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

    Gene ID: 1388, updated on 10-Dec-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: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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