Atf6 activating transcription factor 6 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Atf6provided by RGD
Official Full Name: activating transcription factor 6provided by RGD
Primary source: RGD:1305471
See related: EnsemblRapid:ENSRNOG00000024632 AllianceGenome:RGD:1305471
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable several functions, including DNA-binding transcription activator activity, RNA polymerase II-specific; identical protein binding activity; and protein heterodimerization activity. Predicted to be involved in several processes, including endoplasmic reticulum unfolded protein response; positive regulation of ATF6-mediated unfolded protein response; and visual perception. Predicted to act upstream of or within positive regulation of autophagy and positive regulation of transcription by RNA polymerase II. Located in nucleus. Biomarker of borna disease. Human ortholog(s) of this gene implicated in achromatopsia 7. Orthologous to human ATF6 (activating transcription factor 6). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Kidney (RPKM 188.3), Liver (RPKM 159.4) and 9 other tissues See more
Orthologs: human mouse all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 13q24

Exon count:: 16

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	13	NC_086031.1 (85460312..85639959, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	13	NC_051348.1 (82927579..83106381, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	13	NC_005112.4 (89053457..89242531, complement)

Chromosome 13 - NC_086031.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

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

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Activating transcription factor 6 alleviates secondary brain injury by increasing cystathionine gamma-lyase expression in a rat model of intracerebral hemorrhage.
Title: Activating transcription factor 6 alleviates secondary brain injury by increasing cystathionine γ-lyase expression in a rat model of intracerebral hemorrhage.
CYP2E1 triggered GRP78/ATF6/CHOP signaling axis inhibit apoptosis and promotes progression of hepatocellular carcinoma.
Title: CYP2E1 triggered GRP78/ATF6/CHOP signaling axis inhibit apoptosis and promotes progression of hepatocellular carcinoma.
Dual role of endoplasmic reticulum stress-ATF-6 activation in autophagy and apoptosis induced by cyclic stretch in myoblast.
Title: Dual role of endoplasmic reticulum stress-ATF-6 activation in autophagy and apoptosis induced by cyclic stretch in myoblast.
MiR-195-5p represses inflammation, apoptosis, oxidative stress, and endoplasmic reticulum stress in sepsis-induced myocardial injury by targeting activating transcription factor 6.
Title: MiR-195-5p represses inflammation, apoptosis, oxidative stress, and endoplasmic reticulum stress in sepsis-induced myocardial injury by targeting activating transcription factor 6.
Molecular Mechanism of the ATF6alpha/S1P/S2P Signaling Pathway in Hippocampal Neuronal Apoptosis in SPS Rats.
Title: Molecular Mechanism of the ATF6α/S1P/S2P Signaling Pathway in Hippocampal Neuronal Apoptosis in SPS Rats.
Cardiac hypertrophy caused by hyperthyroidism in rats: the role of ATF-6 and TRPC1 channels.
Title: Cardiac hypertrophy caused by hyperthyroidism in rats: the role of ATF-6 and TRPC1 channels.
MicroRNA-211-5p attenuates spinal cord injury via targeting of activating transcription factor 6.
Title: MicroRNA-211-5p attenuates spinal cord injury via targeting of activating transcription factor 6.
The peroxisomal enzyme, FAR1, is induced during ER stress in an ATF6-dependent manner in cardiac myocytes.
Title: The peroxisomal enzyme, FAR1, is induced during ER stress in an ATF6-dependent manner in cardiac myocytes.
ER stress mediatedautophagy contributes to neurological dysfunction in traumatic brain injury via the ATF6 UPR signaling pathway.
Title: ER stress mediated‑autophagy contributes to neurological dysfunction in traumatic brain injury via the ATF6 UPR signaling pathway.
The results showed that both Unfolded Protein Response (Xbp-1, its spliced variant sXbp-1, Atf-6, Chop, and Grp94) and Toll like receptor (2, 3, 4, 7 and 9) genes were significantly upregulated in the hippocampi of rats who were exposed to restraint stress.
Title: Unfolded protein response and associated alterations in toll-like receptor expression and interaction in the hippocampus of restraint rats.

Submit: New GeneRIF Correction See all GeneRIFs (24)

General gene information

Go to the top of the page Help

Markers

d13rat133 (e-PCR)
- UniSTS:120892

RH134430 (e-PCR)
- UniSTS:217710

AU046924 (e-PCR)
- UniSTS:111010

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription activator activity, RNA polymerase II-specific	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription factor activity	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables enzyme binding	IEA Inferred from Electronic Annotation more info
enables enzyme binding	ISO Inferred from Sequence Orthology 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 protein heterodimerization activity	IEA Inferred from Electronic Annotation more info
enables protein heterodimerization activity	ISO Inferred from Sequence Orthology more info
enables sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables sequence-specific double-stranded DNA binding	ISO Inferred from Sequence Orthology more info
enables transcription cis-regulatory region 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 endoplasmic reticulum unfolded protein response	IBA Inferred from Biological aspect of Ancestor more info
involved_in eye development	IEA Inferred from Electronic Annotation more info
involved_in eye development	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of ATF6-mediated unfolded protein response	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of ATF6-mediated unfolded protein response	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of apoptotic process	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of apoptotic process	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of autophagy	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of autophagy	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within 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	ISO Inferred from Sequence Orthology more info
involved_in regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in response to endoplasmic reticulum stress	IEA Inferred from Electronic Annotation more info
involved_in response to endoplasmic reticulum stress	ISO Inferred from Sequence Orthology more info
involved_in visual perception	IEA Inferred from Electronic Annotation more info
involved_in visual perception	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in Golgi apparatus	IEA Inferred from Electronic Annotation more info
located_in Golgi apparatus	ISO Inferred from Sequence Orthology more info
located_in Golgi membrane	IEA Inferred from Electronic Annotation more info
part_of RNA polymerase II transcription regulator complex	IEA Inferred from Electronic Annotation more info
part_of RNA polymerase II transcription regulator complex	ISO Inferred from Sequence Orthology more info
located_in endoplasmic reticulum	ISO Inferred from Sequence Orthology more info
located_in endoplasmic reticulum membrane	IEA Inferred from Electronic Annotation more info
located_in endoplasmic reticulum membrane	ISO Inferred from Sequence Orthology more info
located_in membrane	ISO Inferred from Sequence Orthology 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	IEA Inferred from Electronic Annotation more info
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

Go to the top of the page Help

Preferred Names: cyclic AMP-dependent transcription factor ATF-6 alpha

Names: ATF6-alpha; activating transcription factor 6 alpha; cAMP-dependent transcription factor ATF-6 alpha

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_001107196.1 → NP_001100666.1 cyclic AMP-dependent transcription factor ATF-6 alpha

See identical proteins and their annotated locations for NP_001100666.1

Status: PROVISIONAL

Source sequence(s)

CH473958

UniProtKB/Swiss-Prot

B5DF18, G3V909

UniProtKB/TrEMBL

A0A8I5ZTX7

Conserved Domains (1) summary

cd14700
Location:296 → 347

bZIP_ATF6; Basic leucine zipper (bZIP) domain of Activating Transcription Factor-6 (ATF-6) and similar proteins: a DNA-binding and dimerization domain

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_086031.1 Reference GRCr8

Range

85460312..85639959 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063272368.1 → XP_063128438.1 cyclic AMP-dependent transcription factor ATF-6 alpha isoform X2
XM_063272367.1 → XP_063128437.1 cyclic AMP-dependent transcription factor ATF-6 alpha isoform X1

UniProtKB/Swiss-Prot

B5DF18, G3V909
XM_008769738.4 → XP_008767960.1 cyclic AMP-dependent transcription factor ATF-6 alpha isoform X3

UniProtKB/TrEMBL

A0A8I5ZTX7, A0A8L2QJM2

Related

ENSRNOP00000032766.5, ENSRNOT00000029202.7

Conserved Domains (1) summary

cd14700
Location:292 → 343

bZIP_ATF6; Basic leucine zipper (bZIP) domain of Activating Transcription Factor-6 (ATF-6) and similar proteins: a DNA-binding and dimerization domain