JMJD6 jumonji domain containing 6, arginine demethylase and lysine hydroxylase [Homo sapiens (human)] - Gene

Summary

Official Symbol: JMJD6provided by HGNC
Official Full Name: jumonji domain containing 6, arginine demethylase and lysine hydroxylaseprovided by HGNC
Primary source: HGNC:HGNC:19355
See related: Ensembl:ENSG00000070495 MIM:604914; AllianceGenome:HGNC:19355
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: PSR; PTDSR; PTDSR1
Summary: 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]
Expression: Ubiquitous expression in bone marrow (RPKM 17.6), heart (RPKM 4.9) and 24 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 17q25.1

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	17	NC_000017.11 (76712836..76726606, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	17	NC_060941.1 (77609799..77623589, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	17	NC_000017.10 (74708918..74722688, complement)

Chromosome 17 - NC_000017.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

JMJD6-BRD4 complex stimulates lncRNA HOTAIR transcription by binding to the promoter region of HOTAIR and induces radioresistance in liver cancer stem cells.
Title: JMJD6-BRD4 complex stimulates lncRNA HOTAIR transcription by binding to the promoter region of HOTAIR and induces radioresistance in liver cancer stem cells.
JMJD6 in tumor-associated macrophage regulates macrophage polarization and cancer progression via STAT3/IL-10 axis.
Title: JMJD6 in tumor-associated macrophage regulates macrophage polarization and cancer progression via STAT3/IL-10 axis.
JMJD6 Shapes a Pro-tumor Microenvironment via ANXA1-Dependent Macrophage Polarization in Breast Cancer.
Title: JMJD6 Shapes a Pro-tumor Microenvironment via ANXA1-Dependent Macrophage Polarization in Breast Cancer.
Predictive network analysis identifies JMJD6 and other potential key drivers in Alzheimer's disease.
Title: Predictive network analysis identifies JMJD6 and other potential key drivers in Alzheimer's disease.
Fibronectin and JMJD6 Signature in Circulating Placental Extracellular Vesicles for the Detection of Preeclampsia.
Title: Fibronectin and JMJD6 Signature in Circulating Placental Extracellular Vesicles for the Detection of Preeclampsia.
JMJD6 orchestrates a transcriptional program in favor of endocrine resistance in ER+ breast cancer cells.
Title: JMJD6 orchestrates a transcriptional program in favor of endocrine resistance in ER+ breast cancer cells.
An oncogenic JMJD6-DGAT1 axis tunes the epigenetic regulation of lipid droplet formation in clear cell renal cell carcinoma.
Title: An oncogenic JMJD6-DGAT1 axis tunes the epigenetic regulation of lipid droplet formation in clear cell renal cell carcinoma.
Widespread hydroxylation of unstructured lysine-rich protein domains by JMJD6.
Title: Widespread hydroxylation of unstructured lysine-rich protein domains by JMJD6.
MiR-298 suppresses the malignant progression of osteosarcoma by targeting JMJD6.
Title: MiR-298 suppresses the malignant progression of osteosarcoma by targeting JMJD6.
Role of the Epigenetic Modifier JMJD6 in Tumor Development and Regulation of Immune Response.
Title: Role of the Epigenetic Modifier JMJD6 in Tumor Development and Regulation of Immune Response.

Submit: New GeneRIF Correction See all GeneRIFs (64)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genetic loci for retinal arteriolar microcirculation. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH93087 (e-PCR)
- UniSTS:85047

PTDSR_9319 (e-PCR)
- UniSTS:468623

D11S3114 (e-PCR)
- UniSTS:152207

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables P-TEFb complex binding	IBA Inferred from Biological aspect of Ancestor more info
enables P-TEFb complex binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA binding	TAS Traceable Author Statement more info	PubMed
enables histone H3R2 demethylase activity	IDA Inferred from Direct Assay more info	PubMed
enables histone H4R3 demethylase activity	IBA Inferred from Biological aspect of Ancestor more info
enables histone H4R3 demethylase activity	IDA Inferred from Direct Assay more info	PubMed
enables histone demethylase activity	IDA Inferred from Direct Assay more info	PubMed
enables histone demethylase activity	TAS Traceable Author Statement more info
enables identical protein binding	IDA Inferred from Direct Assay more info	PubMed
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables iron ion binding	IDA Inferred from Direct Assay more info	PubMed
enables oxidative RNA demethylase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables peptidyl-lysine 5-dioxygenase activity	EXP Inferred from Experiment more info	PubMed
enables peptidyl-lysine 5-dioxygenase activity	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein demethylase activity	IDA Inferred from Direct Assay more info	PubMed
enables signaling receptor activity	IEA Inferred from Electronic Annotation more info
enables single-stranded RNA binding	IDA Inferred from Direct Assay more info	PubMed
enables transcription regulator activator activity	IMP Inferred from Mutant Phenotype more info	PubMed

Process	Evidence Code	Pubs
involved_in RNA splicing	IEA Inferred from Electronic Annotation more info
involved_in T cell differentiation in thymus	IEA Inferred from Electronic Annotation more info
involved_in cell surface receptor signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	IDA Inferred from Direct Assay more info	PubMed
involved_in erythrocyte development	IEA Inferred from Electronic Annotation more info
involved_in heart development	IEA Inferred from Electronic Annotation more info
involved_in kidney development	IEA Inferred from Electronic Annotation more info
involved_in lung development	IEA Inferred from Electronic Annotation more info
involved_in mRNA processing	IEA Inferred from Electronic Annotation more info
involved_in macrophage activation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of protein homooligomerization	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in non-membrane-bounded organelle assembly	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in oxidative RNA demethylation	IDA Inferred from Direct Assay more info	PubMed
involved_in peptidyl-lysine hydroxylation to 5-hydroxy-L-lysine	IDA Inferred from Direct Assay more info	PubMed
involved_in phagocytosis	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of DNA-templated transcription	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in protein homooligomerization	IDA Inferred from Direct Assay more info	PubMed
involved_in recognition of apoptotic cell	IEA Inferred from Electronic Annotation more info
involved_in regulation of mRNA splicing, via spliceosome	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in retina development in camera-type eye	IEA Inferred from Electronic Annotation more info
involved_in sprouting angiogenesis	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in nucleolus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IMP Inferred from Mutant Phenotype more info	PubMed
is_active_in nucleus	ISS Inferred from Sequence or Structural Similarity more info	PubMed
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
part_of ribonucleoprotein complex	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: bifunctional arginine demethylase and lysyl-hydroxylase JMJD6

Names: arginine demethylase and lysine hydroxylase; histone arginine demethylase JMJD6; jmjC domain-containing protein 6; jumonji domain-containing protein 6; lysyl-hydroxylase JMJD6; peptide-lysine 5-dioxygenase JMJD6; phosphatidylserine receptor

NP_001074930.1

EC 1.14.11.-

NP_055982.2

EC 1.14.11.-

XP_047291644.1

EC 1.14.11.-

XP_047291645.1

EC 1.14.11.-

XP_054171569.1

EC 1.14.11.-

XP_054171570.1

EC 1.14.11.-

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001081461.2 → NP_001074930.1 bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 isoform 1

See identical proteins and their annotated locations for NP_001074930.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AA775442, AB011157, AC005837, DB451815

Consensus CDS

CCDS42383.1

UniProtKB/TrEMBL

A0A0S2PZM4

Related

ENSP00000394085.2, ENST00000445478.6

Conserved Domains (1) summary

pfam02373
Location:174 → 288

JmjC; JmjC domain, hydroxylase
NM_015167.3 → NP_055982.2 bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 isoform 2

See identical proteins and their annotated locations for NP_055982.2

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate splice site in the 3' coding region and an alternate polyadenylation site, compared to variant 1. The resulting protein (isoform 2) has a shorter C-terminus, compared to isoform 1.

Source sequence(s)

AA226560, BC066654, DB451815

Consensus CDS

CCDS42384.1

UniProtKB/Swiss-Prot

B3KMN8, B4DGX1, Q6NYC1, Q86VY0, Q8IUM5, Q9Y4E2

UniProtKB/TrEMBL

A0A0S2PZM4

Related

ENSP00000380750.4, ENST00000397625.9

Conserved Domains (1) summary

pfam02373
Location:174 → 288

JmjC; JmjC domain, hydroxylase

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000017.11 Reference GRCh38.p14 Primary Assembly

Range

76712836..76726606 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047435688.1 → XP_047291644.1 bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 isoform X1

UniProtKB/TrEMBL

B2WTI4

Related

ENSP00000442362.1, ENST00000542934.5
XM_047435689.1 → XP_047291645.1 bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 isoform X2

UniProtKB/TrEMBL

B2WTI3

Related

ENSP00000302916.6, ENST00000303996.10

Alternate T2T-CHM13v2.0

Genomic

NC_060941.1 Alternate T2T-CHM13v2.0

Range

77609799..77623589 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054315594.1 → XP_054171569.1 bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 isoform X1

UniProtKB/TrEMBL

B2WTI4
XM_054315595.1 → XP_054171570.1 bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 isoform X2

UniProtKB/TrEMBL

B2WTI3