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ATF3 activating transcription factor 3 [ Homo sapiens (human) ]

Gene ID: 467, updated on 3-Apr-2024

Summary

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Official Symbol
ATF3provided by HGNC
Official Full Name
activating transcription factor 3provided by HGNC
Primary source
HGNC:HGNC:785
See related
Ensembl:ENSG00000162772 MIM:603148; AllianceGenome:HGNC:785
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
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]
Expression
Ubiquitous expression in gall bladder (RPKM 38.3), liver (RPKM 37.5) and 23 other tissues See more
Orthologs
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Genomic context

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Location:
1q32.3
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (212565407..212620777)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (211810345..211865712)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (212738749..212794119)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105372908 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:212687383-212688110 Neighboring gene VISTA enhancer hs2089 Neighboring gene long intergenic non-protein coding RNA 1740 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:212731832-212732569 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2506 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2507 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2508 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_3744 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2509 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:212769225-212770424 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1797 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:212780771-212781728 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:212781729-212782686 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1800 Neighboring gene Sharpr-MPRA regulatory region 14805 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:212799247-212799747 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:212803852-212804383 Neighboring gene long intergenic non-protein coding RNA 2773 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1801 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:212810785-212811984 Neighboring gene golgi associated RAB2 interactor family member 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:212819605-212820114 Neighboring gene RFK pseudogene 5

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Activating transcription factor 3, glucolipid metabolism, and metabolic diseases. Hu S, et al. J Mol Cell Biol, 2023 Mar 29. PMID 36472556, Free PMC Article
  2. ATF3 Reprograms the Bone Marrow Niche in Response to Early Breast Cancer Transformation. Perrone M, et al. Cancer Res, 2023 Jan 4. PMID 36318106, Free PMC Article
  3. ATF3 in atherosclerosis: a controversial transcription factor. Wang B, et al. J Mol Med (Berl), 2022 Nov. PMID 36207452
  4. Decreased expression of ATF3, orchestrated by β-catenin/TCF3, miR-17-5p and HOXA11-AS, promoted gastric cancer progression via increased β-catenin and CEMIP. Xie G, et al. Exp Mol Med, 2021 Nov. PMID 34728784, Free PMC Article
  5. ATF3 regulates oxidative stress and extracellular matrix degradation via p38/Nrf2 signaling pathway in pelvic organ prolapse. Feng J, et al. Tissue Cell, 2021 Dec. PMID 34666282

See all (306) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Role of ATF3 triggering M2 macrophage polarization to protect against the inflammatory injury of sepsis through ILF3/NEAT1 axis.
    Title: Role of ATF3 triggering M2 macrophage polarization to protect against the inflammatory injury of sepsis through ILF3/NEAT1 axis.
  2. Altered expression of activating transcription factor 3 in the hippocampus of patients with mesial temporal lobe epilepsy-hippocampal sclerosis (MTLE-HS).
    Title: Altered expression of activating transcription factor 3 in the hippocampus of patients with mesial temporal lobe epilepsy-hippocampal sclerosis (MTLE-HS).
  3. CircEXOC5 Aggravates Sepsis-Induced Acute Lung Injury by Promoting Ferroptosis Through the IGF2BP2/ATF3 Axis.
    Title: CircEXOC5 Aggravates Sepsis-Induced Acute Lung Injury by Promoting Ferroptosis Through the IGF2BP2/ATF3 Axis.
  4. Activating transcription factor 3 is a new biomarker correlation with renal clear cell carcinoma progression.
    Title: Activating transcription factor 3 is a new biomarker correlation with renal clear cell carcinoma progression.
  5. Methylation-Mediated Silencing of ATF3 Promotes Thyroid Cancer Progression by Regulating Prognostic Genes in the MAPK and PI3K/AKT Pathways.
    Title: Methylation-Mediated Silencing of ATF3 Promotes Thyroid Cancer Progression by Regulating Prognostic Genes in the MAPK and PI3K/AKT Pathways.
  6. Inhibition of inflammation and infiltration of M2 macrophages in NSCLC through the ATF3/CSF1 axis: Role of miR-27a-3p.
    Title: Inhibition of inflammation and infiltration of M2 macrophages in NSCLC through the ATF3/CSF1 axis: Role of miR-27a-3p.
  7. Identification of ATF3 as a novel protective signature of quiescent colorectal tumor cells.
    Title: Identification of ATF3 as a novel protective signature of quiescent colorectal tumor cells.
  8. ATF3 Modulates the Proliferation, Migration, and Apoptosis of Synovial Fibroblasts after Arthroscopy by Promoting RGS1 Transcription.
    Title: ATF3 Modulates the Proliferation, Migration, and Apoptosis of Synovial Fibroblasts after Arthroscopy by Promoting RGS1 Transcription.
  9. Activating transcription factor 3, glucolipid metabolism, and metabolic diseases.
    Title: Activating transcription factor 3, glucolipid metabolism, and metabolic diseases.
  10. ATF3 Reprograms the Bone Marrow Niche in Response to Early Breast Cancer Transformation.
    Title: ATF3 Reprograms the Bone Marrow Niche in Response to Early Breast Cancer Transformation.
Submit: New GeneRIF Correction See all GeneRIFs (228)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Nef nef Expression of activating transcription factor 3 (ATF-3) is upregulated by HIV-1 Nef in HeLa cells PubMed
Tat tat HIV-1 and the viral protein Tat modulate the expression of activating transcription factor 3 (ATF3) in immature dendritic cells and monocyte-derived macrophages PubMed
tat HIV-1 Tat upregulates ATF3 expression in Tat-infected Jurkat T cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ41705

Gene Ontology Provided by GOA

Function Evidence Code Pubs
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 ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
enables DNA-binding transcription factor activity IGI
Inferred from Genetic Interaction
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 factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
  
enables DNA-binding transcription repressor activity, RNA polymerase II-specific IDA
Inferred from Direct Assay
more info
 PubMed 
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 ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein heterodimerization activity IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein homodimerization activity IPI
Inferred from Physical Interaction
more info
 PubMed 
enables sequence-specific double-stranded DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables transcription cis-regulatory region binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in cellular response to amino acid starvation IEA
Inferred from Electronic Annotation
more info
  
involved_in endoplasmic reticulum unfolded protein response IEA
Inferred from Electronic Annotation
more info
  
involved_in gluconeogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of ERK1 and ERK2 cascade IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of transcription by RNA polymerase II TAS
Traceable Author Statement
more info
 PubMed 
involved_in positive regulation of TRAIL-activated apoptotic signaling pathway IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of cell population proliferation IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of gene expression IEA
Inferred from Electronic Annotation
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 ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
involved_in positive regulation of transcription by RNA polymerase II NAS
Non-traceable Author Statement
more info
 PubMed 
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 IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of transcription by RNA polymerase II NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in response to endoplasmic reticulum stress IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in skeletal muscle cell differentiation IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
part_of CHOP-ATF3 complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of RNA polymerase II transcription regulator complex IPI
Inferred from Physical Interaction
more info
 PubMed 
part_of chromatin ISA
Inferred from Sequence Alignment
more info
  
located_in nucleolus IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
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 NAS
Non-traceable Author Statement
more info
 PubMed 

General protein information

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Preferred Names
cyclic AMP-dependent transcription factor ATF-3
Names
cAMP-dependent transcription factor ATF-3

NCBI Reference Sequences (RefSeq)

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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.

Genomic

  1. NG_029871.1 RefSeqGene

    Range
    48407..60421
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001030287.4 → NP_001025458.1  cyclic AMP-dependent transcription factor ATF-3 isoform 1

    See identical proteins and their annotated locations for NP_001025458.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, compared to variant 1. Both variants 1 and 3 encode the same isoform (1), which represses rather than activates transcription from promoters with ATF-binding elements.
    Source sequence(s)
    AI949953, BC006322, CD638624, CD641946, CD742713
    Consensus CDS
    CCDS1506.1
    UniProtKB/Swiss-Prot
    P18847, Q5VTZ2, Q6ICQ9, Q7Z566, Q8WYM6
    UniProtKB/TrEMBL
    Q5VTZ4
    Related
    ENSP00000355954.2, ENST00000366987.6
    Conserved Domains (1) summary
    cd14722
    Location:96 → 149
    bZIP_ATF3; Basic leucine zipper (bZIP) domain of Activating Transcription Factor-3 (ATF-3) and similar proteins: a DNA-binding and dimerization domain

  2. NM_001040619.3 → NP_001035709.1  cyclic AMP-dependent transcription factor ATF-3 isoform 2

    See identical proteins and their annotated locations for NP_001035709.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4, also known as deltaZip2a) contains an alternate terminal exon, and thus differs in the 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (2, also known as deltaZip2) has a distinct and shorter C-terminus, compared to isoform 1. Isoform 2 lacks the leucine zipper protein-dimerization motif and does not bind to DNA, and it stimulates transcription presumably by sequestering inhibitory co-factors away from the promoter.
    Source sequence(s)
    AB078026, AI949953, BC006322, CD742713, DB197400
    Consensus CDS
    CCDS41464.1
    UniProtKB/TrEMBL
    Q7Z567
    Related
    ENSP00000355950.1, ENST00000366983.5
    Conserved Domains (1) summary
    cl21462
    Location:96 → 116
    bZIP; Basic leucine zipper (bZIP) domain of bZIP transcription factors: a DNA-binding and dimerization domain

  3. NM_001206484.3 → NP_001193413.2  cyclic AMP-dependent transcription factor ATF-3 isoform 3

    See identical proteins and their annotated locations for NP_001193413.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR, lacks a portion of the 5' coding region, and uses a downstream in-frame start codon, compared to variant 1. The encoded isoform (3) is shorter at the N-terminus, compared to isoform 1. Both variants 5 and 8 encode isoform 3.
    Source sequence(s)
    AB078026, AI949953, BC006322, CD742713, DA589280
    Consensus CDS
    CCDS58059.1
    UniProtKB/TrEMBL
    A0A0A0MRJ2
    Conserved Domains (1) summary
    cd14722
    Location:39 → 92
    bZIP_ATF3; Basic leucine zipper (bZIP) domain of Activating Transcription Factor-3 (ATF-3) and similar proteins: a DNA-binding and dimerization domain

  4. NM_001206486.2 → NP_001193415.1  cyclic AMP-dependent transcription factor ATF-3 isoform 5

    See identical proteins and their annotated locations for NP_001193415.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) differs in the 5' UTR, lacks an in-frame segment of the 5' coding region, and contains an alternate terminal exon, thus differing in the 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (5, also known as deltaZip2c) has a distinct C-terminus and is shorter than isoform 1.
    Source sequence(s)
    AB078026, AI949953, AY313927, BC006322, CD742713
    Consensus CDS
    CCDS55688.1
    UniProtKB/Swiss-Prot
    P18847
    Related
    ENSP00000336908.4, ENST00000336937.8
    Conserved Domains (1) summary
    cl21462
    Location:67 → 87
    bZIP; Basic leucine zipper (bZIP) domain of bZIP transcription factors: a DNA-binding and dimerization domain

  5. NM_001206488.3 → NP_001193417.2  cyclic AMP-dependent transcription factor ATF-3 isoform 3

    See identical proteins and their annotated locations for NP_001193417.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8) differs in the 5' UTR, lacks a portion of the 5' coding region, and uses a downstream in-frame start codon, compared to variant 1. The encoded isoform (3) is shorter at the N-terminus, compared to isoform 1. Both variants 5 and 8 encode isoform 3.
    Source sequence(s)
    AI949953, AL560585, BC006322, BI524020, CD742713
    Consensus CDS
    CCDS58059.1
    UniProtKB/TrEMBL
    A0A0A0MRJ2
    Related
    ENSP00000480606.1, ENST00000613104.1
    Conserved Domains (1) summary
    cd14722
    Location:39 → 92
    bZIP_ATF3; Basic leucine zipper (bZIP) domain of Activating Transcription Factor-3 (ATF-3) and similar proteins: a DNA-binding and dimerization domain

  6. NM_001674.4 → NP_001665.1  cyclic AMP-dependent transcription factor ATF-3 isoform 1

    See identical proteins and their annotated locations for NP_001665.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1), which represses rather than activates transcription from promoters with ATF-binding elements. Both variants 1 and 3 encode isoform 1.
    Source sequence(s)
    AI949953, AL560585, BC006322, CD742713
    Consensus CDS
    CCDS1506.1
    UniProtKB/Swiss-Prot
    P18847, Q5VTZ2, Q6ICQ9, Q7Z566, Q8WYM6
    UniProtKB/TrEMBL
    Q5VTZ4
    Related
    ENSP00000344352.4, ENST00000341491.9
    Conserved Domains (1) summary
    cd14722
    Location:96 → 149
    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_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    212565407..212620777
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011509579.2 → XP_011507881.1  cyclic AMP-dependent transcription factor ATF-3 isoform X1

    See identical proteins and their annotated locations for XP_011507881.1

    UniProtKB/Swiss-Prot
    P18847, Q5VTZ2, Q6ICQ9, Q7Z566, Q8WYM6
    UniProtKB/TrEMBL
    Q5VTZ4
    Conserved Domains (1) summary
    cd14722
    Location:96 → 149
    bZIP_ATF3; Basic leucine zipper (bZIP) domain of Activating Transcription Factor-3 (ATF-3) and similar proteins: a DNA-binding and dimerization domain

  2. XM_005273146.2 → XP_005273203.1  cyclic AMP-dependent transcription factor ATF-3 isoform X1

    See identical proteins and their annotated locations for XP_005273203.1

    UniProtKB/Swiss-Prot
    P18847, Q5VTZ2, Q6ICQ9, Q7Z566, Q8WYM6
    UniProtKB/TrEMBL
    Q5VTZ4
    Conserved Domains (1) summary
    cd14722
    Location:96 → 149
    bZIP_ATF3; Basic leucine zipper (bZIP) domain of Activating Transcription Factor-3 (ATF-3) and similar proteins: a DNA-binding and dimerization domain

  3. XM_047421211.1 → XP_047277167.1  cyclic AMP-dependent transcription factor ATF-3 isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    211810345..211865712
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054336744.1 → XP_054192719.1  cyclic AMP-dependent transcription factor ATF-3 isoform X1

    UniProtKB/Swiss-Prot
    P18847, Q5VTZ2, Q6ICQ9, Q7Z566, Q8WYM6

  2. XM_054336743.1 → XP_054192718.1  cyclic AMP-dependent transcription factor ATF-3 isoform X1

    UniProtKB/Swiss-Prot
    P18847, Q5VTZ2, Q6ICQ9, Q7Z566, Q8WYM6

  3. XM_054336745.1 → XP_054192720.1  cyclic AMP-dependent transcription factor ATF-3 isoform X2

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001206485.1: Suppressed sequence

    Description
    NM_001206485.1: This RefSeq was permanently suppressed because the transcript is incompletely processed.

  2. NM_004024.4: Suppressed sequence

    Description
    NM_004024.4: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P18847.2 GenPept UniProtKB/Swiss-Prot:P18847

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