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

Gene ID: 467, updated on 21-Jan-2020

Summary

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
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

Genomic context

See ATF3 in Genome Data Viewer
Location:
1q32.3
Exon count:
7
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (212565334..212620777)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (212738676..212794119)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene VISTA enhancer hs2089 Neighboring gene long intergenic non-protein coding RNA 1740 Neighboring gene Sharpr-MPRA regulatory region 14467 Neighboring gene family with sequence similarity 71 member A Neighboring gene long intergenic non-protein coding RNA 2773 Neighboring gene riboflavin kinase pseudogene

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

HIV-1 interactions

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ41705

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA-binding transcription activator activity, RNA polymerase II-specific IC
Inferred by Curator
more info
 
DNA-binding transcription factor activity IGI
Inferred from Genetic Interaction
more info
PubMed 
DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
 
DNA-binding transcription factor activity, RNA polymerase II-specific ISM
Inferred from Sequence Model
more info
PubMed 
DNA-binding transcription factor activity, RNA polymerase II-specific NAS
Non-traceable Author Statement
more info
PubMed 
DNA-binding transcription repressor activity, RNA polymerase II-specific IEA
Inferred from Electronic Annotation
more info
 
RNA polymerase II proximal promoter sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
RNA polymerase II regulatory region sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein heterodimerization activity IPI
Inferred from Physical Interaction
more info
PubMed 
protein homodimerization activity IDA
Inferred from Direct Assay
more info
PubMed 
transcription corepressor activity TAS
Traceable Author Statement
more info
PubMed 
transcription regulatory region DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
transcription regulatory region sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
CHOP-ATF3 complex IDA
Inferred from Direct Assay
more info
PubMed 
nuclear chromatin ISA
Inferred from Sequence Alignment
more info
 
nucleolus IDA
Inferred from Direct Assay
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

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

NCBI Reference Sequences (RefSeq)

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
    4980..60423
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001030287.3NP_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)
    AC092803, AI949953, BC006322, CD638624, CD641946, CD742713
    Consensus CDS
    CCDS1506.1
    UniProtKB/Swiss-Prot
    P18847
    Related
    ENSP00000355954.2, ENST00000366987.6
    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
  2. NM_001040619.3NP_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/Swiss-Prot
    P18847
    Related
    ENSP00000355950.1, ENST00000366983.5
    Conserved Domains (1) summary
    cl21462
    Location:96116
    bZIP; Basic leucine zipper (bZIP) domain of bZIP transcription factors: a DNA-binding and dimerization domain
  3. NM_001206484.3NP_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/Swiss-Prot
    P18847
    Conserved Domains (1) summary
    cd14722
    Location:3992
    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_001206486.2NP_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:6787
    bZIP; Basic leucine zipper (bZIP) domain of bZIP transcription factors: a DNA-binding and dimerization domain
  5. NM_001206488.3NP_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/Swiss-Prot
    P18847
    Related
    ENSP00000483576.1, ENST00000613954.4
    Conserved Domains (1) summary
    cd14722
    Location:3992
    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_001674.4NP_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
    Related
    ENSP00000344352.4, ENST00000341491.9
    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: Homo sapiens Updated Annotation Release 109.20191205

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    212565334..212620777
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011509579.1XP_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
    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
  2. XM_005273146.1XP_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
    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

RNA

  1. XR_001737203.1 RNA Sequence

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.
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