ATF3 Gene (Protein Coding)

Activating Transcription Factor 3

GC01P212565
GIFtS:
44
This gene encodes a member of the mammalian activation transcription factor/cAMP responsive element-binding (CREB) protein family of transcription factors. This gene is induced by a variety of signals, including many of those encountered by cancer cells, and is involved in the complex process of cellular stress response. Multiple transcript variants encoding different isoforms ... See more...

Aliases for ATF3 Gene

Aliases for ATF3 Gene

  • Activating Transcription Factor 3 2 3 4 5
  • Cyclic AMP-Dependent Transcription Factor ATF-3 3 4
  • CAMP-Dependent Transcription Factor ATF-3 3 4
  • ATF3 5

External Ids for ATF3 Gene

Previous GeneCards Identifiers for ATF3 Gene

  • GC01P211461
  • GC01P208625
  • GC01P209398
  • GC01P209838
  • GC01P209170
  • GC01P210805
  • GC01P212738
  • GC01P183415

Summaries for ATF3 Gene

Entrez Gene Summary for ATF3 Gene

  • This gene encodes a member of the mammalian activation transcription factor/cAMP responsive element-binding (CREB) protein family of transcription factors. This gene is induced by a variety of signals, including many of those encountered by cancer cells, and is involved in the complex process of cellular stress response. Multiple transcript variants encoding different isoforms have been found for this gene. It is possible that alternative splicing of this gene may be physiologically important in the regulation of target genes. [provided by RefSeq, Apr 2011]

GeneCards Summary for ATF3 Gene

ATF3 (Activating Transcription Factor 3) is a Protein Coding gene. Diseases associated with ATF3 include Bone Cancer and Hypospadias. Among its related pathways are Photodynamic therapy-induced unfolded protein response and PERK regulates gene expression. Gene Ontology (GO) annotations related to this gene include DNA-binding transcription factor activity and sequence-specific DNA binding. An important paralog of this gene is JDP2.

UniProtKB/Swiss-Prot Summary for ATF3 Gene

  • This protein binds the cAMP response element (CRE) (consensus: 5'-GTGACGT[AC][AG]-3'), a sequence present in many viral and cellular promoters. Represses transcription from promoters with ATF sites. It may repress transcription by stabilizing the binding of inhibitory cofactors at the promoter. Isoform 2 activates transcription presumably by sequestering inhibitory cofactors away from the promoters.

Gene Wiki entry for ATF3 Gene

Additional gene information for ATF3 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for ATF3 Gene

Genomics for ATF3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for ATF3 Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH01J212605 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 612.9 +42.9 42860 6 RNF2 CEBPG HNRNPL CREB1 GATAD2A CTCF ATF7 PRDM10 ZNF629 REST ATF3 lnc-BATF3-8 ANGEL2 DTL FLVCR1 BATF3 FAM71A
GH01J212565 Promoter/Enhancer 1.7 Ensembl ENCODE CraniofacialAtlas dbSUPER 600.7 +1.8 1764 2.2 RNF2 SP1 PRDM10 ZNF629 ZNF512 LEF1 ZNF692 BACH1 JUND FOXA1 ATF3 lnc-BATF3-8 FAM71A
GH01J212615 Promoter 0.6 EPDnew 600.3 +49.9 49910 0.1 ZNF316 POLR2A USF2 AB372749-001 NONHSAG004237.2 lnc-BATF3-5 ATF3 BATF3 FAM71A
GH01J212590 Promoter 0.4 EPDnew 600.3 +25.0 25034 0.1 ZNF316 ATF3 lnc-BATF3-8 FAM71A
GH01J212481 Enhancer 1.5 FANTOM5 ENCODE dbSUPER 39.1 -79.4 -79417 8.2 CREB1 ATF7 PRDM10 ZNF629 RFX1 LEF1 ZNF692 BACH1 JUND FOXA1 lnc-TMEM206-7 LINC02771 ATF3 ANGEL2 BATF3 RPL21P28 lnc-NENF-5 NENF
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around ATF3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for ATF3

Top Transcription factor binding sites by QIAGEN in the ATF3 gene promoter:
  • ATF
  • C/EBPalpha
  • CREB
  • deltaCREB

Genomic Locations for ATF3 Gene

Genomic Locations for ATF3 Gene
chr1:212,565,334-212,620,777
(GRCh38/hg38)
Size:
55,444 bases
Orientation:
Plus strand
chr1:212,738,676-212,794,119
(GRCh37/hg19)
Size:
55,444 bases
Orientation:
Plus strand

Genomic View for ATF3 Gene

Genes around ATF3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ATF3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ATF3 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for ATF3 Gene

Proteins for ATF3 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for ATF3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P18847-ATF3_HUMAN
    Recommended name:
    Cyclic AMP-dependent transcription factor ATF-3
    Protein Accession:
    P18847
    Secondary Accessions:
    • Q5VTZ2
    • Q6ICQ9
    • Q7Z566
    • Q8WYM6

    Protein attributes for ATF3 Gene

    Size:
    181 amino acids
    Molecular mass:
    20576 Da
    Quaternary structure:
    • Binds DNA as a homodimer or a heterodimer.
    Miscellaneous:
    • [Isoform 2]: May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.
    • [Isoform 3]: Stress-induced isoform, counteracts the transcriptional repression of isoform 1.

    Alternative splice isoforms for ATF3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for ATF3 Gene

Protein Expression for ATF3 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for ATF3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for ATF3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for ATF3 Gene

Domains & Families for ATF3 Gene

Gene Families for ATF3 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for ATF3 Gene

InterPro:
Blocks:
  • Fos transforming protein signature
ProtoNet:

Suggested Antigen Peptide Sequences for ATF3 Gene

GenScript: Design optimal peptide antigens:
  • Activating transcription factor 3 (ATF3_HUMAN)
  • cDNA, FLJ93461, Homo sapiens activating transcription factor 3 (ATF3), mRNA (Q6ICQ9_HUMAN)
  • cDNA FLJ57271, highly similar to Cyclic AMP-dependent transcription factorATF-3 (Q7Z567_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P18847

UniProtKB/Swiss-Prot:

ATF3_HUMAN :
  • Belongs to the bZIP family. ATF subfamily.
Family:
  • Belongs to the bZIP family. ATF subfamily.
genes like me logo Genes that share domains with ATF3: view

Function for ATF3 Gene

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  2. CRISPR
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Molecular function for ATF3 Gene

UniProtKB/Swiss-Prot Function:
This protein binds the cAMP response element (CRE) (consensus: 5'-GTGACGT[AC][AG]-3'), a sequence present in many viral and cellular promoters. Represses transcription from promoters with ATF sites. It may repress transcription by stabilizing the binding of inhibitory cofactors at the promoter. Isoform 2 activates transcription presumably by sequestering inhibitory cofactors away from the promoters.

Phenotypes From GWAS Catalog for ATF3 Gene

Gene Ontology (GO) - Molecular Function for ATF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000976 transcription regulatory region sequence-specific DNA binding IDA 8622660
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding IDA 2516827
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IBA 21873635
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific ISM 19274049
GO:0001227 DNA-binding transcription repressor activity, RNA polymerase II-specific IEA --
genes like me logo Genes that share ontologies with ATF3: view
genes like me logo Genes that share phenotypes with ATF3: view

Animal Models for ATF3 Gene

MGI Knock Outs for ATF3:
  • Atf3 Atf3<tm1Dron>
  • Atf3 Atf3<tm2b(EUCOMM)Wtsi>
  • Atf3 Atf3<tm1.1Kitab>

Animal Model Products

CRISPR Products

Targeted motifs for ATF3 Gene
HOMER Transcription Factor Regulatory Elements motif ATF3
  • Consensus sequence: DATGASTCATHN Submotif: canonical Cell Type: GBM GEO ID: GSE33912

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ATF3

Clone Products

  • Addgene plasmids for ATF3

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology and Transcription Factor Targets for ATF3 Gene

Localization for ATF3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ATF3 Gene

Nucleus.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for ATF3 gene
Compartment Confidence
nucleus 5
endoplasmic reticulum 3
cytosol 3
plasma membrane 2
extracellular 2
cytoskeleton 2
mitochondrion 2
endosome 2
lysosome 2
peroxisome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli (3)
  • Nucleoplasm (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for ATF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000790 nuclear chromatin ISA --
GO:0005634 nucleus IDA 8622660
GO:0005654 nucleoplasm TAS --
GO:0005730 nucleolus IDA --
GO:1990622 CHOP-ATF3 complex IDA 8622660
genes like me logo Genes that share ontologies with ATF3: view

Pathways & Interactions for ATF3 Gene

genes like me logo Genes that share pathways with ATF3: view

Pathways by source for ATF3 Gene

2 Sino Biological pathways for ATF3 Gene
1 PharmGKB pathway for ATF3 Gene
8 Qiagen pathways for ATF3 Gene
  • Ceramide Pathway
  • ILK Signaling
  • iNOS Signaling
  • ITK and TCR Signaling
  • MAPK Signaling
1 Cell Signaling Technology pathway for ATF3 Gene

SIGNOR curated interactions for ATF3 Gene

Activates:

Gene Ontology (GO) - Biological Process for ATF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IDA 8622660
GO:0006094 gluconeogenesis IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006357 regulation of transcription by RNA polymerase II IBA 21873635
GO:0008284 positive regulation of cell proliferation IEA --
genes like me logo Genes that share ontologies with ATF3: view

Drugs & Compounds for ATF3 Gene

Products:

  1. Drug

(19) Drugs for ATF3 Gene - From: DrugBank, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Pseudoephedrine Approved Pharma Target, inhibitor 426
cyclic amp Experimental Pharma 0

(12) Additional Compounds for ATF3 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with ATF3: view

Transcripts for ATF3 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for ATF3 Gene

8 REFSEQ mRNAs :
27 NCBI additional mRNA sequence :
11 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ATF3

Clone Products

  • Addgene plasmids for ATF3

Alternative Splicing Database (ASD) splice patterns (SP) for ATF3 Gene

ExUns: 1 ^ 2a · 2b · 2c · 2d ^ 3 ^ 4a · 4b · 4c · 4d ^ 5a · 5b ^ 6a · 6b · 6c · 6d ^ 7a · 7b · 7c ^ 8a · 8b
SP1: - - - - - - - -
SP2: - -
SP3: - - - - -
SP4: - - - -
SP5: - - -
SP6: - - - - - - -
SP7: - - -
SP8: - -
SP9: -
SP10: - - -
SP11: -

Relevant External Links for ATF3 Gene

GeneLoc Exon Structure for
ATF3

Expression for ATF3 Gene

Products:

  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for ATF3 Gene

mRNA expression in normal human tissues for ATF3 Gene
mRNA expression by BioGPS for ATF3 GenemRNA expression by GTEx for ATF3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for ATF3 Gene

This gene is overexpressed in Placenta (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for ATF3 Gene



Protein tissue co-expression partners for ATF3 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for ATF3

SOURCE GeneReport for Unigene cluster for ATF3 Gene:

Hs.460

Evidence on tissue expression from TISSUES for ATF3 Gene

  • Nervous system(4.8)
  • Lung(4.7)
  • Muscle(4.6)
  • Liver(3.4)
  • Heart(3.2)
  • Kidney(3.2)
  • Intestine(3.1)
  • Blood(2.9)
  • Pancreas(2.8)
  • Adrenal gland(2.7)
  • Skin(2.7)
  • Thyroid gland(2.7)
  • Bone marrow(2.6)
  • Spleen(2.6)
  • Lymph node(2.6)
  • Stomach(2.5)
  • Eye(2.3)
genes like me logo Genes that share expression patterns with ATF3: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for ATF3 Gene

Orthologs for ATF3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for ATF3 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia ATF3 30 31
  • 99.63 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia ATF3 30 31
  • 93.74 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia ATF3 30 31
  • 93.37 (n)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia ATF3 31
  • 93 (a)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia ATF3 31
  • 92 (a)
 OneToOne
Mouse
(Mus musculus)
 Mammalia Atf3 30 17 31
  • 88.95 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Atf3 30
  • 88.03 (n)
Chicken
(Gallus gallus)
 Aves ATF3 30 31
  • 76.06 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia ATF3 31
  • 85 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia atf3 30
  • 74.22 (n)
Zebrafish
(Danio rerio)
 Actinopterygii atf3 30 31
  • 67.8 (n)
 OneToOne
zgc55526 30
Sea Squirt
(Ciona savignyi)
 Ascidiacea -- 31
  • 27 (a)
 OneToMany
Species where no ortholog for ATF3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for ATF3 Gene

ENSEMBL:
Gene Tree for ATF3 (if available)
TreeFam:
Gene Tree for ATF3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for ATF3: view image

Paralogs for ATF3 Gene

Paralogs for ATF3 Gene

(7) SIMAP similar genes for ATF3 Gene using alignment to 3 proteins:

  • ATF3_HUMAN
  • Q5VTZ4_HUMAN
  • Q7Z567_HUMAN
genes like me logo Genes that share paralogs with ATF3: view

Variants for ATF3 Gene

Products:

  1. SNP Genotyping and Copy Number Assay

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for ATF3 Gene

SNP ID Clinical significance and condition Chr 01 pos Variation AA Info Type
741892 Benign: not provided 212,619,384(+) T/C SYNONYMOUS_VARIANT,THREE_PRIME_UTR_VARIANT
rs11571541 - p.Thr38Met
VAR_081532 - p.Asn168Thr

Additional dbSNP identifiers (rs#s) for ATF3 Gene

Structural Variations from Database of Genomic Variants (DGV) for ATF3 Gene

Variant ID Type Subtype PubMed ID
esv2758996 CNV loss 17122850
esv3394920 CNV insertion 20981092
nsv549139 CNV gain 21841781

Variation tolerance for ATF3 Gene

Residual Variation Intolerance Score: 63.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.01; 20.77% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ATF3 Gene

Human Gene Mutation Database (HGMD)
ATF3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
ATF3

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ATF3 Gene

Disorders for ATF3 Gene

MalaCards: The human disease database

(7) MalaCards diseases for ATF3 Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
bone cancer
  • bone neoplasm
hypospadias
  • familial hypospadias
cockayne syndrome b
  • csb
pulmonary systemic sclerosis
  • lung disease with systemic sclerosis
wilms tumor 1
  • wt1
- elite association - COSMIC cancer census association via MalaCards
Search ATF3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for ATF3

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with ATF3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for ATF3 Gene

Publications for ATF3 Gene

  1. ATF3 and ATF3 delta Zip. Transcriptional repression versus activation by alternatively spliced isoforms. (PMID: 7515060) Chen BP … Hai T (The Journal of biological chemistry 1994) 2 3 4 23
  2. Genetics of hypospadias: are single-nucleotide polymorphisms in SRD5A2, ESR1, ESR2, and ATF3 really associated with the malformation? (PMID: 20215396) van der Zanden LF … Franke B (The Journal of clinical endocrinology and metabolism 2010) 3 23 41
  3. Activating transcription factor 3: a hormone responsive gene in the etiology of hypospadias. (PMID: 18426833) Beleza-Meireles A … Nordenskjöld A (European journal of endocrinology 2008) 3 23 41
  4. Amino acid deprivation and endoplasmic reticulum stress induce expression of multiple activating transcription factor-3 mRNA species that, when overexpressed in HepG2 cells, modulate transcription by the human asparagine synthetase promoter. (PMID: 12881527) Pan Y … Kilberg MS (The Journal of biological chemistry 2003) 3 4 23
  5. AdipoR2 is transcriptionally regulated by ER stress-inducible ATF3 in HepG2 human hepatocyte cells. (PMID: 20423458) Koh IU … Song J (The FEBS journal 2010) 3 23

ExternalLinks

View latest publications for ATF3 gene in Mastermind

Products for ATF3 Gene

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  • Signalway Proteins for ATF3

Sources for ATF3 Gene