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Q60641 (NR1H4_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 138. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Bile acid receptor
Alternative name(s):
Farnesoid X-activated receptor
Farnesol receptor HRR-1
Nuclear receptor subfamily 1 group H member 4
Retinoid X receptor-interacting protein 14
Short name=RXR-interacting protein 14
Gene names
Name:Nr1h4
Synonyms:Bar, Fxr, Rip14
OrganismMus musculus (Mouse) [Reference proteome]
Taxonomic identifier10090 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus

Protein attributes

Sequence length488 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Ligand-activated transcription factor. Receptor for bile acids such as chenodeoxycholic acid, lithocholic acid and deoxycholic acid. Represses the transcription of the cholesterol 7-alpha-hydroxylase gene (CYP7A1) and activates the intestinal bile acid-binding protein (IBABP). Activates the transcription of bile salt export pump ABCB11 by directly recruiting histone methyltransferase CARM1 within its gene locus By similarity.

Subunit structure

Interacts with CARM1 and SMARD1. After activation by agonist binding, interacts with a coactivator, NCOA1 or NCOA2 By similarity Heterodimer of NR1H4 and RXR. Ref.1

Subcellular location

Nucleus Probable.

Tissue specificity

Expressed specifically in liver and kidney.

Post-translational modification

Methylation may increase transactivation of target genes By similarity.

Sequence similarities

Belongs to the nuclear hormone receptor family. NR1 subfamily.

Contains 1 nuclear receptor DNA-binding domain.

Ontologies

Keywords
   Biological processTranscription
Transcription regulation
   Cellular componentNucleus
   Coding sequence diversityAlternative splicing
   DomainZinc-finger
   LigandDNA-binding
Metal-binding
Zinc
   Molecular functionActivator
Receptor
Repressor
   PTMMethylation
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processbile acid metabolic process

Inferred from mutant phenotype PubMed 12917447. Source: MGI

cellular response to acid

Inferred from mutant phenotype PubMed 21757002. Source: BHF-UCL

cellular response to organonitrogen compound

Inferred from mutant phenotype PubMed 21757002. Source: BHF-UCL

digestive tract development

Inferred from electronic annotation. Source: Ensembl

intracellular bile acid receptor signaling pathway

Inferred from electronic annotation. Source: Ensembl

intracellular receptor signaling pathway

Inferred from mutant phenotype PubMed 21757002. Source: BHF-UCL

negative regulation of bile acid biosynthetic process

Inferred from electronic annotation. Source: Ensembl

negative regulation of transcription from RNA polymerase II promoter

Inferred from mutant phenotype PubMed 21757002. Source: BHF-UCL

nitrogen catabolite activation of transcription from RNA polymerase II promoter

Inferred by curator PubMed 21757002. Source: BHF-UCL

positive regulation of ammonia assimilation cycle

Inferred from mutant phenotype PubMed 21757002. Source: BHF-UCL

positive regulation of glutamate metabolic process

Inferred from mutant phenotype PubMed 21757002. Source: BHF-UCL

positive regulation of transcription from RNA polymerase II promoter

Inferred from mutant phenotype PubMed 21757002. Source: BHF-UCL

regulation of carbohydrate metabolic process

Inferred from electronic annotation. Source: Ensembl

regulation of transcription from RNA polymerase II promoter

Inferred from genetic interaction Ref.1. Source: MGI

regulation of urea metabolic process

Inferred from mutant phenotype PubMed 21757002. Source: BHF-UCL

response to glucose

Inferred from electronic annotation. Source: Ensembl

response to lipopolysaccharide

Inferred from electronic annotation. Source: Ensembl

   Cellular_componentnuclear euchromatin

Inferred from electronic annotation. Source: Ensembl

   Molecular_functionRNA polymerase II distal enhancer sequence-specific DNA binding

Inferred from electronic annotation. Source: Ensembl

RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity

Inferred from electronic annotation. Source: Ensembl

RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription

Inferred from electronic annotation. Source: Ensembl

bile acid binding

Inferred from mutant phenotype PubMed 21757002. Source: BHF-UCL

bile acid receptor activity

Inferred from electronic annotation. Source: Ensembl

chenodeoxycholic acid binding

Inferred from electronic annotation. Source: Ensembl

ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity

Inferred from mutant phenotype PubMed 21757002. Source: BHF-UCL

peptide binding

Inferred from electronic annotation. Source: Ensembl

retinoid X receptor binding

Inferred from direct assay Ref.1. Source: MGI

sequence-specific DNA binding transcription factor activity

Inferred from genetic interaction Ref.1. Source: MGI

steroid hormone receptor activity

Inferred from electronic annotation. Source: Ensembl

thyroid hormone receptor activity

Inferred from electronic annotation. Source: InterPro

zinc ion binding

Inferred from electronic annotation. Source: InterPro

Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q60641-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.
Isoform 2 (identifier: Q60641-2)

The sequence of this isoform differs from the canonical sequence as follows:
     208-211: Missing.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 488488Bile acid receptor
PRO_0000053539

Regions

DNA binding135 – 21076Nuclear receptor
Zinc finger138 – 15821NR C4-type
Zinc finger174 – 19825NR C4-type
Region258 – 476219Ligand-binding By similarity
Region344 – 3529Agonist binding By similarity

Sites

Binding site3771Agonist By similarity
Binding site3851Agonist By similarity
Binding site4631Agonist By similarity
Binding site4851Agonist By similarity

Amino acid modifications

Modified residue2211N6-methyllysine; by SETD7 By similarity

Natural variations

Alternative sequence208 – 2114Missing in isoform 2.
VSP_003666

Experimental info

Sequence conflict281E → D in AAC53066. Ref.1
Sequence conflict281E → D in AAH15261. Ref.3
Sequence conflict1991K → R in AAC53065. Ref.1
Sequence conflict1991K → R in AAC53066. Ref.1
Sequence conflict1991K → R in AAC52978. Ref.1
Sequence conflict1991K → R in AAH15261. Ref.3
Sequence conflict2351A → V in AAC53065. Ref.1
Sequence conflict2351A → V in AAC53066. Ref.1
Sequence conflict2351A → V in AAC52978. Ref.1
Sequence conflict2351A → V in AAH15261. Ref.3

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified July 27, 2011. Version 3.
Checksum: 3E59B7146F8ECC86

FASTA48855,994
        10         20         30         40         50         60 
MVMQFQGLEN PIQISLHHSH RLSGFVPEGM SVKPAKGMLT EHAAGPLGQN LDLESYSPYN 

        70         80         90        100        110        120 
NVPFPQVQPQ ISSSSYYSNL GFYPQQPEDW YSPGIYELRR MPAETGYQGE TEVSEMPVTK 

       130        140        150        160        170        180 
KPRMAAASAG RIKGDELCVV CGDRASGYHY NALTCEGCKG FFRRSITKNA VYKCKNGGNC 

       190        200        210        220        230        240 
VMDMYMRRKC QECRLRKCKE MGMLAECMYT GLLTEIQCKS KRLRKNVKQH ADQTANEDDS 

       250        260        270        280        290        300 
EGRDLRQVTS TTKFCREKTE LTADQQTLLD YIMDSYNKQR MPQEITNKIL KEEFSAEENF 

       310        320        330        340        350        360 
LILTEMATSH VQILVEFTKK LPGFQTLDHE DQIALLKGSA VEAMFLRSAE IFNKKLPAGH 

       370        380        390        400        410        420 
ADLLEERIRK SGISDEYITP MFSFYKSVGE LKMTQEEYAL LTAIVILSPD RQYIKDREAV 

       430        440        450        460        470        480 
EKLQEPLLDV LQKLCKMYQP ENPQHFACLL GRLTELRTFN HHHAEMLMSW RVNDHKFTPL 


LCEIWDVQ 

« Hide

Isoform 2 [UniParc].

Checksum: 06B56494305A438A
Show »

FASTA48455,542

References

« Hide 'large scale' references
[1]"Isolation of proteins that interact specifically with the retinoid X receptor: two novel orphan receptors."
Seol W., Choi H.S., Moore D.D.
Mol. Endocrinol. 9:72-85(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 2), INTERACTION WITH RXR.
Tissue: Liver.
[2]"Lineage-specific biology revealed by a finished genome assembly of the mouse."
Church D.M., Goodstadt L., Hillier L.W., Zody M.C., Goldstein S., She X., Bult C.J., Agarwala R., Cherry J.L., DiCuccio M., Hlavina W., Kapustin Y., Meric P., Maglott D., Birtle Z., Marques A.C., Graves T., Zhou S. expand/collapse author list , Teague B., Potamousis K., Churas C., Place M., Herschleb J., Runnheim R., Forrest D., Amos-Landgraf J., Schwartz D.C., Cheng Z., Lindblad-Toh K., Eichler E.E., Ponting C.P.
PLoS Biol. 7:E1000112-E1000112(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: C57BL/6J.
[3]"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
The MGC Project Team
Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
Tissue: Kidney.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
U09416 mRNA. Translation: AAC53066.1.
U09417 mRNA. Translation: AAC53065.1.
U09418 mRNA. Translation: AAC52978.1.
AC152417 Genomic DNA. No translation available.
BC015261 mRNA. Translation: AAH15261.1.
CCDSCCDS24116.1. [Q60641-2]
CCDS48668.1. [Q60641-1]
PIRI49018.
I49019.
I49020.
RefSeqNP_001157172.1. NM_001163700.1. [Q60641-1]
UniGeneMm.3095.

3D structure databases

ProteinModelPortalQ60641.
SMRQ60641. Positions 129-487.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid203043. 7 interactions.
DIPDIP-443N.

Chemistry

BindingDBQ60641.
ChEMBLCHEMBL5343.

PTM databases

PhosphoSiteQ60641.

Proteomic databases

PRIDEQ60641.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENSMUST00000058126; ENSMUSP00000053092; ENSMUSG00000047638. [Q60641-2]
ENSMUST00000105296; ENSMUSP00000100933; ENSMUSG00000047638. [Q60641-1]
GeneID20186.
KEGGmmu:20186.
UCSCuc007gsg.2. mouse. [Q60641-1]

Organism-specific databases

CTD9971.
MGIMGI:1352464. Nr1h4.

Phylogenomic databases

eggNOGNOG302915.
GeneTreeENSGT00720000108423.
HOGENOMHOG000220843.
HOVERGENHBG108655.
InParanoidQ60641.
KOK08537.
OMAMKPAKGV.
OrthoDBEOG7DC25S.
TreeFamTF316304.

Gene expression databases

BgeeQ60641.
CleanExMM_NR1H4.
GenevestigatorQ60641.

Family and domain databases

Gene3D1.10.565.10. 2 hits.
3.30.50.10. 1 hit.
InterProIPR008946. Nucl_hormone_rcpt_ligand-bd.
IPR000536. Nucl_hrmn_rcpt_lig-bd_core.
IPR001723. Str_hrmn_rcpt.
IPR001728. ThyrH_rcpt.
IPR001628. Znf_hrmn_rcpt.
IPR013088. Znf_NHR/GATA.
[Graphical view]
PfamPF00104. Hormone_recep. 1 hit.
PF00105. zf-C4. 1 hit.
[Graphical view]
PRINTSPR00398. STRDHORMONER.
PR00047. STROIDFINGER.
PR00546. THYROIDHORMR.
SMARTSM00430. HOLI. 1 hit.
SM00399. ZnF_C4. 1 hit.
[Graphical view]
SUPFAMSSF48508. SSF48508. 1 hit.
PROSITEPS00031. NUCLEAR_REC_DBD_1. 1 hit.
PS51030. NUCLEAR_REC_DBD_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

NextBio297725.
PROQ60641.
SOURCESearch...

Entry information

Entry nameNR1H4_MOUSE
AccessionPrimary (citable) accession number: Q60641
Secondary accession number(s): E9QJW2, Q60642, Q60643
Entry history
Integrated into UniProtKB/Swiss-Prot: May 27, 2002
Last sequence update: July 27, 2011
Last modified: July 9, 2014
This is version 138 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

MGD cross-references

Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot