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NR1H4 nuclear receptor subfamily 1 group H member 4 [ Homo sapiens (human) ]

Gene ID: 9971, updated on 12-Jun-2018
Official Symbol
NR1H4provided by HGNC
Official Full Name
nuclear receptor subfamily 1 group H member 4provided by HGNC
Primary source
HGNC:HGNC:7967
See related
Ensembl:ENSG00000012504 MIM:603826; Vega:OTTHUMG00000170359
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
BAR; FXR; HRR1; HRR-1; PFIC5; RIP14
Summary
This gene encodes a ligand-activated transcription factor that shares structural features in common with nuclear hormone receptor family members. This protein functions as a receptor for bile acids, and when bound to bile acids, binds to DNA and regulates the expression of genes involved in bile acid synthesis and transport. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Feb 2016]
Expression
Biased expression in liver (RPKM 14.7), small intestine (RPKM 8.3) and 6 other tissues See more
Orthologs
See NR1H4 in Genome Data Viewer
Location:
12q23.1
Exon count:
14
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 12 NC_000012.12 (100473773..100563867)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (100867486..100957645)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene DEP domain containing 4 Neighboring gene SCY1 like pseudokinase 2 Neighboring gene solute carrier family 17 member 8 Neighboring gene growth arrest specific 2 like 3 Neighboring gene phosphatidylinositol glycan anchor biosynthesis class A pseudogene 1 Neighboring gene anoctamin 4 Neighboring gene sorting nexin 5 pseudogene 2

  • 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 Jun 15 11:32:44 2016

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Associated conditions

Description Tests
Cholestasis, progressive familial intrahepatic, 5
MedGen: C4310747 OMIM: 617049 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

Description
Genome-wide association study identifies a novel susceptibility locus at 12q23.1 for lung squamous cell carcinoma in han chinese.
NHGRI GWA Catalog

Protein interactions

Protein Gene Interaction Pubs
matrix gag Treatment of human PBMCs with HIV-1 MA upregulates the expression of MCP-1, ICAM-1, CD40, CD86 and CD36 and downregulates the expression of nuclear receptors FXR and PPARgamma PubMed

Go to the HIV-1, Human Interaction Database

  • Bile acid and bile salt metabolism, organism-specific biosystem (from REACTOME)
    Bile acid and bile salt metabolism, organism-specific biosystemIn a healthy adult human, about 500 mg of cholesterol is converted to bile salts daily. Newly synthesized bile salts are secreted into the bile and released into the small intestine where they emulsi...
  • Bile secretion, organism-specific biosystem (from KEGG)
    Bile secretion, organism-specific biosystemBile is a vital secretion, essential for digestion and absorption of fats and fat-soluble vitamins in the small intestine. Moreover, bile is an important route of elimination for excess cholesterol a...
  • Bile secretion, conserved biosystem (from KEGG)
    Bile secretion, conserved biosystemBile is a vital secretion, essential for digestion and absorption of fats and fat-soluble vitamins in the small intestine. Moreover, bile is an important route of elimination for excess cholesterol a...
  • Biological oxidations, organism-specific biosystem (from REACTOME)
    Biological oxidations, organism-specific biosystemAll organisms are constantly exposed to foreign chemicals every day. These can be man-made (drugs, industrial chemicals) or natural (alkaloids, toxins from plants and animals). Uptake is usually via ...
  • Cytochrome P450 - arranged by substrate type, organism-specific biosystem (from REACTOME)
    Cytochrome P450 - arranged by substrate type, organism-specific biosystemThe P450 isozyme system is the major phase 1 biotransforming system in man, accounting for more than 90% of drug biotransformations. This system has huge catalytic versatility and a broad substrate s...
  • Drug Induction of Bile Acid Pathway, organism-specific biosystem (from WikiPathways)
    Drug Induction of Bile Acid Pathway, organism-specific biosystem
    Drug Induction of Bile Acid Pathway
  • Endogenous sterols, organism-specific biosystem (from REACTOME)
    Endogenous sterols, organism-specific biosystemA number of CYPs take part in cholesterol biosynthesis and elimination, thus playing an important role in maintaining cholesterol homeostasis. Under normal physiological conditions, cholesterol intak...
  • Farnesoid X Receptor Pathway, organism-specific biosystem (from WikiPathways)
    Farnesoid X Receptor Pathway, organism-specific biosystemThe farnesoid X receptor (FXR, a.k.a. NR1H4) is a nuclear receptor that responds to levels of bile acids present in the body and regulates many processes related to bile acids synthesis and transport
  • Fatty acid, triacylglycerol, and ketone body metabolism, organism-specific biosystem (from REACTOME)
    Fatty acid, triacylglycerol, and ketone body metabolism, organism-specific biosystemThe reactions involved in the metabolism of fatty acids and of the triacylglycerols and ketone bodies derived from them form a closely interrelated, coordinately regulated module that plays a central...
  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • Generic Transcription Pathway, organism-specific biosystem (from REACTOME)
    Generic Transcription Pathway, organism-specific biosystemOVERVIEW OF TRANSCRIPTION REGULATION: Detailed studies of gene transcription regulation in a wide variety of eukaryotic systems has revealed the general principles and mechanisms by which cell- or t...
  • Metabolism, organism-specific biosystem (from REACTOME)
    Metabolism, organism-specific biosystemMetabolic processes in human cells generate energy through the oxidation of molecules consumed in the diet and mediate the synthesis of diverse essential molecules not taken in the diet as well as th...
  • Metabolism of lipids and lipoproteins, organism-specific biosystem (from REACTOME)
    Metabolism of lipids and lipoproteins, organism-specific biosystemLipids are hydrophobic but otherwise chemically diverse molecules that play a wide variety of roles in human biology. They include ketone bodies, fatty acids, triacylglycerols, phospholipids and sphi...
  • Nuclear Receptor transcription pathway, organism-specific biosystem (from REACTOME)
    Nuclear Receptor transcription pathway, organism-specific biosystemA classic example of bifunctional transcription factors is the family of Nuclear Receptor (NR) proteins. These are DNA-binding transcription factors that bind certain hormones, vitamins, and other s...
  • Nuclear Receptors in Lipid Metabolism and Toxicity, organism-specific biosystem (from WikiPathways)
    Nuclear Receptors in Lipid Metabolism and Toxicity, organism-specific biosystemNuclear receptors are transcription factors that are activated upon binding to its ligands. Initially, they had been classified as classic endocrine nuclear hormone receptors and orphan receptors. Ho...
  • PPARA activates gene expression, organism-specific biosystem (from REACTOME)
    PPARA activates gene expression, organism-specific biosystemThe set of genes regulated by PPAR-alpha is not fully known in humans, however many examples have been found in mice. Genes directly activated by PPAR-alpha contain peroxisome proliferator receptor e...
  • Phase 1 - Functionalization of compounds, organism-specific biosystem (from REACTOME)
    Phase 1 - Functionalization of compounds, organism-specific biosystemPhase 1 of metabolism is concerned with functionalization, that is the introduction or exposure of functional groups on the chemical structure of a compound. This provides a 'handle' for phase 2 conj...
  • RXR and RAR heterodimerization with other nuclear receptor, organism-specific biosystem (from Pathway Interaction Database)
    RXR and RAR heterodimerization with other nuclear receptor, organism-specific biosystem
    RXR and RAR heterodimerization with other nuclear receptor
  • Recycling of bile acids and salts, organism-specific biosystem (from REACTOME)
    Recycling of bile acids and salts, organism-specific biosystemOf the 20-40 grams of bile salts released daily by the liver, all but approximately 0.5 grams are reabsorbed from the intestine, returned to the liver, and re-used. This recycling involves a series o...
  • Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha), organism-specific biosystem (from REACTOME)
    Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha), organism-specific biosystemPeroxisome proliferator-activated receptor alpha (PPAR-alpha) is the major regulator of fatty acid oxidation in the liver. PPARalpha is also the target of fibrate drugs used to treat abnormal plasma ...
  • Synthesis of bile acids and bile salts, organism-specific biosystem (from REACTOME)
    Synthesis of bile acids and bile salts, organism-specific biosystemIn a healthy adult human, about 500 mg of cholesterol is converted to bile salts daily (Russell 2003). The major pathway for bile salt synthesis in the liver begins with the conversion of cholesterol...
  • Synthesis of bile acids and bile salts via 27-hydroxycholesterol, organism-specific biosystem (from REACTOME)
    Synthesis of bile acids and bile salts via 27-hydroxycholesterol, organism-specific biosystemIn the body, 27-hydroxycholesterol is synthesized in multiple tissues, exported to the liver, and converted there to bile acids and bile salts. This pathway is only a minor source of bile acids and b...
  • Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol, organism-specific biosystem (from REACTOME)
    Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol, organism-specific biosystemIn the liver, synthesis of bile acids and bile salts is initiated with the conversion of cholesterol to 7alpha-hydroxycholesterol and of 7alpha-hydroxycholesterol to 4-cholesten-7alpha-ol-3-one. The ...
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Clone Names

  • MGC163445

Gene Ontology Provided by GOA

Function Evidence Code Pubs
CONTRIBUTES_TO DNA-binding transcription factor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
DNA-binding transcription factor activity TAS
Traceable Author Statement
more info
PubMed 
RNA polymerase II distal enhancer sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
RNA polymerase II regulatory region 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 
RNA polymerase II transcription factor activity, sequence-specific DNA binding ISA
Inferred from Sequence Alignment
more info
 
RNA polymerase II transcription factor activity, sequence-specific DNA binding ISM
Inferred from Sequence Model
more info
PubMed 
RNA polymerase II transcription factor activity, sequence-specific DNA binding NAS
Non-traceable Author Statement
more info
PubMed 
bile acid binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
bile acid binding ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
bile acid binding TAS
Traceable Author Statement
more info
PubMed 
bile acid receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
bile acid receptor activity IDA
Inferred from Direct Assay
more info
PubMed 
bile acid receptor activity TAS
Traceable Author Statement
more info
PubMed 
chenodeoxycholic acid binding IDA
Inferred from Direct Assay
more info
PubMed 
lipid binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nuclear receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nuclear receptor activity IDA
Inferred from Direct Assay
more info
PubMed 
nuclear receptor activity ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
nuclear receptor binding TAS
Traceable Author Statement
more info
PubMed 
nuclear receptor transcription coactivator activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
retinoid X receptor binding IEA
Inferred from Electronic Annotation
more info
 
sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
steroid hormone receptor activity IEA
Inferred from Electronic Annotation
more info
 
thyroid hormone receptor activity IEA
Inferred from Electronic Annotation
more info
 
transcription coactivator activity TAS
Traceable Author Statement
more info
PubMed 
transcription corepressor activity TAS
Traceable Author Statement
more info
PubMed 
transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding IDA
Inferred from Direct Assay
more info
PubMed 
transcription factor activity, RNA polymerase II transcription factor binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
transcription factor activity, direct ligand regulated sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
transcription factor binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
transcription regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
transcriptional activator activity, RNA polymerase II proximal promoter sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
transcriptional activator activity, RNA polymerase II transcription factor binding IDA
Inferred from Direct Assay
more info
PubMed 
zinc ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
Notch signaling pathway IEA
Inferred from Electronic Annotation
more info
 
bile acid and bile salt transport TAS
Traceable Author Statement
more info
 
bile acid metabolic process IEA
Inferred from Electronic Annotation
more info
 
bile acid signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
bile acid signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
 
bile acid signaling pathway TAS
Traceable Author Statement
more info
PubMed 
cell differentiation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cell-cell junction assembly IEA
Inferred from Electronic Annotation
more info
 
cellular response to fatty acid IDA
Inferred from Direct Assay
more info
PubMed 
cellular response to lipopolysaccharide IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cellular response to lipopolysaccharide IEA
Inferred from Electronic Annotation
more info
 
cellular response to organonitrogen compound ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
cellular triglyceride homeostasis IDA
Inferred from Direct Assay
more info
PubMed 
cholesterol homeostasis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cholesterol homeostasis IEA
Inferred from Electronic Annotation
more info
 
defense response to bacterium IEA
Inferred from Electronic Annotation
more info
 
fatty acid homeostasis IEA
Inferred from Electronic Annotation
more info
 
glucose homeostasis IEA
Inferred from Electronic Annotation
more info
 
histone H3-R17 methylation IDA
Inferred from Direct Assay
more info
PubMed 
inflammatory response IEA
Inferred from Electronic Annotation
more info
 
innate immune response IEA
Inferred from Electronic Annotation
more info
 
interleukin-17 secretion IDA
Inferred from Direct Assay
more info
PubMed 
intracellular bile acid receptor signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
intracellular receptor signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
 
lipid homeostasis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
lipid metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
multicellular organism development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of I-kappaB kinase/NF-kappaB signaling IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of NF-kappaB transcription factor activity IEA
Inferred from Electronic Annotation
more info
 
negative regulation of apoptotic process IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of bile acid biosynthetic process IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of inflammatory response IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of inflammatory response IEA
Inferred from Electronic Annotation
more info
 
negative regulation of interferon-gamma secretion IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of interleukin-1 production IEA
Inferred from Electronic Annotation
more info
 
negative regulation of interleukin-2 production IEA
Inferred from Electronic Annotation
more info
 
negative regulation of interleukin-6 production IEA
Inferred from Electronic Annotation
more info
 
negative regulation of monocyte chemotactic protein-1 production IEA
Inferred from Electronic Annotation
more info
 
negative regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of transcription by RNA polymerase II ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
negative regulation of tumor necrosis factor secretion IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of tumor necrosis factor-mediated signaling pathway IEA
Inferred from Electronic Annotation
more info
 
nitrogen catabolite activation of transcription from RNA polymerase II promoter IC
Inferred by Curator
more info
PubMed 
positive regulation of adipose tissue development IEA
Inferred from Electronic Annotation
more info
 
positive regulation of ammonia assimilation cycle IEA
Inferred from Electronic Annotation
more info
 
positive regulation of glucose import in response to insulin stimulus IEA
Inferred from Electronic Annotation
more info
 
positive regulation of glutamate metabolic process ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
positive regulation of insulin receptor signaling pathway IEA
Inferred from Electronic Annotation
more info
 
positive regulation of insulin secretion involved in cellular response to glucose stimulus IEA
Inferred from Electronic Annotation
more info
 
positive regulation of phosphatidic acid biosynthetic process IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of bile acid biosynthetic process TAS
Traceable Author Statement
more info
PubMed 
regulation of cholesterol metabolic process TAS
Traceable Author Statement
more info
PubMed 
regulation of insulin secretion involved in cellular response to glucose stimulus IDA
Inferred from Direct Assay
more info
PubMed 
regulation of low-density lipoprotein particle clearance IDA
Inferred from Direct Assay
more info
PubMed 
regulation of urea metabolic process ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
response to lipid IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
signal transduction TAS
Traceable Author Statement
more info
PubMed 
steroid hormone mediated signaling pathway IEA
Inferred from Electronic Annotation
more info
 
toll-like receptor 4 signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
toll-like receptor 9 signaling pathway IEA
Inferred from Electronic Annotation
more info
 
transcription initiation from RNA polymerase II promoter TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
RNA polymerase II transcription factor complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nuclear euchromatin IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Preferred Names
bile acid receptor
Names
RXR-interacting protein 14
farnesoid X nuclear receptor
farnesoid X-activated receptor
farnesol receptor HRR-1
retinoid X receptor-interacting protein 14

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_029843.1 RefSeqGene

    Range
    5001..95095
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001206977.1NP_001193906.1  bile acid receptor isoform 1

    See identical proteins and their annotated locations for NP_001193906.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) contains an alternate exon in the 5' UTR compared to variant 1. Variants 1 and 6 encode the same isoform (1, also known as FXRalpha+).
    Source sequence(s)
    AF384555, BC035654, DA011411
    Consensus CDS
    CCDS55873.1
    UniProtKB/Swiss-Prot
    Q96RI1
    UniProtKB/TrEMBL
    F1DAL1
    Conserved Domains (2) summary
    cd06936
    Location:251471
    NR_LBD_Fxr; The ligand binding domain of Farnesoid X receptor:a member of the nuclear receptor superfamily of ligand-activated transcription factors
    cd06962
    Location:124211
    NR_DBD_FXR; DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers
  2. NM_001206978.1NP_001193907.1  bile acid receptor isoform 5

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks an in-frame exon compared to variant 1. This results in a shorter isoform (5) than isoform 1.
    Source sequence(s)
    BC035654, BC130573, BC144183, DA011411
    Consensus CDS
    CCDS55874.1
    UniProtKB/Swiss-Prot
    Q96RI1
    Related
    ENSP00000448978.1, OTTHUMP00000243786, ENST00000549996.5, OTTHUMT00000409137
    Conserved Domains (2) summary
    cd06936
    Location:200420
    NR_LBD_Fxr; The ligand binding domain of Farnesoid X receptor:a member of the nuclear receptor superfamily of ligand-activated transcription factors
    cl02596
    Location:127149
    NR_DBD_like; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers
  3. NM_001206979.1NP_001193908.1  bile acid receptor isoform 1

    See identical proteins and their annotated locations for NP_001193908.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes isoform 1 (also known as FXRalpha+). Variants 1 and 6 encode the same isoform (1).
    Source sequence(s)
    BC035654, BC130573, DA011411
    Consensus CDS
    CCDS55873.1
    UniProtKB/Swiss-Prot
    Q96RI1
    UniProtKB/TrEMBL
    F1DAL1
    Related
    ENSP00000376712.3, OTTHUMP00000243784, ENST00000392986.7, OTTHUMT00000409135
    Conserved Domains (2) summary
    cd06936
    Location:251471
    NR_LBD_Fxr; The ligand binding domain of Farnesoid X receptor:a member of the nuclear receptor superfamily of ligand-activated transcription factors
    cd06962
    Location:124211
    NR_DBD_FXR; DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers
  4. NM_001206992.1NP_001193921.1  bile acid receptor isoform 4

    See identical proteins and their annotated locations for NP_001193921.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs 5' UTR, lacks a portion of the 5' coding region, and uses an alternate in-frame splice site, compared to variant 1. It represents use of an alternate promoter and initiates translation at an alternate start codon. The encoded isoform (4, also known as FXRbeta-) has a distinct N-terminus and is longer than isoform 1.
    Source sequence(s)
    AF478445, BC035654
    Consensus CDS
    CCDS55875.1
    UniProtKB/Swiss-Prot
    Q96RI1
    Related
    ENSP00000188403.7, OTTHUMP00000243790, ENST00000188403.7, OTTHUMT00000409141
    Conserved Domains (2) summary
    cd06936
    Location:257477
    NR_LBD_Fxr; The ligand binding domain of Farnesoid X receptor:a member of the nuclear receptor superfamily of ligand-activated transcription factors
    cd06962
    Location:134217
    NR_DBD_FXR; DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers
  5. NM_001206993.1NP_001193922.1  bile acid receptor isoform 3

    See identical proteins and their annotated locations for NP_001193922.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs 5' UTR and lacks a portion of the 5' coding region compared to variant 1. It represents use of an alternate promoter and initiates translation at an alternate start codon. The encoded isoform (3, also known as FXRbeta+) has a distinct, longer N-terminus, compared to isoform 1.
    Source sequence(s)
    AF478446, BC035654
    Consensus CDS
    CCDS55876.1
    UniProtKB/Swiss-Prot
    Q96RI1
    Related
    ENSP00000447149.1, OTTHUMP00000243789, ENST00000551379.5, OTTHUMT00000409140
    Conserved Domains (2) summary
    cd06936
    Location:261481
    NR_LBD_Fxr; The ligand binding domain of Farnesoid X receptor:a member of the nuclear receptor superfamily of ligand-activated transcription factors
    cd06962
    Location:134221
    NR_DBD_FXR; DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers
  6. NM_005123.3NP_005114.1  bile acid receptor isoform 2

    See identical proteins and their annotated locations for NP_005114.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site compared to variant 1. This results in a shorter isoform (2, also known as FXRalpha-) compared to isoform 1.
    Source sequence(s)
    BC035654, DA011411, U68233
    Consensus CDS
    CCDS9078.1
    UniProtKB/Swiss-Prot
    Q96RI1
    UniProtKB/TrEMBL
    B6ZGS9
    Related
    ENSP00000448506.1, OTTHUMP00000243579, ENST00000548884.5, OTTHUMT00000408677
    Conserved Domains (2) summary
    cd06936
    Location:247467
    NR_LBD_Fxr; The ligand binding domain of Farnesoid X receptor:a member of the nuclear receptor superfamily of ligand-activated transcription factors
    cd06962
    Location:124207
    NR_DBD_FXR; DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers

RNA

  1. NR_135146.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) uses an alternate internal splice site compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK312959, BC035654, BC144187, DA016827

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p12 Primary Assembly

    Range
    100473773..100563867
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011539040.2XP_011537342.1  bile acid receptor isoform X1

    See identical proteins and their annotated locations for XP_011537342.1

    UniProtKB/Swiss-Prot
    Q96RI1
    UniProtKB/TrEMBL
    F1DAL1
    Conserved Domains (2) summary
    cd06936
    Location:251471
    NR_LBD_Fxr; The ligand binding domain of Farnesoid X receptor:a member of the nuclear receptor superfamily of ligand-activated transcription factors
    cd06962
    Location:124211
    NR_DBD_FXR; DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers
  2. XM_011539041.2XP_011537343.1  bile acid receptor isoform X2

    Conserved Domains (2) summary
    cd06936
    Location:210430
    NR_LBD_Fxr; The ligand binding domain of Farnesoid X receptor:a member of the nuclear receptor superfamily of ligand-activated transcription factors
    cl02596
    Location:137159
    NR_DBD_like; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers
  3. XM_006719719.2XP_006719782.1  bile acid receptor isoform X3

    Conserved Domains (1) summary
    cl02596
    Location:134221
    NR_DBD_like; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers
  4. XM_011539042.1XP_011537344.1  bile acid receptor isoform X4

    Conserved Domains (1) summary
    cl02596
    Location:134217
    NR_DBD_like; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers
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