LOCUS       NM_007741               2746 bp    mRNA    linear   ROD 16-OCT-2024
DEFINITION  Mus musculus collagen, type IX, alpha 2 (Col9a2), mRNA.
ACCESSION   NM_007741
VERSION     NM_007741.2
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 2746)
  AUTHORS   Patel,V.N., Aure,M.H., Choi,S.H., Ball,J.R., Lane,E.D., Wang,Z.,
            Xu,Y., Zheng,C., Liu,X., Martin,D., Pailin,J.Y., Prochazkova,M.,
            Kulkarni,A.B., van Kuppevelt,T.H., Ambudkar,I.S., Liu,J. and
            Hoffman,M.P.
  TITLE     Specific 3-O-sulfated heparan sulfate domains regulate salivary
            gland basement membrane metabolism and epithelial differentiation
  JOURNAL   Nat Commun 15 (1), 7584 (2024)
   PUBMED   39217171
  REMARK    Erratum:[Nat Commun. 2024 Oct 10;15(1):8784. doi:
            10.1038/s41467-024-53230-4. PMID: 39389981]
            Publication Status: Online-Only
REFERENCE   2  (bases 1 to 2746)
  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   3  (bases 1 to 2746)
  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   4  (bases 1 to 2746)
  AUTHORS   Vong,K.I., Ma,T.C., Li,B., Leung,T.C.N., Nong,W., Ngai,S.M.,
            Hui,J.H.L., Jiang,L. and Kwan,K.M.
  TITLE     SOX9-COL9A3-dependent regulation of choroid plexus epithelial
            polarity governs blood-cerebrospinal fluid barrier integrity
  JOURNAL   Proc Natl Acad Sci U S A 118 (6) (2021)
   PUBMED   33526661
REFERENCE   5  (bases 1 to 2746)
  AUTHORS   Koppes,E., Shaffer,B., Sadovsky,E., Himes,K., Barak,Y., Sadovsky,Y.
            and Chaillet,J.R.
  TITLE     Klf14 is an imprinted transcription factor that regulates placental
            growth
  JOURNAL   Placenta 88, 61-67 (2019)
   PUBMED   31675530
REFERENCE   6  (bases 1 to 2746)
  AUTHORS   Warman,M.L., McCarthy,M.T., Perala,M., Vuorio,E., Knoll,J.H.,
            McDaniels,C.N., Mayne,R., Beier,D.R. and Olsen,B.R.
  TITLE     The genes encoding alpha 2(IX) collagen (COL9A2) map to human
            chromosome 1p32.3-p33 and mouse chromosome 4
  JOURNAL   Genomics 23 (1), 158-162 (1994)
   PUBMED   7829066
REFERENCE   7  (bases 1 to 2746)
  AUTHORS   Perala,M., Elima,K., Metsaranta,M., Rosati,R., de Crombrugghe,B.
            and Vuorio,E.
  TITLE     The exon structure of the mouse alpha 2(IX) collagen gene shows
            unexpected divergence from the chick gene
  JOURNAL   J Biol Chem 269 (7), 5064-5071 (1994)
   PUBMED   8106484
REFERENCE   8  (bases 1 to 2746)
  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
REFERENCE   9  (bases 1 to 2746)
  AUTHORS   Perala,M., Hanninen,M., Hastbacka,J., Elima,K. and Vuorio,E.
  TITLE     Molecular cloning of the human alpha 2(IX) collagen cDNA and
            assignment of the human COL9A2 gene to chromosome 1
  JOURNAL   FEBS Lett 319 (1-2), 177-180 (1993)
   PUBMED   8454052
REFERENCE   10 (bases 1 to 2746)
  AUTHORS   Elima,K., Metsaranta,M., Kallio,J., Perala,M., Eerola,I.,
            Garofalo,S., De Crombrugghe,B. and Vuorio,E.
  TITLE     Specific hybridization probes for mouse alpha 2(IX) and alpha 1(X)
            collagen mRNAs
  JOURNAL   Biochim Biophys Acta 1130 (1), 78-80 (1992)
   PUBMED   1543751
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            BY732235.1, BY088510.1, BY232299.1, BU512853.1, CJ046324.1,
            AA171281.1, CX243824.1, BQ964231.1, CJ312879.1 and BB732275.1.
            
            On Apr 21, 2009 this sequence version replaced NM_007741.1.
            
            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 :: BC029697.1, SRR7652917.343854.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN00849374, SAMN00849375
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on single protein-coding transcript
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-671               BY732235.1         2-672
            672-749             BY088510.1         307-384
            750-935             BY232299.1         10-195
            936-936             BU512853.1         843-843
            937-1041            BY232299.1         197-301
            1042-1342           CJ046324.1         15-315
            1343-1589           AA171281.1         157-403
            1590-2165           CX243824.1         102-677
            2166-2349           BQ964231.1         404-587
            2350-2740           CJ312879.1         143-533
            2741-2746           BB732275.1         432-437
FEATURES             Location/Qualifiers
     source          1..2746
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="4"
                     /map="4 56.78 cM"
     gene            1..2746
                     /gene="Col9a2"
                     /gene_synonym="Col9a-2"
                     /note="collagen, type IX, alpha 2"
                     /db_xref="GeneID:12840"
                     /db_xref="MGI:MGI:88466"
     exon            1..221
                     /gene="Col9a2"
                     /gene_synonym="Col9a-2"
                     /inference="alignment:Splign:2.1.0"
     exon            222..296
                     /gene="Col9a2"
                     /gene_synonym="Col9a-2"
                     /inference="alignment:Splign:2.1.0"
     exon            297..332
                     /gene="Col9a2"
                     /gene_synonym="Col9a-2"
                     /inference="alignment:Splign:2.1.0"
     exon            333..395
                     /gene="Col9a2"
                     /gene_synonym="Col9a-2"
                     /inference="alignment:Splign:2.1.0"
     exon            396..449
                     /gene="Col9a2"
                     /gene_synonym="Col9a-2"
                     /inference="alignment:Splign:2.1.0"
     exon            450..485
                     /gene="Col9a2"
                     /gene_synonym="Col9a-2"
                     /inference="alignment:Splign:2.1.0"
     exon            486..509
                     /gene="Col9a2"
                     /gene_synonym="Col9a-2"
                     /inference="alignment:Splign:2.1.0"
     exon            510..563
                     /gene="Col9a2"
                     /gene_synonym="Col9a-2"
                     /inference="alignment:Splign:2.1.0"
     exon            564..617
                     /gene="Col9a2"
                     /gene_synonym="Col9a-2"
                     /inference="alignment:Splign:2.1.0"
     exon            618..665
                     /gene="Col9a2"
                     /gene_synonym="Col9a-2"
                     /inference="alignment:Splign:2.1.0"
     exon            666..722
                     /gene="Col9a2"
                     /gene_synonym="Col9a-2"
                     /inference="alignment:Splign:2.1.0"
     exon            723..776
                     /gene="Col9a2"
                     /gene_synonym="Col9a-2"
                     /inference="alignment:Splign:2.1.0"
     exon            777..830
                     /gene="Col9a2"
                     /gene_synonym="Col9a-2"
                     /inference="alignment:Splign:2.1.0"
     exon            831..884
                     /gene="Col9a2"
                     /gene_synonym="Col9a-2"
                     /inference="alignment:Splign:2.1.0"
     exon            885..938
                     /gene="Col9a2"
                     /gene_synonym="Col9a-2"
                     /inference="alignment:Splign:2.1.0"
     exon            939..992
                     /gene="Col9a2"
                     /gene_synonym="Col9a-2"
                     /inference="alignment:Splign:2.1.0"
     exon            993..1046
                     /gene="Col9a2"
                     /gene_synonym="Col9a-2"
                     /inference="alignment:Splign:2.1.0"
     exon            1047..1100
                     /gene="Col9a2"
                     /gene_synonym="Col9a-2"
                     /inference="alignment:Splign:2.1.0"
     exon            1101..1154
                     /gene="Col9a2"
                     /gene_synonym="Col9a-2"
                     /inference="alignment:Splign:2.1.0"
     exon            1155..1199
                     /gene="Col9a2"
                     /gene_synonym="Col9a-2"
                     /inference="alignment:Splign:2.1.0"
     exon            1200..1253
                     /gene="Col9a2"
                     /gene_synonym="Col9a-2"
                     /inference="alignment:Splign:2.1.0"
     exon            1254..1307
                     /gene="Col9a2"
                     /gene_synonym="Col9a-2"
                     /inference="alignment:Splign:2.1.0"
     exon            1308..1361
                     /gene="Col9a2"
                     /gene_synonym="Col9a-2"
                     /inference="alignment:Splign:2.1.0"
     exon            1362..1433
                     /gene="Col9a2"
                     /gene_synonym="Col9a-2"
                     /inference="alignment:Splign:2.1.0"
     exon            1434..1469
                     /gene="Col9a2"
                     /gene_synonym="Col9a-2"
                     /inference="alignment:Splign:2.1.0"
     exon            1470..1514
                     /gene="Col9a2"
                     /gene_synonym="Col9a-2"
                     /inference="alignment:Splign:2.1.0"
     exon            1515..1547
                     /gene="Col9a2"
                     /gene_synonym="Col9a-2"
                     /inference="alignment:Splign:2.1.0"
     exon            1548..1694
                     /gene="Col9a2"
                     /gene_synonym="Col9a-2"
                     /inference="alignment:Splign:2.1.0"
     exon            1695..1749
                     /gene="Col9a2"
                     /gene_synonym="Col9a-2"
                     /inference="alignment:Splign:2.1.0"
     exon            1750..1938
                     /gene="Col9a2"
                     /gene_synonym="Col9a-2"
                     /inference="alignment:Splign:2.1.0"
     exon            1939..2016
                     /gene="Col9a2"
                     /gene_synonym="Col9a-2"
                     /inference="alignment:Splign:2.1.0"
     exon            2017..2746
                     /gene="Col9a2"
                     /gene_synonym="Col9a-2"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2717..2722
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Col9a2"
                     /gene_synonym="Col9a-2"
                     /note="hexamer: AATAAA"
     polyA_site      2743
                     /gene="Col9a2"
                     /gene_synonym="Col9a-2"
                     /note="major polyA site"
ORIGIN      
        1 agttcctccc cacagtgctc tcaggtgaca ggcctgcagg tccccgcccc ggcccgtcta
       61 gctgcgtttt cgggagatcc agtccgaggc tccgaaagca gcccccgcca tcggtgcttg
      121 gacccccgct ccagaacccg ctgttcgcca tgaccgccgt gcccgcgccc cgcagcctgt
      181 tcgttctcct ccaggtgctg tggctcgccc tggctcagat cagaggtcca ccaggggagc
      241 cgggtcctcc agggccacca gggccaccag gagtgcctgg ttcagatggc atcgacggtg
      301 acaaggggcc tccaggtaaa gttggtcctc cgggatccaa aggagagcct ggcaaacctg
      361 gcccagatgg tccagatggg aaacctggca ttgatggttt aatgggagcc aagggagagc
      421 ctggtcccgt ggggacccct ggagtcaagg gccagcctgg gctcccaggg ccccctggcc
      481 tgccgggccc tggttttgct ggacctcccg gaccccctgg acctgttggc ctccctggtg
      541 agattggaac cccaggcccc aagggggatc caggaccaga gggaccatca gggcccccag
      601 ggccccctgg gaaaccaggc cgaccaggaa ccatccaggg cttggaaggg agtgcggatt
      661 tcttgtgtcc aaccaactgt ccagctggtg tgaagggtcc tcagggtttg caaggagtga
      721 agggtcatcc aggcaaacgg gggattctgg gtgatcctgg tcgccagggg aagccaggtc
      781 ccaagggaga tgtgggtgcc tctggagagc aaggcatccc tggaccaccg ggcccccaag
      841 gcatcagggg ctacccgggc atggcaggac ccaagggaga gatgggtcct cgtggctata
      901 aaggcatggt gggctccatc ggggctgctg ggccaccggg tgaagaaggc ccaagagggc
      961 caccaggccg agccggtgag aagggggatg tggggagcca aggtgccaga ggaccccagg
     1021 ggataacagg cccaaaggga acaaccggtc caccaggcat tgatggcaag gatgggaccc
     1081 caggcattcc tggcatgaag ggcagtgcag gacaagtggg acggccagga agcccaggcc
     1141 accagggctt agcgggtgtg ccgggtcagc ctggaacaaa aggaggtcct ggagacaagg
     1201 gtgaaccagg ccagcagggc ttgccgggag tctctggtcc ccctgggaaa gaaggggagc
     1261 cagggcctcg aggagaaatt ggtccacagg gcatcatggg acagaagggt gaccagggcg
     1321 agagggggcc agtgggacag ccaggccctc aaggacgaca gggccccaaa ggagagcagg
     1381 gccctccagg aattccagga ccccaaggct tgccaggcat caaaggagat aagggttccc
     1441 cagggaagac cgggccccga ggcggagtgg gtgacccggg ggtggccggc ctcccgggag
     1501 agaaaggaga gaagggccaa tcaggcgagc cagggcttaa gggacagcaa ggagtccgtg
     1561 gagagaccgg ctaccccggc cccagcggag atgccggtgc cccaggagtg cagggctacc
     1621 ccgggcttcc cgggccccga ggactggtgg gagatcgagg cgtgccagga caacccggga
     1681 gacagggtgt ggtgggccga gccgccagtg accagcacat cgtggatgtg gtgctgaaga
     1741 tgattcaaga gcaacttgct gaggtagctg tgagtgccaa gcgagaagcc ctgggtgcag
     1801 cagggatggt gggccttcca ggacctcctg ggccccctgg atatccaggc aaacaggggc
     1861 ccaatgggca tcccggcccc cgaggcattc ctggcatcgt gggagcagtg ggtcagattg
     1921 gcaacactgg acccaaggga aagcgtggag agaaggggga tcgaggagaa atgggtcgtg
     1981 gccatcccgg gatgcctggg cccccaggga tcccaggtct tcctggccgg cctggccagg
     2041 caatcaatgg caaggatggg gaccgaggat ccccaggggc tccaggagag gctgggagac
     2101 ctggccggcc aggcccagtg gggctaccag gtttctgtga gcctgccgca tgcctggggg
     2161 cttcagccta tacctctgct cgcctcacag agcctgggtc catcaagggg ccatgagcaa
     2221 ccagccagga cagagcctat tagtgtctag ggtcacttct gggtggacat gtactccaga
     2281 cccaggaggc tagatttctc aggatcttct ggaaacccaa gatccagggg ttctgaagac
     2341 aagttcagtg agggaggggt tgggggaggg agagcacggg agtaaaggtg aggccaacag
     2401 agccaagtat tggagagcca cccctcccaa gggaagaggg tagcttctct tcctggagta
     2461 ccaactaccc ctcacccatg cctttcagca ctgggccatc ccaccctcgg ggcagggggg
     2521 actgaggctt ctggtggtcc ttaccctatt cttattctct ggacttattt ttattgggta
     2581 tcttttgggg gagaatacct tgaggtggca gttcttaggc cagccctgct attgcctgtc
     2641 tcccatccca gtatttaaac atccatcttc cctgttcccc agtctctttt gcccacacca
     2701 ctctggcctt tgtgtaaata aaagttcctc agttggttac aaagtg
//
