LOCUS       NM_030820               4173 bp    mRNA    linear   PRI 04-APR-2024
DEFINITION  Homo sapiens collagen type XXI alpha 1 chain (COL21A1), transcript
            variant 1, mRNA.
ACCESSION   NM_030820
VERSION     NM_030820.4
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 4173)
  AUTHORS   Liang,Y., Lv,Z., Huang,G., Qin,J., Li,H., Nong,F. and Wen,B.
  TITLE     Prognostic significance of abnormal matrix collagen remodeling in
            colorectal cancer based on histologic and bioinformatics analysis
  JOURNAL   Oncol Rep 44 (4), 1671-1685 (2020)
   PUBMED   32945508
  REMARK    GeneRIF: Prognostic significance of abnormal matrix collagen
            remodeling in colorectal cancer based on histologic and
            bioinformatics analysis.
REFERENCE   2  (bases 1 to 4173)
  AUTHORS   Al-Qarni,R., Iqbal,M., Al-Otaibi,M., Al-Saif,F., Alfadda,A.A.,
            Alkhalidi,H., Bamehriz,F. and Hassanain,M.
  TITLE     Validating candidate biomarkers for different stages of
            non-alcoholic fatty liver disease
  JOURNAL   Medicine (Baltimore) 99 (36), e21463 (2020)
   PUBMED   32898995
  REMARK    GeneRIF: Validating candidate biomarkers for different stages of
            non-alcoholic fatty liver disease.
REFERENCE   3  (bases 1 to 4173)
  AUTHORS   Mohamad Shah,N.S., Sulong,S., Wan Sulaiman,W.A. and Halim,A.S.
  TITLE     Two novel genes TOX3 and COL21A1 in large extended Malay families
            with nonsyndromic cleft lip and/or palate
  JOURNAL   Mol Genet Genomic Med 7 (5), e635 (2019)
   PUBMED   30924295
  REMARK    GeneRIF: Low copy number of Col21A1 is associated with nonsyndromic
            cleft lip and/or palate.
REFERENCE   4  (bases 1 to 4173)
  AUTHORS   Naba,A., Pearce,O.M.T., Del Rosario,A., Ma,D., Ding,H., Rajeeve,V.,
            Cutillas,P.R., Balkwill,F.R. and Hynes,R.O.
  TITLE     Characterization of the Extracellular Matrix of Normal and Diseased
            Tissues Using Proteomics
  JOURNAL   J Proteome Res 16 (8), 3083-3091 (2017)
   PUBMED   28675934
REFERENCE   5  (bases 1 to 4173)
  AUTHORS   Naba,A., Clauser,K.R., Whittaker,C.A., Carr,S.A., Tanabe,K.K. and
            Hynes,R.O.
  TITLE     Extracellular matrix signatures of human primary metastatic colon
            cancers and their metastases to liver
  JOURNAL   BMC Cancer 14, 518 (2014)
   PUBMED   25037231
  REMARK    Publication Status: Online-Only
REFERENCE   6  (bases 1 to 4173)
  AUTHORS   Januchowski,R., Zawierucha,P., Rucinski,M., Nowicki,M. and Zabel,M.
  TITLE     Extracellular matrix proteins expression profiling in
            chemoresistant variants of the A2780 ovarian cancer cell line
  JOURNAL   Biomed Res Int 2014, 365867 (2014)
   PUBMED   24804215
  REMARK    GeneRIF: Extracellular matrix proteins expression profiling in
            chemoresistant variants of the A2780 ovarian cancer cell line.
REFERENCE   7  (bases 1 to 4173)
  AUTHORS   Chou,M.Y. and Li,H.C.
  TITLE     Genomic organization and characterization of the human type XXI
            collagen (COL21A1) gene
  JOURNAL   Genomics 79 (3), 395-401 (2002)
   PUBMED   11863369
REFERENCE   8  (bases 1 to 4173)
  AUTHORS   Tuckwell,D.
  TITLE     Identification and analysis of collagen alpha 1(XXI), a novel
            member of the FACIT collagen family
  JOURNAL   Matrix Biol 21 (1), 63-66 (2002)
   PUBMED   11827793
REFERENCE   9  (bases 1 to 4173)
  AUTHORS   Fitzgerald,J. and Bateman,J.F.
  TITLE     A new FACIT of the collagen family: COL21A1
  JOURNAL   FEBS Lett 505 (2), 275-280 (2001)
   PUBMED   11566190
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from BP231679.1, AF330693.1 and
            AL136624.1.
            
            On Nov 22, 2018 this sequence version replaced NM_030820.3.
            
            Summary: This gene encodes the alpha chain of type XXI collagen, a
            member of the FACIT (fibril-associated collagens with interrupted
            helices) collagen family. Type XXI collagen is localized to tissues
            containing type I collagen and maintains the integrity of the
            extracellular matrix. Alternative splicing results in multiple
            transcript variants. [provided by RefSeq, Jan 2016].
            
            Transcript Variant: This variant (1) encodes the longest isoform
            (a). Variants 1 and 2 encode the same isoform (a).
            
            ##Evidence-Data-START##
            Transcript exon combination :: AF414088.1, SRR1803612.119950.1
                                           [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA1965299,
                                           SAMEA1966682 [ECO:0006172]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000244728.10/ ENSP00000244728.5
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-442               BP231679.1         3-444
            443-1510            AF330693.1         373-1440
            1511-2241           AL136624.1         1481-2211
            2242-4173           AF330693.1         2163-4094
FEATURES             Location/Qualifiers
     source          1..4173
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="6"
                     /map="6p12.1"
     gene            1..4173
                     /gene="COL21A1"
                     /gene_synonym="COLA1L; FP633"
                     /note="collagen type XXI alpha 1 chain"
                     /db_xref="GeneID:81578"
                     /db_xref="HGNC:HGNC:17025"
                     /db_xref="MIM:610002"
     exon            1..194
                     /gene="COL21A1"
                     /gene_synonym="COLA1L; FP633"
                     /inference="alignment:Splign:2.1.0"
     exon            195..320
                     /gene="COL21A1"
                     /gene_synonym="COLA1L; FP633"
                     /inference="alignment:Splign:2.1.0"
     CDS             233..3106
                     /gene="COL21A1"
                     /gene_synonym="COLA1L; FP633"
                     /note="isoform a precursor is encoded by transcript
                     variant 1; collagen alpha-1(XXI) chain; alpha 1 chain-like
                     collagen; collagen, type XXI, alpha 1"
                     /codon_start=1
                     /product="collagen alpha-1(XXI) chain isoform a precursor"
                     /protein_id="NP_110447.2"
                     /db_xref="CCDS:CCDS55025.1"
                     /db_xref="GeneID:81578"
                     /db_xref="HGNC:HGNC:17025"
                     /db_xref="MIM:610002"
                     /translation="MAHYITFLCMVLVLLLQNSVLAEDGEVRSSCRTAPTDLVFILDG
                     SYSVGPENFEIVKKWLVNITKNFDIGPKFIQVGVVQYSDYPVLEIPLGSYDSGEHLTA
                     AVESILYLGGNTKTGKAIQFALDYLFAKSSRFLTKIAVVLTDGKSQDDVKDAAQAARD
                     SKITLFAIGVGSETEDAELRAIANKPSSTYVFYVEDYIAISKIREVMKQKLCEESVCP
                     TRIPVAARDERGFDILLGLDVNKKVKKRIQLSPKKIKGYEVTSKVDLSELTSNVFPEG
                     LPPSYVFVSTQRFKVKKIWDLWRILTIDGRPQIAVTLNGVDKILLFTTTSVINGSQVV
                     TFANPQVKTLFDEGWHQIRLLVTEQDVTLYIDDQQIENKPLHPVLGILINGQTQIGKY
                     SGKEETVQFDVQKLRIYCDPEQNNRETACEIPGFNGECLNGPSDVGSTPAPCICPPGK
                     PGLQGPKGDPGLPGNPGYPGQPGQDGKPGYQGIAGTPGVPGSPGIQGARGLPGYKGEP
                     GRDGDKGDRGLPGFPGLHGMPGSKGEMGAKGDKGSPGFYGKKGAKGEKGNAGFPGLPG
                     PAGEPGRHGKDGLMGSPGFKGEAGSPGAPGQDGTRGEPGIPGFPGNRGLMGQKGEIGP
                     PGQQGKKGAPGMPGLMGSNGSPGQPGTPGSKGSKGEPGIQGMPGASGLKGEPGATGSP
                     GEPGYMGLPGIQGKKGDKGNQGEKGIQGQKGENGRQGIPGQQGIQGHHGAKGERGEKG
                     EPGVRGAIGSKGESGVDGLMGPAGPKGQPGDPGPQGPPGLDGKPGREFSEQFIRQVCT
                     DVIRAQLPVLLQSGRIRNCDHCLSQHGSPGIPGPPGPIGPEGPRGLPGLPGRDGVPGL
                     VGVPGRPGVRGLKGLPGRNGEKGSQGFGYPGEQGPPGPPGPEGPPGISKEGPPGDPGL
                     PGKDGDHGKPGIQGQPGPPGICDPSLCFSVIARRDPFRKGPNY"
     exon            321..872
                     /gene="COL21A1"
                     /gene_synonym="COLA1L; FP633"
                     /inference="alignment:Splign:2.1.0"
     exon            873..1041
                     /gene="COL21A1"
                     /gene_synonym="COLA1L; FP633"
                     /inference="alignment:Splign:2.1.0"
     exon            1042..1258
                     /gene="COL21A1"
                     /gene_synonym="COLA1L; FP633"
                     /inference="alignment:Splign:2.1.0"
     exon            1259..1432
                     /gene="COL21A1"
                     /gene_synonym="COLA1L; FP633"
                     /inference="alignment:Splign:2.1.0"
     exon            1433..1510
                     /gene="COL21A1"
                     /gene_synonym="COLA1L; FP633"
                     /inference="alignment:Splign:2.1.0"
     exon            1511..1519
                     /gene="COL21A1"
                     /gene_synonym="COLA1L; FP633"
                     /inference="alignment:Splign:2.1.0"
     exon            1520..1603
                     /gene="COL21A1"
                     /gene_synonym="COLA1L; FP633"
                     /inference="alignment:Splign:2.1.0"
     exon            1604..1666
                     /gene="COL21A1"
                     /gene_synonym="COLA1L; FP633"
                     /inference="alignment:Splign:2.1.0"
     exon            1667..1720
                     /gene="COL21A1"
                     /gene_synonym="COLA1L; FP633"
                     /inference="alignment:Splign:2.1.0"
     exon            1721..1774
                     /gene="COL21A1"
                     /gene_synonym="COLA1L; FP633"
                     /inference="alignment:Splign:2.1.0"
     exon            1775..1828
                     /gene="COL21A1"
                     /gene_synonym="COLA1L; FP633"
                     /inference="alignment:Splign:2.1.0"
     exon            1829..1882
                     /gene="COL21A1"
                     /gene_synonym="COLA1L; FP633"
                     /inference="alignment:Splign:2.1.0"
     exon            1883..1936
                     /gene="COL21A1"
                     /gene_synonym="COLA1L; FP633"
                     /inference="alignment:Splign:2.1.0"
     exon            1937..1990
                     /gene="COL21A1"
                     /gene_synonym="COLA1L; FP633"
                     /inference="alignment:Splign:2.1.0"
     exon            1991..2044
                     /gene="COL21A1"
                     /gene_synonym="COLA1L; FP633"
                     /inference="alignment:Splign:2.1.0"
     exon            2045..2089
                     /gene="COL21A1"
                     /gene_synonym="COLA1L; FP633"
                     /inference="alignment:Splign:2.1.0"
     exon            2090..2143
                     /gene="COL21A1"
                     /gene_synonym="COLA1L; FP633"
                     /inference="alignment:Splign:2.1.0"
     exon            2144..2197
                     /gene="COL21A1"
                     /gene_synonym="COLA1L; FP633"
                     /inference="alignment:Splign:2.1.0"
     exon            2198..2251
                     /gene="COL21A1"
                     /gene_synonym="COLA1L; FP633"
                     /inference="alignment:Splign:2.1.0"
     exon            2252..2323
                     /gene="COL21A1"
                     /gene_synonym="COLA1L; FP633"
                     /inference="alignment:Splign:2.1.0"
     exon            2324..2359
                     /gene="COL21A1"
                     /gene_synonym="COLA1L; FP633"
                     /inference="alignment:Splign:2.1.0"
     exon            2360..2404
                     /gene="COL21A1"
                     /gene_synonym="COLA1L; FP633"
                     /inference="alignment:Splign:2.1.0"
     exon            2405..2437
                     /gene="COL21A1"
                     /gene_synonym="COLA1L; FP633"
                     /inference="alignment:Splign:2.1.0"
     exon            2438..2584
                     /gene="COL21A1"
                     /gene_synonym="COLA1L; FP633"
                     /inference="alignment:Splign:2.1.0"
     exon            2585..2639
                     /gene="COL21A1"
                     /gene_synonym="COLA1L; FP633"
                     /inference="alignment:Splign:2.1.0"
     exon            2640..2840
                     /gene="COL21A1"
                     /gene_synonym="COLA1L; FP633"
                     /inference="alignment:Splign:2.1.0"
     exon            2841..2918
                     /gene="COL21A1"
                     /gene_synonym="COLA1L; FP633"
                     /inference="alignment:Splign:2.1.0"
     exon            2919..4173
                     /gene="COL21A1"
                     /gene_synonym="COLA1L; FP633"
                     /inference="alignment:Splign:2.1.0"
     regulatory      4151..4156
                     /regulatory_class="polyA_signal_sequence"
                     /gene="COL21A1"
                     /gene_synonym="COLA1L; FP633"
                     /note="hexamer: AATAAA"
     polyA_site      4173
                     /gene="COL21A1"
                     /gene_synonym="COLA1L; FP633"
                     /note="major polyA site"
ORIGIN      
        1 gagagcgagt ttctgagcct ctgagctctg cactggccgc tgcagggaga acggactccg
       61 ggcggagggc agccaatccg tttcagcgca ggtcttgctc gggttgggct tgccactgcc
      121 tggaacatac ctgtccccct ggcgcaacac tcagctggct gcgacggcaa ccccgagcct
      181 ggacactgcg ccaggaatcc taaaaccaaa atattagaac gaaaacagaa acatggctca
      241 ctatattaca tttctctgca tggttttggt gctgcttctt cagaattctg tgttagctga
      301 agatggggaa gtaagatcaa gttgtcgtac tgctccgaca gatttagttt tcatcttaga
      361 tggctcttat agtgttggcc cagaaaactt tgaaatagtg aaaaagtggc ttgtcaatat
      421 cacaaaaaac tttgacatag ggccgaagtt tattcaagtt ggagtggttc aatatagtga
      481 ctaccctgtg ctggagattc ctctcggaag ctatgattca ggagaacatt tgacggcagc
      541 agtggaatcc atactctact taggaggaaa cacaaagaca gggaaggcca tccagtttgc
      601 gctcgattac ctttttgcca agtcctcacg atttctgact aagatagcag tggtacttac
      661 ggatggcaaa tcccaagatg acgtcaagga tgcagctcaa gcagcaagag atagtaagat
      721 aacattattt gctattggtg ttggttcaga aacagaagat gccgaactta gagctattgc
      781 caacaagcct tcgtctactt atgtgtttta tgtggaagac tatattgcaa tatccaaaat
      841 aagggaagtg atgaagcaga aactttgtga agaatctgtc tgtccaacac gaattccagt
      901 ggcagctcgt gatgaaaggg gatttgatat tcttttaggt ttagatgtaa ataaaaaggt
      961 taagaaaaga atacagcttt caccaaaaaa gataaaagga tatgaagtaa catcaaaagt
     1021 tgatttatca gaactcacaa gcaatgtttt cccagaaggt cttcctccat catatgtatt
     1081 tgtgtctact caaagattta aagtcaagaa aatttgggat ttatggagaa tattaactat
     1141 tgatggaagg ccacaaatag cagttacctt aaatggtgtg gacaaaatct tattatttac
     1201 aacaaccagc gtaattaatg gctcacaagt ggttaccttt gctaaccctc aagttaagac
     1261 gttgtttgat gaaggctggc accaaattcg tctcttagta acagaacaag atgtgacttt
     1321 gtatattgat gaccaacaaa ttgaaaacaa gcccttacat ccagttttag ggatcttgat
     1381 caatgggcaa acccaaattg gaaaatattc tggaaaagaa gaaactgttc agtttgatgt
     1441 ccaaaagttg cgaatctact gtgacccaga acagaacaac cgggagacag catgtgagat
     1501 tcctggattt aatggagagt gccttaatgg tcccagtgat gtaggttcaa ctccagctcc
     1561 ctgtatttgt cctccgggaa aaccaggact tcaaggcccc aaaggtgacc ctggactgcc
     1621 tgggaaccct ggctaccctg gacaacctgg tcaagatggt aagcctggat atcagggaat
     1681 tgcagggaca ccaggtgttc caggatctcc aggaatacaa ggagctcgag gactaccagg
     1741 ttacaaagga gaaccagggc gagatggtga caagggtgat cgtggacttc ctggttttcc
     1801 tgggcttcat ggcatgccag gatcaaaggg tgaaatgggt gccaaaggag acaaaggatc
     1861 acctggattt tatggcaaaa agggtgcaaa aggtgaaaag gggaatgctg gcttccctgg
     1921 cctccctgga cctgctggag aaccaggaag acatggaaag gatggattaa tgggtagtcc
     1981 cggtttcaag ggagaagcag gatcccctgg tgctccgggg caggatggaa cacggggaga
     2041 gcctggaatc ccaggatttc ctggaaaccg aggattaatg ggccaaaagg gagaaattgg
     2101 gcctccagga cagcaaggaa aaaaaggagc cccagggatg cctggtttaa tgggaagcaa
     2161 tggctcacca ggccagcctg gaacaccggg atctaaggga agcaaaggtg aacctggaat
     2221 tcaagggatg cctggggctt ctgggctcaa gggagaacca ggagcaacgg gttccccagg
     2281 agaaccagga tacatgggtt tacccgggat tcaaggaaaa aagggggaca aaggaaatca
     2341 aggtgaaaaa ggtattcagg gtcaaaaggg agaaaatgga agacagggaa ttccagggca
     2401 acagggaatt caaggccatc atggtgcaaa aggagagaga ggtgaaaagg gagaacctgg
     2461 tgtccgaggt gccattggat caaaaggaga atctggggtg gatggcttga tggggcccgc
     2521 aggtcctaag gggcaacctg gggatccagg tcctcaggga cccccaggtt tggatgggaa
     2581 gcccggaaga gagttttcag aacaatttat tcgacaagtt tgcacagatg taataagagc
     2641 ccagctacca gtcttacttc agagtggaag aattagaaat tgtgatcatt gcctgtccca
     2701 acatggctcc ccgggtattc ctgggccacc tggtccgata ggcccagagg gtcccagagg
     2761 attacctggt ttgccaggaa gagatggtgt tcctggatta gtgggtgtcc ctggacgtcc
     2821 aggtgtcaga ggattaaaag gcctaccagg aagaaatggg gaaaaaggga gccaagggtt
     2881 tgggtatcct ggagaacaag gtcctcctgg tcccccaggt ccagagggcc ctcctggaat
     2941 aagcaaagaa ggtcctccag gagacccagg tctccctggc aaagatggag accatggaaa
     3001 acctggaatc caagggcaac caggcccccc aggcatctgc gacccatcac tatgttttag
     3061 tgtaattgcc agaagagatc cgttcagaaa aggaccaaac tattagtgtc tgatgcctca
     3121 ttcagcagcc taggcatggt gctttttctg tggtcttttg catctcagga agataaccaa
     3181 cagtaatccc ttgaaaagaa acttaagtac ctcggtgttt ttattttttt tttcttatgg
     3241 aaaaaaatat aaaagatcac atatactgat tttaaaggct cctcagtcat ttggagccct
     3301 tggattagca gcattaatta aatctcaagg gtttcttgta aagtccattt atgttaatca
     3361 aagttgaata taaaaatcca ccattgcctg ttagccagtc agttttagtc actgtgaaat
     3421 atttcacatt cagcctccat gcagtagaga tttgagttta atttcatgtc catgtgactt
     3481 tcatgtttcc tatctcatag ctcatgctac tacataagcc aaaacatgta tctcatcatt
     3541 ggaagtaaga tcagggctga tattcacctg ggatagacag tattggtgaa ctactcattt
     3601 actacagtgt ctcagccttg ataaggggca gtggattgcc tgttgttcgg tgttgtgaat
     3661 agcacctctg aataagatta gagtgtttct taattcattt caaactctaa aattagatta
     3721 atggtggtgc taagaaagag tattaattac tttgggaatg gtcaaaatta acattaaaaa
     3781 cattttagac aaaaagtttc attgtacatt caaagaaaat gtaagtttgg aagtactaaa
     3841 agactatttt atacttgttg attaatcgga atgtttgttg tatgccttca ttttccattt
     3901 cacttatatg tgtatgtcca tatatgttaa ttttcattgt agcaaagcta atggaaataa
     3961 agctaatgct ctagttgaaa gaaaaggaaa actcctgaaa tcctagaatg tcttgttatt
     4021 tttagctgac tgtaaaatat tatgaacagt ctttgtgtat tgtgcttaat gcttttgtaa
     4081 gaaacagaat ttgaaatatt tcatccttgt catgctcaaa attttgttac atgcttgtta
     4141 ttcagagtat aataaagttt tgtacaggcc tga
//
