JMJD6 Gene (Protein Coding)

Jumonji Domain Containing 6, Arginine Demethylase And Lysine Hydroxylase

GC17M076718
GIFtS:
43
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 o... See more...

Aliases for JMJD6 Gene

Aliases for JMJD6 Gene

  • Jumonji Domain Containing 6, Arginine Demethylase And Lysine Hydroxylase 2 3 5
  • Phosphatidylserine Receptor 2 3 4
  • Bifunctional Arginine Demethylase And Lysyl-Hydroxylase JMJD6 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
  • KIAA0585 2 4
  • PTDSR1 2 3
  • PTDSR 3 4
  • PSR 3 4
  • Arginine Demethylase And Lysine Hydroxylase 3
  • Jumonji Domain Containing 6 2
  • Protein PTDSR 4
  • EC 1.14.11.- 4
  • EC 1.14.11 51
  • JMJD6 5

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 (Jumonji Domain Containing 6, Arginine Demethylase And Lysine Hydroxylase) is a Protein Coding gene. Diseases associated with JMJD6 include Myasthenic Syndrome, Congenital, 9, Associated With Acetylcholine Receptor Deficiency and Pancreatitis. Among its related pathways are Chromatin organization and Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3. Gene Ontology (GO) annotations related to this gene include identical protein binding. An important paralog of this gene is JMJD4.

UniProtKB/Swiss-Prot Summary for JMJD6 Gene

  • Dioxygenase that can both act as a arginine demethylase and a lysyl-hydroxylase (PubMed:24498420, PubMed:17947579, PubMed:20684070, PubMed:21060799, PubMed:22189873). Acts as a lysyl-hydroxylase that catalyzes 5-hydroxylation on specific lysine residues of target proteins such as U2AF2/U2AF65 and LUC7L2. Regulates RNA splicing by mediating 5-hydroxylation of U2AF2/U2AF65, affecting the pre-mRNA splicing activity of U2AF2/U2AF65 (PubMed:19574390). Hydroxylates its own N-terminus, which is required for homooligomerization (PubMed:22189873). In addition to peptidyl-lysine 5-dioxygenase activity, may act as an RNA hydroxylase, as suggested by its ability to bind single strand RNA (PubMed:20679243, PubMed:29176719). Also acts as an arginine demethylase which preferentially demethylates asymmetric dimethylation (PubMed:17947579, PubMed:24498420, PubMed:24360279). Demethylates histone H3 at 'Arg-2' (H3R2me) and histone H4 at 'Arg-3' (H4R3me), including mono-, symmetric di- and asymmetric dimethylated forms, thereby playing a role in histone code (PubMed:17947579, PubMed:24360279). However, histone arginine demethylation may not constitute the primary activity in vivo (PubMed:17947579, PubMed:21060799, PubMed:22189873). In collaboration with BRD4, interacts with the positive transcription elongation factor b (P-TEFb) complex in its active form to regulate polymerase II promoter-proximal pause release for transcriptional activation of a large cohort of genes. On distal enhancers, so called anti-pause enhancers, demethylates both histone H4R3me2 and the methyl cap of 7SKsnRNA leading to the dismissal of the 7SKsnRNA:HEXIM1 inhibitor complex. After removal of repressive marks, the complex BRD4:JMJD6 attract and retain the P-TEFb complex on chromatin, leading to its activation, promoter-proximal polymerase II pause release, and transcriptional activation (PubMed:24360279). Demethylates other arginine methylated-proteins such as ESR1 (PubMed:24498420). Has no histone lysine demethylase activity (PubMed:21060799). 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 (By similarity). Seems to be necessary for the regulation of macrophage cytokine responses (PubMed:15622002).

Gene Wiki entry for JMJD6 Gene

Additional gene information for JMJD6 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for JMJD6 Gene

Genomics for JMJD6 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for JMJD6 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around JMJD6 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for JMJD6

Top Transcription factor binding sites by QIAGEN in the JMJD6 gene promoter:
  • AML1a
  • c-Myc
  • Max
  • Max1
  • MyoD

Genomic Locations for JMJD6 Gene

Latest Assembly
chr17:76,712,830-76,726,799
(GRCh38/hg38)
Size:
13,970 bases
Orientation:
Minus strand

Previous Assembly
chr17:74,708,918-74,722,688
(GRCh37/hg19 by Entrez Gene)
Size:
13,771 bases
Orientation:
Minus strand

chr17:74,708,919-74,722,866
(GRCh37/hg19 by Ensembl)
Size:
13,948 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 Structure • Gene Density

RefSeq DNA sequence for JMJD6 Gene

Proteins for JMJD6 Gene

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  • 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:
    • Homooligomerizes; requires lysyl-hydroxylase activity (PubMed:22189873, PubMed:24360279). Interacts with LUC7L2, LUC7L3 and U2AF2/U2AF65 (PubMed:19574390). Interacts with LIAT1 (By similarity). Interacts with CDK9 and CCNT1; the interaction is direct with CDK9 and associates the P-TEFb complex when active (PubMed:24360279). Interacts (via JmjC and N-terminal domains) with BRD4 (via NET domain); the interaction is stronger in presence of ssRNA and recruits JMJD6 on distal enhancers (PubMed:21555454, PubMed:24360279, PubMed:29176719).
    SequenceCaution:
    • Sequence=AAH47003.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305}; Sequence=BAA25511.1; Type=Erroneous initiation; Note=Extended N-terminus.; 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

Protein Expression for JMJD6 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Selected DME Specific Peptides for JMJD6 Gene

Q6NYC1:
  • KRRKLLEDY
  • EDYKVPKFF
  • EAKRSARPELKDS
  • GHKRWCLFPT
  • DEAITWF
  • IHIDPLGTSAWN
  • TPRELIKV
  • YPRTQLP
  • KTVRGRPKLS
  • ASDSSSDSSSSSSSSSS
  • DDSPLYIFD
  • EKWTLERL
  • RWFVMGP
  • DNVERADALQL
  • HRRKKRRT
  • GETVFVPGGWWHVVLN
  • GSEGDGT
  • TIAITQNF
  • GNGDTTSQDDCVSKERSSSR
  • KYRNQKFK

Post-translational modifications for JMJD6 Gene

  • Hydroxylates its own N-terminus; hydroxylation is required for homooligomerization.
  • Ubiquitination at Lys167 and Lys204
  • Modification sites at PhosphoSitePlus

Other Protein References for JMJD6 Gene

ENSEMBL proteins:
REFSEQ proteins:

Domains & Families for JMJD6 Gene

Gene Families for JMJD6 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for JMJD6 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for JMJD6 Gene

GenScript: Design optimal peptide antigens:
  • Phosphatidylserine receptor, isoform CRA_d (B2WTI3_HUMAN)
  • Phosphatidylserine receptor (JMJD6_HUMAN)

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.
Family:
  • Belongs to the JMJD6 family.
genes like me logo Genes that share domains with JMJD6: view

Function for JMJD6 Gene

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Molecular function for JMJD6 Gene

UniProtKB/Swiss-Prot Function:
Dioxygenase that can both act as a arginine demethylase and a lysyl-hydroxylase (PubMed:24498420, PubMed:17947579, PubMed:20684070, PubMed:21060799, PubMed:22189873). Acts as a lysyl-hydroxylase that catalyzes 5-hydroxylation on specific lysine residues of target proteins such as U2AF2/U2AF65 and LUC7L2. Regulates RNA splicing by mediating 5-hydroxylation of U2AF2/U2AF65, affecting the pre-mRNA splicing activity of U2AF2/U2AF65 (PubMed:19574390). Hydroxylates its own N-terminus, which is required for homooligomerization (PubMed:22189873). In addition to peptidyl-lysine 5-dioxygenase activity, may act as an RNA hydroxylase, as suggested by its ability to bind single strand RNA (PubMed:20679243, PubMed:29176719). Also acts as an arginine demethylase which preferentially demethylates asymmetric dimethylation (PubMed:17947579, PubMed:24498420, PubMed:24360279). Demethylates histone H3 at 'Arg-2' (H3R2me) and histone H4 at 'Arg-3' (H4R3me), including mono-, symmetric di- and asymmetric dimethylated forms, thereby playing a role in histone code (PubMed:17947579, PubMed:24360279). However, histone arginine demethylation may not constitute the primary activity in vivo (PubMed:17947579, PubMed:21060799, PubMed:22189873). In collaboration with BRD4, interacts with the positive transcription elongation factor b (P-TEFb) complex in its active form to regulate polymerase II promoter-proximal pause release for transcriptional activation of a large cohort of genes. On distal enhancers, so called anti-pause enhancers, demethylates both histone H4R3me2 and the methyl cap of 7SKsnRNA leading to the dismissal of the 7SKsnRNA:HEXIM1 inhibitor complex. After removal of repressive marks, the complex BRD4:JMJD6 attract and retain the P-TEFb complex on chromatin, leading to its activation, promoter-proximal polymerase II pause release, and transcriptional activation (PubMed:24360279). Demethylates other arginine methylated-proteins such as ESR1 (PubMed:24498420). Has no histone lysine demethylase activity (PubMed:21060799). 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 (By similarity). Seems to be necessary for the regulation of macrophage cytokine responses (PubMed:15622002).
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=2-oxoglutarate + L-lysyl-[protein] + O2 = (5S)-5-hydroxy-L-lysyl-[protein] + CO2 + succinate; Xref=Rhea:RHEA:58360, Rhea:RHEA-COMP:9752, Rhea:RHEA-COMP:15144, ChEBI:CHEBI:15379, ChEBI:CHEBI:16526, ChEBI:CHEBI:16810, ChEBI:CHEBI:29969, ChEBI:CHEBI:30031, ChEBI:CHEBI:141843; Evidence={ECO:0000269|PubMed:19574390, ECO:0000269|PubMed:20684070, ECO:0000269|PubMed:22189873};.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=2 2-oxoglutarate + N(omega),N(omega)'-dimethyl-L-arginyl-[protein] + 2 O2 = 2 CO2 + 2 formaldehyde + L-arginyl-[protein] + 2 succinate; Xref=Rhea:RHEA:58348, Rhea:RHEA-COMP:10532, Rhea:RHEA-COMP:11992, ChEBI:CHEBI:15379, ChEBI:CHEBI:16526, ChEBI:CHEBI:16810, ChEBI:CHEBI:16842, ChEBI:CHEBI:29965, ChEBI:CHEBI:30031, ChEBI:CHEBI:88221; Evidence={ECO:0000269|PubMed:17947579, ECO:0000269|PubMed:24360279};.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=2-oxoglutarate + N(omega),N(omega)'-dimethyl-L-arginyl-[protein] + O2 = CO2 + formaldehyde + N(omega)-methyl-L-arginyl-[protein] + succinate; Xref=Rhea:RHEA:58472, Rhea:RHEA-COMP:11990, Rhea:RHEA-COMP:11992, ChEBI:CHEBI:15379, ChEBI:CHEBI:16526, ChEBI:CHEBI:16810, ChEBI:CHEBI:16842, ChEBI:CHEBI:30031, ChEBI:CHEBI:65280, ChEBI:CHEBI:88221; Evidence={ECO:0000269|PubMed:17947579, ECO:0000269|PubMed:24360279};.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=2-oxoglutarate + a 5'-methyltriphosphate-guanosine-ribonucleotide-snRNA + O2 = a 5'-triphospho-guanosine-ribonucleotide-snRNA + CO2 + formaldehyde + H(+) + succinate; Xref=Rhea:RHEA:58784, Rhea:RHEA-COMP:15220, Rhea:RHEA-COMP:15221, ChEBI:CHEBI:15378, ChEBI:CHEBI:15379, ChEBI:CHEBI:16526, ChEBI:CHEBI:16810, ChEBI:CHEBI:16842, ChEBI:CHEBI:30031, ChEBI:CHEBI:138278, ChEBI:CHEBI:142789; Evidence={ECO:0000269|PubMed:24360279};.
UniProtKB/Swiss-Prot Induction:
Up-regulated upon cytokine treatment, but not upon TNF treatment.
UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=39 uM for 2-oxoglutarate {ECO:0000269|PubMed:20684070};

Enzyme Numbers (IUBMB) for JMJD6 Gene

Phenotypes From GWAS Catalog 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:0005506 iron ion binding IDA 20679243
GO:0005515 protein binding IPI 19574390
GO:0016491 oxidoreductase activity IEA --
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 Models for research

  • Taconic Biosciences Mouse Models for JMJD6

miRNA for JMJD6 Gene

miRTarBase miRNAs that target JMJD6

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for JMJD6

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. Cytoplasm. 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. {ECO:0000269 PubMed:21060799}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for JMJD6 gene
Compartment Confidence
nucleus 5
plasma membrane 3
cytosol 3
extracellular 2
cytoskeleton 2
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1
endosome 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for JMJD6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IMP 21555454
GO:0005654 nucleoplasm IDA,TAS --
GO:0005730 nucleolus IEA,IDA 21060799
GO:0005737 cytoplasm IEA,IDA 24498420
GO:0005829 cytosol IEA --
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

SIGNOR curated interactions for JMJD6 Gene

Inactivates:

Gene Ontology (GO) - Biological Process for JMJD6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001568 blood vessel development IEA --
GO:0001822 kidney development IEA --
GO:0002040 sprouting angiogenesis ISS --
GO:0006325 chromatin organization IEA --
GO:0006397 mRNA processing IEA --
genes like me logo Genes that share ontologies with JMJD6: view

Drugs & Compounds for JMJD6 Gene

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(2) Drugs for JMJD6 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

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

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(28:0)
  • pSer(14:0/14:0)
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(30:0)
  • pSer(14:0/16:0)
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(32:0)
  • pSer(14:0/18:0)
genes like me logo Genes that share compounds with JMJD6: view

Transcripts for JMJD6 Gene

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mRNA/cDNA for JMJD6 Gene

2 REFSEQ mRNAs :
13 NCBI additional mRNA sequence :
8 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for JMJD6

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

Expression for JMJD6 Gene

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mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for JMJD6 Gene

mRNA expression in normal human tissues for JMJD6 Gene
mRNA expression by GTEx for JMJD6 GenemRNA expression by BioGPS 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, MaxQB, and MOPED for JMJD6 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for JMJD6

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.

Evidence on tissue expression from TISSUES for JMJD6 Gene

  • Nervous system(4.8)
  • Skin(4.4)
  • Lung(2.7)
  • Bone marrow(2.6)
  • Kidney(2.4)
  • Heart(2.4)
  • Spleen(2.3)
  • Lymph node(2.2)
  • Muscle(2.2)
  • Blood(2.2)
  • Intestine(2.2)
  • Liver(2.1)
genes like me logo Genes that share expression patterns with JMJD6: view

Primer products for research

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer 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 30 31
  • 99.76 (n)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia JMJD6 31
  • 99 (a)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia JMJD6 31
  • 97 (a)
 OneToOne
Dog
(Canis familiaris)
 Mammalia JMJD6 30 31
  • 92.75 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia JMJD6 30 31
  • 91.81 (n)
 OneToOne
Mouse
(Mus musculus)
 Mammalia Jmjd6 30 17 31
  • 89.99 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Jmjd6 30
  • 89.5 (n)
Chicken
(Gallus gallus)
 Aves JMJD6 30 31
  • 82.69 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia JMJD6 31
  • 91 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia jmjd6 30
  • 75.1 (n)
Str.7456 30
African clawed frog
(Xenopus laevis)
 Amphibia cg5383-prov 30
Zebrafish
(Danio rerio)
 Actinopterygii jmjd6 30 31
  • 72.13 (n)
 OneToOne
LOC266962 30
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP000158 30
  • 63.39 (n)
Fruit Fly
(Drosophila melanogaster)
 Insecta PSR 30 31
  • 62.63 (n)
 OneToOne
Worm
(Caenorhabditis elegans)
 Secernentea psr-1 30 31
  • 58.21 (n)
 OneToOne
Sea Squirt
(Ciona savignyi)
 Ascidiacea CSA.6953 31
  • 68 (a)
 OneToOne
Sea Vase
(Ciona intestinalis)
 Ascidiacea Cin.8912 30
Species where no ortholog for JMJD6 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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)
Aminode:
Evolutionary constrained regions (ECRs) for JMJD6: view image

Paralogs for JMJD6 Gene

Paralogs for JMJD6 Gene

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

Variants for JMJD6 Gene

Products:

  1. SNP Genotyping and Copy Number Assays for research

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for JMJD6 Gene

SNP ID Clinical significance and condition Chr 17 pos Variation AA Info Type
rs200613423 Benign: not provided 76,725,508(-) G/A
NM_001081461.2(JMJD6):c.477C>T (p.Asp159=) 		SYNONYMOUS

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for JMJD6 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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

Variant ID Type Subtype PubMed ID
esv28006 CNV gain 19812545
nsv1123145 CNV deletion 24896259
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)

Additional Variant Information for JMJD6 Gene

Human Gene Mutation Database (HGMD)
JMJD6
SNPedia medical, phenotypic, and genealogical associations of SNPs for
JMJD6

SNP Genotyping and Copy Number Assays for research

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

Disorders for JMJD6 Gene

MalaCards: The human disease database

(3) MalaCards diseases for JMJD6 Gene - From: COP and GCD

- elite association - COSMIC cancer census association via MalaCards
Search JMJD6 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for JMJD6

Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
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) Köninger J … Friess H (Annals of surgery 2005) 3 4 23
  2. Phosphatidylserine receptor cooperates with high-density lipoprotein receptor in recognition of apoptotic cells by thymic nurse cells. (PMID: 15072554) Cao WM … Ishida T (Journal of molecular endocrinology 2004) 3 4 23
  3. Elastase-mediated phosphatidylserine receptor cleavage impairs apoptotic cell clearance in cystic fibrosis and bronchiectasis. (PMID: 11877474) Vandivier RW … Henson PM (The Journal of clinical investigation 2002) 2 3 23
  4. Structural Mechanism of the Oxygenase JMJD6 Recognition by the Extraterminal (ET) Domain of BRD4. (PMID: 29176719) Konuma T … Zeng L (Scientific reports 2017) 3 4
  5. JMJD6 regulates ERα methylation on arginine. (PMID: 24498420) Poulard C … Le Romancer M (PloS one 2014) 3 4

ExternalLinks

View latest publications for JMJD6 gene in Mastermind

Products for JMJD6 Gene

  • Addgene plasmids for JMJD6

Sources for JMJD6 Gene