Jmjd6 jumonji domain containing 6, arginine demethylase and lysine hydroxylase [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Jmjd6provided by RGD
Official Full Name: jumonji domain containing 6, arginine demethylase and lysine hydroxylaseprovided by RGD
Primary source: RGD:1305395
See related: EnsemblRapid:ENSRNOG00000000250 AllianceGenome:RGD:1305395
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Ptdsr
Summary: Predicted to enable several functions, including 2-oxoglutarate-dependent dioxygenase activity; P-TEFb complex binding activity; and transcription regulator activator activity. Predicted to be involved in several processes, including oxidative RNA demethylation; peptidyl-lysine hydroxylation to 5-hydroxy-L-lysine; and regulation of RNA metabolic process. Predicted to act upstream of or within several processes, including circulatory system development; hemopoiesis; and recognition of apoptotic cell. Predicted to be located in cytosol; nuclear lumen; and plasma membrane. Predicted to be part of ribonucleoprotein complex. Predicted to be active in cytoplasm and nucleus. Orthologous to human JMJD6 (jumonji domain containing 6, arginine demethylase and lysine hydroxylase). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Thymus (RPKM 77.8), Heart (RPKM 75.5) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 10q32.2

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	10	NC_086028.1 (102539935..102545986, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	10	NC_051345.1 (102041131..102047182, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	10	NC_005109.4 (105781752..105787803, complement)

Chromosome 10 - NC_086028.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

JMJD6 may exert its therapeutic function in neuropathic pain by regulating NFkappaB following chronic constriction injury.
Title: JMJD6 exerts function in neuropathic pain by regulating NF‑κB following peripheral nerve injury in rats.

Submit: New GeneRIF Correction

General gene information

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Markers

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

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

RH131428 (e-PCR)
- UniSTS:214711

Gene Ontology Provided by RGD

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	ISO Inferred from Sequence Orthology more info
enables dioxygenase activity	IEA Inferred from Electronic Annotation more info
enables histone H3R2 demethylase activity	IEA Inferred from Electronic Annotation more info
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	IEA Inferred from Electronic Annotation 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	IEA Inferred from Electronic Annotation more info
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 metal ion binding	IEA Inferred from Electronic Annotation more info
enables oxidative RNA demethylase activity	IEA Inferred from Electronic Annotation 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	IEA Inferred from Electronic Annotation 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 demethylase activity	ISO Inferred from Sequence Orthology more info
enables signaling receptor activity	IEA Inferred from Electronic Annotation more info
enables signaling receptor activity	ISO Inferred from Sequence Orthology more info
enables single-stranded RNA binding	IEA Inferred from Electronic Annotation more info
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	IEA Inferred from Electronic Annotation 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
involved_in T cell differentiation in thymus	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within T cell differentiation in thymus	ISO Inferred from Sequence Orthology more info
NOT acts_upstream_of_or_within apoptotic cell clearance	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within apoptotic cell clearance	ISO Inferred from Sequence Orthology more info
involved_in biological_process	ND No biological Data available more info
acts_upstream_of_or_within blood vessel development	ISO Inferred from Sequence Orthology more info
involved_in cell surface receptor signaling pathway	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cell surface receptor signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in chromatin organization	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	ISO Inferred from Sequence Orthology more info
involved_in erythrocyte development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within erythrocyte development	ISO Inferred from Sequence Orthology more info
involved_in heart development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within heart development	ISO Inferred from Sequence Orthology more info
involved_in kidney development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within kidney development	ISO Inferred from Sequence Orthology more info
involved_in lung development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within lung development	ISO Inferred from Sequence Orthology more info
involved_in mRNA processing	IEA Inferred from Electronic Annotation more info
involved_in macrophage activation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within macrophage activation	ISO Inferred from Sequence Orthology more info
involved_in membraneless organelle assembly	IEA Inferred from Electronic Annotation more info
involved_in membraneless organelle assembly	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of protein homooligomerization	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of protein homooligomerization	ISO Inferred from Sequence Orthology more info
involved_in oxidative RNA demethylation	IEA Inferred from Electronic Annotation more info
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	IEA Inferred from Electronic Annotation 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	IEA Inferred from Electronic Annotation 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
involved_in recognition of apoptotic cell	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within recognition of apoptotic cell	ISO Inferred from Sequence Orthology more info
involved_in regulation of mRNA splicing, via spliceosome	IEA Inferred from Electronic Annotation more info
involved_in regulation of mRNA splicing, via spliceosome	ISO Inferred from Sequence Orthology more info
involved_in regulation of mRNA splicing, via spliceosome	ISS Inferred from Sequence or Structural Similarity more info
involved_in retina development in camera-type eye	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within retina development in camera-type eye	ISO Inferred from Sequence Orthology more info
involved_in sprouting angiogenesis	IEA Inferred from Electronic Annotation more info
involved_in sprouting angiogenesis	ISO Inferred from Sequence Orthology 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	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in nucleolus	IEA Inferred from Electronic Annotation more info
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	IEA Inferred from Electronic Annotation more info
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
located_in nucleus	IEA Inferred from Electronic Annotation more info
is_active_in nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info
part_of ribonucleoprotein complex	IEA Inferred from Electronic Annotation more info
part_of ribonucleoprotein complex	ISO Inferred from Sequence Orthology 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_001012143.2

EC 1.14.11.-

XP_006247868.1

EC 1.14.11.-

XP_063125543.1

EC 1.14.11.-

XP_063125544.1

EC 1.14.11.-

XP_063125545.1

EC 1.14.11.-

XP_063125546.1

EC 1.14.11.-

XP_063125547.1

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_001012143.2 → NP_001012143.2 bifunctional arginine demethylase and lysyl-hydroxylase JMJD6

See identical proteins and their annotated locations for NP_001012143.2

Status: VALIDATED

Source sequence(s)

BC079012, BM391923, CB789826

UniProtKB/Swiss-Prot

Q6AYK2

UniProtKB/TrEMBL

A0A8I6AJV5, A6HKZ3

Conserved Domains (1) summary

pfam02373
Location:174 → 288

JmjC; JmjC domain, hydroxylase

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086028.1 Reference GRCr8

Range

102539935..102545986 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006247806.2 → XP_006247868.1 bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 isoform X1

See identical proteins and their annotated locations for XP_006247868.1

UniProtKB/TrEMBL

A0A8I6AJV5, A6HKZ2

Conserved Domains (1) summary

pfam02373
Location:174 → 288

JmjC; JmjC domain, hydroxylase
XM_063269475.1 → XP_063125545.1 bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 isoform X4
XM_063269473.1 → XP_063125543.1 bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 isoform X2

Related

ENSRNOP00000062806.4, ENSRNOT00000064671.4
XM_063269474.1 → XP_063125544.1 bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 isoform X3

UniProtKB/TrEMBL

A0A8I5Y5A5

Related

ENSRNOP00000077039.1, ENSRNOT00000116096.2
XM_063269477.1 → XP_063125547.1 bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 isoform X6
XM_063269476.1 → XP_063125546.1 bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 isoform X5

UniProtKB/TrEMBL

A0A8L2QWD0