LOCUS       NM_011281               2572 bp    mRNA    linear   ROD 09-JAN-2024
DEFINITION  Mus musculus RAR-related orphan receptor gamma (Rorc), transcript
            variant 1, mRNA.
ACCESSION   NM_011281
VERSION     NM_011281.3
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 2572)
  AUTHORS   Valle-Noguera A, Sancho-Temino L, Castillo-Gonzalez R, Villa-Gomez
            C, Gomez-Sanchez MJ, Ochoa-Ramos A, Yague-Fernandez P, Soler
            Palacios B, Zorita V, Raposo-Ponce B, Gonzalez-Granado JM, Aragones
            J and Cruz-Adalia A.
  TITLE     IL-18-induced HIF-1alpha in ILC3s ameliorates the inflammation of
            C. rodentium-induced colitis
  JOURNAL   Cell Rep 42 (12), 113508 (2023)
   PUBMED   38019650
REFERENCE   2  (bases 1 to 2572)
  AUTHORS   Yang T, Barros-Martins J, Wang Z, Wencker M, Zhang J, Smout J,
            Gambhir P, Janssen A, Schimrock A, Georgiev H, Leon-Lara X, Weiss
            S, Huehn J, Prinz I, Krueger A, Foerster R, Walzer T and Ravens S.
  TITLE     RORgammat+ c-Maf+ Vgamma4+ gammadelta T cells are generated in the
            adult thymus but do not reach the periphery
  JOURNAL   Cell Rep 42 (10), 113230 (2023)
   PUBMED   37815917
  REMARK    GeneRIF: RORgammat[+] c-Maf[+] Vgamma4[+] gammadelta T cells are
            generated in the adult thymus but do not reach the periphery.
REFERENCE   3  (bases 1 to 2572)
  AUTHORS   Herppich S, Hoenicke L, Kern F, Kruse F, Smout J, Greweling-Pils
            MC, Geffers R, Burton OT, Liston A, Keller A, Floess S and Huehn J.
  TITLE     Zfp362 potentiates murine colonic inflammation by constraining Treg
            cell function rather than promoting Th17 cell differentiation
  JOURNAL   Eur J Immunol 53 (10), e2250270 (2023)
   PUBMED   37366299
REFERENCE   4  (bases 1 to 2572)
  AUTHORS   Wang Y, Wang M, Chen J, Li Y, Kuang Z, Dende C, Raj P, Quinn G, Hu
            Z, Srinivasan T, Hassell B, Ruhn KA, Behrendt CL, Liang T, Dou X,
            Song Z and Hooper LV.
  TITLE     The gut microbiota reprograms intestinal lipid metabolism through
            long noncoding RNA Snhg9
  JOURNAL   Science 381 (6660), 851-857 (2023)
   PUBMED   37616368
REFERENCE   5  (bases 1 to 2572)
  AUTHORS   Chang D, Zhang H, Ge J, Xing Q, Guo X, Wang X and Dong C.
  TITLE     A cis-element at the Rorc locus regulates the development of type 3
            innate lymphoid cells
  JOURNAL   Front Immunol 14, 1105145 (2023)
   PUBMED   36969227
  REMARK    GeneRIF: A cis-element at the Rorc locus regulates the development
            of type 3 innate lymphoid cells.
            Publication Status: Online-Only
REFERENCE   6  (bases 1 to 2572)
  AUTHORS   Austin S, Medvedev A, Yan ZH, Adachi H, Hirose T and Jetten AM.
  TITLE     Induction of the nuclear orphan receptor RORgamma during adipocyte
            differentiation of D1 and 3T3-L1 cells
  JOURNAL   Cell Growth Differ 9 (3), 267-276 (1998)
   PUBMED   9543393
REFERENCE   7  (bases 1 to 2572)
  AUTHORS   Medvedev A, Chistokhina A, Hirose T and Jetten AM.
  TITLE     Genomic structure and chromosomal mapping of the nuclear orphan
            receptor ROR gamma (RORC) gene
  JOURNAL   Genomics 46 (1), 93-102 (1997)
   PUBMED   9403063
REFERENCE   8  (bases 1 to 2572)
  AUTHORS   Medvedev A, Yan ZH, Hirose T, Giguere V and Jetten AM.
  TITLE     Cloning of a cDNA encoding the murine orphan receptor RZR/ROR gamma
            and characterization of its response element
  JOURNAL   Gene 181 (1-2), 199-206 (1996)
   PUBMED   8973331
REFERENCE   9  (bases 1 to 2572)
  AUTHORS   Ortiz MA, Piedrafita FJ, Pfahl M and Maki R.
  TITLE     TOR: a new orphan receptor expressed in the thymus that can
            modulate retinoid and thyroid hormone signals
  JOURNAL   Mol Endocrinol 9 (12), 1679-1691 (1995)
   PUBMED   8614404
REFERENCE   10 (bases 1 to 2572)
  AUTHORS   Hirose T, Smith RJ and Jetten AM.
  TITLE     ROR gamma: the third member of ROR/RZR orphan receptor subfamily
            that is highly expressed in skeletal muscle
  JOURNAL   Biochem Biophys Res Commun 205 (3), 1976-1983 (1994)
   PUBMED   7811290
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AC164562.4.
            
            [WARNING] On Jan 17, 2024 this sequence was replaced by
            NM_011281.4.
            
            On Jun 18, 2014 this sequence version replaced NM_011281.2.
            
            Transcript Variant: This variant (1) represents the shortest
            transcript and encodes the longer isoform (1).
            
            Sequence Note: The RefSeq transcript and protein were derived from
            genomic sequence to make the sequence consistent with the reference
            genome assembly. The genomic coordinates used for the transcript
            record were based on 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 :: U39071.1, U43508.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN00849374, SAMN00849375
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-138               AC164562.4         173874-174011
            139-168             AC164562.4         176115-176144
            169-254             AC164562.4         188201-188286
            255-396             AC164562.4         188540-188681
            397-903             AC164562.4         189831-190337
            904-1025            AC164562.4         190555-190676
            1026-1158           AC164562.4         192154-192286
            1159-1266           AC164562.4         192460-192567
            1267-1377           AC164562.4         192725-192835
            1378-1487           AC164562.4         194111-194220
            1488-2572           AC164562.4         198272-199356
FEATURES             Location/Qualifiers
     source          1..2572
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="3"
                     /map="3 40.56 cM"
     gene            1..2572
                     /gene="Rorc"
                     /gene_synonym="Nr1f3; RORgamma; Thor; TOR"
                     /note="RAR-related orphan receptor gamma"
                     /db_xref="GeneID:19885"
                     /db_xref="MGI:MGI:104856"
     exon            1..138
                     /gene="Rorc"
                     /gene_synonym="Nr1f3; RORgamma; Thor; TOR"
                     /inference="alignment:Splign:2.1.0"
     CDS             99..1649
                     /gene="Rorc"
                     /gene_synonym="Nr1f3; RORgamma; Thor; TOR"
                     /note="isoform 1 is encoded by transcript variant 1;
                     nuclear receptor ROR-gamma; nuclear receptor RZR-gamma;
                     retinoid-related orphan receptor-gamma; nuclear receptor
                     subfamily 1 group F member 3; thymus orphan receptor;
                     RAR-related orphan receptor C"
                     /codon_start=1
                     /product="nuclear receptor ROR-gamma isoform 1"
                     /protein_id="NP_035411.2"
                     /db_xref="CCDS:CCDS17591.1"
                     /db_xref="GeneID:19885"
                     /db_xref="MGI:MGI:104856"
                     /translation="MDRAPQRHHRTSRELLAAKKTHTSQIEVIPCKICGDKSSGIHYG
                     VITCEGCKGFFRRSQQCNVAYSCTRQQNCPIDRTSRNRCQHCRLQKCLALGMSRDAVK
                     FGRMSKKQRDSLHAEVQKQLQQQQQQEQVAKTPPAGSRGADTLTYTLGLSDGQLPLGA
                     SPDLPEASACPPGLLRASGSGPPYSNTLAKTEVQGASCHLEYSPERGKAEGRDSIYST
                     DGQLTLGRCGLRFEETRHPELGEPEQGPDSHCIPSFCSAPEVPYASLTDIEYLVQNVC
                     KSFRETCQLRLEDLLRQRTNLFSREEVTSYQRKSMWEMWERCAHHLTEAIQYVVEFAK
                     RLSGFMELCQNDQIILLKAGAMEVVLVRMCRAYNANNHTVFFEGKYGGVELFRALGCS
                     ELISSIFDFSHFLSALCFSEDEIALYTALVLINANRPGLQEKRRVEHLQYNLELAFHH
                     HLCKTHRQGLLAKLPPKGKLRSLCSQHVEKLQIFQHLHPIVVQAAFPPLYKELFSTDV
                     ESPEGLSK"
     exon            139..168
                     /gene="Rorc"
                     /gene_synonym="Nr1f3; RORgamma; Thor; TOR"
                     /inference="alignment:Splign:2.1.0"
     exon            169..254
                     /gene="Rorc"
                     /gene_synonym="Nr1f3; RORgamma; Thor; TOR"
                     /inference="alignment:Splign:2.1.0"
     exon            255..396
                     /gene="Rorc"
                     /gene_synonym="Nr1f3; RORgamma; Thor; TOR"
                     /inference="alignment:Splign:2.1.0"
     exon            397..903
                     /gene="Rorc"
                     /gene_synonym="Nr1f3; RORgamma; Thor; TOR"
                     /inference="alignment:Splign:2.1.0"
     exon            904..1025
                     /gene="Rorc"
                     /gene_synonym="Nr1f3; RORgamma; Thor; TOR"
                     /inference="alignment:Splign:2.1.0"
     exon            1026..1158
                     /gene="Rorc"
                     /gene_synonym="Nr1f3; RORgamma; Thor; TOR"
                     /inference="alignment:Splign:2.1.0"
     exon            1159..1266
                     /gene="Rorc"
                     /gene_synonym="Nr1f3; RORgamma; Thor; TOR"
                     /inference="alignment:Splign:2.1.0"
     exon            1267..1377
                     /gene="Rorc"
                     /gene_synonym="Nr1f3; RORgamma; Thor; TOR"
                     /inference="alignment:Splign:2.1.0"
     exon            1378..1487
                     /gene="Rorc"
                     /gene_synonym="Nr1f3; RORgamma; Thor; TOR"
                     /inference="alignment:Splign:2.1.0"
     exon            1488..2572
                     /gene="Rorc"
                     /gene_synonym="Nr1f3; RORgamma; Thor; TOR"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      
        1 aggtgctccc tccctcttcc ctcctccctc ccttgggccc tgctccctgc cctcctgggc
       61 agccagggca gcaaggacgg caccaaggga gctaccccat ggacagggcc ccacagagac
      121 accaccggac atctcgggag ctgctggctg caaagaagac ccacacctca caaattgaag
      181 tgatcccttg caagatctgt ggggacaagt catctgggat ccactacggg gttatcacct
      241 gtgaggggtg caagggcttc ttccgccgca gccagcagtg taatgtggcc tactcctgca
      301 cgcgtcagca gaactgcccc attgaccgaa ccagccgcaa ccgatgccag cattgccgcc
      361 tgcagaagtg cctggctctg ggcatgtccc gagatgctgt caagtttggc cgaatgtcca
      421 agaagcagag ggacagtcta catgcagaag tgcagaaaca actgcaacag cagcagcaac
      481 aggaacaagt ggccaagact cctccagctg ggagccgcgg agcagacaca cttacataca
      541 ctttagggct ctcagatggg cagctaccac tgggcgcctc acctgaccta cccgaggcct
      601 ctgcttgtcc ccctggcctc ctgagagcct caggctctgg cccaccatat tccaatacct
      661 tggccaaaac agaggtccag ggggcctcct gccaccttga gtatagtcca gaacgaggca
      721 aagctgaagg cagagacagc atctatagca ctgacggcca acttactctt ggaagatgtg
      781 gacttcgttt tgaggaaacc aggcatcctg aacttgggga accagaacag ggtccagaca
      841 gccactgcat tcccagtttc tgcagtgccc cagaggtacc atatgcctct ctgacagaca
      901 tagagtacct ggtacagaat gtctgcaagt ccttccgaga gacatgccag ctgcgactgg
      961 aggaccttct acggcagcgc accaacctct tttcacggga ggaggtgacc agctaccaga
     1021 ggaagtcaat gtgggagatg tgggagcgct gtgcccacca cctcactgag gccattcagt
     1081 atgtggtgga gtttgccaag cggctttcag gcttcatgga gctctgccag aatgaccaga
     1141 tcatactact gaaagcagga gcaatggaag tcgtcctagt cagaatgtgc agggcctaca
     1201 atgccaacaa ccacacagtc ttttttgaag gcaaatacgg tggtgtggag ctgtttcgag
     1261 ccttgggctg cagcgagctc atcagctcca tatttgactt ttcccacttc ctcagcgccc
     1321 tgtgtttttc tgaggatgag attgccctct acacggccct ggttctcatc aatgccaacc
     1381 gtcctgggct ccaagagaag aggagagtgg aacatctgca atacaatttg gaactggctt
     1441 tccatcatca tctctgcaag actcatcgac aaggcctcct agccaagctg ccacccaaag
     1501 gaaaactccg gagcctgtgc agccaacatg tggaaaagct gcagatcttc cagcacctcc
     1561 accccatcgt ggtccaagcc gccttccctc cactctataa ggaactcttc agcactgatg
     1621 ttgaatcccc tgaggggctg tcaaagtgat ctggaggaag gacaactttc tatttccttc
     1681 agccctctga cccgtctccc tggactccct tcacccagcc tttccctttc tgcactctat
     1741 gaagggtggt atccctagga gtaagcaaat cctaagactg attttctgcc cctaggcttg
     1801 ccttgtagga caacagcagc aagtgatgga gaaaaggctt gttatgtttg atttcccata
     1861 agttccaccc tggcttctgg aagctgtggg gtagatggga tagagatagg atgaccaagt
     1921 caaataaaaa acagactgac aatcagcagg gataaatcca ggtacctggg ataaggagaa
     1981 ctcaaatcta ggcttgaaag ctaataacag tcctttcaat acctcattgt atttccccat
     2041 gggtcctcct ggggggacat ggatctagct cagagactgg tggcaagccc ccagaaggac
     2101 ctgtatataa taagaatata gattcctgag acttttctgc ctttcttctt cctagttaag
     2161 aaatgttgtt gaccccctct gcctgttttc tgggacctaa aatgcctgga tgtgtaaaga
     2221 atgagggtgg ggtggagata aggtcccaag ataactgttt tatggggttt gggtatgaag
     2281 aaaaacatca ctggaaaaat tagaatggaa acctctttgc acactttaaa agtgtcagat
     2341 tcgttagcag tctaatcaga gacacacatc cacacaggtg gagcacacag aggctctgcc
     2401 cccagtgaca ccattctgta gactttccct ctggcacaca atctcttcct tgaggttgca
     2461 gctctgagaa gcctgaggtt ctaattcata caggacacca gaattcatcc cagctccagc
     2521 tgtcctctgt ccctaagaga agcagaggac cggatactaa ccagccggaa aa
//
