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Atf3 activating transcription factor 3 [ Rattus norvegicus (Norway rat) ]

Gene ID: 25389, updated on 28-Oct-2024

Summary

Symbol
Atf3provided by RGD
Full Name
activating transcription factor 3provided by RGD
Primary source
RGD:2165
See related
EnsemblRapid:ENSRNOG00000003745 AllianceGenome:RGD:2165
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
Also known as
LRFI; LRF-1
Summary
Enables DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in positive regulation of cell population proliferation and positive regulation of transcription by RNA polymerase II. Predicted to be located in nucleolus and nucleoplasm. Predicted to be part of CHOP-ATF3 complex and RNA polymerase II transcription regulator complex. Predicted to be active in nucleus. Orthologous to human ATF3 (activating transcription factor 3). [provided by Alliance of Genome Resources, Oct 2024]
Expression
Biased expression in Muscle (RPKM 49.0), Lung (RPKM 40.1) and 9 other tissues See more
Orthologs
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Genomic context

See Atf3 in Genome Data Viewer
Location:
13q27
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 13 NC_086031.1 (105274103..105331653, complement)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 13 NC_051348.1 (102751278..102800520, complement)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 13 NC_005112.4 (109817892..109849632, complement)

Chromosome 13 - NC_086031.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC120096350 Neighboring gene basic leucine zipper ATF-like transcription factor 3 Neighboring gene golgi associated RAB2 interactor family member 4 Neighboring gene uncharacterized LOC102555043 Neighboring gene uncharacterized LOC102555129 Neighboring gene neudesin neurotrophic factor

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pathways from PubChem

General gene information

Markers

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables DNA binding ISO
Inferred from Sequence Orthology
more info
 
enables DNA-binding transcription activator activity, RNA polymerase II-specific IDA
Inferred from Direct Assay
more info
PubMed 
enables DNA-binding transcription activator activity, RNA polymerase II-specific ISO
Inferred from Sequence Orthology
more info
 
enables DNA-binding transcription factor activity ISO
Inferred from Sequence Orthology
more info
 
enables DNA-binding transcription factor activity TAS
Traceable Author Statement
more info
PubMed 
enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
 
enables DNA-binding transcription repressor activity, RNA polymerase II-specific ISO
Inferred from Sequence Orthology
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 IDA
Inferred from Direct Assay
more info
PubMed 
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 identical protein binding ISO
Inferred from Sequence Orthology
more info
 
enables protein heterodimerization activity ISO
Inferred from Sequence Orthology
more info
 
enables protein homodimerization activity 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 cell fate determination TAS
Traceable Author Statement
more info
PubMed 
involved_in cellular response to amino acid starvation ISO
Inferred from Sequence Orthology
more info
 
involved_in endoplasmic reticulum unfolded protein response ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within gluconeogenesis ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within negative regulation of DNA-templated transcription ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of ERK1 and ERK2 cascade ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of TRAIL-activated apoptotic signaling pathway ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of cell population proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of gene expression ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
involved_in response to endoplasmic reticulum stress ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within skeletal muscle cell differentiation ISO
Inferred from Sequence Orthology
more info
 
Component Evidence Code Pubs
part_of CHOP-ATF3 complex ISO
Inferred from Sequence Orthology
more info
 
part_of RNA polymerase II transcription regulator complex 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 nucleoplasm IEA
Inferred from Electronic Annotation
more info
 
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in nucleus ISO
Inferred from Sequence Orthology
more info
 

General protein information

Preferred Names
cyclic AMP-dependent transcription factor ATF-3
Names
cAMP-dependent transcription factor ATF-3
cyclic AMP-dependent transcription factor ATF-3-like
liver regeneration factor 1

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)

  1. NM_012912.2NP_037044.1  cyclic AMP-dependent transcription factor ATF-3

    See identical proteins and their annotated locations for NP_037044.1

    Status: PROVISIONAL

    Source sequence(s)
    BC078903
    UniProtKB/Swiss-Prot
    P29596
    Related
    ENSRNOP00000005085.1, ENSRNOT00000005085.5
    Conserved Domains (1) summary
    cd14722
    Location:96149
    bZIP_ATF3; Basic leucine zipper (bZIP) domain of Activating Transcription Factor-3 (ATF-3) 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

  1. NC_086031.1 Reference GRCr8

    Range
    105274103..105331653 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_039090385.2XP_038946313.1  cyclic AMP-dependent transcription factor ATF-3 isoform X1

    UniProtKB/Swiss-Prot
    P29596
    Conserved Domains (1) summary
    cd14722
    Location:96149
    bZIP_ATF3; Basic leucine zipper (bZIP) domain of Activating Transcription Factor-3 (ATF-3) and similar proteins: a DNA-binding and dimerization domain