LOCUS       NM_009108               1973 bp    mRNA    linear   ROD 07-FEB-2025
DEFINITION  Mus musculus nuclear receptor subfamily 1, group H, member 4
            (Nr1h4), transcript variant 3, mRNA.
ACCESSION   NM_009108
VERSION     NM_009108.2
KEYWORDS    RefSeq; RefSeq Select.
SOURCE      Mus musculus (house mouse)
  ORGANISM  Mus musculus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
            Muroidea; Muridae; Murinae; Mus; Mus.
REFERENCE   1  (bases 1 to 1973)
  AUTHORS   Tomioka,I., Ota,C., Tanahashi,Y., Ikegami,K., Ishihara,A.,
            Kohri,N., Fujii,H. and Morohaku,K.
  TITLE     Loss of the DNA-binding domain of the farnesoid X receptor gene
            causes severe liver and kidney injuries
  JOURNAL   Biochem Biophys Res Commun 721, 150125 (2024)
   PUBMED   38762930
  REMARK    GeneRIF: Loss of the DNA-binding domain of the farnesoid X receptor
            gene causes severe liver and kidney injuries.
REFERENCE   2  (bases 1 to 1973)
  AUTHORS   Liu,Y., Zhou,Y., Ahodantin,J., Jin,Y., Zhu,J., Sun,Z., Wu,X., Su,L.
            and Yang,Y.
  TITLE     Generation and characterization of mature hepatocyte organoids for
            liver metabolic studies
  JOURNAL   J Cell Sci 137 (10) (2024)
   PUBMED   38700490
REFERENCE   3  (bases 1 to 1973)
  AUTHORS   Qin,X., Tan,Y., Ren,W., Zhou,W., Niu,R., Liang,L., Li,J., Cao,K.,
            Wei,G., Zhu,X. and Huang,M.
  TITLE     Elevated expression of LCN13 through FXR activation ameliorates
            hepatocellular lipid accumulation and inflammation
  JOURNAL   Int Immunopharmacol 131, 111812 (2024)
   PUBMED   38493698
  REMARK    GeneRIF: Elevated expression of LCN13 through FXR activation
            ameliorates hepatocellular lipid accumulation and inflammation.
REFERENCE   4  (bases 1 to 1973)
  AUTHORS   Ahuja,N., Gupta,S., Arora,R., Bhagyaraj,E., Tiwari,D., Kumar,S. and
            Gupta,P.
  TITLE     Nr1h4 and Thrb ameliorate ER stress and provide protection in the
            MPTP mouse model of Parkinson's
  JOURNAL   Life Sci Alliance 7 (7), e202302416 (2024)
   PUBMED   38609183
  REMARK    GeneRIF: Nr1h4 and Thrb ameliorate ER stress and provide protection
            in the MPTP mouse model of Parkinson's.
            Publication Status: Online-Only
REFERENCE   5  (bases 1 to 1973)
  AUTHORS   Cong,J., Liu,P., Han,Z., Ying,W., Li,C., Yang,Y., Wang,S., Yang,J.,
            Cao,F., Shen,J., Zeng,Y., Bai,Y., Zhou,C., Ye,L., Zhou,R., Guo,C.,
            Cang,C., Kasper,D.L., Song,X., Dai,L., Sun,L., Pan,W. and Zhu,S.
  TITLE     Bile acids modified by the intestinal microbiota promote colorectal
            cancer growth by suppressing CD8+ T cell effector functions
  JOURNAL   Immunity 57 (4), 876-889 (2024)
   PUBMED   38479384
REFERENCE   6  (bases 1 to 1973)
  AUTHORS   Shih,D.Q., Bussen,M., Sehayek,E., Ananthanarayanan,M.,
            Shneider,B.L., Suchy,F.J., Shefer,S., Bollileni,J.S.,
            Gonzalez,F.J., Breslow,J.L. and Stoffel,M.
  TITLE     Hepatocyte nuclear factor-1alpha is an essential regulator of bile
            acid and plasma cholesterol metabolism
  JOURNAL   Nat Genet 27 (4), 375-382 (2001)
   PUBMED   11279518
REFERENCE   7  (bases 1 to 1973)
  AUTHORS   Lammert,F., Carey,M.C. and Paigen,B.
  TITLE     Chromosomal organization of candidate genes involved in cholesterol
            gallstone formation: a murine gallstone map
  JOURNAL   Gastroenterology 120 (1), 221-238 (2001)
   PUBMED   11208732
  REMARK    Review article
REFERENCE   8  (bases 1 to 1973)
  AUTHORS   Sinal,C.J., Tohkin,M., Miyata,M., Ward,J.M., Lambert,G. and
            Gonzalez,F.J.
  TITLE     Targeted disruption of the nuclear receptor FXR/BAR impairs bile
            acid and lipid homeostasis
  JOURNAL   Cell 102 (6), 731-744 (2000)
   PUBMED   11030617
REFERENCE   9  (bases 1 to 1973)
  AUTHORS   Kozak,C.A., Adamson,M.C. and Weinberger,C.
  TITLE     Genetic mapping of gene encoding the farnesoid receptor, Fxr, to
            mouse Chromosome 10
  JOURNAL   Mamm Genome 7 (2), 164-165 (1996)
   PUBMED   8835541
REFERENCE   10 (bases 1 to 1973)
  AUTHORS   Seol,W., Choi,H.S. and Moore,D.D.
  TITLE     Isolation of proteins that interact specifically with the retinoid
            X receptor: two novel orphan receptors
  JOURNAL   Mol Endocrinol 9 (1), 72-85 (1995)
   PUBMED   7760852
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AC152417.3 and AK132255.1.
            
            On Jul 30, 2009 this sequence version replaced NM_009108.1.
            
            Transcript Variant: This variant (3), alternatively referred to as
            beta 2 and alpha 4, uses an alternate in-frame splice site in the
            coding region, compared to variant 1. This results in a shorter
            isoform (2), compared to isoform 1.
            
            Sequence Note: This RefSeq record was created from transcript and
            genomic sequence data to make the sequence consistent with the
            reference genome assembly. The genomic coordinates used for the
            transcript record were based on transcript alignments.
            
            Publication Note:  This RefSeq record includes a subset of the
            publications that are available for this gene. Please see the Gene
            record to access additional publications.
            
            ##Evidence-Data-START##
            Transcript exon combination :: AK132255.1, U09416.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN00849386, SAMN01164135
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-9                 AC152417.3         196852-196860       c
            10-1829             AK132255.1         2-1821
            1830-1973           AC152417.3         144436-144579       c
FEATURES             Location/Qualifiers
     source          1..1973
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="10"
                     /map="10 44.98 cM"
     gene            1..1973
                     /gene="Nr1h4"
                     /gene_synonym="Fxr; HRR1; RIP14; Rxrip14"
                     /note="nuclear receptor subfamily 1, group H, member 4"
                     /db_xref="GeneID:20186"
                     /db_xref="MGI:MGI:1352464"
     exon            1..151
                     /gene="Nr1h4"
                     /gene_synonym="Fxr; HRR1; RIP14; Rxrip14"
                     /inference="alignment:Splign:2.1.0"
     exon            152..520
                     /gene="Nr1h4"
                     /gene_synonym="Fxr; HRR1; RIP14; Rxrip14"
                     /inference="alignment:Splign:2.1.0"
     exon            521..661
                     /gene="Nr1h4"
                     /gene_synonym="Fxr; HRR1; RIP14; Rxrip14"
                     /inference="alignment:Splign:2.1.0"
     exon            662..798
                     /gene="Nr1h4"
                     /gene_synonym="Fxr; HRR1; RIP14; Rxrip14"
                     /inference="alignment:Splign:2.1.0"
     exon            799..897
                     /gene="Nr1h4"
                     /gene_synonym="Fxr; HRR1; RIP14; Rxrip14"
                     /inference="alignment:Splign:2.1.0"
     exon            898..997
                     /gene="Nr1h4"
                     /gene_synonym="Fxr; HRR1; RIP14; Rxrip14"
                     /inference="alignment:Splign:2.1.0"
     exon            998..1144
                     /gene="Nr1h4"
                     /gene_synonym="Fxr; HRR1; RIP14; Rxrip14"
                     /inference="alignment:Splign:2.1.0"
     exon            1145..1258
                     /gene="Nr1h4"
                     /gene_synonym="Fxr; HRR1; RIP14; Rxrip14"
                     /inference="alignment:Splign:2.1.0"
     exon            1259..1973
                     /gene="Nr1h4"
                     /gene_synonym="Fxr; HRR1; RIP14; Rxrip14"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1705..1710
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Nr1h4"
                     /gene_synonym="Fxr; HRR1; RIP14; Rxrip14"
                     /note="hexamer: ATTAAA"
     polyA_site      1731
                     /gene="Nr1h4"
                     /gene_synonym="Fxr; HRR1; RIP14; Rxrip14"
     regulatory      1813..1818
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Nr1h4"
                     /gene_synonym="Fxr; HRR1; RIP14; Rxrip14"
                     /note="hexamer: AATAAA"
     polyA_site      1834
                     /gene="Nr1h4"
                     /gene_synonym="Fxr; HRR1; RIP14; Rxrip14"
                     /note="major polyA site"
     regulatory      1929..1934
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Nr1h4"
                     /gene_synonym="Fxr; HRR1; RIP14; Rxrip14"
                     /note="hexamer: AGTAAA"
     regulatory      1942..1947
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Nr1h4"
                     /gene_synonym="Fxr; HRR1; RIP14; Rxrip14"
                     /note="hexamer: AATAGA"
     polyA_site      1950
                     /gene="Nr1h4"
                     /gene_synonym="Fxr; HRR1; RIP14; Rxrip14"
     polyA_site      1970
                     /gene="Nr1h4"
                     /gene_synonym="Fxr; HRR1; RIP14; Rxrip14"
ORIGIN      
        1 tcttacctcg gctccttctc agttgccgtg aggaagctaa ggatggtgat gcagtttcag
       61 ggtttagaaa atccaattca gattagtctt caccacagcc accggctgtc aggatttgtg
      121 ccggaaggga tgagtgtgaa gccagctaaa ggtatgctaa cagaacacgc ggcaggccct
      181 ctggggcaga atctggattt ggaatcgtac tccccataca acaatgtccc gtttcctcaa
      241 gttcagccac agatttcctc ctcgtcttac tattccaacc tgggcttcta cccccaacaa
      301 ccggaagact ggtattctcc tggcatctat gaactcaggc gaatgcccgc tgagactggg
      361 taccagggag agactgaggt atcagagatg cctgtgacaa agaagccgcg aatggccgcg
      421 gcatcggcag gcagaataaa aggggatgag ctgtgtgttg tctgtggaga cagggcctct
      481 gggtaccact acaacgcgct cacctgtgag ggctgcaaag gtttcttccg aagaagcatt
      541 accaagaacg ccgtgtacaa gtgtaagaac gggggcaact gcgtgatgga catgtacatg
      601 cgcaggaagt gccaggagtg ccggctaagg aagtgcaaag agatggggat gttggctgaa
      661 tgtttgttaa ctgaaatcca gtgtaaatct aaacggctaa ggaaaaatgt gaagcagcac
      721 gctgatcaga cagctaatga ggacgacagc gaagggcgtg acttgcgaca agtgacctcc
      781 acaaccaagt tttgcaggga gaaaacggaa ctcacggcag accaacagac cctcctggat
      841 tatattatgg attcgtacaa caaacagaga atgcctcagg aaatcacaaa taaaatctta
      901 aaagaagaat ttagtgcaga agaaaatttt ctcatattaa cagaaatggc aaccagtcat
      961 gtacagattc tcgtagaatt cacaaaaaag cttccagggt ttcagacact ggatcacgaa
     1021 gatcagattg ctttgctcaa agggtccgca gtggaggcca tgtttcttcg ttcggcggag
     1081 attttcaata agaaacttcc tgccggtcat gcagacctgt tggaagaaag aattcgaaag
     1141 agtggtatct ctgatgagta tataaccccg atgttcagtt tctataaaag tgttggagaa
     1201 ctcaaaatga ctcaggagga gtacgctctg ctcacagcga tcgtcatcct ctctccagac
     1261 agacaataca tcaaggacag agaggcggtg gagaagctgc aggagcccct gcttgatgtg
     1321 ctacaaaagc tgtgcaagat gtaccagcct gagaacccgc agcatttcgc ctgcctcctg
     1381 ggtcgcctga cggaactccg gacattcaac catcaccacg ctgagatgct gatgtcttgg
     1441 agagtgaatg atcacaagtt caccccgctc ctctgtgaga tctgggatgt gcagtgatgg
     1501 acaccagtgg ggctggctcc ttgtcctcct cggaacagaa accttgtttc gtttgtacct
     1561 ggtttcactc aagaatctca atgaatattt atgtggcaat tatacacctc ccacggttgt
     1621 aaatacagac tagatagaac tgctttcccc acactgtatt ttacaaggct tcaggaaacc
     1681 ccactggcat gcccttttgg cctaattaaa tcaattgtta cttcaattct atctactgag
     1741 ctaggggcat tttattcttc attcgacaat attatatata ttttataaag ttgagctgtt
     1801 ttcaactgag acaataaact gaatgtaata gcaaggagac ttctcatttg gacaaaaaga
     1861 aattgaggag tatctcttta agtgatgacg ggaatcttat tgagttggag ggcaggtcat
     1921 ttccagaaag taaactctta caatagaaaa gtaatgtttc catccctgca gaa
//
