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ATF6B activating transcription factor 6 beta [ Homo sapiens (human) ]

Gene ID: 1388, updated on 2-Nov-2024

Summary

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Official Symbol
ATF6Bprovided by HGNC
Official Full Name
activating transcription factor 6 betaprovided by HGNC
Primary source
HGNC:HGNC:2349
See related
Ensembl:ENSG00000213676 MIM:600984; AllianceGenome:HGNC:2349
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
Also known as
G13; CREBL1; CREB-RP; ATF6beta
Summary
The protein encoded by this gene is a transcription factor in the unfolded protein response (UPR) pathway during ER stress. Either as a homodimer or as a heterodimer with ATF6-alpha, the encoded protein binds to the ER stress response element, interacting with nuclear transcription factor Y to activate UPR target genes. The protein is normally found in the membrane of the endoplasmic reticulum; however, under ER stress, the N-terminal cytoplasmic domain is cleaved from the rest of the protein and translocates to the nucleus. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2008]
Expression
Ubiquitous expression in spleen (RPKM 32.2), skin (RPKM 32.1) and 25 other tissues See more
Orthologs
mouse all
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Genomic context

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See ATF6B in Genome Data Viewer
Location:
6p21.32
Exon count:
18
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (32115264..32128246, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (31968456..31981438, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (32083041..32096023, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene CYP21A2 5' regulatory region Neighboring gene CYP21A2 recombination region Neighboring gene tenascin XB recombination region Neighboring gene ReSE screen-validated silencer GRCh37_chr6:32013699-32013950 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:32014364-32015563 Neighboring gene cytochrome P450 family 21 subfamily A member 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:32015753-32016386 Neighboring gene tenascin XB Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:32038327-32039327 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:32040222-32041078 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:32041114-32041614 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:32049385-32049900 Neighboring gene RNA, 5S ribosomal pseudogene 206 Neighboring gene Sharpr-MPRA regulatory region 2290 Neighboring gene CRISPRi-validated cis-regulatory element chr6.1802 Neighboring gene FKBP prolyl isomerase like Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:32116858-32117395 Neighboring gene uncharacterized LOC100507547 Neighboring gene proline rich transmembrane protein 1

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 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. Establishment of a reporter system for monitoring activation of the ER stress transducer ATF6β. Hien LT, et al. Biochem Biophys Res Commun, 2021 Jun 18. PMID 33894672
  2. Tenascin-X: a novel extracellular matrix protein encoded by the human XB gene overlapping P450c21B. Bristow J, et al. J Cell Biol, 1993 Jul. PMID 7686164, Free PMC Article
  3. N-glycosylation of ATF6beta is essential for its proteolytic cleavage and transcriptional repressor function to ATF6alpha. Guan D, et al. J Cell Biochem, 2009 Nov 1. PMID 19693772
  4. The gene G13 in the class III region of the human MHC encodes a potential DNA-binding protein. Khanna A, et al. Biochem J, 1996 Oct 1. PMID 8870652, Free PMC Article
  5. Alternate promoters and alternate splicing of human tenascin-X, a gene with 5' and 3' ends buried in other genes. Speek M, et al. Hum Mol Genet, 1996 Nov. PMID 8923003

See all (47) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Loss of ATF6alpha in a human carcinoma cell line is compensated not by its paralogue ATF6beta but by sustained activation of the IRE1 and PERK arms for tumor growth in nude mice.
    Title: Loss of ATF6α in a human carcinoma cell line is compensated not by its paralogue ATF6β but by sustained activation of the IRE1 and PERK arms for tumor growth in nude mice.
  2. Establishment of a reporter system for monitoring activation of the ER stress transducer ATF6beta.
    Title: Establishment of a reporter system for monitoring activation of the ER stress transducer ATF6β.
  3. Polymorphism in the 3'-UTR of LIF but Not in the ATF6B Gene Associates with Schizophrenia Susceptibility: a Case-Control Study and In Silico Analyses.
    Title: Polymorphism in the 3'-UTR of LIF but Not in the ATF6B Gene Associates with Schizophrenia Susceptibility: a Case-Control Study and In Silico Analyses.
  4. ATF4 and ATF6beta act synergistically in the negative regulation of placental growth factor mRNA expression
    Title: Placental endoplasmic reticulum stress negatively regulates transcription of placental growth factor via ATF4 and ATF6β: implications for the pathophysiology of human pregnancy complications.
  5. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
    Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
  6. unglycosylated ATF6beta may directly facilitate the expression of ERSR genes by losing its repressor function to ATF6alpha
    Title: N-glycosylation of ATF6beta is essential for its proteolytic cleavage and transcriptional repressor function to ATF6alpha.
  7. Observational study of gene-disease association. (HuGE Navigator)
    Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
Submit: New GeneRIF Correction

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

EBI GWAS Catalog

Description
A genome-wide association study of atopic dermatitis identifies loci with overlapping effects on asthma and psoriasis.
EBI GWAS Catalog
Genetic factors in nonsmokers with age-related macular degeneration revealed through genome-wide gene-environment interaction analysis.
EBI GWAS Catalog
Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

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

Potential readthrough

Included gene: TNXB

Homology

Clone Names

  • FLJ10066

Gene Ontology Provided by GOA

Function Evidence Code Pubs
contributes_to DNA-binding transcription activator activity, RNA polymerase II-specific IDA
Inferred from Direct Assay
more info
 PubMed 
enables DNA-binding transcription factor activity IDA
Inferred from Direct Assay
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
  
contributes_to RNA polymerase II cis-regulatory region sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding 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 ATF6-mediated unfolded protein response NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in ATF6-mediated unfolded protein response TAS
Traceable Author Statement
more info
 PubMed 
involved_in endoplasmic reticulum unfolded protein response IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of ATF6-mediated unfolded protein response IDA
Inferred from Direct Assay
more info
 PubMed 
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 TAS
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 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 response to endoplasmic reticulum stress TAS
Traceable Author Statement
more info
 PubMed 
involved_in signal transduction TAS
Traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
located_in Golgi apparatus TAS
Traceable Author Statement
more info
 PubMed 
located_in Golgi membrane TAS
Traceable Author Statement
more info
  
part_of RNA polymerase II transcription regulator 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 
located_in chromatin ISA
Inferred from Sequence Alignment
more info
  
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in endoplasmic reticulum membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in endoplasmic reticulum membrane NAS
Non-traceable Author Statement
more info
 PubMed 
located_in endoplasmic reticulum membrane TAS
Traceable Author Statement
more info
 PubMed 
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 
located_in nucleus TAS
Traceable Author Statement
more info
 PubMed 
part_of protein-DNA complex IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
cyclic AMP-dependent transcription factor ATF-6 beta
Names
Creb-related protein
cAMP response element-binding protein-related protein
cAMP-dependent transcription factor ATF-6 beta
cAMP-responsive element-binding protein-like 1
protein G13

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.

Genomic

  1. NG_033940.1 RefSeqGene

    Range
    4995..17977
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001136153.2 → NP_001129625.1  cyclic AMP-dependent transcription factor ATF-6 beta isoform b

    See identical proteins and their annotated locations for NP_001129625.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site at the 3' end of exon 1 compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is 3 aa shorter compared to isoform a.
    Source sequence(s)
    AL662884, U31903, X98054
    Consensus CDS
    CCDS47408.1
    UniProtKB/TrEMBL
    A0A1U9X796, A0A1U9X799
    Related
    ENSP00000364347.4, ENST00000375201.8
    Conserved Domains (2) summary
    cd14700
    Location:325 → 376
    bZIP_ATF6; Basic leucine zipper (bZIP) domain of Activating Transcription Factor-6 (ATF-6) and similar proteins: a DNA-binding and dimerization domain
    pfam14362
    Location:301 → 411
    DUF4407; Domain of unknown function (DUF4407)

  2. NM_004381.5 → NP_004372.3  cyclic AMP-dependent transcription factor ATF-6 beta isoform a

    See identical proteins and their annotated locations for NP_004372.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
    Source sequence(s)
    AL662884, BC077075, X98054
    Consensus CDS
    CCDS4737.1
    UniProtKB/Swiss-Prot
    B0UYX6, Q13269, Q14343, Q14345, Q5SSW7, Q99635, Q99637, Q99941, Q9H3V9, Q9H3W1, Q9NPL0
    UniProtKB/TrEMBL
    Q6AZW6
    Related
    ENSP00000364349.3, ENST00000375203.8
    Conserved Domains (1) summary
    cd14700
    Location:328 → 379
    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_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    32115264..32128246 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_2

Genomic

  1. NT_113891.3 Reference GRCh38.p14 ALT_REF_LOCI_2

    Range
    3553597..3566577 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_3

Genomic

  1. NT_167245.2 Reference GRCh38.p14 ALT_REF_LOCI_3

    Range
    3356630..3369610 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_5

Genomic

  1. NT_167247.2 Reference GRCh38.p14 ALT_REF_LOCI_5

    Range
    3457284..3470266 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    31968456..31981438 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q99941.2 GenPept UniProtKB/Swiss-Prot:Q99941

Gene LinkOut

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