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Aliases for JMJD6 Gene

Aliases for JMJD6 Gene

  • Arginine Demethylase And Lysine Hydroxylase 2 3
  • Phosphatidylserine Receptor 2 3 4
  • Jumonji Domain Containing 6 2 3 5
  • 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
  • Protein PTDSR 4
  • EC 1.14.11.- 4
  • EC 1.14.11 63
  • KIAA0585 4
  • PTDSR1 3
  • PSR 3

External Ids for JMJD6 Gene

Previous HGNC Symbols for JMJD6 Gene

  • PTDSR

Previous GeneCards Identifiers for JMJD6 Gene

  • GC17M072221
  • GC17M074708
  • GC17M070137

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 (Arginine Demethylase And Lysine Hydroxylase) is a Protein Coding gene. Diseases associated with JMJD6 include deep angioma and intramuscular hemangioma. Among its related pathways are Chromatin organization and Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3. GO annotations related to this gene include identical protein 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

Regulatory Elements for JMJD6 Gene

Promoters for JMJD6 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around JMJD6 on UCSC Golden Path with GeneCards custom track

Genomic Location for JMJD6 Gene

Chromosome:
17
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

Genes around JMJD6 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
JMJD6 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for JMJD6 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence 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;
    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

  • Ubiquitination at Lys 167 and Lys 204
  • Modification sites at PhosphoSitePlus

Other Protein References for JMJD6 Gene

Antibody Products

Domains & Families for JMJD6 Gene

Protein Domains for JMJD6 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for JMJD6 Gene

Graphical View of Domain Structure for InterPro Entry

Q6NYC1

UniProtKB/Swiss-Prot:

JMJD6_HUMAN :
  • The nuclear localization signal motifs are necessary and sufficient to target it into the nucleus.
  • Belongs to the JMJD6 family.
Domain:
  • The nuclear localization signal motifs are necessary and sufficient to target it into the nucleus.
  • Contains 1 JmjC domain.
Family:
  • Belongs to the JMJD6 family.
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:0032452 histone demethylase activity TAS --
GO:0070815 peptidyl-lysine 5-dioxygenase activity IDA 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:

Animal Model Products

  • Taconic Biosciences Mouse Models for JMJD6

CRISPR Products

miRNA for JMJD6 Gene

miRTarBase miRNAs that target JMJD6

Inhibitory RNA Products

In Situ Assay Products

Flow Cytometry Products

No data available for Human Phenotype Ontology , Transcription Factor Targets 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
cytosol 3
plasma membrane 3
extracellular 1

Gene Ontology (GO) - Cellular Components for JMJD6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005730 nucleolus IDA 21060799
genes like me logo Genes that share ontologies with JMJD6: view

Pathways & Interactions for JMJD6 Gene

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

Pathways by source for JMJD6 Gene

1 GeneTex pathway for JMJD6 Gene

Gene Ontology (GO) - Biological Process for JMJD6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002040 sprouting angiogenesis ISS --
GO:0006325 chromatin organization TAS --
GO:0006397 mRNA processing IEA --
GO:0007507 heart development IEA --
GO:0030324 lung development IEA --
genes like me logo Genes that share ontologies with JMJD6: view

No data available for SIGNOR curated interactions for JMJD6 Gene

Drugs & Compounds for JMJD6 Gene

(1) Drugs for JMJD6 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(127) Additional Compounds for JMJD6 Gene - From: Novoseek and HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
PS(14:0/14:0)
  • 1-Myristoyl-2-myristoyl-sn-glycero-3-phosphoserine
  • Phosphatidylserine(14:0/14:0)
  • Phosphatidylserine(28:0)
  • PS(14:0/14:0)
  • PS(28:0)
PS(14:0/14:1(9Z))
  • 1-Myristoyl-2-myristoleoyl-sn-glycero-3-phosphoserine
  • Phosphatidylserine(14:0/14:1)
  • Phosphatidylserine(14:0/14:1n5)
  • Phosphatidylserine(14:0/14:1w5)
  • Phosphatidylserine(28:1)
PS(14:0/16:0)
  • 1-Myristoyl-2-palmitoyl-sn-glycero-3-phosphoserine
  • Phosphatidylserine(14:0/16:0)
  • Phosphatidylserine(30:0)
  • PS(14:0/16:0)
  • PS(30:0)
PS(14:0/16:1(9Z))
  • 1-Myristoyl-2-palmitoleoyl-sn-glycero-3-phosphoserine
  • Phosphatidylserine(14:0/16:1)
  • Phosphatidylserine(14:0/16:1n7)
  • Phosphatidylserine(14:0/16:1w7)
  • Phosphatidylserine(30:1)
PS(14:0/18:0)
  • 1-Myristoyl-2-stearoyl-sn-glycero-3-phosphoserine
  • Phosphatidylserine(14:0/18:0)
  • Phosphatidylserine(32:0)
  • PS(14:0/18:0)
  • PS(32:0)
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:

CRISPR Products

Inhibitory RNA Products

Flow Cytometry Products

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 differential expression in normal tissues according to GTEx for JMJD6 Gene

This gene is overexpressed in Whole Blood (x4.8).

Protein differential expression in normal tissues from HIPED for JMJD6 Gene

This gene is overexpressed in Lung (36.2) and Peripheral blood mononuclear cells (10.6).

Integrated Proteomics: protein expression in normal tissues and cell lines 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 expression patterns with JMJD6: view

Primer Products

In Situ Assay Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and Protein tissue co-expression partners for JMJD6 Gene

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
  • 100 (a)
OneToOne
JMJD6 35
  • 99.76 (n)
  • 100 (a)
cow
(Bos Taurus)
Mammalia JMJD6 35
  • 91.81 (n)
  • 98.01 (a)
JMJD6 36
  • 98 (a)
OneToOne
dog
(Canis familiaris)
Mammalia JMJD6 36
  • 98 (a)
OneToOne
JMJD6 35
  • 92.75 (n)
  • 98.31 (a)
mouse
(Mus musculus)
Mammalia Jmjd6 36
  • 98 (a)
OneToOne
Jmjd6 16
Jmjd6 35
  • 89.99 (n)
  • 97.77 (a)
oppossum
(Monodelphis domestica)
Mammalia JMJD6 36
  • 99 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia JMJD6 36
  • 97 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Jmjd6 35
  • 89.5 (n)
  • 98.01 (a)
chicken
(Gallus gallus)
Aves JMJD6 35
  • 82.69 (n)
  • 94.2 (a)
JMJD6 36
  • 94 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia JMJD6 36
  • 91 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia cg5383-prov 35
tropical clawed frog
(Silurana tropicalis)
Amphibia jmjd6 35
  • 75.1 (n)
  • 84.62 (a)
Str.7456 35
zebrafish
(Danio rerio)
Actinopterygii jmjd6 36
  • 85 (a)
OneToOne
jmjd6 35
  • 72.13 (n)
  • 84.86 (a)
LOC266962 35
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP000158 35
  • 63.39 (n)
  • 66.5 (a)
fruit fly
(Drosophila melanogaster)
Insecta PSR 36
  • 64 (a)
OneToOne
PSR 35
  • 62.63 (n)
  • 68.43 (a)
worm
(Caenorhabditis elegans)
Secernentea psr-1 35
  • 58.21 (n)
  • 56.19 (a)
psr-1 36
  • 48 (a)
OneToOne
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.8912 35
sea squirt
(Ciona savignyi)
Ascidiacea CSA.6953 36
  • 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
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
rs2240774 -- 76,714,490(-) GGCCA(A/G)GGTAG utr-variant-3-prime
rs2240775 -- 76,714,046(-) TCTTA(A/G)TAATT 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

Variation tolerance for JMJD6 Gene

Residual Variation Intolerance Score: 18% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.71; 15.14% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for JMJD6 Gene

HapMap Linkage Disequilibrium report
JMJD6

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for JMJD6 Gene

Disorders for JMJD6 Gene

MalaCards: The human disease database

(6) MalaCards diseases for JMJD6 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
deep angioma
  • deep hemangioma
intramuscular hemangioma
  • intramuscular angioma
chorioretinal scar
primary cutaneous amyloidosis
  • familial primary localized cutaneous amyloidosis
congenital heart block
  • heart block congenital
- elite association - COSMIC cancer census association via MalaCards
Search JMJD6 in MalaCards View complete list of genes associated with diseases

Relevant External Links for JMJD6

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
JMJD6
genes like me logo Genes that share disorders with JMJD6: view

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

Publications for JMJD6 Gene

  1. Phosphatidylserine receptor in chronic pancreatitis: evidence for a macrophage independent role. (PMID: 15622002) Koeninger J. … Friess H. (Ann. Surg. 2005) 3 4 23 67
  2. 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
  3. Endogenous Jmjd6 gene product is expressed at the cell surface and regulates phagocytosis in immature monocyte-like activated THP-1 cells. (PMID: 19492415) Zakharova L. … Fomina A.F. (J. Cell. Physiol. 2009) 3 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. 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 23

Products for JMJD6 Gene

Sources for JMJD6 Gene

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