LOCUS       NM_001108611            2587 bp    mRNA    linear   ROD 01-APR-2024
DEFINITION  Rattus norvegicus collagen type IX alpha 3 chain (Col9a3), mRNA.
ACCESSION   NM_001108611 XM_001059028 XM_003749640 XM_003753842 XM_342599
VERSION     NM_001108611.3
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 2587)
  AUTHORS   Zhang,P. and Chang,B.G.
  TITLE     Inhibitory effect on the apoptosis of disc nucleus pulposus cells
            in rats by silencing COL9A3 gene to mediate MAPK signaling pathway:
            a study on the function and mechanism
  JOURNAL   Eur Rev Med Pharmacol Sci 24 (17), 8653-8664 (2020)
   PUBMED   32964953
  REMARK    GeneRIF: Inhibitory effect on the apoptosis of disc nucleus
            pulposus cells in rats by silencing COL9A3 gene to mediate MAPK
            signaling pathway: a study on the function and mechanism.
REFERENCE   2  (bases 1 to 2587)
  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 alpha3 was found within the tectorial
            membrane as well as fibrocytes in the spiral ligament.
REFERENCE   3  (bases 1 to 2587)
  AUTHORS   Perera,E.M., Martin,H., Seeherunvong,T., Kos,L., Hughes,I.A.,
            Hawkins,J.R. and Berkovitz,G.D.
  TITLE     Tescalcin, a novel gene encoding a putative EF-hand Ca(2+)-binding
            protein, Col9a3, and renin are expressed in the mouse testis during
            the early stages of gonadal differentiation
  JOURNAL   Endocrinology 142 (1), 455-463 (2001)
   PUBMED   11145610
REFERENCE   4  (bases 1 to 2587)
  AUTHORS   Paassilta,P., Lohiniva,J., Annunen,S., Bonaventure,J., Le
            Merrer,M., Pai,L. and Ala-Kokko,L.
  TITLE     COL9A3: A third locus for multiple epiphyseal dysplasia
  JOURNAL   Am J Hum Genet 64 (4), 1036-1044 (1999)
   PUBMED   10090888
  REMARK    Erratum:[Am J Hum Genet 1999 Oct;65(4):1214]
REFERENCE   5  (bases 1 to 2587)
  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
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            JAXUCZ010000003.1.
            
            On Nov 27, 2020 this sequence version replaced NM_001108611.2.
            
            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. This RefSeq transcript is based on
            transcript alignments from orthologous data.
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR26643285.14733.1,
                                           SRR26643295.16764.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA5760393, SAMEA5760433
                                           [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
            1-80                JAXUCZ010000003.1  188089410-188089489
            81-149              JAXUCZ010000003.1  188090039-188090107
            150-185             JAXUCZ010000003.1  188091180-188091215
            186-257             JAXUCZ010000003.1  188091736-188091807
            258-311             JAXUCZ010000003.1  188092394-188092447
            312-347             JAXUCZ010000003.1  188093449-188093484
            348-371             JAXUCZ010000003.1  188093715-188093738
            372-425             JAXUCZ010000003.1  188093968-188094021
            426-479             JAXUCZ010000003.1  188094371-188094424
            480-521             JAXUCZ010000003.1  188094692-188094733
            522-578             JAXUCZ010000003.1  188095925-188095981
            579-632             JAXUCZ010000003.1  188096412-188096465
            633-686             JAXUCZ010000003.1  188097121-188097174
            687-740             JAXUCZ010000003.1  188097305-188097358
            741-794             JAXUCZ010000003.1  188097585-188097638
            795-848             JAXUCZ010000003.1  188098104-188098157
            849-902             JAXUCZ010000003.1  188098838-188098891
            903-956             JAXUCZ010000003.1  188099682-188099735
            957-1010            JAXUCZ010000003.1  188099837-188099890
            1011-1055           JAXUCZ010000003.1  188100425-188100469
            1056-1109           JAXUCZ010000003.1  188100566-188100619
            1110-1163           JAXUCZ010000003.1  188101005-188101058
            1164-1217           JAXUCZ010000003.1  188101647-188101700
            1218-1289           JAXUCZ010000003.1  188101816-188101887
            1290-1325           JAXUCZ010000003.1  188103658-188103693
            1326-1370           JAXUCZ010000003.1  188104888-188104932
            1371-1403           JAXUCZ010000003.1  188106056-188106088
            1404-1550           JAXUCZ010000003.1  188106187-188106333
            1551-1605           JAXUCZ010000003.1  188106518-188106572
            1606-1788           JAXUCZ010000003.1  188107182-188107364
            1789-1866           JAXUCZ010000003.1  188109786-188109863
            1867-2587           JAXUCZ010000003.1  188111314-188112034
FEATURES             Location/Qualifiers
     source          1..2587
                     /organism="Rattus norvegicus"
                     /mol_type="mRNA"
                     /strain="BN"
                     /db_xref="taxon:10116"
                     /chromosome="3"
                     /map="3q43"
     gene            1..2587
                     /gene="Col9a3"
                     /note="collagen type IX alpha 3 chain"
                     /db_xref="GeneID:362285"
                     /db_xref="RGD:1310255"
     exon            1..80
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     CDS             15..2057
                     /gene="Col9a3"
                     /note="procollagen, type IX, alpha 3; collagen alpha-3(IX)
                     chain; collagen, type IX, alpha 3"
                     /codon_start=1
                     /product="collagen alpha-3(IX) chain precursor"
                     /protein_id="NP_001102081.2"
                     /db_xref="GeneID:362285"
                     /db_xref="RGD:1310255"
                     /translation="MTGAPALALLLLGQLLTATSAQKVGPRGPPGPQGPPGKPGKDGI
                     DGEAGPPGLPGPPGPKGTSGKPGKPGEAGLPGLPGVDGLTGRDGPAGPKGAPGERGSL
                     GPPGPPGLGGKGLPGPPGEAGVSGLPGGIGLRGPPGPSGLPGLPGPPGPPGPPGNPGV
                     LPEGATDLQCPAICPPGPPGPPGMPGFKGPTGYKGEQGEVGKDGEKGNPGPPGPPGIP
                     GTVGLQGPRGLQGLPGPLGPPGDRGPIGFRGPPGIPGAPGKAGDRGDRGPEGFRGPKG
                     DLGRPGPKGIPGVAGPGGEPGMPGKDGKDGVPGLDGEKGEAGRTGAPGEKGPNGLPGL
                     PGRAGSKGEKGEVGRTGELGEAGPSGEPGIPGDVGVPGERGEAGHRGSVGALGPQGPP
                     GAPGIRGFQGQKGSIGDPGLPGPQGLRGDVGDRGPGGATGPKGDQGIAGSDGLPGDKG
                     ELGPNGPVGQKGESGSRGELGPKGIQGPNGTSGVQGVPGPPGPLGFQGVQGVPGITGK
                     PGVPGKEASEQRIRELCGGMISEQIAQLAAHLRKPLAPGSIGRPGPAGPPGPPGPPGS
                     IGHPGARGPPGYRGPTGELGDPGPRGSQGDRGDKGAIGVGLDGPAGDQGYRGPQGVPG
                     ISKDGRDGAHGEPGLPGDPGLPGAAGAQGTPGICDTSACQGAVLGGGGEKSGPRSS"
     exon            81..149
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     exon            150..185
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     exon            186..257
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     exon            258..311
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     exon            312..347
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     exon            348..371
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     exon            372..425
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     exon            426..479
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     exon            480..521
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     exon            522..578
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     exon            579..632
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     exon            633..686
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     exon            687..740
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     exon            741..794
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     exon            795..848
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     exon            849..902
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     exon            903..956
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     exon            957..1010
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     exon            1011..1055
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     exon            1056..1109
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     exon            1110..1163
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     exon            1164..1217
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     exon            1218..1289
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     exon            1290..1325
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     exon            1326..1370
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     exon            1371..1403
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     exon            1404..1550
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     exon            1551..1605
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     exon            1606..1788
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     exon            1789..1866
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
     exon            1867..2587
                     /gene="Col9a3"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      
        1 agcgcctgcc agccatgacc ggagcgcctg ccctagccct gctgctgctg gggcagctcc
       61 tgacggccac ctccgcgcag aaagtgggac ctcgaggccc ccctggtccc caagggcctc
      121 ctggaaaacc cggcaaggat ggcatcgatg gagaagctgg ccctccaggt ctgcctggcc
      181 ctccaggacc caaagggacc tcagggaagc cggggaagcc gggagaggca ggactgccag
      241 gactgcctgg tgtagatggt ctgacaggga gagatggacc cgcaggaccc aaaggtgccc
      301 cgggagaacg gggaagtcta ggacctccag ggccaccagg acttggaggc aaaggcctcc
      361 ctggacctcc tggagaggca ggagtgagtg gcctcccagg tgggattggt ctacgtggcc
      421 ccccgggacc ctctggactt ccaggcctgc ctggcccccc aggacctcct ggacctcctg
      481 gaaaccctgg agtcctccct gaaggtgcta ctgatctgca gtgtcctgcc atctgccctc
      541 caggccctcc agggccccca ggaatgccgg ggttcaaggg gcctactggc tacaaagggg
      601 aacaaggaga agtcggcaaa gatggtgaga agggtaatcc tggcccccct ggacctccag
      661 gaatcccagg cactgtgggg ctacagggcc caagaggatt gcaaggactt ccagggccac
      721 ttggaccccc tggggaccgg ggtcccattg ggtttcgggg ccccccaggg atcccaggag
      781 cacctgggaa agcgggtgac aggggtgata ggggaccaga agggttccgt ggccctaagg
      841 gtgacctggg caggcctggt cccaaaggaa tccctggagt ggctgggcca ggcggagaac
      901 caggcatgcc aggcaaggat ggcaaggacg gtgtgccggg acttgacggt gagaagggag
      961 aggctggtcg cactggtgcc ccaggagaaa aaggccccaa tgggctgccg gggctccctg
     1021 gacgagcagg gtccaaaggc gagaagggag aagtgggtag aactggggag ctgggcgagg
     1081 ctggcccctc tggagaacca ggtattcctg gagacgttgg tgttccgggg gagcgtggcg
     1141 aggctggtca caggggctca gtgggggccc tcggcccaca aggtcctcct ggggctcctg
     1201 gcattcgtgg cttccagggc caaaaaggca gcataggaga ccctggcctt ccaggccccc
     1261 aaggcctacg gggagatgtg ggtgaccggg gtccaggagg tgccacaggt cctaagggag
     1321 accagggcat cgcgggttct gatggtcttc caggggacaa aggagagctg ggtcctaatg
     1381 gccccgttgg acaaaaagga gagtccggca gccgagggga actgggcccc aaaggcatcc
     1441 agggccccaa tggtaccagt ggggtccagg gtgtgcctgg tcccccaggt ccactgggct
     1501 tccaaggcgt gcagggtgtc ccaggcatca cggggaaacc tggagttccg ggcaaggaag
     1561 ccagtgaaca acgcatcagg gagctgtgtg gggggatgat cagtgagcaa attgcacagc
     1621 tggctgcaca cctgaggaag cccttagcac caggctccat tggcaggcct ggtccagctg
     1681 gccccccagg ccctccaggc cccccaggct ccattggcca ccctggcgct cggggtcctc
     1741 ctggataccg tggtcccact ggggaactag gagatcctgg accaagagga agccagggtg
     1801 acagaggaga caagggagca ataggtgtag ggttggatgg acctgctggg gaccagggct
     1861 accgagggcc tcaaggtgtg cctggcatca gcaaagatgg tcgagatggt gctcatggtg
     1921 agcctggcct tcctggtgat cctggccttc ctggagctgc tggtgctcaa ggaaccccgg
     1981 ggatttgcga cacctcagcc tgccaaggag ctgtgttagg gggaggtggg gaaaagtcag
     2041 gtcctcggag ctcataagca agaactaaag taggaaatga cagagcactc cagcaggcag
     2101 cagggatgag cagtgtgatg gctatggaca ggaatggaca gtggctggct acagtcagct
     2161 agtccttcct ggcctgctgc ttggccccaa gagcatctat tggcgccact gtcactgtcc
     2221 catcttcagg atttatggca gcccattcat ctgtgacagc atacctcaga cacagacctt
     2281 agggatggag actttaaacc cagcatctgg gaggattggt gttattgaag agttttgtac
     2341 aattccatga gataaaaaca ctcaagagac ttgtttacac atttatataa agcctatgac
     2401 agactaccaa taaagcgatc ttctaaccct tcagattagt actggctaca gtgtgatgaa
     2461 ggcaaggaac ttaatgtctg cttcacctgc tttctattgc aagttagtat aatctttgat
     2521 gcccagtatt tattcaagga actacactgt accatatgtc acaataaata aagctactca
     2581 ctggaaa
//
