LOCUS       NM_009936               2846 bp    mRNA    linear   ROD 30-APR-2024
DEFINITION  Mus musculus collagen, type IX, alpha 3 (Col9a3), transcript
            variant 2, mRNA.
ACCESSION   NM_009936
VERSION     NM_009936.2
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 2846)
  AUTHORS   Adams,D.J., Barlas,B., McIntyre,R.E., Salguero,I., van der
            Weyden,L., Barros,A., Vicente,J.R., Karimpour,N., Haider,A.,
            Ranzani,M., Turner,G., Thompson,N.A., Harle,V., Olvera-Leon,R.,
            Robles-Espinoza,C.D., Speak,A.O., Geisler,N., Weninger,W.J.,
            Geyer,S.H., Hewinson,J., Karp,N.A., Fu,B., Yang,F., Kozik,Z.,
            Choudhary,J., Yu,L., van Ruiten,M.S., Rowland,B.D., Lelliott,C.J.,
            Del Castillo Velasco-Herrera,M., Verstraten,R., Bruckner,L.,
            Henssen,A.G., Rooimans,M.A., de Lange,J., Mohun,T.J., Arends,M.J.,
            Kentistou,K.A., Coelho,P.A., Zhao,Y., Zecchini,H., Perry,J.R.B.,
            Jackson,S.P. and Balmus,G.
  CONSRTM   Sanger Mouse Genetics Project
  TITLE     Genetic determinants of micronucleus formation in vivo
  JOURNAL   Nature 627 (8002), 130-136 (2024)
   PUBMED   38355793
REFERENCE   2  (bases 1 to 2846)
  AUTHORS   Prokopuk,L., Jarred,E.G., Blucher,R.O., McLaughlin,E.A.,
            Stringer,J.M. and Western,P.S.
  TITLE     An essential role for Polycomb Repressive Complex 2 in the mouse
            ovary
  JOURNAL   Reproduction 163 (3), 167-182 (2022)
   PUBMED   35084365
  REMARK    Publication Status: Online-Only
REFERENCE   3  (bases 1 to 2846)
  AUTHORS   Wen,Y., Ma,X., Wang,X., Wang,F., Dong,J., Wu,Y., Lv,C., Liu,K.,
            Zhang,Y., Zhang,Z. and Yuan,S.
  TITLE     hnRNPU in Sertoli cells cooperates with WT1 and is essential for
            testicular development by modulating transcriptional factors Sox8/9
  JOURNAL   Theranostics 11 (20), 10030-10046 (2021)
   PUBMED   34815802
  REMARK    Publication Status: Online-Only
REFERENCE   4  (bases 1 to 2846)
  AUTHORS   Martinez,M.E. and Hernandez,A.
  TITLE     The Type 3 Deiodinase Is a Critical Modulator of Thyroid Hormone
            Sensitivity in the Fetal Brain
  JOURNAL   Front Neurosci 15, 703730 (2021)
   PUBMED   34248495
  REMARK    Publication Status: Online-Only
REFERENCE   5  (bases 1 to 2846)
  AUTHORS   Wilkerson,B.A., Zebroski,H.L., Finkbeiner,C.R., Chitsazan,A.D.,
            Beach,K.E., Sen,N., Zhang,R.C. and Bermingham-McDonogh,O.
  TITLE     Novel cell types and developmental lineages revealed by single-cell
            RNA-seq analysis of the mouse crista ampullaris
  JOURNAL   Elife 10, e60108 (2021)
   PUBMED   34003106
  REMARK    Publication Status: Online-Only
REFERENCE   6  (bases 1 to 2846)
  AUTHORS   Llor,X., Serfas,M.S., Bie,W., Vasioukhin,V., Polonskaia,M.,
            Derry,J., Abbott,C.M. and Tyner,A.L.
  TITLE     BRK/Sik expression in the gastrointestinal tract and in colon
            tumors
  JOURNAL   Clin Cancer Res 5 (7), 1767-1777 (1999)
   PUBMED   10430081
REFERENCE   7  (bases 1 to 2846)
  AUTHORS   Aszodi,A., Chan,D., Hunziker,E., Bateman,J.F. and Fassler,R.
  TITLE     Collagen II is essential for the removal of the notochord and the
            formation of intervertebral discs
  JOURNAL   J Cell Biol 143 (5), 1399-1412 (1998)
   PUBMED   9832566
REFERENCE   8  (bases 1 to 2846)
  AUTHORS   Savontaus,M., Metsaranta,M. and Vuorio,E.
  TITLE     Mutation in type II collagen gene disturbs spinal development and
            gene expression patterns in transgenic Del1 mice
  JOURNAL   Lab Invest 77 (6), 591-600 (1997)
   PUBMED   9426396
REFERENCE   9  (bases 1 to 2846)
  AUTHORS   Perala,M., Savontaus,M., Metsaranta,M. and Vuorio,E.
  TITLE     Developmental regulation of mRNA species for types II, IX and XI
            collagens during mouse embryogenesis
  JOURNAL   Biochem J 324 (Pt 1) (Pt 1), 209-216 (1997)
   PUBMED   9164858
REFERENCE   10 (bases 1 to 2846)
  AUTHORS   Abe,N., Yoshioka,H., Inoue,H. and Ninomiya,Y.
  TITLE     The complete primary structure of the long form of mouse alpha
            1(IX) collagen chain and its expression during limb development
  JOURNAL   Biochim Biophys Acta 1204 (1), 61-67 (1994)
   PUBMED   8305476
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            CK623954.1, AK030350.1 and AK038481.1.
            
            On Aug 16, 2006 this sequence version replaced NM_009936.1.
            
            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 :: AK030350.1, AF349718.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN00849375, SAMN00849383
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-22                CK623954.1         1-22
            23-1049             AK030350.1         2-1028
            1050-1349           AK038481.1         827-1126
            1350-2846           AK030350.1         1329-2825
FEATURES             Location/Qualifiers
     source          1..2846
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="2"
                     /map="2 103.14 cM"
     gene            1..2846
                     /gene="Col9a3"
                     /note="collagen, type IX, alpha 3"
                     /db_xref="GeneID:12841"
                     /db_xref="MGI:MGI:894686"
     exon            1..104
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     exon            105..173
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     exon            174..209
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     exon            210..281
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     exon            282..335
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     exon            336..371
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     exon            372..395
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     exon            396..449
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     exon            450..503
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     exon            504..545
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     exon            546..602
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     exon            603..656
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     exon            657..710
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     exon            711..764
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     exon            765..818
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     exon            819..872
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     exon            873..926
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     exon            927..980
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     exon            981..1034
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     exon            1035..1079
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     exon            1080..1133
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     exon            1134..1187
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     exon            1188..1241
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     exon            1242..1313
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     exon            1314..1349
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     exon            1350..1394
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     exon            1395..1427
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     exon            1428..1574
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     exon            1575..1629
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     exon            1630..1812
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     exon            1813..1890
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     exon            1891..2846
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2082..2087
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Col9a3"
                     /note="hexamer: AACAAG"
     polyA_site      2102
                     /gene="Col9a3"
                     /note="major polyA site"
     regulatory      2438..2443
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Col9a3"
                     /note="hexamer: AATAAA"
     polyA_site      2462
                     /gene="Col9a3"
                     /note="major polyA site"
     regulatory      2594..2599
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Col9a3"
                     /note="hexamer: AATAAA"
     polyA_site      2614
                     /gene="Col9a3"
                     /note="major polyA site"
ORIGIN      
        1 cgtcgctcgg cgcctgccgc tcagagcgcc tgccagccat gaccggagcg cctgccctag
       61 ccctgctgct gctggggcag ctcctgacgg ccacctccgc gcagaaagtg ggaccccgag
      121 gcccccctgg tccccaaggg cctcctggaa aacccggcaa ggatggcatt gatggagaag
      181 ctggccctcc aggtctgcct ggccttccag gacccaaagg gacctcaggg aagccaggga
      241 agccgggaga ggcaggactg ccaggactgc ctggtgtaga tggtctgaca gggagagatg
      301 gacccgcagg acccaaaggt gcccctggag aacggggaag tctaggaccc ccagggccac
      361 caggacttgg gggcaaaggc ctccctggac ctcctggaga ggcaggagtg agtggcctcc
      421 caggtgggat tggtctacgt ggccccccgg gaccctctgg acttccagga ctgcctggcc
      481 tcccaggacc tcctggacct cctggaaacc ctggagtcct ccctgaaggt gctactgatc
      541 tgcagtgtcc cgccatctgc ccgccaggcc ctccgggacc cccaggaatg ccggggttca
      601 aggggcctac tggctacaaa ggggaacaag gagaagttgg caaagatggt gagaagggta
      661 gtcctggccc ccccgggcct cctggaatcc caggcaccgt ggggctacag ggcccacgag
      721 gattaagagg acttccaggg ccactcgggc cccctgggga ccggggtccc attgggtttc
      781 ggggcccccc tgggacccca ggagcacctg ggaaagtggg tgacaggggt gaaaggggac
      841 cagaagggtt ccgtggccct aagggtgacc tgggcaggcc tggtcccaaa ggaatccctg
      901 gaatggctgg gccaggcgga gaaccaggca tgccaggcaa ggatggcaaa gatggtgtgc
      961 cgggacttga tggtgagaag ggagaggctg gtcgcaatgg tggccaagga gagaaaggcc
     1021 ccaatgggct gccggggctc cctggacgag cagggtccaa aggcgagaag ggagaaccgg
     1081 gtagaactgg cgagctgggt gaggctggcc cctctggaga gccaggtatc cctggagatg
     1141 ttggtgttcc aggggagcgt ggtgaggctg gtcacagggg ctccgtggga gctcttggcc
     1201 cacaaggtcc tcctggtgct cctggcatcc gtggctttca gggacaaaaa ggcagcacag
     1261 gagaccctgg ccttccgggc ccccaaggcc tacggggaga tgtgggtgac cggggtccag
     1321 gaggtgccac aggccctaag ggagaccagg gcattgcagg ttccgatggt cttccagggg
     1381 acaaaggcga gctgggtcct aatggccccg ttggacaaaa aggagagtct ggcagccgag
     1441 gggaactggg ccccaaaggc atccagggcc ccaatggcac cagtggagtc cagggtgtac
     1501 ctggtccccc aggtccactg ggcctccaag gtgtgcaggg tgtcccaggc atcaccggga
     1561 agcctggagt tccgggcaag gaagccagtg aacagcgcat cagggagcta tgcgggggta
     1621 tgatcagtga gcaaattgca cagttggctg cacacctgag gaagccctta gcaccaggct
     1681 ccatcggcag gcctggtcca gctggccccc caggccctcc aggccctcca ggctctattg
     1741 gccaccctgg cgctcggggt ccccctggat accgtggtcc cactggggaa ctaggagatc
     1801 ctggaccaag agggagccag ggtgacagag gggacaaggg agcaacaggt gcagggctgg
     1861 atgggcctgc tggggaccag ggctaccaag ggcctcaagg tgtacctggc atcagcaaag
     1921 atggtcgaga tggtgctcat ggtgagcctg gccttcccgg tgatcctggc cttcctggag
     1981 ctgctggtgc tcagggtacc ccagggatct gcgacacttc agcctgccaa ggagctgtgt
     2041 tagggggagg tggggaaaag tcgggtcctc ggagctcata aaacaaggac ttcagtagga
     2101 aatggctcca tatttcctac tgaaatacga gagcactcca gcaggcagca gggatgagcg
     2161 gtgtggctat ggacagaaat ggacagtggc tggctacagt tggtccttca tggcctgctg
     2221 cttggcccca agaacatcta ttggcagcac tgtcactgtc ccatctccaa gatttatggc
     2281 agcccaatac ctcagacaca ggccttaggg atggagactt taaacccagc atctgggagg
     2341 gatggtgtta tctaagagtt ttgtacaatt ccatgagata aaaacactca agagacttgt
     2401 ttacataaca tttatataaa gcctatgata gactaccaat aaagtgatct tctaaccctt
     2461 cagattagta ctggttatag tgtgatgaag gcaaggaact taatgtctac tttgcctgct
     2521 ttctattgca aacttagtat ctctgatgcc tagtgtttat tcaaggaact acactgcacc
     2581 atctgttaaa ataaataaag cgactcactg ggaacctttg ttccaaacat acagtttatt
     2641 acacataaag cactgcctca caatatggaa atgtgggcat taaagcaatg tactgcgaaa
     2701 atgtttatgg gcaaaaggag ctttaaaaga agtctctgga aaattcttag caaagtttta
     2761 aaatggcact gcattttcca atagagtacc atgagactgg aaataggggg gacagaacaa
     2821 atgaaataaa gtttccaaac ctcttc
//
