Xbp1 X-box binding protein 1 [ Rattus norvegicus (Norway rat) ]

Gene ID: 289754, updated on 18-Sep-2024

Summary

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Official Symbol: Xbp1provided by RGD
Official Full Name: X-box binding protein 1provided by RGD
Primary source: RGD:1303073
See related: EnsemblRapid:ENSRNOG00000010298 AllianceGenome:RGD:1303073
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: HTF
Summary: Enables DNA-binding transcription factor activity and sequence-specific DNA binding activity. Involved in several processes, including endoplasmic reticulum unfolded protein response; negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway; and serotonin secretion, neurotransmission. Located in cytoplasm and nucleus. Biomarker of borna disease. Orthologous to human XBP1 (X-box binding protein 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Liver (RPKM 597.1), Lung (RPKM 544.4) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

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See Xbp1 in Genome Data Viewer

Location:: 14q21

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	14	NC_086032.1 (84604623..84609707)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	14	NC_051349.1 (80390629..80395713)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	14	NC_005113.4 (85753736..85758820)

Chromosome 14 - NC_086032.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Exosomal miR-205-5p derived from periodontal ligament stem cells attenuates the inflammation of chronic periodontitis via targeting XBP1.
Title: Exosomal miR-205-5p derived from periodontal ligament stem cells attenuates the inflammation of chronic periodontitis via targeting XBP1.
Proteomic analysis reveals that Xbp1s promotes hypoxic pulmonary hypertension through the p-JNK MAPK pathway.
Title: Proteomic analysis reveals that Xbp1s promotes hypoxic pulmonary hypertension through the p-JNK MAPK pathway.
Downregulated XBP-1 Rescues Cerebral Ischemia/Reperfusion Injury-Induced Pyroptosis via the NLRP3/Caspase-1/GSDMD Axis.
Title: Downregulated XBP-1 Rescues Cerebral Ischemia/Reperfusion Injury-Induced Pyroptosis via the NLRP3/Caspase-1/GSDMD Axis.
Effect of Denervation on XBP1 in Skeletal Muscle and the Neuromuscular Junction.
Title: Effect of Denervation on XBP1 in Skeletal Muscle and the Neuromuscular Junction.
Xbp1s-Ddit3 promotes MCT-induced pulmonary hypertension.
Title: Xbp1s-Ddit3 promotes MCT-induced pulmonary hypertension.
Porphyromonas gingivalis lipopolysaccharide (Pg-LPS) influences adipocytes injuries through triggering XBP1 and activating mitochondria-mediated apoptosis.
Title: Porphyromonas gingivalis lipopolysaccharide (Pg-LPS) influences adipocytes injuries through triggering XBP1 and activating mitochondria-mediated apoptosis.
Astaxanthin mediated regulation of VEGF through HIF1alpha and XBP1 signaling pathway: An insight from ARPE-19 cell and streptozotocin mediated diabetic rat model.
Title: Astaxanthin mediated regulation of VEGF through HIF1α and XBP1 signaling pathway: An insight from ARPE-19 cell and streptozotocin mediated diabetic rat model.
XBP1s repression regulates Kupffer cell polarization leading to immune suppressive effects protecting liver allograft in rats.
Title: XBP1s repression regulates Kupffer cell polarization leading to immune suppressive effects protecting liver allograft in rats.
Bile acid toxicity in Paneth cells contributes to gut dysbiosis induced by high-fat feeding.
Title: Bile acid toxicity in Paneth cells contributes to gut dysbiosis induced by high-fat feeding.
Palmitate induces cardiomyocyte death via inositol requiring enzyme-1 (IRE1)-mediated signaling independent of X-box binding protein 1 (XBP1).
Title: Palmitate induces cardiomyocyte death via inositol requiring enzyme-1 (IRE1)-mediated signaling independent of X-box binding protein 1 (XBP1).

Submit: New GeneRIF Correction See all GeneRIFs (35)

General gene information

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Markers

RH130248 (e-PCR)
- UniSTS:213535

Xbp1 (e-PCR), detects polymorphism
- UniSTS:525968

Xbp1 (e-PCR), detects polymorphism
- UniSTS:531428

D14Wox29 (e-PCR)
- UniSTS:518909

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA binding	TAS Traceable Author Statement more info	PubMed
enables DNA-binding transcription factor activity	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription factor activity	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription factor activity	TAS Traceable Author Statement 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	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables chromatin DNA binding	ISO Inferred from Sequence Orthology more info
enables chromatin DNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables cis-regulatory region sequence-specific DNA binding	IEA Inferred from Electronic Annotation more info
enables cis-regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables cis-regulatory region sequence-specific DNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables histone deacetylase binding	ISO Inferred from Sequence Orthology more info
enables identical protein binding	IEA Inferred from Electronic Annotation more info
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables phosphatidylinositol 3-kinase regulatory subunit binding	ISO Inferred from Sequence Orthology more info
enables protease binding	ISO Inferred from Sequence Orthology more info
enables protein heterodimerization activity	IEA Inferred from Electronic Annotation more info
enables protein heterodimerization activity	ISO Inferred from Sequence Orthology more info
enables protein heterodimerization activity	ISS Inferred from Sequence or Structural Similarity more info
enables protein kinase binding	ISO Inferred from Sequence Orthology more info
enables sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables sequence-specific double-stranded DNA binding	ISO Inferred from Sequence Orthology more info
enables transcription cis-regulatory region binding	ISO Inferred from Sequence Orthology more info
enables ubiquitin protein ligase binding	ISO Inferred from Sequence Orthology more info
enables ubiquitin-like protein ligase binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in adipose tissue development	ISO Inferred from Sequence Orthology more info
involved_in adipose tissue development	ISS Inferred from Sequence or Structural Similarity more info
involved_in angiogenesis	ISO Inferred from Sequence Orthology more info
involved_in angiogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in cellular response to amino acid stimulus	ISO Inferred from Sequence Orthology more info
involved_in cellular response to amino acid stimulus	ISS Inferred from Sequence or Structural Similarity more info
involved_in cellular response to antibiotic	IEP Inferred from Expression Pattern more info	PubMed
involved_in cellular response to fluid shear stress	ISO Inferred from Sequence Orthology more info
involved_in cellular response to fluid shear stress	ISS Inferred from Sequence or Structural Similarity more info
involved_in cellular response to fructose stimulus	ISO Inferred from Sequence Orthology more info
involved_in cellular response to glucose starvation	ISO Inferred from Sequence Orthology more info
involved_in cellular response to glucose starvation	ISS Inferred from Sequence or Structural Similarity more info
involved_in cellular response to glucose stimulus	ISO Inferred from Sequence Orthology more info
involved_in cellular response to insulin stimulus	ISO Inferred from Sequence Orthology more info
involved_in cellular response to interleukin-4	ISO Inferred from Sequence Orthology more info
involved_in cellular response to interleukin-4	ISS Inferred from Sequence or Structural Similarity more info
involved_in cellular response to laminar fluid shear stress	ISO Inferred from Sequence Orthology more info
involved_in cellular response to laminar fluid shear stress	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within cellular response to leukemia inhibitory factor	ISO Inferred from Sequence Orthology more info
involved_in cellular response to lipopolysaccharide	IEA Inferred from Electronic Annotation more info
involved_in cellular response to lipopolysaccharide	ISO Inferred from Sequence Orthology more info
involved_in cellular response to lipopolysaccharide	ISS Inferred from Sequence or Structural Similarity more info
involved_in cellular response to nutrient	ISO Inferred from Sequence Orthology more info
involved_in cellular response to oxidative stress	ISO Inferred from Sequence Orthology more info
involved_in cellular response to peptide hormone stimulus	ISO Inferred from Sequence Orthology more info
involved_in cellular response to peptide hormone stimulus	ISS Inferred from Sequence or Structural Similarity more info
involved_in cellular response to vascular endothelial growth factor stimulus	ISO Inferred from Sequence Orthology more info
involved_in cholesterol homeostasis	ISO Inferred from Sequence Orthology more info
involved_in cholesterol homeostasis	ISS Inferred from Sequence or Structural Similarity more info
involved_in endoplasmic reticulum unfolded protein response	IDA Inferred from Direct Assay more info	PubMed
involved_in endoplasmic reticulum unfolded protein response	IEA Inferred from Electronic Annotation more info
involved_in endoplasmic reticulum unfolded protein response	ISO Inferred from Sequence Orthology more info
involved_in endoplasmic reticulum unfolded protein response	ISS Inferred from Sequence or Structural Similarity more info
involved_in endothelial cell proliferation	ISO Inferred from Sequence Orthology more info
involved_in endothelial cell proliferation	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within epithelial cell maturation involved in salivary gland development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within exocrine pancreas development	ISO Inferred from Sequence Orthology more info
involved_in fatty acid homeostasis	ISO Inferred from Sequence Orthology more info
involved_in fatty acid homeostasis	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within glandular epithelial cell maturation	ISO Inferred from Sequence Orthology more info
involved_in intracellular triglyceride homeostasis	ISO Inferred from Sequence Orthology more info
involved_in intracellular triglyceride homeostasis	ISS Inferred from Sequence or Structural Similarity more info
involved_in intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress	ISO Inferred from Sequence Orthology more info
involved_in liver development	ISO Inferred from Sequence Orthology more info
involved_in liver development	ISS Inferred from Sequence or Structural Similarity more info
involved_in muscle organ development	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of ERK1 and ERK2 cascade	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of SMAD protein signal transduction	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of apoptotic process	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of apoptotic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of endoplasmic reticulum unfolded protein response	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of myotube differentiation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transforming growth factor beta receptor signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in neuron development	ISO Inferred from Sequence Orthology more info
involved_in phosphatidylinositol 3-kinase/protein kinase B signal transduction	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of B cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of B cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of MHC class II biosynthetic process	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of MHC class II biosynthetic process	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of MHC class II biosynthetic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of T cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of T cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of T cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of TOR signaling	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of angiogenesis	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of autophagy	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cell migration	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of cell migration	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cell population proliferation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of cell population proliferation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of endoplasmic reticulum unfolded protein response	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of endoplasmic reticulum unfolded protein response	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of endothelial cell apoptotic process	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of fat cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of fat cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of hepatocyte proliferation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of hepatocyte proliferation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of immunoglobulin production	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of immunoglobulin production	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of immunoglobulin production	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of interleukin-6 production	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of lactation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of lactation	ISS Inferred from Sequence or Structural Similarity more info
NOT involved_in positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of plasma cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of plasma cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of plasma cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of protein acetylation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of protein import into nucleus	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of protein phosphorylation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
NOT involved_in positive regulation of vascular associated smooth muscle cell migration	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of vascular associated smooth muscle cell migration	ISO Inferred from Sequence Orthology more info
NOT involved_in positive regulation of vascular associated smooth muscle cell proliferation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of vascular associated smooth muscle cell proliferation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of vascular wound healing	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of vascular wound healing	ISO Inferred from Sequence Orthology more info
involved_in protein destabilization	ISO Inferred from Sequence Orthology more info
involved_in protein destabilization	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in regulation of DNA-templated transcription	TAS Traceable Author Statement more info	PubMed
involved_in regulation of autophagy	ISO Inferred from Sequence Orthology more info
involved_in regulation of autophagy	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of cell growth	ISO Inferred from Sequence Orthology more info
involved_in regulation of protein stability	ISO Inferred from Sequence Orthology more info
involved_in regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in response to electrical stimulus	IDA Inferred from Direct Assay more info	PubMed
involved_in response to endoplasmic reticulum stress	ISO Inferred from Sequence Orthology more info
involved_in response to insulin-like growth factor stimulus	ISO Inferred from Sequence Orthology more info
involved_in response to insulin-like growth factor stimulus	ISS Inferred from Sequence or Structural Similarity more info
involved_in response to nutrient	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to xenobiotic stimulus	IDA Inferred from Direct Assay more info	PubMed
involved_in serotonin secretion, neurotransmission	IDA Inferred from Direct Assay more info	PubMed
involved_in sterol homeostasis	ISO Inferred from Sequence Orthology more info
involved_in sterol homeostasis	ISS Inferred from Sequence or Structural Similarity more info
involved_in transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in ubiquitin-dependent protein catabolic process	ISO Inferred from Sequence Orthology more info
involved_in ubiquitin-dependent protein catabolic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in vascular endothelial growth factor receptor signaling pathway	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of RNA polymerase II transcription regulator complex	IEA Inferred from Electronic Annotation more info
part_of RNA polymerase II transcription regulator complex	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in endoplasmic reticulum	IEA Inferred from Electronic Annotation more info
located_in endoplasmic reticulum	ISO Inferred from Sequence Orthology more info
located_in endoplasmic reticulum	ISS Inferred from Sequence or Structural Similarity more info
located_in endoplasmic reticulum membrane	IEA Inferred from Electronic Annotation more info
located_in endoplasmic reticulum membrane	ISO Inferred from Sequence Orthology more info
located_in membrane	IEA Inferred from Electronic Annotation more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
is_active_in nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in presynapse	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: X-box-binding protein 1

Names: hepatocarcinogenesis-related transcription factor

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.

mRNA and Protein(s)

NM_001004210.2 → NP_001004210.1 X-box-binding protein 1 isoform XBP1(U)

See identical proteins and their annotated locations for NP_001004210.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript but encodes the shorter isoform, XBP1(U).

Source sequence(s)

BC079450, BU670819

UniProtKB/Swiss-Prot

Q9R1S4

UniProtKB/TrEMBL

A6IKL9

Conserved Domains (1) summary

cd14691
Location:63 → 119

bZIP_XBP1; Basic leucine zipper (bZIP) domain of X-box binding protein 1 (XBP1) and similar proteins: a DNA-binding and dimerization domain
NM_001271731.1 → NP_001258660.1 X-box-binding protein 1 isoform XBP1(S)

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks a 26 nt segment in the CDS compared to variant 1, that causes a frameshift. The resulting isoform, XBP1(S), has the same N-terminus, but a longer and distinct C-terminus compared to isoform XBP1(U). Isoform XBP1(S) functions as a transcription factor.

Source sequence(s)

BC079450, BU670819, CB691171

UniProtKB/TrEMBL

A0A140TAA7

Related

ENSRNOP00000014044.7, ENSRNOT00000014044.8

Conserved Domains (1) summary

cd14691
Location:63 → 119

bZIP_XBP1; Basic leucine zipper (bZIP) domain of X-box binding protein 1 (XBP1) and similar proteins: a DNA-binding and dimerization domain