Browse JMJD6

Summary
SymbolJMJD6
Namejumonji domain containing 6
Aliases PTDSR1; KIAA0585; PTDSR; phosphatidylserine receptor; PSR; histone arginine demethylase JMJD6; jmjC domain-c ......
Chromosomal Location17q25
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Basic function annotation.
> Subcellular Location, Domain and Function
> Gene Ontology
> KEGG and Reactome Pathway
> Subcellular Location, Domain and Function
 
Subcellular Location 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.
Domain PF02373 JmjC domain
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.

> Gene Ontology
 
Biological Process GO:0000375 RNA splicing, via transesterification reactions
GO:0000377 RNA splicing, via transesterification reactions with bulged adenosine as nucleophile
GO:0000398 mRNA splicing, via spliceosome
GO:0001525 angiogenesis
GO:0001654 eye development
GO:0001655 urogenital system development
GO:0001822 kidney development
GO:0002040 sprouting angiogenesis
GO:0002262 myeloid cell homeostasis
GO:0002274 myeloid leukocyte activation
GO:0002521 leukocyte differentiation
GO:0006397 mRNA processing
GO:0006482 protein demethylation
GO:0006909 phagocytosis
GO:0006910 phagocytosis, recognition
GO:0007159 leukocyte cell-cell adhesion
GO:0007423 sensory organ development
GO:0007507 heart development
GO:0008037 cell recognition
GO:0008214 protein dealkylation
GO:0008380 RNA splicing
GO:0016570 histone modification
GO:0016577 histone demethylation
GO:0017185 peptidyl-lysine hydroxylation
GO:0018126 protein hydroxylation
GO:0018205 peptidyl-lysine modification
GO:0018395 peptidyl-lysine hydroxylation to 5-hydroxy-L-lysine
GO:0030098 lymphocyte differentiation
GO:0030099 myeloid cell differentiation
GO:0030217 T cell differentiation
GO:0030218 erythrocyte differentiation
GO:0030323 respiratory tube development
GO:0030324 lung development
GO:0033077 T cell differentiation in thymus
GO:0034101 erythrocyte homeostasis
GO:0042110 T cell activation
GO:0042116 macrophage activation
GO:0043010 camera-type eye development
GO:0043277 apoptotic cell clearance
GO:0043484 regulation of RNA splicing
GO:0043654 recognition of apoptotic cell
GO:0048024 regulation of mRNA splicing, via spliceosome
GO:0048514 blood vessel morphogenesis
GO:0048821 erythrocyte development
GO:0048872 homeostasis of number of cells
GO:0050684 regulation of mRNA processing
GO:0060041 retina development in camera-type eye
GO:0060541 respiratory system development
GO:0061515 myeloid cell development
GO:0070077 histone arginine demethylation
GO:0070078 histone H3-R2 demethylation
GO:0070079 histone H4-R3 demethylation
GO:0070486 leukocyte aggregation
GO:0070489 T cell aggregation
GO:0070988 demethylation
GO:0071593 lymphocyte aggregation
GO:0071594 thymocyte aggregation
GO:0072001 renal system development
GO:1903311 regulation of mRNA metabolic process
Molecular Function GO:0003727 single-stranded RNA binding
GO:0005506 iron ion binding
GO:0016705 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
GO:0016706 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors
GO:0032451 demethylase activity
GO:0032452 histone demethylase activity
GO:0033746 histone demethylase activity (H3-R2 specific)
GO:0033749 histone demethylase activity (H4-R3 specific)
GO:0051213 dioxygenase activity
GO:0070815 peptidyl-lysine 5-dioxygenase activity
Cellular Component -
> KEGG and Reactome Pathway
 
KEGG -
Reactome R-HSA-3247509: Chromatin modifying enzymes
R-HSA-4839726: Chromatin organization
R-HSA-3214842: HDMs demethylate histones
Summary
SymbolJMJD6
Namejumonji domain containing 6
Aliases PTDSR1; KIAA0585; PTDSR; phosphatidylserine receptor; PSR; histone arginine demethylase JMJD6; jmjC domain-c ......
Chromosomal Location17q25
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Literatures that report relations between JMJD6 and anti-tumor immunity. The specific mechanism were also collected if the literature reports that a gene specifically promotes or inhibits the infiltration or function of T/NK cells.
> Text Mining
 

There is no record.

Summary
SymbolJMJD6
Namejumonji domain containing 6
Aliases PTDSR1; KIAA0585; PTDSR; phosphatidylserine receptor; PSR; histone arginine demethylase JMJD6; jmjC domain-c ......
Chromosomal Location17q25
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content High-throughput screening data (e.g. CRISPR-Cas9, shRNA and RNAi) for T cell-mediated killing. Genetic screen techniques can identify mechanisms of tumor cell resistance (e.g., PTPN2) and sensitivity (e.g., APLNR) to killing by cytotoxic T cells, the central effectors of anti-tumor immunity. After comprehensively searching, eight groups of screening data sets were collected in the current database. In this tab, users can check whether their selected genes cause resistance or increase sensitivity to T cell-mediated killing in various data sets.
> High-throughput Screening
  Statistical results of JMJD6 in screening data sets for detecting immune reponses.
PMID Screening System Cancer Type Cell Line Data Set Statistical Results Relation to immunity
29301958CRISPR-Cas9 melanomaB16F10Pmel-1 T cell logFC: -2.95; FDR: 0.00942 Resistant to T cell-mediated killing
29301958CRISPR-Cas9 melanomaB16F10OT-1 T cell NA/NS NA/NS
28783722CRISPR-Cas9 melanomaMel6242CT-CRISPR NA/NS NA/NS
28723893CRISPR-Cas9 melanomaB16GVAX+Anti-PD1 NA/NS NA/NS
28723893CRISPR-Cas9 melanomaB16GVAX NA/NS NA/NS
25691366RNAiBreast cancerMCF7Luc-CTL assay NA/NS NA/NS
24476824shRNAmelanomaB16Primary screen NA/NS NA/NS
24476824shRNAmelanomaB16Secondary screen NA/NS NA/NS
Summary
SymbolJMJD6
Namejumonji domain containing 6
Aliases PTDSR1; KIAA0585; PTDSR; phosphatidylserine receptor; PSR; histone arginine demethylase JMJD6; jmjC domain-c ......
Chromosomal Location17q25
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Transcriptomic and genomic profiling of pre-treated tumor biopsies from responders and non-responders to immunotherapy. These data were used to identify signatures and mechanisms of response to checkpoint blockade (e.g., anti-PDL1 and anti-PD1). One example is that mutations in the gene PBRM1 benefit clinical survival of patients with clear cell renal cell carcinoma. After comprehensively searching, we collected 5 and 6 of transcriptomic and genomic data sets, respectively. In this tab, users can check whether their selected genes have significant difference of expression or mutation between responders and non-responders in various data sets.
> Expression difference between responders and non-responders
> Mutation difference between responders and non-responders
> Expression difference between responders and non-responders
 
Points in the above scatter plot represent the expression difference of JMJD6 in various data sets.
No PMID Cancer type Group Drug # Res # NRes Log2 (Fold Change) P value Anno
126997480MelanomaallAnti-PD-1 (pembrolizumab and nivolumab)1412-0.0860.724
226997480MelanomaMAPKiAnti-PD-1 (pembrolizumab and nivolumab)650.2520.892
326997480Melanomanon-MAPKiAnti-PD-1 (pembrolizumab and nivolumab)87-0.3370.812
428552987Urothelial cancerallAnti-PD-L1 (atezolizumab) 916-0.1890.56
528552987Urothelial cancersmokingAnti-PD-L1 (atezolizumab) 59-0.5880.721
628552987Urothelial cancernon-smokingAnti-PD-L1 (atezolizumab) 470.3220.887
729033130MelanomaallAnti-PD-1 (nivolumab) 26230.0840.82
829033130MelanomaNIV3-PROGAnti-PD-1 (nivolumab) 1511-0.0230.986
929033130MelanomaNIV3-NAIVEAnti-PD-1 (nivolumab) 11120.240.869
1029301960Clear cell renal cell carcinoma (ccRCC)allAnti-PD-1 (nivolumab) 480.3970.785
1129301960Clear cell renal cell carcinoma (ccRCC)VEGFRiAnti-PD-1 (nivolumab) 2001
1229301960Clear cell renal cell carcinoma (ccRCC)non-VEGFRiAnti-PD-1 (nivolumab) 280.9020.671
1329443960Urothelial cancerallAnti-PD-L1 (atezolizumab) 68230-0.0120.844
> Mutation difference between responders and non-responders
 
Points in the above scatter plot represent the mutation difference of JMJD6 in various data sets.
No PMID Cancer type Group Drug # Res # NRes % Mut/Res % Mut/NRes % Diff (R vs NR) Pval Anno
125765070Non-small cell lung cancer (NSCLC)allAnti-PD-1 (pembrolizumab) 14170001
225765070Non-small cell lung cancer (NSCLC)smokingAnti-PD-1 (pembrolizumab) 1030001
325765070Non-small cell lung cancer (NSCLC)non-smokingAnti-PD-1 (pembrolizumab) 4140001
426359337MelanomaallAnti-CTLA-4 (ipilimumab) 27737.41.460.177
526359337MelanomaBRAFiAnti-CTLA-4 (ipilimumab) 0140001
626359337Melanomanon-BRAFiAnti-CTLA-4 (ipilimumab) 27597.41.75.70.231
726997480MelanomaallAnti-PD-1 (pembrolizumab and nivolumab)211705.9-5.90.447
826997480MelanomaMAPKiAnti-PD-1 (pembrolizumab and nivolumab)860001
926997480Melanomanon-MAPKiAnti-PD-1 (pembrolizumab and nivolumab)131109.1-9.10.458
1028552987Urothelial cancerallAnti-PD-L1 (atezolizumab) 9160001
1128552987Urothelial cancersmokingAnti-PD-L1 (atezolizumab) 590001
1228552987Urothelial cancernon-smokingAnti-PD-L1 (atezolizumab) 470001
1329033130MelanomaallAnti-PD-1 (nivolumab) 38270001
1429033130MelanomaNIV3-PROGAnti-PD-1 (nivolumab) 22130001
1529033130MelanomaNIV3-NAIVEAnti-PD-1 (nivolumab) 16140001
1629301960Clear cell renal cell carcinoma (ccRCC)allAnti-PD-1 (nivolumab) 11130001
1729301960Clear cell renal cell carcinoma (ccRCC)VEGFRiAnti-PD-1 (nivolumab) 610001
1829301960Clear cell renal cell carcinoma (ccRCC)non-VEGFRiAnti-PD-1 (nivolumab) 5120001
Summary
SymbolJMJD6
Namejumonji domain containing 6
Aliases PTDSR1; KIAA0585; PTDSR; phosphatidylserine receptor; PSR; histone arginine demethylase JMJD6; jmjC domain-c ......
Chromosomal Location17q25
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Relations between abundance of tumor-infiltrating lymphocytes (TILs) and expression, copy number, methylation, or mutation of JMJD6. The immune-related signatures of 28 TIL types from Charoentong's study, which can be viewed in the download page. For each cancer type, the relative abundance of TILs were inferred by using gene set variation analysis (GSVA) based on gene expression profile. In this tab, users can examine which kinds of TILs might be regulated by the current gene.
> Lymphocyte
 
Summary
SymbolJMJD6
Namejumonji domain containing 6
Aliases PTDSR1; KIAA0585; PTDSR; phosphatidylserine receptor; PSR; histone arginine demethylase JMJD6; jmjC domain-c ......
Chromosomal Location17q25
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Relations between three kinds of immunomodulators and expression, copy number, methylation, or mutation of JMJD6. These immunomo-dulators were collected from Charoentong's study. In this tab, users can examine which immunomodulators might be regulated by JMJD6.
> Immunoinhibitor
> Immunostimulator
> MHC molecule
> Immunoinhibitor
 
> Immunostimulator
 
> MHC molecule
 
Summary
SymbolJMJD6
Namejumonji domain containing 6
Aliases PTDSR1; KIAA0585; PTDSR; phosphatidylserine receptor; PSR; histone arginine demethylase JMJD6; jmjC domain-c ......
Chromosomal Location17q25
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Relations between chemokines (or receptors) and expression, copy number, methylation, or mutation of JMJD6. In this tab, users can examine which chemokines (or receptors) might be regulated by the current gene.
> Chemokine
> Receptor
> Chemokine
 
> Receptor
 
Summary
SymbolJMJD6
Namejumonji domain containing 6
Aliases PTDSR1; KIAA0585; PTDSR; phosphatidylserine receptor; PSR; histone arginine demethylase JMJD6; jmjC domain-c ......
Chromosomal Location17q25
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Distribution of JMJD6 expression across immune and molecular subtypes.
> Immune subtype
> Molecular subtype
> Immune subtype
 
> Molecular subtype
 
Summary
SymbolJMJD6
Namejumonji domain containing 6
Aliases PTDSR1; KIAA0585; PTDSR; phosphatidylserine receptor; PSR; histone arginine demethylase JMJD6; jmjC domain-c ......
Chromosomal Location17q25
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Associations between JMJD6 and clinical features.
> Overall survival analysis
> Cancer stage
> Tumor grade
> Overall survival
 
> Stage
 
> Grade
 
Summary
SymbolJMJD6
Namejumonji domain containing 6
Aliases PTDSR1; KIAA0585; PTDSR; phosphatidylserine receptor; PSR; histone arginine demethylase JMJD6; jmjC domain-c ......
Chromosomal Location17q25
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Drugs targeting JMJD6 collected from DrugBank database.
> Drugs from DrugBank database
 

There is no record.