LOCUS       NM_007740               3888 bp    mRNA    linear   ROD 19-NOV-2024
DEFINITION  Mus musculus collagen, type IX, alpha 1 (Col9a1), transcript
            variant 1, mRNA.
ACCESSION   NM_007740
VERSION     NM_007740.3
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 3888)
  AUTHORS   Wu,B., Wu,B., Benkaci,S., Shi,L., Lu,P., Park,T., Morrow,B.E.,
            Wang,Y. and Zhou,B.
  TITLE     Crk and Crkl Are Required in the Endocardial Lineage for Heart
            Valve Development
  JOURNAL   J Am Heart Assoc 12 (18), e029683 (2023)
   PUBMED   37702066
REFERENCE   2  (bases 1 to 3888)
  AUTHORS   Szakats,S., McAtamney,A., Cross,H. and Wilson,M.J.
  TITLE     Sex-biased gene and microRNA expression in the developing mouse
            brain is associated with neurodevelopmental functions and
            neurological phenotypes
  JOURNAL   Biol Sex Differ 14 (1), 57 (2023)
   PUBMED   37679839
  REMARK    Publication Status: Online-Only
REFERENCE   3  (bases 1 to 3888)
  AUTHORS   Bonet,F., Anez,S.B., Inacio,J.M., Futschik,M.E. and Belo,J.A.
  TITLE     CCBE1 Is Essential for Epicardial Function during Myocardium
            Development
  JOURNAL   Int J Mol Sci 23 (20), 12642 (2022)
   PUBMED   36293499
  REMARK    Publication Status: Online-Only
REFERENCE   4  (bases 1 to 3888)
  AUTHORS   Ye,Q., Bhojwani,A. and Hu,J.K.
  TITLE     Understanding the development of oral epithelial organs through
            single cell transcriptomic analysis
  JOURNAL   Development 149 (16) (2022)
   PUBMED   35831953
REFERENCE   5  (bases 1 to 3888)
  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   6  (bases 1 to 3888)
  AUTHORS   Hiltunen,A., Metsaranta,M., Perala,M., Saamanen,A.M., Aro,H.T. and
            Vuorio,E.
  TITLE     Expression of type VI, IX and XI collagen genes and alternative
            splicing of type II collagen transcripts in fracture callus tissue
            in mice
  JOURNAL   FEBS Lett 364 (2), 171-174 (1995)
   PUBMED   7750564
REFERENCE   7  (bases 1 to 3888)
  AUTHORS   Giros,B., Pohl,M., Rochelle,J.M. and Seldin,M.F.
  TITLE     Chromosomal localization of opioid peptide and receptor genes in
            the mouse
  JOURNAL   Life Sci 56 (18), PL369-PL375 (1995)
   PUBMED   7752808
REFERENCE   8  (bases 1 to 3888)
  AUTHORS   Rokos,I., Muragaki,Y., Warman,M. and Olsen,B.R.
  TITLE     Assembly and sequencing of a cDNA covering the entire mouse alpha
            1(IX) collagen chain
  JOURNAL   Matrix Biol 14 (1), 1-8 (1994)
   PUBMED   8061915
REFERENCE   9  (bases 1 to 3888)
  AUTHORS   Metsaranta,M., Toman,D., De Crombrugghe,B. and Vuorio,E.
  TITLE     Specific hybridization probes for mouse type I, II, III and IX
            collagen mRNAs
  JOURNAL   Biochim Biophys Acta 1089 (2), 241-243 (1991)
   PUBMED   2054384
REFERENCE   10 (bases 1 to 3888)
  AUTHORS   Muragaki,Y., Nishimura,I., Henney,A., Ninomiya,Y. and Olsen,B.R.
  TITLE     The alpha 1 (IX) collagen gene gives rise to two different
            transcripts in both mouse embryonic and human fetal RNA
  JOURNAL   Proc Natl Acad Sci U S A 87 (7), 2400-2404 (1990)
   PUBMED   1690886
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            CX207941.1, AK031071.1, L12215.1, AK004383.1 and AK017395.1.
            
            On Apr 14, 2009 this sequence version replaced NM_007740.2.
            
            Transcript Variant: This variant (1) represents the longer
            transcript and encodes the longer isoform (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 :: AK031071.1, D17511.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN01164134, SAMN01164137
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-90                CX207941.1         1-90
            91-1530             AK031071.1         1-1440
            1531-1948           L12215.1           1286-1703
            1949-2952           AK031071.1         1859-2862
            2953-3409           AK004383.1         410-866
            3410-3888           AK017395.1         433-911
FEATURES             Location/Qualifiers
     source          1..3888
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="1"
                     /map="1 9.95 cM"
     gene            1..3888
                     /gene="Col9a1"
                     /gene_synonym="Col9a-1"
                     /note="collagen, type IX, alpha 1"
                     /db_xref="GeneID:12839"
                     /db_xref="MGI:MGI:88465"
     exon            1..259
                     /gene="Col9a1"
                     /gene_synonym="Col9a-1"
                     /inference="alignment:Splign:2.1.0"
     CDS             246..3011
                     /gene="Col9a1"
                     /gene_synonym="Col9a-1"
                     /note="isoform 1 precursor is encoded by transcript
                     variant 1; collagen alpha-1(IX) chain; alpha 1 type IX
                     collagen; procollagen, type IX, alpha 1"
                     /codon_start=1
                     /product="collagen alpha-1(IX) chain isoform 1 precursor"
                     /protein_id="NP_031766.3"
                     /db_xref="CCDS:CCDS35527.1"
                     /db_xref="GeneID:12839"
                     /db_xref="MGI:MGI:88465"
                     /translation="MKNFWKISVFFCVCSCLGPWVSATLKRRARFPANSISNGGSELC
                     PKIRIGQDDLPGFDLISQFQIEKAASRRTIQRVVGSTALQVAYKLGSNVDFRIPTRHL
                     YPSGLPEEYSFLTTFRMTGSTLEKHWNIWQIQDSAGREQVGVKINGQTKSVAFSYKGL
                     DGSLQTAAFLNLPSLFDSRWHKLMIGVERTSATLFIDCIRIESLPIKPRGQIDADGFA
                     VLGKLVDNPQVSVPFELQWMLIHCDPLRPRRETCHELPIRITTSQTTDERGPPGEQGP
                     PGPPGPPGVPGIDGIDGDRGPKGPPGPPGPPGDPGKPGAPGKPGTPGADGLTGPDGSP
                     GSVGPRGQKGEPGVPGSRGFPGRGIPGPPGPPGTTGLPGELGRVGPIGDPGKRGPPGP
                     PGPPGPSGTIGFHDGDPLCPNSCPPGRSGYPGLPGMRGHKGAKGEIGEPGRQGHKGEE
                     GDQGELGEVGDQGPPGPQGLRGITGIVGDKGEKGARGFDGEPGPQGIPGAAGDQGQRG
                     PPGETGPEGDRGIQGSRGIPGSPGPKGDTGLPGVDGRDGIPGMPGTKGEAGKPGPPGD
                     VGLQGLPGVPGIPGAKGVAGEKGNTGAPGKPGQLGSSGKPGQQGPPGEVGPRGPRGLP
                     GSRGPVGPEGSPGIPGKLGSVGSPGLPGLPGPPGLPGMKGDRGVFGEPGPKGEQGASG
                     EEGEAGARGDLGDMGQPGPKGSVGNPGEPGLRGPEGIRGLPGVEGPRGPPGPRGMQGD
                     QGATGLPGIQGPPGRAPTDQHIKQVCMRVVQEHFAEMAASLKRPDTGASGLPGRPGPP
                     GPPGPPGENGFPGQMGIRGLPGIKGPPGALGLRGPKGDLGEKGERGPPGRGPKGLPGA
                     IGLPGDPGPASYGKNGRDGEQGPPGVAGIPGVPGPPGPPGPPGFCEPASCTLQSGQRA
                     FSKGPDK"
     exon            260..333
                     /gene="Col9a1"
                     /gene_synonym="Col9a-1"
                     /inference="alignment:Splign:2.1.0"
     exon            334..411
                     /gene="Col9a1"
                     /gene_synonym="Col9a-1"
                     /inference="alignment:Splign:2.1.0"
     exon            412..544
                     /gene="Col9a1"
                     /gene_synonym="Col9a-1"
                     /inference="alignment:Splign:2.1.0"
     exon            545..941
                     /gene="Col9a1"
                     /gene_synonym="Col9a-1"
                     /inference="alignment:Splign:2.1.0"
     exon            942..1025
                     /gene="Col9a1"
                     /gene_synonym="Col9a-1"
                     /inference="alignment:Splign:2.1.0"
     exon            1026..1046
                     /gene="Col9a1"
                     /gene_synonym="Col9a-1"
                     /inference="alignment:Splign:2.1.0"
     exon            1047..1121
                     /gene="Col9a1"
                     /gene_synonym="Col9a-1"
                     /inference="alignment:Splign:2.1.0"
     exon            1122..1157
                     /gene="Col9a1"
                     /gene_synonym="Col9a-1"
                     /inference="alignment:Splign:2.1.0"
     exon            1158..1220
                     /gene="Col9a1"
                     /gene_synonym="Col9a-1"
                     /inference="alignment:Splign:2.1.0"
     exon            1221..1274
                     /gene="Col9a1"
                     /gene_synonym="Col9a-1"
                     /inference="alignment:Splign:2.1.0"
     exon            1275..1310
                     /gene="Col9a1"
                     /gene_synonym="Col9a-1"
                     /inference="alignment:Splign:2.1.0"
     exon            1311..1334
                     /gene="Col9a1"
                     /gene_synonym="Col9a-1"
                     /inference="alignment:Splign:2.1.0"
     exon            1335..1388
                     /gene="Col9a1"
                     /gene_synonym="Col9a-1"
                     /inference="alignment:Splign:2.1.0"
     exon            1389..1442
                     /gene="Col9a1"
                     /gene_synonym="Col9a-1"
                     /inference="alignment:Splign:2.1.0"
     exon            1443..1475
                     /gene="Col9a1"
                     /gene_synonym="Col9a-1"
                     /inference="alignment:Splign:2.1.0"
     exon            1476..1532
                     /gene="Col9a1"
                     /gene_synonym="Col9a-1"
                     /inference="alignment:Splign:2.1.0"
     exon            1533..1586
                     /gene="Col9a1"
                     /gene_synonym="Col9a-1"
                     /inference="alignment:Splign:2.1.0"
     exon            1587..1640
                     /gene="Col9a1"
                     /gene_synonym="Col9a-1"
                     /inference="alignment:Splign:2.1.0"
     exon            1641..1694
                     /gene="Col9a1"
                     /gene_synonym="Col9a-1"
                     /inference="alignment:Splign:2.1.0"
     exon            1695..1748
                     /gene="Col9a1"
                     /gene_synonym="Col9a-1"
                     /inference="alignment:Splign:2.1.0"
     exon            1749..1802
                     /gene="Col9a1"
                     /gene_synonym="Col9a-1"
                     /inference="alignment:Splign:2.1.0"
     exon            1803..1856
                     /gene="Col9a1"
                     /gene_synonym="Col9a-1"
                     /inference="alignment:Splign:2.1.0"
     exon            1857..1910
                     /gene="Col9a1"
                     /gene_synonym="Col9a-1"
                     /inference="alignment:Splign:2.1.0"
     exon            1911..1964
                     /gene="Col9a1"
                     /gene_synonym="Col9a-1"
                     /inference="alignment:Splign:2.1.0"
     exon            1965..2009
                     /gene="Col9a1"
                     /gene_synonym="Col9a-1"
                     /inference="alignment:Splign:2.1.0"
     exon            2010..2063
                     /gene="Col9a1"
                     /gene_synonym="Col9a-1"
                     /inference="alignment:Splign:2.1.0"
     exon            2064..2117
                     /gene="Col9a1"
                     /gene_synonym="Col9a-1"
                     /inference="alignment:Splign:2.1.0"
     exon            2118..2171
                     /gene="Col9a1"
                     /gene_synonym="Col9a-1"
                     /inference="alignment:Splign:2.1.0"
     exon            2172..2243
                     /gene="Col9a1"
                     /gene_synonym="Col9a-1"
                     /inference="alignment:Splign:2.1.0"
     exon            2244..2279
                     /gene="Col9a1"
                     /gene_synonym="Col9a-1"
                     /inference="alignment:Splign:2.1.0"
     exon            2280..2324
                     /gene="Col9a1"
                     /gene_synonym="Col9a-1"
                     /inference="alignment:Splign:2.1.0"
     exon            2325..2357
                     /gene="Col9a1"
                     /gene_synonym="Col9a-1"
                     /inference="alignment:Splign:2.1.0"
     exon            2358..2504
                     /gene="Col9a1"
                     /gene_synonym="Col9a-1"
                     /inference="alignment:Splign:2.1.0"
     exon            2505..2559
                     /gene="Col9a1"
                     /gene_synonym="Col9a-1"
                     /inference="alignment:Splign:2.1.0"
     exon            2560..2748
                     /gene="Col9a1"
                     /gene_synonym="Col9a-1"
                     /inference="alignment:Splign:2.1.0"
     exon            2749..2826
                     /gene="Col9a1"
                     /gene_synonym="Col9a-1"
                     /inference="alignment:Splign:2.1.0"
     exon            2827..3888
                     /gene="Col9a1"
                     /gene_synonym="Col9a-1"
                     /inference="alignment:Splign:2.1.0"
     regulatory      3473..3478
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Col9a1"
                     /gene_synonym="Col9a-1"
                     /note="hexamer: AATAAA"
     polyA_site      3498
                     /gene="Col9a1"
                     /gene_synonym="Col9a-1"
                     /note="major polyA site"
     regulatory      3802..3807
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Col9a1"
                     /gene_synonym="Col9a-1"
                     /note="hexamer: ATTAAA"
     polyA_site      3834
                     /gene="Col9a1"
                     /gene_synonym="Col9a-1"
                     /note="major polyA site"
ORIGIN      
        1 cccctggctg ggcctgggtt acaggctgcc tctccccacc cctttccttt gcttcagctt
       61 aaagggttat tgcatgcctc caattcactc tttttgcctt tagccctgag aggggcaaga
      121 aggagcaagc ttggggccaa aactcgaagt ccgagaaggg tagagagggg gtcttaggga
      181 gtagtgaccc cccctccaaa ccctttacgg tgactcttat aaaccacaga gaacccactg
      241 ggaaaatgaa gaacttctgg aaaatctcag ttttcttctg tgtgtgcagt tgtctgggac
      301 cctgggtatc cgcaactctt aagcgtcgtg caagatttcc tgccaattcc atttctaatg
      361 gtggaagtga actgtgtccc aagatcagga ttggccaaga tgacttacca gggtttgacc
      421 tgatttctca gttccaaatt gagaaggctg catctcgaag gactatccag agggtggtgg
      481 gatccacagc cttacaagtg gcttacaagc tgggaagtaa tgtagacttc aggattccaa
      541 caaggcattt gtatcccagt ggactgcctg aagaatattc ctttttaact actttccgga
      601 tgactggaag cacacttgaa aagcactgga acatttggca gatccaggat tccgcaggga
      661 gagagcaagt tggcgtgaag ataaatggcc aaacaaagtc tgtcgcattt tcatacaagg
      721 gactggatgg gagtctccaa acggctgcct tcttgaattt gccgtccttg tttgactccc
      781 ggtggcataa gctcatgatt ggcgtggaaa gaacaagcgc cactcttttt attgactgca
      841 tcaggatcga atctttacct ataaagccaa gaggccagat tgatgcggat ggctttgcag
      901 tgctgggaaa acttgtggac aatcctcagg tttctgttcc ttttgaactc cagtggatgc
      961 tgattcattg tgaccccctg agacccagga gagaaacctg tcatgagctg ccaatcagaa
     1021 tcacaaccag ccagaccact gatgagagag gtcctccggg tgagcagggg cctccagggc
     1081 ctcctgggcc tcctggagtt ccgggcatag atggcattga tggtgaccga ggtccaaagg
     1141 gtcccccagg acctccgggt cctcctggag acccaggcaa gccaggagca ccaggcaagc
     1201 caggcacacc aggagctgat ggattaacag gacctgatgg atcccctggc tctgttggac
     1261 caaggggaca aaaaggagaa cctggtgtac ctgggtctcg tggatttcca ggccgtggta
     1321 ttccaggacc ccctggtcct cctgggacca caggacttcc tggagaactt ggccgagtag
     1381 gccctattgg agaccctggg aaaagaggac cacctggccc tcctggacct ccaggaccca
     1441 gtggaacaat tggatttcat gatggagacc cattgtgccc caattcctgc ccaccaggtc
     1501 gctctggata tccaggccta ccaggcatga ggggccataa aggggcgaaa ggagaaatcg
     1561 gcgagccagg aagacaagga cacaagggtg aagagggtga ccagggggaa ctgggagaag
     1621 ttggcgatca aggacctcca ggacctcagg gtctgagagg catcactggc atagttggag
     1681 acaaaggaga aaagggtgct cggggatttg atggagagcc tggacctcag ggcattccag
     1741 gtgcagctgg tgatcaagga cagcgaggcc ctccaggaga aacaggtcct gagggagaca
     1801 gaggcattca aggttcccga ggaattcctg gatccccagg gccaaaagga gacacgggct
     1861 tgccaggtgt agatggccga gatggaatac caggaatgcc cgggacaaag ggtgaagcag
     1921 ggaagcctgg accccccggg gacgtgggat tgcagggctt accaggtgtc cctggaatcc
     1981 ctggtgcaaa aggtgttgcc ggtgaaaagg gtaacacggg tgctccagga aagcccggtc
     2041 agttgggaag ttcagggaaa ccaggccaac aagggccccc aggagaggtt ggacctcggg
     2101 gacccagggg ccttccaggc agtagaggcc cggtaggacc agaagggtct ccaggcatac
     2161 cagggaaact gggatctgtt ggcagccctg gccttcctgg cttgcctggg ccccctggac
     2221 ttcctggaat gaaaggagac aggggtgtat ttggtgaacc gggtcccaag ggtgaacagg
     2281 gtgcctctgg tgaagaaggt gaagcaggag caaggggtga ccttggagat atgggacaac
     2341 ctggcccaaa gggatctgtg ggtaaccccg gggagccggg tctgaggggg cctgaaggaa
     2401 tcagagggct tcctggagtg gaaggaccaa gaggaccacc tggaccccgg ggcatgcagg
     2461 gagatcaggg tgccactggg ctgcctggta tccagggccc tccgggcaga gcgccgaccg
     2521 accagcacat caagcaggtt tgcatgagag tcgtgcaaga gcattttgcg gaaatggcag
     2581 ccagcctcaa gagaccagac acaggagcct ctggtcttcc tgggaggcct ggcccccctg
     2641 ggcctccggg cccccctgga gagaatggtt tccctggtca gatgggaatc cgtggtctcc
     2701 caggcattaa gggtccccct ggtgctcttg gcttaagagg acctaaagga gacttgggag
     2761 aaaaaggaga acgtggtcct ccaggaagag gtcctaaggg tttgcctgga gcgataggtc
     2821 tcccaggtga cccaggccct gccagctatg ggaaaaatgg ccgtgacgga gagcaaggtc
     2881 ccccgggagt ggcaggaatt cctggtgtgc ctggaccccc aggtcctcca ggccctcctg
     2941 ggttctgtga gccagcctct tgcaccctgc agtctggtca aagagcattt agcaaagggc
     3001 cggacaagtg aaatccgtag cgttgtaggc tccctgcaca aagcacacct gttagcagag
     3061 tgtgggggga gaaacgatac caaaactggg gcaaagcctc aaaggtttca cctctgacat
     3121 cattacataa gtgctacttg acaatcagat ttagagcaac tggtgctatt cagtaagtct
     3181 tgttccttgt ccatggaagg aaggtaggag agtcaacaga caagagtcaa attcaatttc
     3241 tctttagcca aatttatata tcctcttccc aggagtttga attttagtgt gctatgaatg
     3301 gatatatgat gtgttgtggg tcactgtgcc aacaacaaca acaacaacaa gctgttcaca
     3361 ttacctcagt tgctgtcatt atttttattt caattaagat attgatctca gattattcat
     3421 tcagttatat caagtattgc taggatacta aggaacagac cccactacat tcaataaaat
     3481 tggtgcttaa aatcttcatc agggctgtgt cccaaaagtg gtctctatac atcgcatggt
     3541 ggttttgata tttactatga atttgtgaat agtgtgtact gcatccaatc ccatttgtat
     3601 tctaaaatcc acgtgaaagc aaagaagtaa taccctgaca cacatatgtt ttgtggctga
     3661 cattatttat tttaaaagtt tgaggtaaca tgtctggttg taccaaagaa aaaataaaca
     3721 cggtttccta gtcttttgtg tgttctaaaa taagtagtca tgttaaatgt ggttacatgt
     3781 taattgaact ggtttagagt cattaaaatt ttgacttact gctacttcta aaaatgtatt
     3841 tattttactg gtttattcta tctgaagaaa tctgaagagt tcccactg
//
