Human Gene XBP1 (ENST00000344347.6_13) from GENCODE V47lift37
  Description: X-box binding protein 1, transcript variant 2 (from RefSeq NM_001079539.2)
Gencode Transcript: ENST00000344347.6_13
Gencode Gene: ENSG00000100219.17_19
Transcript (Including UTRs)
   Position: hg19 chr22:29,190,548-29,196,557 Size: 6,010 Total Exon Count: 6 Strand: -
Coding Region
   Position: hg19 chr22:29,191,163-29,196,512 Size: 5,350 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr22:29,190,548-29,196,557)mRNA (may differ from genome)Protein (376 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCHuman Cortex Gene ExpressionMalacardsMGIOMIMPubMed
ReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: XBP1_HUMAN
DESCRIPTION: RecName: Full=X-box-binding protein 1; Short=XBP-1; AltName: Full=Tax-responsive element-binding protein 5;
FUNCTION: Transcription factor essential for hepatocyte growth, the differentiation of plasma cells, the immunoglobulin secretion, and the unfolded protein response (UPR). Acts during endoplasmic reticulum stress (ER) by activating unfolded protein response (UPR) target genes via direct binding to the UPR element (UPRE). Binds DNA preferably to the CRE-like element 5'- GATGACGTG[TG]N(3)[AT]T-3', and also to some TPA response elements (TRE). Binds to the HLA DR-alpha promoter. Binds to the Tax- responsive element (TRE) of HTLV-I.
SUBCELLULAR LOCATION: Nucleus.
INDUCTION: Up-regulated by ATF6 via direct binding to the ERSE in response to endoplasmic reticulum stress.
DISEASE: Genetic variations in XBP1 could be associated with susceptibility to major affective disorder type 7 (MAFD7) [MIM:612371]. Major affective disorders represent a class of mental disorders characterized by a disturbance in mood as their predominant feature.
SIMILARITY: Belongs to the bZIP family.
SIMILARITY: Contains 1 bZIP (basic-leucine zipper) domain.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: XBP1
Diseases sorted by gene-association score: major affective disorder-7* (569), bipolar disorder (11), fatty liver disease (9), metaphyseal chondrodysplasia, schmid type (5), breast cancer (5), corneal dystrophy, subepithelial mucinous (4), obesity (2), amyotrophic lateral sclerosis 1 (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 456.20 RPKM in Pancreas
Total median expression: 3426.07 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -21.5045-0.478 Picture PostScript Text
3' UTR -154.70615-0.252 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR004827 - bZIP

Pfam Domains:
PF00170 - bZIP transcription factor
PF03131 - bZIP Maf transcription factor
PF07716 - Basic region leucine zipper

SCOP Domains:
47454 - A DNA-binding domain in eukaryotic transcription factors
57959 - Leucine zipper domain

ModBase Predicted Comparative 3D Structure on P17861
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologGenome BrowserNo ortholog
Gene DetailsGene Details Gene DetailsGene Details 
Gene SorterGene Sorter Gene SorterGene Sorter 
 RGD  WormBase 
    Protein Sequence 
    Alignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0001047 core promoter binding
GO:0001085 RNA polymerase II transcription factor binding
GO:0001158 enhancer sequence-specific DNA binding
GO:0002020 protease binding
GO:0003677 DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0005515 protein binding
GO:0019901 protein kinase binding
GO:0030331 estrogen receptor binding
GO:0031490 chromatin DNA binding
GO:0031625 ubiquitin protein ligase binding
GO:0042803 protein homodimerization activity
GO:0043565 sequence-specific DNA binding
GO:0044212 transcription regulatory region DNA binding
GO:0046982 protein heterodimerization activity

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0001525 angiogenesis
GO:0001889 liver development
GO:0001934 positive regulation of protein phosphorylation
GO:0001935 endothelial cell proliferation
GO:0002070 epithelial cell maturation
GO:0002639 positive regulation of immunoglobulin production
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006366 transcription from RNA polymerase II promoter
GO:0006511 ubiquitin-dependent protein catabolic process
GO:0006629 lipid metabolic process
GO:0006633 fatty acid biosynthetic process
GO:0006914 autophagy
GO:0006915 apoptotic process
GO:0006955 immune response
GO:0006986 response to unfolded protein
GO:0006990 positive regulation of transcription from RNA polymerase II promoter involved in unfolded protein response
GO:0006996 organelle organization
GO:0007275 multicellular organism development
GO:0007517 muscle organ development
GO:0008284 positive regulation of cell proliferation
GO:0010506 regulation of autophagy
GO:0010508 positive regulation of autophagy
GO:0010832 negative regulation of myotube differentiation
GO:0014065 phosphatidylinositol 3-kinase signaling
GO:0015031 protein transport
GO:0016049 cell growth
GO:0030154 cell differentiation
GO:0030335 positive regulation of cell migration
GO:0030512 negative regulation of transforming growth factor beta receptor signaling pathway
GO:0030968 endoplasmic reticulum unfolded protein response
GO:0031017 exocrine pancreas development
GO:0031062 positive regulation of histone methylation
GO:0031647 regulation of protein stability
GO:0031648 protein destabilization
GO:0031670 cellular response to nutrient
GO:0032008 positive regulation of TOR signaling
GO:0032869 cellular response to insulin stimulus
GO:0034599 cellular response to oxidative stress
GO:0034976 response to endoplasmic reticulum stress
GO:0035356 cellular triglyceride homeostasis
GO:0035470 positive regulation of vascular wound healing
GO:0035924 cellular response to vascular endothelial growth factor stimulus
GO:0036498 IRE1-mediated unfolded protein response
GO:0036500 ATF6-mediated unfolded protein response
GO:0042149 cellular response to glucose starvation
GO:0042307 positive regulation of protein import into nucleus
GO:0042593 glucose homeostasis
GO:0042632 cholesterol homeostasis
GO:0043066 negative regulation of apoptotic process
GO:0045348 positive regulation of MHC class II biosynthetic process
GO:0045579 positive regulation of B cell differentiation
GO:0045582 positive regulation of T cell differentiation
GO:0045600 positive regulation of fat cell differentiation
GO:0045766 positive regulation of angiogenesis
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0048010 vascular endothelial growth factor receptor signaling pathway
GO:0048666 neuron development
GO:0051024 positive regulation of immunoglobulin secretion
GO:0051897 positive regulation of protein kinase B signaling
GO:0055089 fatty acid homeostasis
GO:0055092 sterol homeostasis
GO:0060394 negative regulation of pathway-restricted SMAD protein phosphorylation
GO:0060612 adipose tissue development
GO:0060691 epithelial cell maturation involved in salivary gland development
GO:0070059 intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress
GO:0070373 negative regulation of ERK1 and ERK2 cascade
GO:0071222 cellular response to lipopolysaccharide
GO:0071230 cellular response to amino acid stimulus
GO:0071332 cellular response to fructose stimulus
GO:0071333 cellular response to glucose stimulus
GO:0071353 cellular response to interleukin-4
GO:0071375 cellular response to peptide hormone stimulus
GO:0071498 cellular response to fluid shear stress
GO:0071499 cellular response to laminar fluid shear stress
GO:1900100 positive regulation of plasma cell differentiation
GO:1900102 negative regulation of endoplasmic reticulum unfolded protein response
GO:1900103 positive regulation of endoplasmic reticulum unfolded protein response
GO:1900413 positive regulation of phospholipid biosynthetic process by positive regulation of transcription from RNA polymerase II promoter
GO:1901800 positive regulation of proteasomal protein catabolic process
GO:1901985 positive regulation of protein acetylation
GO:1902236 negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway
GO:1903071 positive regulation of ER-associated ubiquitin-dependent protein catabolic process
GO:1903489 positive regulation of lactation
GO:1904707 positive regulation of vascular smooth muscle cell proliferation
GO:1904754 positive regulation of vascular associated smooth muscle cell migration
GO:1990418 response to insulin-like growth factor stimulus
GO:1990440 positive regulation of transcription from RNA polymerase II promoter in response to endoplasmic reticulum stress
GO:1990830 cellular response to leukemia inhibitory factor
GO:2000347 positive regulation of hepatocyte proliferation
GO:2000353 positive regulation of endothelial cell apoptotic process
GO:2000778 positive regulation of interleukin-6 secretion

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0005829 cytosol
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030176 integral component of endoplasmic reticulum membrane


-  Descriptions from all associated GenBank mRNAs
  M31627 - Human X box binding protein-1 (XBP-1) mRNA, complete cds.
BC000938 - Homo sapiens X-box binding protein 1, mRNA (cDNA clone MGC:5436 IMAGE:3449394), complete cds.
AK093842 - Homo sapiens cDNA FLJ36523 fis, clone TRACH2002664.
AX748333 - Sequence 1858 from Patent EP1308459.
BC012841 - Homo sapiens X-box binding protein 1, mRNA (cDNA clone MGC:8980 IMAGE:3856898), complete cds.
BC015709 - Homo sapiens, clone IMAGE:3911945, mRNA, partial cds.
AB076383 - Homo sapiens XBP1 mRNA for X box-binding protein unspliced form, complete cds.
AB076384 - Homo sapiens XBP1 mRNA for X box-binding protein spliced form, complete cds.
JD236970 - Sequence 217994 from Patent EP1572962.
JD078698 - Sequence 59722 from Patent EP1572962.
JD259829 - Sequence 240853 from Patent EP1572962.
JD045765 - Sequence 26789 from Patent EP1572962.
JD300576 - Sequence 281600 from Patent EP1572962.
AK292188 - Homo sapiens cDNA FLJ77362 complete cds, highly similar to Homo sapiens X-box binding protein 1 (XBP1), mRNA.
JD469546 - Sequence 450570 from Patent EP1572962.
HV325275 - JP 2011505850-A/41: SM-PROTEIN BASED SECRETION ENGINEERING.
JD320486 - Sequence 301510 from Patent EP1572962.
JD080770 - Sequence 61794 from Patent EP1572962.
JD334531 - Sequence 315555 from Patent EP1572962.
JD022866 - Sequence 3890 from Patent EP1572962.
JD032189 - Sequence 13213 from Patent EP1572962.
JD160424 - Sequence 141448 from Patent EP1572962.
JD073668 - Sequence 54692 from Patent EP1572962.
JD304977 - Sequence 286001 from Patent EP1572962.
JD090587 - Sequence 71611 from Patent EP1572962.
CR456611 - Homo sapiens XBP1 full length open reading frame (ORF) cDNA clone (cDNA clone C22ORF:pGEM.XBP1.V2).
JD349767 - Sequence 330791 from Patent EP1572962.
CU013207 - Homo sapiens XBP1, mRNA (cDNA clone IMAGE:100000560), complete cds, with stop codon, in Gateway system.
AK313761 - Homo sapiens cDNA, FLJ94362.
DQ890989 - Synthetic construct clone IMAGE:100003619; FLH168296.01X; RZPDo839E1292D X-box binding protein 1 (XBP1) gene, encodes complete protein.
KJ904588 - Synthetic construct Homo sapiens clone ccsbBroadEn_13982 XBP1 gene, encodes complete protein.
DQ894165 - Synthetic construct Homo sapiens clone IMAGE:100008625; FLH168292.01L; RZPDo839E1291D X-box binding protein 1 (XBP1) gene, encodes complete protein.
AB463352 - Synthetic construct DNA, clone: pF1KB9553, Homo sapiens XBP1 gene for X-box binding protein 1, without stop codon, in Flexi system.
AM393640 - Synthetic construct Homo sapiens clone IMAGE:100002604 for hypothetical protein (XBP1 gene).
CU013495 - Homo sapiens XBP1, mRNA (cDNA clone IMAGE:100000464), complete cds, without stop codon, in Gateway system.
CU674466 - Synthetic construct Homo sapiens gateway clone IMAGE:100018649 5' read XBP1 mRNA.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein P17861 (Reactome details) participates in the following event(s):

R-HSA-381070 IRE1alpha activates chaperones
R-HSA-381183 ATF6 (ATF6-alpha) activates chaperone genes
R-HSA-381119 Unfolded Protein Response (UPR)
R-HSA-381033 ATF6 (ATF6-alpha) activates chaperones
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000344347.1, ENST00000344347.2, ENST00000344347.3, ENST00000344347.4, ENST00000344347.5, NM_001079539, P17861, Q8WYK6, Q969P1, Q96BD7, TREB5 , uc317wxl.1, uc317wxl.2, XBP1 , XBP1_HUMAN, XBP2
UCSC ID: ENST00000344347.6_13
RefSeq Accession: NM_001079539.2
Protein: P17861 (aka XBP1_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.