LOCUS       NM_001100842            3830 bp    mRNA    linear   ROD 03-APR-2024
DEFINITION  Rattus norvegicus collagen type IX alpha 1 chain (Col9a1), mRNA.
ACCESSION   NM_001100842
VERSION     NM_001100842.1
KEYWORDS    RefSeq; RefSeq Select.
SOURCE      Rattus norvegicus (Norway rat)
  ORGANISM  Rattus norvegicus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
            Muroidea; Muridae; Murinae; Rattus.
REFERENCE   1  (bases 1 to 3830)
  AUTHORS   Usami,S., Takumi,Y., Suzuki,N., Oguchi,T., Oshima,A., Suzuki,H.,
            Kitoh,R., Abe,S., Sasaki,A. and Matsubara,A.
  TITLE     The localization of proteins encoded by CRYM, KIAA1199, UBA52,
            COL9A3, and COL9A1, genes highly expressed in the cochlea
  JOURNAL   Neuroscience 154 (1), 22-28 (2008)
   PUBMED   18448257
  REMARK    GeneRIF: Collagen type IX alpha1 was found within the tectorial
            membrane as well as fibrocytes in the spiral ligament.
REFERENCE   2  (bases 1 to 3830)
  AUTHORS   Posey,K.L., Hankenson,K., Veerisetty,A.C., Bornstein,P., Lawler,J.
            and Hecht,J.T.
  TITLE     Skeletal abnormalities in mice lacking extracellular matrix
            proteins, thrombospondin-1, thrombospondin-3, thrombospondin-5, and
            type IX collagen
  JOURNAL   Am J Pathol 172 (6), 1664-1674 (2008)
   PUBMED   18467703
REFERENCE   3  (bases 1 to 3830)
  AUTHORS   Blumbach,K., Niehoff,A., Paulsson,M. and Zaucke,F.
  TITLE     Ablation of collagen IX and COMP disrupts epiphyseal cartilage
            architecture
  JOURNAL   Matrix Biol 27 (4), 306-318 (2008)
   PUBMED   18191556
REFERENCE   4  (bases 1 to 3830)
  AUTHORS   Czarny-Ratajczak,M., Lohiniva,J., Rogala,P., Kozlowski,K.,
            Perala,M., Carter,L., Spector,T.D., Kolodziej,L., Seppanen,U.,
            Glazar,R., Krolewski,J., Latos-Bielenska,A. and Ala-Kokko,L.
  TITLE     A mutation in COL9A1 causes multiple epiphyseal dysplasia: further
            evidence for locus heterogeneity
  JOURNAL   Am J Hum Genet 69 (5), 969-980 (2001)
   PUBMED   11565064
REFERENCE   5  (bases 1 to 3830)
  AUTHORS   Aszodi,A., Hunziker,E.B., Olsen,B.R. and Fassler,R.
  TITLE     The role of collagen II and cartilage fibril-associated molecules
            in skeletal development
  JOURNAL   Osteoarthritis Cartilage 9 Suppl A, S150-S159 (2001)
   PUBMED   11680679
REFERENCE   6  (bases 1 to 3830)
  AUTHORS   Aikawa,T., Shirasuna,K., Iwamoto,M., Watatani,K., Nakamura,T.,
            Okura,M., Yoshioka,H. and Matsuya,T.
  TITLE     Establishment of bone morphogenetic protein 2 responsive
            chondrogenic cell line
  JOURNAL   J Bone Miner Res 11 (4), 544-553 (1996)
   PUBMED   8992886
REFERENCE   7  (bases 1 to 3830)
  AUTHORS   Diab,M., Wu,J.J. and Eyre,D.R.
  TITLE     Collagen type IX from human cartilage: a structural profile of
            intermolecular cross-linking sites
  JOURNAL   Biochem J 314 (Pt 1) (Pt 1), 327-332 (1996)
   PUBMED   8660302
REFERENCE   8  (bases 1 to 3830)
  AUTHORS   Fassler,R., Schnegelsberg,P.N., Dausman,J., Shinya,T., Muragaki,Y.,
            McCarthy,M.T., Olsen,B.R. and Jaenisch,R.
  TITLE     Mice lacking alpha 1 (IX) collagen develop noninflammatory
            degenerative joint disease
  JOURNAL   Proc Natl Acad Sci U S A 91 (11), 5070-5074 (1994)
   PUBMED   8197187
REFERENCE   9  (bases 1 to 3830)
  AUTHORS   Ting,K., Petropulos,L.A., Iwatsuki,M. and Nishimura,I.
  TITLE     Altered cartilage phenotype expressed during intramembranous bone
            formation
  JOURNAL   J Bone Miner Res 8 (11), 1377-1387 (1993)
   PUBMED   8266829
REFERENCE   10 (bases 1 to 3830)
  AUTHORS   Kimura,T., Mattei,M.G., Stevens,J.W., Goldring,M.B., Ninomiya,Y.
            and Olsen,B.R.
  TITLE     Molecular cloning of rat and human type IX collagen cDNA and
            localization of the alpha 1(IX) gene on the human chromosome 6
  JOURNAL   Eur J Biochem 179 (1), 71-78 (1989)
   PUBMED   2465149
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            JAXUCZ010000009.1, DY316977.1, DY313373.1 and BQ191679.1.
            
            Sequence Note: This RefSeq record was created from transcript and
            genomic sequence data because no single transcript was available
            for the full length of the gene. The extent of this transcript is
            supported by transcript alignments and orthologous data.
            
            ##Evidence-Data-START##
            RNAseq introns :: mixed sample support SAMEA5760383, SAMEA5760386
                              [ECO:0006172]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on conservation, longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-259               JAXUCZ010000009.1  34081364-34081622
            260-333             JAXUCZ010000009.1  34082046-34082119
            334-411             JAXUCZ010000009.1  34083080-34083157
            412-544             JAXUCZ010000009.1  34083270-34083402
            545-941             JAXUCZ010000009.1  34090052-34090448
            942-1025            JAXUCZ010000009.1  34100980-34101063
            1026-1046           JAXUCZ010000009.1  34101827-34101847
            1047-1121           JAXUCZ010000009.1  34103236-34103310
            1122-1157           JAXUCZ010000009.1  34103644-34103679
            1158-1220           JAXUCZ010000009.1  34103795-34103857
            1221-1274           JAXUCZ010000009.1  34108117-34108170
            1275-1310           JAXUCZ010000009.1  34108445-34108480
            1311-1334           JAXUCZ010000009.1  34110953-34110976
            1335-1388           JAXUCZ010000009.1  34111347-34111400
            1389-1442           JAXUCZ010000009.1  34112969-34113022
            1443-1475           JAXUCZ010000009.1  34113863-34113895
            1476-1532           JAXUCZ010000009.1  34114668-34114724
            1533-1586           JAXUCZ010000009.1  34115937-34115990
            1587-1640           JAXUCZ010000009.1  34121797-34121850
            1641-1694           JAXUCZ010000009.1  34124366-34124419
            1695-1748           JAXUCZ010000009.1  34127567-34127620
            1749-1802           JAXUCZ010000009.1  34129701-34129754
            1803-1856           JAXUCZ010000009.1  34129891-34129944
            1857-1910           JAXUCZ010000009.1  34130075-34130128
            1911-1964           JAXUCZ010000009.1  34130547-34130600
            1965-2009           JAXUCZ010000009.1  34131774-34131818
            2010-2063           JAXUCZ010000009.1  34132688-34132741
            2064-2703           DY316977.1         41-680
            2704-3136           DY313373.1         301-733
            3137-3830           BQ191679.1         1-694               c
FEATURES             Location/Qualifiers
     source          1..3830
                     /organism="Rattus norvegicus"
                     /mol_type="mRNA"
                     /strain="BN"
                     /db_xref="taxon:10116"
                     /chromosome="9"
                     /map="9q21"
     gene            1..3830
                     /gene="Col9a1"
                     /note="collagen type IX alpha 1 chain"
                     /db_xref="GeneID:305104"
                     /db_xref="RGD:1309425"
     exon            1..259
                     /gene="Col9a1"
                     /inference="alignment:Splign:2.1.0"
     CDS             207..3011
                     /gene="Col9a1"
                     /note="collagen alpha-1(IX) chain; procollagen, type IX,
                     alpha 1; collagen, type IX, alpha 1"
                     /codon_start=1
                     /product="collagen alpha-1(IX) chain precursor"
                     /protein_id="NP_001094312.1"
                     /db_xref="GeneID:305104"
                     /db_xref="RGD:1309425"
                     /translation="MVTLINPREPTGKMKNFWKIPLFFFACSFLGPCVSATPKRRARF
                     PANSVSHGGSELCPKIRIGQDDLPGFDLISQFQIEKAASRRTIQRVVGSTALQVAYKL
                     GSNVDFRIPTRHLYPSGLPEEYSFLTTFRMTGSTLEKQWNIWQIQDSSGREQVGVKIN
                     GQTKSVAFSYKGLDGSLQTAAFLNLQSLFDSRWHKLMIGVERTRATLFIDCIQIDSLP
                     IKPRAQIDADGFAVLGKLVDNPQVSVPFELQWMLIHCDPLRPRRETCHELPVRITTSQ
                     TTDERGPPGEQGPPGPPGPPGVPGIDGIDGDRGPKGPPGPPGPPGDPGKPGAPGKPGT
                     PGADGLTGPDGSPGSVGPRGQKGEPGVPGSRGFPGRGIPGPPGPPGTTGLPGELGRVG
                     PAGDPGKRGPPGPPGPPGPSGTIGFHDGDPLCPNSCPPGRSGYPGLPGMRGHKGAKGE
                     IGEPGRQGHKGEEGDQGELGEVGAQGPPGAQGLRGITGIVGDKGEKGARGFDGDPGPQ
                     GVPGAAGDQGQRGPPGETGPKGDRGIQGSRGIPGSPGPKGDTGLPGVDGRDGIPGMPG
                     TKGEAGKPGPPGDAGLQGLPGVPGIPGAKGVAGEKGNTGPPGKPGQLGSSGKPGQQGP
                     PGEVGPRGPRGLPGSRGPVGPEGSPGIPGKLGPLGSPGLPGLPGPPGLPGMKGDRGVF
                     GEPGPKGEQGASGEEGEAGVRGDLGDMGQPGPKGSVGNPGEPGLRGPEGIRGLPGVEG
                     PRGPPGPRGVQGEQGATGLPGIQGPPGRAPTDQHIKQVCMRVVQEHFAEMAASLKRPD
                     TGASGLPGRPGPPGPPGPPGENGFPGQMGIRGLPGIKGPPGALGLRGPKGDLGEKGER
                     GPPGRGPKGLPGAIGLPGDPGPASYGKNGRDGEQGPPGVAGIPGVPGPPGPPGPPGFC
                     EPASCTLQAGQRAFSKGPDK"
     exon            260..333
                     /gene="Col9a1"
                     /inference="alignment:Splign:2.1.0"
     exon            334..411
                     /gene="Col9a1"
                     /inference="alignment:Splign:2.1.0"
     exon            412..544
                     /gene="Col9a1"
                     /inference="alignment:Splign:2.1.0"
     exon            545..941
                     /gene="Col9a1"
                     /inference="alignment:Splign:2.1.0"
     exon            942..1025
                     /gene="Col9a1"
                     /inference="alignment:Splign:2.1.0"
     exon            1026..1046
                     /gene="Col9a1"
                     /inference="alignment:Splign:2.1.0"
     exon            1047..1121
                     /gene="Col9a1"
                     /inference="alignment:Splign:2.1.0"
     exon            1122..1157
                     /gene="Col9a1"
                     /inference="alignment:Splign:2.1.0"
     exon            1158..1220
                     /gene="Col9a1"
                     /inference="alignment:Splign:2.1.0"
     exon            1221..1274
                     /gene="Col9a1"
                     /inference="alignment:Splign:2.1.0"
     exon            1275..1310
                     /gene="Col9a1"
                     /inference="alignment:Splign:2.1.0"
     exon            1311..1334
                     /gene="Col9a1"
                     /inference="alignment:Splign:2.1.0"
     exon            1335..1388
                     /gene="Col9a1"
                     /inference="alignment:Splign:2.1.0"
     exon            1389..1442
                     /gene="Col9a1"
                     /inference="alignment:Splign:2.1.0"
     exon            1443..1475
                     /gene="Col9a1"
                     /inference="alignment:Splign:2.1.0"
     exon            1476..1532
                     /gene="Col9a1"
                     /inference="alignment:Splign:2.1.0"
     exon            1533..1586
                     /gene="Col9a1"
                     /inference="alignment:Splign:2.1.0"
     exon            1587..1640
                     /gene="Col9a1"
                     /inference="alignment:Splign:2.1.0"
     exon            1641..1694
                     /gene="Col9a1"
                     /inference="alignment:Splign:2.1.0"
     exon            1695..1748
                     /gene="Col9a1"
                     /inference="alignment:Splign:2.1.0"
     exon            1749..1802
                     /gene="Col9a1"
                     /inference="alignment:Splign:2.1.0"
     exon            1803..1856
                     /gene="Col9a1"
                     /inference="alignment:Splign:2.1.0"
     exon            1857..1910
                     /gene="Col9a1"
                     /inference="alignment:Splign:2.1.0"
     exon            1911..1964
                     /gene="Col9a1"
                     /inference="alignment:Splign:2.1.0"
     exon            1965..2009
                     /gene="Col9a1"
                     /inference="alignment:Splign:2.1.0"
     exon            2010..2063
                     /gene="Col9a1"
                     /inference="alignment:Splign:2.1.0"
     exon            2064..2117
                     /gene="Col9a1"
                     /inference="alignment:Splign:2.1.0"
     exon            2118..2171
                     /gene="Col9a1"
                     /inference="alignment:Splign:2.1.0"
     exon            2172..2243
                     /gene="Col9a1"
                     /inference="alignment:Splign:2.1.0"
     exon            2244..2279
                     /gene="Col9a1"
                     /inference="alignment:Splign:2.1.0"
     exon            2280..2324
                     /gene="Col9a1"
                     /inference="alignment:Splign:2.1.0"
     exon            2325..2357
                     /gene="Col9a1"
                     /inference="alignment:Splign:2.1.0"
     exon            2358..2504
                     /gene="Col9a1"
                     /inference="alignment:Splign:2.1.0"
     exon            2505..2559
                     /gene="Col9a1"
                     /inference="alignment:Splign:2.1.0"
     exon            2560..2748
                     /gene="Col9a1"
                     /inference="alignment:Splign:2.1.0"
     exon            2749..2826
                     /gene="Col9a1"
                     /inference="alignment:Splign:2.1.0"
     exon            2827..3813
                     /gene="Col9a1"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      
        1 cccctggctg ggcctgggct tactggctgt ttctctccac ccctttcctt tgcttcagct
       61 taaagagtta ttacatgcca tcagttcact ctttttgctt ttagccctaa gaggggcaag
      121 aaggagcaag cttggggcca aatctcagag ccagagaagg atagagaagg ggtgttgggg
      181 agtagggact cccctccaac cccctcatgg tgactcttat aaacccaaga gaacccactg
      241 ggaaaatgaa gaacttctgg aaaattccac ttttcttctt tgcatgcagt tttctgggac
      301 cctgtgtatc tgcaactcct aagcgtcgtg caagatttcc tgccaattct gtttctcatg
      361 gtggaagtga actgtgtccc aagatcagga ttggccagga tgacttgcca ggatttgacc
      421 tgatttctca gttccaaatt gagaaggctg catctcgaag gactatccag agggtggtgg
      481 ggtccacagc gttacaagtg gcttacaagc tgggaagtaa tgtagacttc aggattccaa
      541 caaggcattt gtatcccagt ggactgcctg aagaatattc ctttttaact actttccgga
      601 tgactggaag cacacttgaa aagcaatgga acatttggca gatccaggat tcctcaggga
      661 gggagcaagt tggcgtgaag ataaatggcc aaacaaagtc tgtcgcgttt tcatacaagg
      721 gactggacgg gagtctccaa acggcagcct tcttgaattt gcagtccttg tttgactccc
      781 gttggcataa gctcatgatt ggcgtggaga gaacaagagc tactcttttt attgactgca
      841 tccagatcga ttccttacct ataaagccga gagcccagat cgatgctgat ggctttgctg
      901 tgctgggaaa acttgtggac aatcctcagg tttctgttcc ctttgaactc cagtggatgc
      961 tgattcactg tgaccccctg agaccccgga gagagacgtg ccatgaactg ccagtcagaa
     1021 tcacaaccag ccagaccacc gatgagagag gtcctccggg tgagcagggg cctccggggc
     1081 ctcccgggcc tcctggagtt ccgggcatag atggtattga tggtgaccga ggtccaaagg
     1141 gtccccccgg acctccgggt cctcctggag acccgggcaa gccaggagca ccaggcaagc
     1201 caggcactcc aggagctgat ggattaacag gacctgatgg gtccccgggc tccgttggac
     1261 caaggggaca aaaaggagaa cctggtgtgc ctgggtctcg tggatttcca ggccgtggca
     1321 ttccaggacc ccctggccct cctgggacca caggacttcc tggagaactt ggccgagtag
     1381 gccctgctgg cgaccctggg aaaagaggac cacctggtcc tcctggaccc ccaggaccta
     1441 gtggaacaat tggatttcat gatggagacc cattgtgccc caattcctgc ccaccaggtc
     1501 gctctggcta tccaggccta ccaggcatga gaggccacaa aggggcgaaa ggagaaattg
     1561 gcgagccagg aagacaagga cacaagggtg aagagggtga ccagggggaa ctgggagaag
     1621 ttggagctca aggacctcca ggagctcaag gtctgagagg catcactggc atagttggag
     1681 acaaaggaga aaaaggtgct cggggattcg atggagatcc tgggcctcag ggcgttccag
     1741 gtgcagctgg tgatcaaggg cagcgaggac ctccaggaga aacaggtcct aagggagaca
     1801 ggggcattca aggttcccga ggaattcctg gatccccggg tccaaaagga gacacgggct
     1861 tgccaggtgt cgatggtcga gacggaatcc cgggaatgcc tggaacaaag ggtgaagcag
     1921 gaaagcctgg acctcccggt gatgcgggat tgcagggttt accgggtgta cctgggattc
     1981 ctggtgcaaa aggtgtggcc ggcgaaaagg gtaacacggg tcctccgggg aagcctggtc
     2041 agttgggaag ttcaggaaaa ccaggccaac aaggaccgcc gggagaggtt ggacctcggg
     2101 gacccagggg ccttccaggc agcagaggcc cggtaggacc agaaggctct ccaggcatac
     2161 cagggaaact gggacctctt ggcagccctg gccttcctgg cttgcctggg ccccctggac
     2221 ttcctggaat gaaaggagac aggggtgtat ttggtgaacc aggtcccaag ggcgaacagg
     2281 gtgcctctgg tgaagaaggt gaagcaggag taaggggtga ccttggagat atgggacaac
     2341 ctggcccaaa gggatcagtg ggtaaccctg gggagcccgg cctgagggga cctgaaggaa
     2401 tcagagggct tcctggagtg gaaggaccaa gaggaccacc tggaccccga ggtgtgcaag
     2461 gagaacaggg tgccactgga ctgcctggta tccagggacc tccgggcaga gcgccgacgg
     2521 accagcacat caagcaggtt tgcatgagag ttgtgcaaga gcattttgca gaaatggcag
     2581 ctagcctcaa gagaccagac acaggagctt ctggtcttcc tgggaggcct ggtcccccag
     2641 ggcctcccgg ccctccagga gagaatggtt tccctggtca gatgggaatc cgtggccttc
     2701 caggcattaa gggtccccct ggtgctcttg gcttaagggg acctaaaggt gacttgggag
     2761 aaaaaggaga acgtggtcct ccaggaagag gtcctaaggg tttgcctgga gctatcggtc
     2821 tcccaggtga tccaggccct gccagctatg ggaaaaatgg ccgagatgga gagcaaggtc
     2881 ccccaggagt ggcaggaatt cctggtgtgc ctgggccccc aggtcctcca ggccctcctg
     2941 gtttctgtga gccagcctct tgcacccttc aggcaggtca aagagcattt agcaaagggc
     3001 ctgacaagtg aaagccttcg tgttctagac tcccctatac acaccgtgcc tggtagagga
     3061 gcatgtggga gaaacaatat atccaacagt ggggcaacga ctaaaaggtt tcacctcaga
     3121 catcactaca cacgtgctat atgacaatcg gatttagaag aactggtgct attccgttaa
     3181 gtcttgttcc ttcaggagcg tcatcagaca aaagtcaaat tcaatttctc tttaggcaaa
     3241 tttataaatc ctcctcctgg gcttttggat tttagtgtgc tatgagtgca tatatgatgt
     3301 attgtgggcc actgtgccaa caacagcagc agcagcagca aactgttcag tttacctcac
     3361 ttgctgtcat tgtttttatt tcaattaaga tattgacctg agatttgaac aatcagttgt
     3421 gtcaagtact gctaaggaac aaaacccact acattcaaca aaattggtgc ttaaaatctt
     3481 catcagggcc gtgtcacaga agtggtctct atagatggtg gttctcatct ttattctgaa
     3541 tttgtgaata tactgcgccc caaacgcact cgcattgtaa gatccacgtg aaagcaaaga
     3601 agtgataccc caacgtgcat atgttttgtg gctgacatta tttattttaa aagtttgaga
     3661 taacatgtct ggttgtacca aagaagaaat aaacatgatt tcataatctt ttgtacgttc
     3721 taagataagt cgtcatgtta aatgtggttg catgttaatc gaacttgttt agattcatta
     3781 aatttttgac ttattgctac ttttaaaaat gtaaaaaaaa aaaaaaaaaa
//
