Jmjd6 jumonji domain containing 6 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Jmjd6provided by MGI
Official Full Name: jumonji domain containing 6provided by MGI
Primary source: MGI:MGI:1858910
See related: Ensembl:ENSMUSG00000056962 AllianceGenome:MGI:1858910
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: PSR; Ptdsr; PtdSerR; mKIAA0585; D11Ertd195e; 5730436I23Rik
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 functions in differentiation of multiple tissues during development, and in anti-inflammatory cytokine signaling. It was first identified as a putative phosphatidylserine receptor involved in phagocytosis of apoptotic cells; however, subsequent studies have indicated that this protein does not directly function in the clearance of apoptotic cells, and questioned whether it is a true phosphatidylserine receptor. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in testis adult (RPKM 19.2), CNS E11.5 (RPKM 14.3) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 11 E2; 11 81.49 cM

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	11	NC_000077.7 (116728258..116734593, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	11	NC_000077.6 (116837432..116843767, complement)

Chromosome 11 - NC_000077.7 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: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

JMJD6 cleaves MePCE to release positive transcription elongation factor b (P-TEFb) in higher eukaryotes.
Title: JMJD6 cleaves MePCE to release positive transcription elongation factor b (P-TEFb) in higher eukaryotes.
Knocking down JMJD6 reduces neuroblastoma cell proliferation and survival in vitro and tumor progression in mice.
Title: JMJD6 is a tumorigenic factor and therapeutic target in neuroblastoma.
TEC-specific deletion of Jmjd6 exacerbates development of autoimmune diabetes in a mouse model, which express both ovalbumin (OVA) under the control of the rat insulin gene promoter and OT-I T cell receptor specific for OVA peptide bound to major histocompatibility complex class I K(b) molecules.
Title: Thymic epithelial cell-specific deletion of Jmjd6 reduces Aire protein expression and exacerbates disease development in a mouse model of autoimmune diabetes.
Although Jmjd6 deficiency does not affect abundance of Aire transcript, the intron 2 of Aire gene is not effectively spliced out in the absence of Jmjd6, resulting in reduction of mature Aire protein and spontaneous multi-organ autoimmunity in mice.
Title: Intronic regulation of Aire expression by Jmjd6 for self-tolerance induction in the thymus.
The results indicate dual roles for JMJD6 in promoting adipogenic gene expression program by post-transcriptional regulation of C/EBPbeta and C/EBPdelta and direct transcriptional activation of Ppargamma2 and Cebpalpha during adipocyte differentiation.
Title: Transcriptional and post-transcriptional control of adipocyte differentiation by Jumonji domain-containing protein 6.
histones are additional substrates of JMJD6 in vivo. Because 5-hydroxylation of lysyl residues inhibited N-acetylation and N-methylation by an acetyltransferase and a methyltransferase
Title: Lysyl 5-hydroxylation, a novel histone modification, by Jumonji domain containing 6 (JMJD6).
confirmed that Jmjd6 forms multimers and showed that nuclear localization of the protein involves association with a nucleic acid matrix
Title: Analysis of Jmjd6 cellular localization and testing for its involvement in histone demethylation.
protein kinase C beta activation is dependent upon phosphatidylserine receptor action
Title: Activation of protein kinase C beta II by the stereo-specific phosphatidylserine receptor is required for phagocytosis of apoptotic thymocytes by resident murine tissue macrophages.
during embryonic development, phosphatidylserine receptor-mediated apoptotic cell uptake is required for definitive erythropoiesis and T lymphopoiesis, independently of the prevention of inflammatory responses
Title: Defective fetal liver erythropoiesis and T lymphopoiesis in mice lacking the phosphatidylserine receptor.
data demonstrate a critical role for PSR in early stages of mammalian organogenesis and suggest that this receptor may be involved in respiratory distress syndromes and congenital brain malformations
Title: Phosphatidylserine receptor is required for clearance of apoptotic cells.

Submit: New GeneRIF Correction See all GeneRIFs (14)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (3)
Gene trapped (1) 1 citation
Targeted (6) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Jmjd6 (e-PCR), detects polymorphism
- UniSTS:526972

D11Ertd195e (e-PCR), detects polymorphism
- UniSTS:167046

Jmjd6 (e-PCR), detects polymorphism
- UniSTS:526998

Jmjd6 (e-PCR), detects polymorphism
- UniSTS:526999

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables P-TEFb complex binding	IBA Inferred from Biological aspect of Ancestor more info
enables P-TEFb complex binding	IEA Inferred from Electronic Annotation more info
enables P-TEFb complex binding	ISO Inferred from Sequence Orthology more info
enables RNA binding	IDA Inferred from Direct Assay more info	PubMed
enables histone H3R2 demethylase activity	ISO Inferred from Sequence Orthology more info
enables histone H3R2 demethylase activity	ISS Inferred from Sequence or Structural Similarity more info
enables histone H4R3 demethylase activity	IBA Inferred from Biological aspect of Ancestor more info
enables histone H4R3 demethylase activity	ISO Inferred from Sequence Orthology more info
enables histone H4R3 demethylase activity	ISS Inferred from Sequence or Structural Similarity more info
enables histone demethylase activity	ISO Inferred from Sequence Orthology more info
enables histone demethylase activity	ISS Inferred from Sequence or Structural Similarity more info
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables iron ion binding	IEA Inferred from Electronic Annotation more info
enables iron ion binding	ISO Inferred from Sequence Orthology more info
enables oxidative RNA demethylase activity	ISO Inferred from Sequence Orthology more info
enables oxidative RNA demethylase activity	ISS Inferred from Sequence or Structural Similarity more info
enables peptidyl-lysine 5-dioxygenase activity	ISO Inferred from Sequence Orthology more info
enables peptidyl-lysine 5-dioxygenase activity	ISS Inferred from Sequence or Structural Similarity more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein demethylase activity	ISO Inferred from Sequence Orthology more info
enables signaling receptor activity	IDA Inferred from Direct Assay more info	PubMed
enables single-stranded RNA binding	ISO Inferred from Sequence Orthology more info
enables single-stranded RNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables transcription regulator activator activity	ISO Inferred from Sequence Orthology more info
enables transcription regulator activator activity	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in RNA splicing	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within T cell differentiation in thymus	IMP Inferred from Mutant Phenotype more info	PubMed
NOT acts_upstream_of_or_within apoptotic cell clearance	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within apoptotic cell clearance	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within blood vessel development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cell surface receptor signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within erythrocyte development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within heart development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within kidney development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within lung development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mRNA processing	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within macrophage activation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in membraneless organelle assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of protein homooligomerization	IDA Inferred from Direct Assay more info	PubMed
involved_in oxidative RNA demethylation	ISO Inferred from Sequence Orthology more info
involved_in oxidative RNA demethylation	ISS Inferred from Sequence or Structural Similarity more info
involved_in peptidyl-lysine hydroxylation to 5-hydroxy-L-lysine	ISO Inferred from Sequence Orthology more info
involved_in peptidyl-lysine hydroxylation to 5-hydroxy-L-lysine	ISS Inferred from Sequence or Structural Similarity more info
involved_in phagocytosis	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein homooligomerization	ISO Inferred from Sequence Orthology more info
involved_in protein homooligomerization	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within recognition of apoptotic cell	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within recognition of apoptotic cell	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of mRNA splicing, via spliceosome	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of mRNA splicing, via spliceosome	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within retina development in camera-type eye	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in sprouting angiogenesis	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytosol	IDA Inferred from Direct Assay more info	PubMed
located_in nucleolus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleolus	ISO Inferred from Sequence Orthology more info
located_in nucleolus	ISS Inferred from Sequence or Structural Similarity more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISS Inferred from Sequence or Structural Similarity more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
is_active_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
part_of ribonucleoprotein complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: bifunctional arginine demethylase and lysyl-hydroxylase JMJD6

Names: apoptotic cell clearance receptor PtdSerR; 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_001350292.1

EC 1.14.11.-

NP_203971.2

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_001363363.1 → NP_001350292.1 bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 isoform 1

Status: VALIDATED

Source sequence(s)

AL645542, EF527405

UniProtKB/TrEMBL

B2WTI2

Conserved Domains (1) summary

pfam02373
Location:174 → 288

JmjC; JmjC domain, hydroxylase
NM_033398.3 → NP_203971.2 bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 isoform 2

See identical proteins and their annotated locations for NP_203971.2

Status: VALIDATED

Source sequence(s)

AL645542, BP769727, CX210791

Consensus CDS

CCDS25678.1

UniProtKB/Swiss-Prot

A2AA26, A8Y5I2, Q80TX1, Q9ERI5

Related

ENSMUSP00000047570.4, ENSMUST00000047616.10

Conserved Domains (1) summary

pfam02373
Location:174 → 288

JmjC; JmjC domain, hydroxylase

RNA

NR_156486.1 RNA Sequence

Status: VALIDATED

Source sequence(s)

EF527404
NR_156487.1 RNA Sequence

Status: VALIDATED

Source sequence(s)

AL645542

Related

ENSMUST00000142495.8