LOCUS       NM_001852               2852 bp    mRNA    linear   PRI 08-OCT-2024
DEFINITION  Homo sapiens collagen type IX alpha 2 chain (COL9A2), mRNA.
ACCESSION   NM_001852
VERSION     NM_001852.4
KEYWORDS    RefSeq; MANE Select.
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 2852)
  AUTHORS   Kjellstrom,U., Martell,S., Brobeck,C. and Andreasson,S.
  TITLE     Autosomal recessive Stickler syndrome associated with homozygous
            mutations in the COL9A2 gene
  JOURNAL   Ophthalmic Genet 42 (2), 161-169 (2021)
   PUBMED   33356723
  REMARK    GeneRIF: Autosomal recessive Stickler syndrome associated with
            homozygous mutations in the COL9A2 gene.
REFERENCE   2  (bases 1 to 2852)
  AUTHORS   Hanaei,S., Abdollahzade,S., Sadr,M., Fattahi,E., Mirbolouk,M.H.,
            Khoshnevisan,A. and Rezaei,N.
  TITLE     Lack of association between COL1A1 and COL9A2 single nucleotide
            polymorphisms and intervertebral disc degeneration
  JOURNAL   Br J Neurosurg 35 (1), 77-79 (2021)
   PUBMED   32419506
  REMARK    GeneRIF: Lack of association between COL1A1 and COL9A2 single
            nucleotide polymorphisms and intervertebral disc degeneration.
REFERENCE   3  (bases 1 to 2852)
  AUTHORS   Luck,K., Kim,D.K., Lambourne,L., Spirohn,K., Begg,B.E., Bian,W.,
            Brignall,R., Cafarelli,T., Campos-Laborie,F.J., Charloteaux,B.,
            Choi,D., Cote,A.G., Daley,M., Deimling,S., Desbuleux,A., Dricot,A.,
            Gebbia,M., Hardy,M.F., Kishore,N., Knapp,J.J., Kovacs,I.A.,
            Lemmens,I., Mee,M.W., Mellor,J.C., Pollis,C., Pons,C.,
            Richardson,A.D., Schlabach,S., Teeking,B., Yadav,A., Babor,M.,
            Balcha,D., Basha,O., Bowman-Colin,C., Chin,S.F., Choi,S.G.,
            Colabella,C., Coppin,G., D'Amata,C., De Ridder,D., De Rouck,S.,
            Duran-Frigola,M., Ennajdaoui,H., Goebels,F., Goehring,L., Gopal,A.,
            Haddad,G., Hatchi,E., Helmy,M., Jacob,Y., Kassa,Y., Landini,S.,
            Li,R., van Lieshout,N., MacWilliams,A., Markey,D., Paulson,J.N.,
            Rangarajan,S., Rasla,J., Rayhan,A., Rolland,T., San-Miguel,A.,
            Shen,Y., Sheykhkarimli,D., Sheynkman,G.M., Simonovsky,E., Tasan,M.,
            Tejeda,A., Tropepe,V., Twizere,J.C., Wang,Y., Weatheritt,R.J.,
            Weile,J., Xia,Y., Yang,X., Yeger-Lotem,E., Zhong,Q., Aloy,P.,
            Bader,G.D., De Las Rivas,J., Gaudet,S., Hao,T., Rak,J.,
            Tavernier,J., Hill,D.E., Vidal,M., Roth,F.P. and Calderwood,M.A.
  TITLE     A reference map of the human binary protein interactome
  JOURNAL   Nature 580 (7803), 402-408 (2020)
   PUBMED   32296183
REFERENCE   4  (bases 1 to 2852)
  AUTHORS   Nixon,T.R.W., Alexander,P., Richards,A., McNinch,A.,
            Bearcroft,P.W.P., Cobben,J. and Snead,M.P.
  TITLE     Homozygous Type IX collagen variants (COL9A1, COL9A2, and COL9A3)
            causing recessive Stickler syndrome-Expanding the phenotype
  JOURNAL   Am J Med Genet A 179 (8), 1498-1506 (2019)
   PUBMED   31090205
  REMARK    GeneRIF: Homozygous type IX collagen variants, COL9A1, COL9A2, and
            COL9A3, causing recessive Stickler syndrome, expand the disease
            phenotype.
REFERENCE   5  (bases 1 to 2852)
  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   6  (bases 1 to 2852)
  AUTHORS   Mortier,G.
  TITLE     Stickler Syndrome
  JOURNAL   (in) Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE and
            Amemiya A (Eds.);
            GENEREVIEWS(R);
            (1993)
   PUBMED   20301479
REFERENCE   7  (bases 1 to 2852)
  AUTHORS   Briggs,M.D., Wright,M.J. and Mortier,G.R.
  TITLE     Multiple Epiphyseal Dysplasia, Autosomal Dominant
  JOURNAL   (in) Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE and
            Amemiya A (Eds.);
            GENEREVIEWS(R);
            (1993)
   PUBMED   20301302
REFERENCE   8  (bases 1 to 2852)
  AUTHORS   Wu,J.J., Woods,P.E. and Eyre,D.R.
  TITLE     Identification of cross-linking sites in bovine cartilage type IX
            collagen reveals an antiparallel type II-type IX molecular
            relationship and type IX to type IX bonding
  JOURNAL   J Biol Chem 267 (32), 23007-23014 (1992)
   PUBMED   1429648
REFERENCE   9  (bases 1 to 2852)
  AUTHORS   Fahrig,T., Landa,C., Pesheva,P., Kuhn,K. and Schachner,M.
  TITLE     Characterization of binding properties of the myelin-associated
            glycoprotein to extracellular matrix constituents
  JOURNAL   EMBO J 6 (10), 2875-2883 (1987)
   PUBMED   2446864
REFERENCE   10 (bases 1 to 2852)
  AUTHORS   McCormick,D., van der Rest,M., Goodship,J., Lozano,G., Ninomiya,Y.
            and Olsen,B.R.
  TITLE     Structure of the glycosaminoglycan domain in the type IX
            collagen-proteoglycan
  JOURNAL   Proc Natl Acad Sci U S A 84 (12), 4044-4048 (1987)
   PUBMED   3473493
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from CD722372.1, BC136326.1 and
            CB305733.1.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Nov 28, 2018 this sequence version replaced NM_001852.3.
            
            Summary: This gene encodes one of the three alpha chains of type IX
            collagen, the major collagen component of hyaline cartilage. Type
            IX collagen, a heterotrimeric molecule, is usually found in tissues
            containing type II collagen, a fibrillar collagen. This chain is
            unusual in that, unlike the other two type IX alpha chains, it
            contains a covalently attached glycosaminoglycan side chain.
            Mutations in this gene are associated with multiple epiphyseal
            dysplasia. [provided by RefSeq, Jul 2008].
            
            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 :: M95610.1, BC136326.1 [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA1965299,
                                           SAMEA1966682 [ECO:0006172]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000372748.8/ ENSP00000361834.3
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-26                CD722372.1         9-34
            27-2263             BC136326.1         1-2237
            2264-2796           CB305733.1         75-607              c
            2797-2852           CB305733.1         18-73               c
FEATURES             Location/Qualifiers
     source          1..2852
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="1"
                     /map="1p34.2"
     gene            1..2852
                     /gene="COL9A2"
                     /gene_synonym="DJ39G22.4; EDM2; MED; STL5"
                     /note="collagen type IX alpha 2 chain"
                     /db_xref="GeneID:1298"
                     /db_xref="HGNC:HGNC:2218"
                     /db_xref="MIM:120260"
     exon            1..164
                     /gene="COL9A2"
                     /gene_synonym="DJ39G22.4; EDM2; MED; STL5"
                     /inference="alignment:Splign:2.1.0"
     CDS             90..2159
                     /gene="COL9A2"
                     /gene_synonym="DJ39G22.4; EDM2; MED; STL5"
                     /note="collagen IX, alpha-2 polypeptide; collagen, type
                     IX, alpha 2; alpha 2 type IX collagen; collagen
                     alpha-2(IX) chain"
                     /codon_start=1
                     /product="collagen alpha-2(IX) chain precursor"
                     /protein_id="NP_001843.1"
                     /db_xref="CCDS:CCDS450.1"
                     /db_xref="GeneID:1298"
                     /db_xref="HGNC:HGNC:2218"
                     /db_xref="MIM:120260"
                     /translation="MAAATASPRSLLVLLQVVVLALAQIRGPPGERGPPGPPGPPGVP
                     GSDGIDGDNGPPGKAGPPGPKGEPGKAGPDGPDGKPGIDGLTGAKGEPGPMGIPGVKG
                     QPGLPGPPGLPGPGFAGPPGPPGPVGLPGEIGIRGPKGDPGPDGPSGPPGPPGKPGRP
                     GTIQGLEGSADFLCPTNCPPGMKGPPGLQGVKGHAGKRGILGDPGHQGKPGPKGDVGA
                     SGEQGIPGPPGPQGIRGYPGMAGPKGETGPHGYKGMVGAIGATGPPGEEGPRGPPGRA
                     GEKGDEGSPGIRGPQGITGPKGATGPPGINGKDGTPGTPGMKGSAGQAGQPGSPGHQG
                     LAGVPGQPGTKGGPGDQGEPGPQGLPGFSGPPGKEGEPGPRGEIGPQGIMGQKGDQGE
                     RGPVGQPGPQGRQGPKGEQGPPGIPGPQGLPGVKGDKGSPGKTGPRGKVGDPGVAGLP
                     GEKGEKGESGEPGPKGQQGVRGEPGYPGPSGDAGAPGVQGYPGPPGPRGLAGNRGVPG
                     QPGRQGVEGRDATDQHIVDVALKMLQEQLAEVAVSAKREALGAVGMMGPPGPPGPPGY
                     PGKQGPHGHPGPRGVPGIVGAVGQIGNTGPKGKRGEKGDPGEVGRGHPGMPGPPGIPG
                     LPGRPGQAINGKDGDRGSPGAPGEAGRPGLPGPVGLPGFCEPAACLGASAYASARLTE
                     PGSIKGP"
     exon            165..239
                     /gene="COL9A2"
                     /gene_synonym="DJ39G22.4; EDM2; MED; STL5"
                     /inference="alignment:Splign:2.1.0"
     exon            240..275
                     /gene="COL9A2"
                     /gene_synonym="DJ39G22.4; EDM2; MED; STL5"
                     /inference="alignment:Splign:2.1.0"
     exon            276..338
                     /gene="COL9A2"
                     /gene_synonym="DJ39G22.4; EDM2; MED; STL5"
                     /inference="alignment:Splign:2.1.0"
     exon            339..392
                     /gene="COL9A2"
                     /gene_synonym="DJ39G22.4; EDM2; MED; STL5"
                     /inference="alignment:Splign:2.1.0"
     exon            393..428
                     /gene="COL9A2"
                     /gene_synonym="DJ39G22.4; EDM2; MED; STL5"
                     /inference="alignment:Splign:2.1.0"
     exon            429..452
                     /gene="COL9A2"
                     /gene_synonym="DJ39G22.4; EDM2; MED; STL5"
                     /inference="alignment:Splign:2.1.0"
     exon            453..506
                     /gene="COL9A2"
                     /gene_synonym="DJ39G22.4; EDM2; MED; STL5"
                     /inference="alignment:Splign:2.1.0"
     exon            507..560
                     /gene="COL9A2"
                     /gene_synonym="DJ39G22.4; EDM2; MED; STL5"
                     /inference="alignment:Splign:2.1.0"
     exon            561..608
                     /gene="COL9A2"
                     /gene_synonym="DJ39G22.4; EDM2; MED; STL5"
                     /inference="alignment:Splign:2.1.0"
     exon            609..665
                     /gene="COL9A2"
                     /gene_synonym="DJ39G22.4; EDM2; MED; STL5"
                     /inference="alignment:Splign:2.1.0"
     exon            666..719
                     /gene="COL9A2"
                     /gene_synonym="DJ39G22.4; EDM2; MED; STL5"
                     /inference="alignment:Splign:2.1.0"
     exon            720..773
                     /gene="COL9A2"
                     /gene_synonym="DJ39G22.4; EDM2; MED; STL5"
                     /inference="alignment:Splign:2.1.0"
     exon            774..827
                     /gene="COL9A2"
                     /gene_synonym="DJ39G22.4; EDM2; MED; STL5"
                     /inference="alignment:Splign:2.1.0"
     exon            828..881
                     /gene="COL9A2"
                     /gene_synonym="DJ39G22.4; EDM2; MED; STL5"
                     /inference="alignment:Splign:2.1.0"
     exon            882..935
                     /gene="COL9A2"
                     /gene_synonym="DJ39G22.4; EDM2; MED; STL5"
                     /inference="alignment:Splign:2.1.0"
     exon            936..989
                     /gene="COL9A2"
                     /gene_synonym="DJ39G22.4; EDM2; MED; STL5"
                     /inference="alignment:Splign:2.1.0"
     exon            990..1043
                     /gene="COL9A2"
                     /gene_synonym="DJ39G22.4; EDM2; MED; STL5"
                     /inference="alignment:Splign:2.1.0"
     exon            1044..1097
                     /gene="COL9A2"
                     /gene_synonym="DJ39G22.4; EDM2; MED; STL5"
                     /inference="alignment:Splign:2.1.0"
     exon            1098..1142
                     /gene="COL9A2"
                     /gene_synonym="DJ39G22.4; EDM2; MED; STL5"
                     /inference="alignment:Splign:2.1.0"
     exon            1143..1196
                     /gene="COL9A2"
                     /gene_synonym="DJ39G22.4; EDM2; MED; STL5"
                     /inference="alignment:Splign:2.1.0"
     exon            1197..1250
                     /gene="COL9A2"
                     /gene_synonym="DJ39G22.4; EDM2; MED; STL5"
                     /inference="alignment:Splign:2.1.0"
     exon            1251..1304
                     /gene="COL9A2"
                     /gene_synonym="DJ39G22.4; EDM2; MED; STL5"
                     /inference="alignment:Splign:2.1.0"
     exon            1305..1376
                     /gene="COL9A2"
                     /gene_synonym="DJ39G22.4; EDM2; MED; STL5"
                     /inference="alignment:Splign:2.1.0"
     exon            1377..1412
                     /gene="COL9A2"
                     /gene_synonym="DJ39G22.4; EDM2; MED; STL5"
                     /inference="alignment:Splign:2.1.0"
     exon            1413..1457
                     /gene="COL9A2"
                     /gene_synonym="DJ39G22.4; EDM2; MED; STL5"
                     /inference="alignment:Splign:2.1.0"
     exon            1458..1490
                     /gene="COL9A2"
                     /gene_synonym="DJ39G22.4; EDM2; MED; STL5"
                     /inference="alignment:Splign:2.1.0"
     exon            1491..1637
                     /gene="COL9A2"
                     /gene_synonym="DJ39G22.4; EDM2; MED; STL5"
                     /inference="alignment:Splign:2.1.0"
     exon            1638..1692
                     /gene="COL9A2"
                     /gene_synonym="DJ39G22.4; EDM2; MED; STL5"
                     /inference="alignment:Splign:2.1.0"
     exon            1693..1881
                     /gene="COL9A2"
                     /gene_synonym="DJ39G22.4; EDM2; MED; STL5"
                     /inference="alignment:Splign:2.1.0"
     exon            1882..1959
                     /gene="COL9A2"
                     /gene_synonym="DJ39G22.4; EDM2; MED; STL5"
                     /inference="alignment:Splign:2.1.0"
     exon            1960..2852
                     /gene="COL9A2"
                     /gene_synonym="DJ39G22.4; EDM2; MED; STL5"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2786..2791
                     /regulatory_class="polyA_signal_sequence"
                     /gene="COL9A2"
                     /gene_synonym="DJ39G22.4; EDM2; MED; STL5"
                     /note="hexamer: AATAAA"
     polyA_site      2818
                     /gene="COL9A2"
                     /gene_synonym="DJ39G22.4; EDM2; MED; STL5"
                     /note="major polyA site"
     polyA_site      2852
                     /gene="COL9A2"
                     /gene_synonym="DJ39G22.4; EDM2; MED; STL5"
ORIGIN      
        1 gaacagccag cgctggagga gcgccgggag actctgccgt cggtgcgtgc gcggacacgc
       61 acccgtcccc cttggtctcg ccgccagcca tggccgccgc tacggcctcc ccccgcagcc
      121 tccttgttct cctccaggtg gtagtgctcg ctctggcgca gattagaggt ccaccgggag
      181 agcggggccc cccgggtccc ccgggaccgc cgggagtgcc tggatccgac ggcatcgacg
      241 gtgacaatgg gccccctgga aaagctggcc ctccgggacc caagggcgag cctggcaaag
      301 ctgggccaga tgggccagac gggaagcccg ggattgatgg tttaactgga gccaaggggg
      361 agcctggccc catggggatc cctggagtca agggccagcc cgggcttcct ggtcctcctg
      421 gccttccggg ccctggtttt gctggacctc ctgggcctcc tggacctgtt ggcctccctg
      481 gtgagattgg aatccgaggc cccaaggggg accctggacc agatggacca tcggggcccc
      541 caggaccccc tgggaaacct ggtcgcccgg gaaccatcca gggtctggaa ggcagtgcgg
      601 atttcctgtg tccaaccaac tgtccacccg gaatgaaagg tcccccaggg ctgcagggag
      661 tgaaggggca tgcgggcaaa cgcgggattc tgggtgatcc tggccaccag gggaagccgg
      721 gtcccaaggg agatgtgggt gcctctggag agcaaggcat ccctggacca ccgggtcccc
      781 agggcatcag gggctaccca ggcatggcag ggcccaaggg agagacgggc cctcatggat
      841 ataaaggcat ggtgggcgct atcggtgcca ctgggccacc gggtgaggaa ggtcctaggg
      901 gaccgccagg ccgagctggg gagaagggtg acgagggcag cccaggtatt cgtggacccc
      961 aggggatcac aggcccgaaa ggagcaacgg gccccccagg catcaacggc aaggatggga
     1021 ccccaggcac gcctggcatg aagggcagtg caggacaggc gggacagccc ggaagtccag
     1081 gccaccaggg cctagcgggt gtgccaggcc agcctgggac aaaaggaggc cctggagacc
     1141 agggtgagcc gggcccgcag ggccttcctg gattctctgg tccccctggg aaagagggag
     1201 agccagggcc tcgaggagaa attggtcccc agggcatcat gggacagaag ggtgaccaag
     1261 gcgagagggg tccagtgggg caaccaggcc ctcagggaag gcagggccct aagggggagc
     1321 agggcccccc cggaattcca gggccccaag gcttgccagg cgtcaaagga gacaagggct
     1381 ccccagggaa gaccgggccc cgcggcaaag tgggtgaccc aggggtggcc ggcctccccg
     1441 gagagaaagg cgagaagggc gagtccggcg agccggggcc caagggacag caaggagtac
     1501 gtggagaacc cggctaccct ggccccagcg gggatgcggg cgccccaggg gttcagggct
     1561 accctggtcc ccccggccct cgaggactgg ccgggaaccg aggcgtgcca ggacagcccg
     1621 ggagacaggg cgtggagggc cgggatgcca ctgaccagca catcgtggat gtggcgctga
     1681 agatgctgca agagcaactg gcagaggtcg ccgtgagtgc caagcgggaa gccctgggtg
     1741 cggtgggcat gatgggtcct ccaggacctc ctgggccccc tgggtaccca ggcaagcagg
     1801 gcccccatgg gcaccctggc cctcggggcg ttcctggcat cgtgggagcc gtgggtcaga
     1861 tcggcaacac ggggcccaag ggaaaacgtg gagagaaggg tgatccagga gaagtgggac
     1921 gggggcaccc cgggatgcct gggcccccag ggatcccagg actccctggc cggcctggcc
     1981 aggcaatcaa cggcaaggat ggagatcgag ggtccccagg ggctccagga gaggcaggtc
     2041 gacctggcct gccaggcccc gtggggctgc cgggcttctg tgaacctgcc gcctgccttg
     2101 gagcttcggc ctatgcctct gcccgcctta cagagcctgg atccatcaag gggccttgag
     2161 catcaggccc agacagagcc tggcaggcat cctggcggga aggaccaggt cccctctggg
     2221 tggacatgca cccatcccca gtccaggaaa ccatctcccc caggaccttc tgtctgggac
     2281 tcaggagtcc taaggaaaag gaattctaaa acatggggga aggggaggta gagcactgat
     2341 gggtgaaaaa gtgaggccaa cacacagggc aagtggtgtc gatggagtcg aagcgctgaa
     2401 ggaatagggc ggctttcctt ccagcgagca tcattcggct gttaccaaaa caaacatctt
     2461 aatctgcacc tttctccact ggccatcttg tccttgggtc agtgggacat gggcacctcg
     2521 ggaggcccgg gccctgccca gctacagttc cacccctcag cttgaggacc aatgactgag
     2581 gtctatgcca gttcctgatc ccatctcact ctctggacct accaggtgac tgctgctggg
     2641 tgactcccct gaggcggcta tacccttaag ccagccccac tacttccttc cctgcctccc
     2701 agctcagtat ttaaacatca tctcccttct ctttctcgca taactcccca cccctttctc
     2761 cccgatccac ccaggccttt ctgtaaataa aagctcccaa gttgggtaca aaccaggata
     2821 ttggagttac tctatcctgg agttaactag ga
//
