Tet3 tet methylcytosine dioxygenase 3 [Rattus norvegicus (Norway rat)] - Gene

Summary

Symbol: Tet3provided by RGD
Full Name: tet methylcytosine dioxygenase 3provided by RGD
Primary source: RGD:1590584
See related: EnsemblRapid:ENSRNOG00000011387 AllianceGenome:RGD:1590584
Gene type: protein coding
RefSeq status: MODEL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable methyl-CpG binding activity; methylcytosine dioxygenase activity; and zinc ion binding activity. Predicted to be involved in several processes, including DNA methylation or demethylation; cellular protein modification process; and oxidative demethylation. Predicted to be located in cytoplasm; female pronucleus; and male pronucleus. Predicted to be active in nucleus. Orthologous to human TET3 (tet methylcytosine dioxygenase 3). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Lung (RPKM 53.7), Spleen (RPKM 52.7) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 4q34

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	4	NC_086022.1 (117425106..117525495, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	4	NC_051339.1 (115867412..115964433, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	4	NC_005103.4 (115060702..115160800, complement)

Chromosome 4 - NC_086022.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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 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?

MiR-26b-5p/TET3 regulates the osteogenic differentiation of human bone mesenchymal stem cells and bone reconstruction in female rats with calvarial defects.
Title: MiR-26b-5p/TET3 regulates the osteogenic differentiation of human bone mesenchymal stem cells and bone reconstruction in female rats with calvarial defects.
Tet3 enhanced IL-6 expression though up-regulating 5-hmC percentage in the IL-6 promoter.
Title: Tet3 enhances IL-6 expression through up-regulation of 5-hmC in IL-6 promoter in chronic hypoxia induced atherosclerosis in offspring rats.
alterations in the Tet3 gene expression and the level of 5-hydroxymethylcytosine may play an important role in extinction learning and the reduction of subsequent cocaine seeking.
Title: Increased 5-hydroxymethylation levels in the hippocampus of rat extinguished from cocaine self-administration.

Submit: New GeneRIF Correction

General gene information

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Markers

d4rat124 (e-PCR)
- UniSTS:121949

Homology

NCBI Orthologs

Orthologs from OrthoDB

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables 5-methylcytosine dioxygenase activity	IBA Inferred from Biological aspect of Ancestor more info
enables 5-methylcytosine dioxygenase activity	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables methyl-CpG binding	ISO Inferred from Sequence Orthology more info
enables zinc ion binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in biological_process	ND No biological Data available more info
involved_in chromosomal 5-methylcytosine DNA demethylation pathway	IEA Inferred from Electronic Annotation more info
involved_in epigenetic programing of male pronucleus	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of gene expression via chromosomal CpG island demethylation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in protein O-linked glycosylation	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in chromosome	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in female pronucleus	ISO Inferred from Sequence Orthology more info
located_in male pronucleus	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: probable methylcytosine dioxygenase TET3; methylcytosine dioxygenase TET3

Names: astrotactin-2-like; tet oncogene family member 3

NCBI Reference Sequences (RefSeq)

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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_086022.1 Reference GRCr8

Range

117425106..117525495 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063286845.1 → XP_063142915.1 methylcytosine dioxygenase TET3 isoform X2

UniProtKB/TrEMBL

A0A8I6A3Q7
XM_008763095.4 → XP_008761317.1 methylcytosine dioxygenase TET3 isoform X1

See identical proteins and their annotated locations for XP_008761317.1

UniProtKB/TrEMBL

D3ZQT7

Conserved Domains (2) summary

pfam02008
Location:50 → 89

zf-CXXC; CXXC zinc finger domain

pfam12851
Location:992 → 1119

Tet_JBP; Oxygenase domain of the 2OGFeDO superfamily
XM_039108717.2 → XP_038964645.1 methylcytosine dioxygenase TET3 isoform X2

UniProtKB/TrEMBL

A0A8I6A3Q7

Related

ENSRNOP00000087089.1, ENSRNOT00000111758.2

Conserved Domains (4) summary

PHA03247
Location:281 → 740

PHA03247; large tegument protein UL36; Provisional

pfam02008
Location:50 → 89

zf-CXXC; CXXC zinc finger domain

cd18897
Location:816 → 1140

TET3; oxygenase domain of ten-eleven translocation (TET)3 methylcytosine dioxygenase and similar proteins

cl40427
Location:1592 → 1754

Tet_JBP; oxygenase domain of ten-eleven translocation (TET) enzymes, J-binding proteins (JBPs), and similar proteins
XM_008763094.4 → XP_008761316.1 methylcytosine dioxygenase TET3 isoform X1

See identical proteins and their annotated locations for XP_008761316.1

UniProtKB/TrEMBL

D3ZQT7

Conserved Domains (2) summary

pfam02008
Location:50 → 89

zf-CXXC; CXXC zinc finger domain

pfam12851
Location:992 → 1119

Tet_JBP; Oxygenase domain of the 2OGFeDO superfamily
XM_063286844.1 → XP_063142914.1 methylcytosine dioxygenase TET3 isoform X1

UniProtKB/TrEMBL

D3ZQT7

Related

ENSRNOP00000015296.6, ENSRNOT00000015296.9
XM_001057850.8 → XP_001057850.2 methylcytosine dioxygenase TET3 isoform X3

See identical proteins and their annotated locations for XP_001057850.2

UniProtKB/TrEMBL

A6IAM2

Related

ENSRNOP00000110839.1, ENSRNOT00000131739.1

Conserved Domains (1) summary

pfam12851
Location:857 → 984

Tet_JBP; Oxygenase domain of the 2OGFeDO superfamily