LOCUS       NM_003889               2802 bp    mRNA    linear   PRI 10-JUN-2024
DEFINITION  Homo sapiens nuclear receptor subfamily 1 group I member 2 (NR1I2),
            transcript variant 1, mRNA.
ACCESSION   NM_003889
VERSION     NM_003889.4
KEYWORDS    RefSeq; MANE Select.
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 2802)
  AUTHORS   Mitamura,R., Nakano,M., Isono,M., Kurosawa,K., Fukami,T. and
            Nakajima,M.
  TITLE     NEAT1_2 and DAZAP1, Paraspeckle Components, Interact with PXR to
            Negatively Regulate CYP3A4 Induction
  JOURNAL   Drug Metab Dispos 51 (10), 1230-1237 (2023)
   PUBMED   37349114
  REMARK    GeneRIF: NEAT1_2 and DAZAP1, Paraspeckle Components, Interact with
            PXR to Negatively Regulate CYP3A4 Induction.
REFERENCE   2  (bases 1 to 2802)
  AUTHORS   Nakagawa,J., Kinjo,T., Aiuchi,N., Ueno,K., Tomita,H. and Niioka,T.
  TITLE     Effect of pregnane X receptor and cytochrome P450 oxidoreductase
            gene polymorphisms on trough concentrations of rivaroxaban and
            edoxaban in patients with nonvalvular atrial fibrillation
  JOURNAL   Eur J Clin Pharmacol 79 (5), 703-705 (2023)
   PUBMED   36951964
  REMARK    GeneRIF: Effect of pregnane X receptor and cytochrome P450
            oxidoreductase gene polymorphisms on trough concentrations of
            rivaroxaban and edoxaban in patients with nonvalvular atrial
            fibrillation.
REFERENCE   3  (bases 1 to 2802)
  AUTHORS   Karajamaki,A.J., Hukkanen,J. and Ukkola,O.
  TITLE     Pregnane X receptor gene variant rs7643645 and total mortality in
            subjects with nonalcoholic fatty liver disease
  JOURNAL   Pharmacogenet Genomics 33 (2), 35-39 (2023)
   PUBMED   36503926
  REMARK    GeneRIF: Pregnane X receptor gene variant rs7643645 and total
            mortality in subjects with nonalcoholic fatty liver disease.
REFERENCE   4  (bases 1 to 2802)
  AUTHORS   Yagishita,H., Kagaya,H., Saito,M., Numakura,K., Yamamoto,R.,
            Sagehashi,R., Habuchi,T., Satoh,S. and Miura,M.
  TITLE     Effects of NR1I2 and ABCB1 Genetic Polymorphisms on Everolimus
            Pharmacokinetics in Japanese Renal Transplant Patients
  JOURNAL   Int J Mol Sci 23 (19), 11742 (2022)
   PUBMED   36233042
  REMARK    GeneRIF: Effects of NR1I2 and ABCB1 Genetic Polymorphisms on
            Everolimus Pharmacokinetics in Japanese Renal Transplant Patients.
            Publication Status: Online-Only
REFERENCE   5  (bases 1 to 2802)
  AUTHORS   Li,W., Osman,E., Forssell,C. and Yuan,X.M.
  TITLE     Protease-Activated Receptor 1 in Human Carotid Atheroma Is
            Significantly Related to Iron Metabolism, Plaque Vulnerability, and
            the Patient's Age
  JOURNAL   Int J Mol Sci 23 (12), 6363 (2022)
   PUBMED   35742805
  REMARK    GeneRIF: Protease-Activated Receptor 1 in Human Carotid Atheroma Is
            Significantly Related to Iron Metabolism, Plaque Vulnerability, and
            the Patient's Age.
            Publication Status: Online-Only
REFERENCE   6  (bases 1 to 2802)
  AUTHORS   Dotzlaw,H., Leygue,E., Watson,P. and Murphy,L.C.
  TITLE     The human orphan receptor PXR messenger RNA is expressed in both
            normal and neoplastic breast tissue
  JOURNAL   Clin Cancer Res 5 (8), 2103-2107 (1999)
   PUBMED   10473093
REFERENCE   7  (bases 1 to 2802)
  AUTHORS   Blumberg,B., Sabbagh,W. Jr., Juguilon,H., Bolado,J. Jr., van
            Meter,C.M., Ong,E.S. and Evans,R.M.
  TITLE     SXR, a novel steroid and xenobiotic-sensing nuclear receptor
  JOURNAL   Genes Dev 12 (20), 3195-3205 (1998)
   PUBMED   9784494
REFERENCE   8  (bases 1 to 2802)
  AUTHORS   Bertilsson,G., Heidrich,J., Svensson,K., Asman,M., Jendeberg,L.,
            Sydow-Backman,M., Ohlsson,R., Postlind,H., Blomquist,P. and
            Berkenstam,A.
  TITLE     Identification of a human nuclear receptor defines a new signaling
            pathway for CYP3A induction
  JOURNAL   Proc Natl Acad Sci U S A 95 (21), 12208-12213 (1998)
   PUBMED   9770465
REFERENCE   9  (bases 1 to 2802)
  AUTHORS   Lehmann,J.M., McKee,D.D., Watson,M.A., Willson,T.M., Moore,J.T. and
            Kliewer,S.A.
  TITLE     The human orphan nuclear receptor PXR is activated by compounds
            that regulate CYP3A4 gene expression and cause drug interactions
  JOURNAL   J Clin Invest 102 (5), 1016-1023 (1998)
   PUBMED   9727070
  REMARK    GeneRIF: In-vitro transcription/translation studies show that
            translation of pregnane X receptor mRNA initiates at a non-AUG
            (CUG) codon.
REFERENCE   10 (bases 1 to 2802)
  AUTHORS   Kliewer,S.A., Moore,J.T., Wade,L., Staudinger,J.L., Watson,M.A.,
            Jones,S.A., McKee,D.D., Oliver,B.B., Willson,T.M.,
            Zetterstrom,R.H., Perlmann,T. and Lehmann,J.M.
  TITLE     An orphan nuclear receptor activated by pregnanes defines a novel
            steroid signaling pathway
  JOURNAL   Cell 92 (1), 73-82 (1998)
   PUBMED   9489701
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AC069444.17 and KF457674.1.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Aug 11, 2020 this sequence version replaced NM_003889.3.
            
            Summary: This gene product belongs to the nuclear receptor
            superfamily, members of which are transcription factors
            characterized by a ligand-binding domain and a DNA-binding domain.
            The encoded protein is a transcriptional regulator of the
            cytochrome P450 gene CYP3A4, binding to the response element of the
            CYP3A4 promoter as a heterodimer with the 9-cis retinoic acid
            receptor RXR. It is activated by a range of compounds that induce
            CYP3A4, including dexamethasone and rifampicin. Several
            alternatively spliced transcripts encoding different isoforms, some
            of which use non-AUG (CUG) translation initiation codon, have been
            described for this gene. Additional transcript variants exist,
            however, they have not been fully characterized. [provided by
            RefSeq, Jul 2008].
            
            Transcript Variant: This variant (1) contains an alternate 5'
            terminal exon compared to transcript variant 2, and initiates
            translation from an in-frame, downstream non-AUG (CUG) codon,
            resulting in a shorter isoform (1) with a different N-terminus
            compared to isoform 2.
            
            Sequence Note: This RefSeq record was created from transcript and
            genomic sequence data because no quality transcript was available
            for the full length of the gene. The extent of this transcript is
            supported by 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 :: AJ009936.1, AF084645.2 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1968540, SAMEA2142348
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match       :: ENST00000393716.8/ ENSP00000377319.3
            non-AUG initiation codon :: PMID: 9727070
            RefSeq Select criteria   :: based on conservation, expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-200               AC069444.17        107736-107935       c
            201-419             AC069444.17        82589-82807         c
            420-553             AC069444.17        79842-79975         c
            554-741             AC069444.17        78310-78497         c
            742-1016            AC069444.17        77076-77350         c
            1017-1047           AC069444.17        75027-75057         c
            1048-1145           KF457674.1         1-98
            1146-1159           AC069444.17        74915-74928         c
            1160-1276           AC069444.17        74597-74713         c
            1277-1382           AC069444.17        74205-74310         c
            1383-2802           AC069444.17        71549-72968         c
FEATURES             Location/Qualifiers
     source          1..2802
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="3"
                     /map="3q13.33"
     gene            1..2802
                     /gene="NR1I2"
                     /gene_synonym="BXR; ONR1; PAR; PAR1; PAR2; PARq; PRR; PXR;
                     SAR; SXR"
                     /note="nuclear receptor subfamily 1 group I member 2"
                     /db_xref="GeneID:8856"
                     /db_xref="HGNC:HGNC:7968"
                     /db_xref="MIM:603065"
     exon            1..200
                     /gene="NR1I2"
                     /gene_synonym="BXR; ONR1; PAR; PAR1; PAR2; PARq; PRR; PXR;
                     SAR; SXR"
                     /inference="alignment:Splign:2.1.0"
     exon            201..419
                     /gene="NR1I2"
                     /gene_synonym="BXR; ONR1; PAR; PAR1; PAR2; PARq; PRR; PXR;
                     SAR; SXR"
                     /inference="alignment:Splign:2.1.0"
     CDS             223..1527
                     /gene="NR1I2"
                     /gene_synonym="BXR; ONR1; PAR; PAR1; PAR2; PARq; PRR; PXR;
                     SAR; SXR"
                     /note="isoform 1 is encoded by transcript variant 1;
                     non-AUG (CUG) translation initiation codon; steroid and
                     xenobiotic receptor; orphan nuclear receptor PXR; pregnane
                     X receptor; orphan nuclear receptor PAR1"
                     /codon_start=1
                     /product="nuclear receptor subfamily 1 group I member 2
                     isoform 1"
                     /protein_id="NP_003880.3"
                     /db_xref="CCDS:CCDS43136.1"
                     /db_xref="GeneID:8856"
                     /db_xref="HGNC:HGNC:7968"
                     /db_xref="MIM:603065"
                     /translation="MEVRPKESWNHADFVHCEDTESVPGKPSVNADEEVGGPQICRVC
                     GDKATGYHFNVMTCEGCKGFFRRAMKRNARLRCPFRKGACEITRKTRRQCQACRLRKC
                     LESGMKKEMIMSDEAVEERRALIKRKKSERTGTQPLGVQGLTEEQRMMIRELMDAQMK
                     TFDTTFSHFKNFRLPGVLSSGCELPESLQAPSREEAAKWSQVRKDLCSLKVSLQLRGE
                     DGSVWNYKPPADSGGKEIFSLLPHMADMSTYMFKGIISFAKVISYFRDLPIEDQISLL
                     KGAAFELCQLRFNTVFNAETGTWECGRLSYCLEDTAGGFQQLLLEPMLKFHYMLKKLQ
                     LHEEEYVLMQAISLFSPDRPGVLQHRVVDQLQEQFAITLKSYIECNRPQPAHRFLFLK
                     IMAMLTELRSINAQHTQRLLRIQDIHPFATPLMQELFGITGS"
     exon            420..553
                     /gene="NR1I2"
                     /gene_synonym="BXR; ONR1; PAR; PAR1; PAR2; PARq; PRR; PXR;
                     SAR; SXR"
                     /inference="alignment:Splign:2.1.0"
     exon            554..741
                     /gene="NR1I2"
                     /gene_synonym="BXR; ONR1; PAR; PAR1; PAR2; PARq; PRR; PXR;
                     SAR; SXR"
                     /inference="alignment:Splign:2.1.0"
     exon            742..1016
                     /gene="NR1I2"
                     /gene_synonym="BXR; ONR1; PAR; PAR1; PAR2; PARq; PRR; PXR;
                     SAR; SXR"
                     /inference="alignment:Splign:2.1.0"
     exon            1017..1159
                     /gene="NR1I2"
                     /gene_synonym="BXR; ONR1; PAR; PAR1; PAR2; PARq; PRR; PXR;
                     SAR; SXR"
                     /inference="alignment:Splign:2.1.0"
     exon            1160..1276
                     /gene="NR1I2"
                     /gene_synonym="BXR; ONR1; PAR; PAR1; PAR2; PARq; PRR; PXR;
                     SAR; SXR"
                     /inference="alignment:Splign:2.1.0"
     exon            1277..1382
                     /gene="NR1I2"
                     /gene_synonym="BXR; ONR1; PAR; PAR1; PAR2; PARq; PRR; PXR;
                     SAR; SXR"
                     /inference="alignment:Splign:2.1.0"
     exon            1383..2802
                     /gene="NR1I2"
                     /gene_synonym="BXR; ONR1; PAR; PAR1; PAR2; PARq; PRR; PXR;
                     SAR; SXR"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2778..2783
                     /regulatory_class="polyA_signal_sequence"
                     /gene="NR1I2"
                     /gene_synonym="BXR; ONR1; PAR; PAR1; PAR2; PARq; PRR; PXR;
                     SAR; SXR"
                     /note="hexamer: ATTAAA"
     polyA_site      2802
                     /gene="NR1I2"
                     /gene_synonym="BXR; ONR1; PAR; PAR1; PAR2; PARq; PRR; PXR;
                     SAR; SXR"
                     /note="major polyA site"
ORIGIN      
        1 ctttacttca gtgggaatct cggcctcagc ctgcaagcca agtgttcaca gtgagaaaag
       61 caagagaata agctaatact cctgtcctga acaaggcagc ggctccttgg taaagctact
      121 ccttgatcga tcctttgcac cggattgttc aaagtggacc ccaggggaga agtcggagca
      181 aagaacttac caccaagcag tccaagaggc ccagaagcaa acctggaggt gagacccaaa
      241 gaaagctgga accatgctga ctttgtacac tgtgaggaca cagagtctgt tcctggaaag
      301 cccagtgtca acgcagatga ggaagtcgga ggtccccaaa tctgccgtgt atgtggggac
      361 aaggccactg gctatcactt caatgtcatg acatgtgaag gatgcaaggg ctttttcagg
      421 agggccatga aacgcaacgc ccggctgagg tgccccttcc ggaagggcgc ctgcgagatc
      481 acccggaaga cccggcgaca gtgccaggcc tgccgcctgc gcaagtgcct ggagagcggc
      541 atgaagaagg agatgatcat gtccgacgag gccgtggagg agaggcgggc cttgatcaag
      601 cggaagaaaa gtgaacggac agggactcag ccactgggag tgcaggggct gacagaggag
      661 cagcggatga tgatcaggga gctgatggac gctcagatga aaacctttga cactaccttc
      721 tcccatttca agaatttccg gctgccaggg gtgcttagca gtggctgcga gttgccagag
      781 tctctgcagg ccccatcgag ggaagaagct gccaagtgga gccaggtccg gaaagatctg
      841 tgctctttga aggtctctct gcagctgcgg ggggaggatg gcagtgtctg gaactacaaa
      901 cccccagccg acagtggcgg gaaagagatc ttctccctgc tgccccacat ggctgacatg
      961 tcaacctaca tgttcaaagg catcatcagc tttgccaaag tcatctccta cttcagggac
     1021 ttgcccatcg aggaccagat ctccctgctg aagggggccg ctttcgagct gtgtcaactg
     1081 agattcaaca cagtgttcaa cgcggagact ggaacctggg agtgtggccg gctgtcctac
     1141 tgcttggaag acactgcagg tggcttccag caacttctac tggagcccat gctgaaattc
     1201 cactacatgc tgaagaagct gcagctgcat gaggaggagt atgtgctgat gcaggccatc
     1261 tccctcttct ccccagaccg cccaggtgtg ctgcagcacc gcgtggtgga ccagctgcag
     1321 gagcaattcg ccattactct gaagtcctac attgaatgca atcggcccca gcctgctcat
     1381 aggttcttgt tcctgaagat catggctatg ctcaccgagc tccgcagcat caatgctcag
     1441 cacacccagc ggctgctgcg catccaggac atacacccct ttgctacgcc cctcatgcag
     1501 gagttgttcg gcatcacagg tagctgagcg gctgcccttg ggtgacacct ccgagaggca
     1561 gccagaccca gagccctctg agccgccact cccgggccaa gacagatgga cactgccaag
     1621 agccgacaat gccctgctgg cctgtctccc tagggaattc ctgctatgac agctggctag
     1681 cattcctcag gaaggacatg ggtgcccccc acccccagtt cagtctgtag ggagtgaagc
     1741 cacagactct tacgtggaga gtgcactgac ctgtaggtca ggaccatcag agaggcaagg
     1801 ttgccctttc cttttaaaag gccctgtggt ctggggagaa atccctcaga tcccactaaa
     1861 gtgtcaaggt gtggaaggga ccaagcgacc aaggatgggc catctggggt ctatgcccac
     1921 atacccacgt ttgttcgctt cctgagtctt ttcattgcta cctctaatag tcctgtctcc
     1981 cacttcccac tcgttcccct cctcttccga gctgctttgt gggctccagg cctgtactca
     2041 tcggcaggcg catgagtatc tgtgggagtc ctctagagag atgagaagcc aggaggcctg
     2101 caccaaatgt cagaagcttg gcatgacctc attccggcca catcattctg tgtctctgca
     2161 tccatttgaa cacattatta agcaccgata ataggtagcc tgctgtgggg tatacagcat
     2221 tgactcagat atagatcctg agctcacaga gtttatagtt aaaaaaacaa acagaaacac
     2281 aaacgatttg gatcaaaagg agaaatgata agtgacaaaa gcagcacaag gaatttccct
     2341 gtgtggatgc tgagctgtga tggcgggcac tgggtaccca agtgaaggtt cccaaggaca
     2401 tgagtctgta ggagcaaggg cacaaactgc agctgtgagt gcgtgtgtgt gatttggtgt
     2461 aggtaggtct gtttgccact tgatggggcc tgggtttgtt cctggggctg gaatgctggg
     2521 tatgctctgt gacaaggcta cgctgacaat cagttaaaca caccggagaa gaaccattta
     2581 catgcacctt atatttctgt gtacacatct attctcaaag ctaaagggta tgaaagtgcc
     2641 tgccttgttt atagccactt gtgagtaaaa atttttttgc attttcacaa attatacttt
     2701 atataaggca ttccacacct aagaactagt tttgggaaat gtagccctgg gtttaatgtc
     2761 aaatcaaggc aaaaggaatt aaataatgta cttttggcta ga
//
