jmjd6 jumonji domain containing 6, arginine demethylase and lysine hydroxylase [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: jmjd6provided by ZNC
Official Full Name: jumonji domain containing 6, arginine demethylase and lysine hydroxylaseprovided by ZNC
Primary source: ZFIN:ZDB-GENE-040426-17
See related: Ensembl:ENSDARG00000102896 AllianceGenome:ZFIN:ZDB-GENE-040426-17
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: psr; ptdsr; zfpsr; jmjd6a; zgc:66264
Summary: Predicted to enable 2-oxoglutarate-dependent dioxygenase activity; P-TEFb complex binding activity; and single-stranded RNA binding activity. Acts upstream of or within phagocytosis. Predicted to be located in nucleolus and nucleoplasm. Predicted to be active in cytoplasm and nucleus. Is expressed in brain; hatching gland; heart; pronephros; and somite. Orthologous to human JMJD6 (jumonji domain containing 6, arginine demethylase and lysine hydroxylase). [provided by Alliance of Genome Resources, Dec 2024]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 3

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	3	NC_007114.7 (60577513..60589538, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	3	NC_007114.6 (60497709..60509734, complement)

Chromosome 3 - NC_007114.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

results suggest that YY1a regulates PS receptor expression that linked to function of PSR-phagocyte mediated apoptotic cell engulfment during development
Title: Knockdown of zebrafish YY1a can downregulate the phosphatidylserine (PS) receptor expression, leading to induce the abnormal brain and heart development.
PSR-dependent system in zebrafish embryos that engulfs apoptotic cells mediated by PSR-phagocytes during development, with the system assuming an important role in the normal development of tissues such as the brain, heart, notochord and somite
Title: Phosphatidylserine receptor is required for the engulfment of dead apoptotic cells and for normal embryonic development in zebrafish.

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General gene information

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Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables 2-oxoglutarate-dependent dioxygenase activity	IEA Inferred from Electronic Annotation more info
enables P-TEFb complex binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA binding	IEA Inferred from Electronic Annotation more info
enables dioxygenase activity	IEA Inferred from Electronic Annotation 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	ISS Inferred from Sequence or Structural Similarity more info
enables histone demethylase activity	ISS Inferred from Sequence or Structural Similarity more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables oxidoreductase activity	IEA Inferred from Electronic Annotation more info
enables peptidyl-lysine 5-dioxygenase activity	ISS Inferred from Sequence or Structural Similarity more info
enables single-stranded RNA binding	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within RNA splicing	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cell differentiation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within chromatin organization	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within mRNA processing	IEA Inferred from Electronic Annotation 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
acts_upstream_of_or_within phagocytosis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein homooligomerization	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of mRNA splicing, via spliceosome	ISS Inferred from Sequence or Structural Similarity 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	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
located_in nucleolus	ISS Inferred from Sequence or Structural Similarity 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
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: bifunctional arginine demethylase and lysyl-hydroxylase JMJD6

Names: 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_739567.3

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_170761.3 → NP_739567.3 bifunctional arginine demethylase and lysyl-hydroxylase JMJD6

Status: VALIDATED

Source sequence(s)

CU463857

UniProtKB/Swiss-Prot

Q6PFM0, Q8JI07, Q8JI08

Related

ENSDARP00000139813.1, ENSDART00000157822.2

Conserved Domains (1) summary

pfam02373
Location:174 → 288

JmjC; JmjC domain, hydroxylase