMJD6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA 14729065
GO:0005654 nucleoplasm IDA 21060799
GO:0005730 nucleolus IDA 21060799
GO:0005886 plasma membrane IEA --
genes like me logo Genes that share ontologies with JMJD6: view

Pathways for JMJD6 Gene

SuperPathways for JMJD6 Gene

No Data Available

Gene Ontology (GO) - Biological Process for JMJD6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001568 blood vessel development --
GO:0001822 kidney development IEA --
GO:0002040 sprouting angiogenesis ISS --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
genes like me logo Genes that share ontologies with JMJD6: view

No data available for Pathways by source for JMJD6 Gene

Compounds for JMJD6 Gene

(124) HMDB Compounds for JMJD6 Gene

Compound Synonyms Cas Number PubMed IDs
PS(14:0/14:0)
  • Phosphatidylserine(14:0/14:0)
Not Available
PS(14:0/14:1(9Z))
  • Phosphatidylserine(14:0/14:1n5)
Not Available
PS(14:0/16:0)
  • 1-myristoyl-2-palmitoyl-sn-glycero-3-phosphoserine
Not Available
PS(14:0/16:1(9Z))
  • PS(14:0/16:1n7)
Not Available
PS(14:0/18:0)
  • Phosphatidylserine(32:0)
Not Available

(4) Novoseek inferred chemical compound relationships for JMJD6 Gene

Compound -log(P) Hits PubMed IDs
phosphatidylserine 89.7 61
phosphoserine 58.3 2
phospholipid 26.7 2
lipid 3.1 1
genes like me logo Genes that share compounds with JMJD6: view

Transcripts for JMJD6 Gene

Unigene Clusters for JMJD6 Gene

Jumonji domain containing 6:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for JMJD6 Gene

ExUns: 1 ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7
SP1: -
SP2:

Relevant External Links for JMJD6 Gene

GeneLoc Exon Structure for
JMJD6
ECgene alternative splicing isoforms for
JMJD6

Expression for JMJD6 Gene

mRNA expression in normal human tissues for JMJD6 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for JMJD6 Gene

This gene is overexpressed in Whole Blood (4.8).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for JMJD6 Gene

SOURCE GeneReport for Unigene cluster for JMJD6 Gene Hs.514505

mRNA Expression by UniProt/SwissProt for JMJD6 Gene

Q6NYC1-JMJD6_HUMAN
Tissue specificity: Highly expressed in the heart, skeletal muscle and kidney. Expressed at moderate or low level in brain, placenta, lung, liver, pancreas, spleen, thymus, prostate, testis and ovary. Up-regulated in many patients with chronic pancreatitis. Expressed in nursing thymic epithelial cells.
genes like me logo Genes that share expressions with JMJD6: view

Orthologs for JMJD6 Gene

This gene was present in the common ancestor of animals.

Orthologs for JMJD6 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia JMJD6 36
  • 99.76 (n)
  • 100 (a)
JMJD6 37
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia JMJD6 36
  • 91.81 (n)
  • 98.01 (a)
JMJD6 37
  • 98 (a)
OneToOne
dog
(Canis familiaris)
Mammalia JMJD6 36
  • 92.75 (n)
  • 98.31 (a)
JMJD6 37
  • 98 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Jmjd6 36
  • 89.99 (n)
  • 97.77 (a)
Jmjd6 16
Jmjd6 37
  • 98 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia JMJD6 37
  • 99 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia JMJD6 37
  • 97 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Jmjd6 36
  • 89.5 (n)
  • 98.01 (a)
chicken
(Gallus gallus)
Aves JMJD6 36
  • 82.69 (n)
  • 94.2 (a)
JMJD6 37
  • 94 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia JMJD6 37
  • 91 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia cg5383-prov 36
tropical clawed frog
(Silurana tropicalis)
Amphibia jmjd6 36
  • 75.1 (n)
  • 84.62 (a)
Str.7456 36
zebrafish
(Danio rerio)
Actinopterygii jmjd6 36
  • 72.13 (n)
  • 84.86 (a)
jmjd6 37
  • 85 (a)
OneToOne
LOC266962 36
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP000158 36
  • 63.39 (n)
  • 66.5 (a)
fruit fly
(Drosophila melanogaster)
Insecta PSR 36
  • 62.63 (n)
  • 68.43 (a)
PSR 37
  • 64 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea psr-1 36
  • 58.21 (n)
  • 56.19 (a)
psr-1 37
  • 48 (a)
OneToOne
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.8912 36
sea squirt
(Ciona savignyi)
Ascidiacea CSA.6953 37
  • 68 (a)
OneToOne
Species with no ortholog for JMJD6:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for JMJD6 Gene

ENSEMBL:
Gene Tree for JMJD6 (if available)
TreeFam:
Gene Tree for JMJD6 (if available)

Paralogs for JMJD6 Gene

Paralogs for JMJD6 Gene

genes like me logo Genes that share paralogs with JMJD6: view

Variants for JMJD6 Gene

Sequence variations from dbSNP and Humsavar for JMJD6 Gene

SNP ID Clin Chr 17 pos Sequence Context AA Info Type MAF
rs1014390 -- 76,716,804(-) GGGTC(C/T)TGCTT intron-variant
rs2240769 -- 76,722,073(-) TCCCT(A/G)GATCA intron-variant
rs2240770 -- 76,721,522(-) TTTGT(A/G)TTTTG intron-variant
rs2240771 -- 76,718,909(-) AAGAA(A/G/T)TGGGT intron-variant
rs2240772 -- 76,715,641(-) GAGGC(A/G)TTGGC utr-variant-3-prime

Structural Variations from Database of Genomic Variants (DGV) for JMJD6 Gene

Variant ID Type Subtype PubMed ID
nsv908833 CNV Loss 21882294
esv28006 CNV Gain 19812545
nsv833550 CNV Loss 17160897

Relevant External Links for JMJD6 Gene

HapMap Linkage Disequilibrium report
JMJD6

Disorders for JMJD6 Gene

(1) Novoseek inferred disease relationships for JMJD6 Gene

Disease -log(P) Hits PubMed IDs
inflammation 37 2
genes like me logo Genes that share disorders with JMJD6: view

No data available for UniProtKB/Swiss-Prot for JMJD6 Gene

Publications for JMJD6 Gene

  1. Elastase-mediated phosphatidylserine receptor cleavage impairs apoptotic cell clearance in cystic fibrosis and bronchiectasis. (PMID: 11877474) Vandivier R.W. … Henson P.M. (J. Clin. Invest. 2002) 2 3 23
  2. Phosphatidylserine receptor cooperates with high-density lipoprotein receptor in recognition of apoptotic cells by thymic nurse cells. (PMID: 15072554) Cao W.M. … Ishida T. (J. Mol. Endocrinol. 2004) 3 4 23
  3. Phosphatidylserine receptor in chronic pancreatitis: evidence for a macrophage independent role. (PMID: 15622002) Koeninger J. … Friess H. (Ann. Surg. 2005) 3 4 23
  4. Characterization of the biochemical and biophysical properties of the phosphatidylserine receptor (PS-R) gene product. (PMID: 17534701) Tibrewal N. … Birge R.B. (Mol. Cell. Biochem. 2007) 3 23
  5. The phosphatidylserine receptor from Hydra is a nuclear protein with potential Fe(II) dependent oxygenase activity. (PMID: 15193161) Cikala M. … BAPttger A. (BMC Cell Biol. 2004) 3 23

Products for JMJD6 Gene

  • Addgene plasmids for JMJD6

Sources for JMJD6 Gene

Back to Top

Content