LOCUS       NM_031050               1728 bp    mRNA    linear   ROD 15-JUN-2024
DEFINITION  Rattus norvegicus lumican (Lum), mRNA.
ACCESSION   NM_031050
VERSION     NM_031050.2
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 1728)
  AUTHORS   Hayes,A.J. and Melrose,J.
  TITLE     Immunolocalization of Keratan Sulfate in Rat Spinal Tissues Using
            the Keratanase Generated BKS-1(+) Neoepitope: Correlation of
            Expression Patterns with the Class II SLRPs, Lumican and Keratocan
  JOURNAL   Cells 9 (4), 826 (2020)
   PUBMED   32235499
  REMARK    GeneRIF: Immunolocalization of Keratan Sulfate in Rat Spinal
            Tissues Using the Keratanase Generated BKS-1(+) Neoepitope:
            Correlation of Expression Patterns with the Class II SLRPs, Lumican
            and Keratocan.
            Publication Status: Online-Only
REFERENCE   2  (bases 1 to 1728)
  AUTHORS   Barallobre-Barreiro,J., Gupta,S.K., Zoccarato,A.,
            Kitazume-Taneike,R., Fava,M., Yin,X., Werner,T., Hirt,M.N.,
            Zampetaki,A., Viviano,A., Chong,M., Bern,M., Kourliouros,A.,
            Domenech,N., Willeit,P., Shah,A.M., Jahangiri,M., Schaefer,L.,
            Fischer,J.W., Iozzo,R.V., Viner,R., Thum,T., Heineke,J.,
            Kichler,A., Otsu,K. and Mayr,M.
  TITLE     Glycoproteomics Reveals Decorin Peptides With Anti-Myostatin
            Activity in Human Atrial Fibrillation
  JOURNAL   Circulation 134 (11), 817-832 (2016)
   PUBMED   27559042
REFERENCE   3  (bases 1 to 1728)
  AUTHORS   Barallobre-Barreiro,J., Oklu,R., Lynch,M., Fava,M., Baig,F.,
            Yin,X., Barwari,T., Potier,D.N., Albadawi,H., Jahangiri,M.,
            Porter,K.E., Watkins,M.T., Misra,S., Stoughton,J. and Mayr,M.
  TITLE     Extracellular matrix remodelling in response to venous
            hypertension: proteomics of human varicose veins
  JOURNAL   Cardiovasc Res 110 (3), 419-430 (2016)
   PUBMED   27068509
REFERENCE   4  (bases 1 to 1728)
  AUTHORS   Abonnenc,M., Nabeebaccus,A.A., Mayr,U., Barallobre-Barreiro,J.,
            Dong,X., Cuello,F., Sur,S., Drozdov,I., Langley,S.R., Lu,R.,
            Stathopoulou,K., Didangelos,A., Yin,X., Zimmermann,W.H., Shah,A.M.,
            Zampetaki,A. and Mayr,M.
  TITLE     Extracellular matrix secretion by cardiac fibroblasts: role of
            microRNA-29b and microRNA-30c
  JOURNAL   Circ Res 113 (10), 1138-1147 (2013)
   PUBMED   24006456
REFERENCE   5  (bases 1 to 1728)
  AUTHORS   Bubenek,S., Nastase,A., Niculescu,A.M., Baila,S., Herlea,V.,
            Lazar,V., Paslaru,L., Botezatu,A., Tomescu,D., Popescu,I. and
            Dima,S.
  TITLE     Assessment of gene expression profiles in peripheral occlusive
            arterial disease
  JOURNAL   Can J Cardiol 28 (6), 712-720 (2012)
   PUBMED   22721676
REFERENCE   6  (bases 1 to 1728)
  AUTHORS   Onda,M., Ishiwata,T., Kawahara,K., Wang,R., Naito,Z. and
            Sugisaki,Y.
  TITLE     Expression of lumican in thickened intima and smooth muscle cells
            in human coronary atherosclerosis
  JOURNAL   Exp Mol Pathol 72 (2), 142-149 (2002)
   PUBMED   11890723
REFERENCE   7  (bases 1 to 1728)
  AUTHORS   Baba,H., Ishiwata,T., Takashi,E., Xu,G. and Asano,G.
  TITLE     Expression and localization of lumican in the ischemic and
            reperfused rat heart
  JOURNAL   Jpn Circ J 65 (5), 445-450 (2001)
   PUBMED   11348051
REFERENCE   8  (bases 1 to 1728)
  AUTHORS   Neame,P.J., Kay,C.J., McQuillan,D.J., Beales,M.P. and Hassell,J.R.
  TITLE     Independent modulation of collagen fibrillogenesis by decorin and
            lumican
  JOURNAL   Cell Mol Life Sci 57 (5), 859-863 (2000)
   PUBMED   10892350
REFERENCE   9  (bases 1 to 1728)
  AUTHORS   Svensson,L., Narlid,I. and Oldberg,A.
  TITLE     Fibromodulin and lumican bind to the same region on collagen type I
            fibrils
  JOURNAL   FEBS Lett 470 (2), 178-182 (2000)
   PUBMED   10734230
REFERENCE   10 (bases 1 to 1728)
  AUTHORS   Krull,N.B. and Gressner,A.M.
  TITLE     Differential expression of keratan sulphate proteoglycans
            fibromodulin, lumican and aggrecan in normal and fibrotic rat liver
  JOURNAL   FEBS Lett 312 (1), 47-52 (1992)
   PUBMED   1385211
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from
            JAXUCZ010000007.1.
            
            On Nov 26, 2020 this sequence version replaced NM_031050.1.
            
            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 :: X84039.1, BC061878.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA5760386, SAMEA5760389
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-24                JAXUCZ010000007.1  34245706-34245729
            25-907              JAXUCZ010000007.1  34248082-34248964
            908-1728            JAXUCZ010000007.1  34251690-34252510
FEATURES             Location/Qualifiers
     source          1..1728
                     /organism="Rattus norvegicus"
                     /mol_type="mRNA"
                     /strain="BN"
                     /db_xref="taxon:10116"
                     /chromosome="7"
                     /map="7q13"
     gene            1..1728
                     /gene="Lum"
                     /note="lumican"
                     /db_xref="GeneID:81682"
                     /db_xref="RGD:620984"
     exon            1..24
                     /gene="Lum"
                     /inference="alignment:Splign:2.1.0"
     exon            25..907
                     /gene="Lum"
                     /inference="alignment:Splign:2.1.0"
     CDS             46..1062
                     /gene="Lum"
                     /note="KSPG lumican; keratan sulfate proteoglycan lumican"
                     /codon_start=1
                     /product="lumican precursor"
                     /protein_id="NP_112312.1"
                     /db_xref="GeneID:81682"
                     /db_xref="RGD:620984"
                     /translation="

MNVCTFTLVLALVGSVSGQYYDYDAPLFMYGELSPNCAPECNCPHSYPTAMYCDDLKLKSVPMVPPGIKYLYLRNNQIDHIDEKAFENVTDLQWLILDHNLLENSKIKGKVFSKLKQLKKLHINYNNLTESVGPLPKSLQDLQLANNKISKLGSFDGLVNLTFIYLQHNQLKEEAVSASLKGLKSLEYLDLSFNQMSKLPAGLPTSLLTLYLDNNKITNIPDEYFNRFTGLQYLRLSHNELADSGVPGNSFNISSLLELDLSYNKLKSIPTVNENLENYYLEVNKLEKFDVKSFCKILGPLSYSKIKHLRLDGNPLTQSSLPPDMYECLRVANEITVN"

     sig_peptide     46..99
                     /gene="Lum"
                     /inference="COORDINATES: ab initio prediction:SignalP:6.0"
     mat_peptide     100..1059
                     /gene="Lum"
                     /product="Lumican. /id=PRO_0000032735"
                     /note="propagated from UniProtKB/Swiss-Prot (P51886.1)"
     misc_feature    100..102
                     /gene="Lum"
                     /note="Pyrrolidone carboxylic acid.
                     /evidence=ECO:0000250|UniProtKB:P51884; propagated from
                     UniProtKB/Swiss-Prot (P51886.1);
                     pyrrolidone-carboxylic-acid site"
     misc_feature    103..105
                     /gene="Lum"
                     /note="Sulfotyrosine.
                     /evidence=ECO:0000250|UniProtKB:P51885; propagated from
                     UniProtKB/Swiss-Prot (P51886.1); sulfatation site"
     misc_feature    106..108
                     /gene="Lum"
                     /note="Sulfotyrosine.
                     /evidence=ECO:0000250|UniProtKB:P51885; propagated from
                     UniProtKB/Swiss-Prot (P51886.1); sulfatation site"
     misc_feature    112..114
                     /gene="Lum"
                     /note="Sulfotyrosine.
                     /evidence=ECO:0000250|UniProtKB:P51885; propagated from
                     UniProtKB/Swiss-Prot (P51886.1); sulfatation site"
     misc_feature    133..135
                     /gene="Lum"
                     /note="Sulfotyrosine.
                     /evidence=ECO:0000250|UniProtKB:P51885; propagated from
                     UniProtKB/Swiss-Prot (P51886.1); sulfatation site"
     misc_feature    154..258
                     /gene="Lum"
                     /note="Leucine rich repeat N-terminal domain; Region:
                     LRRNT; smart00013"
                     /db_xref="CDD:214470"
     misc_feature    244..309
                     /gene="Lum"
                     /note="propagated from UniProtKB/Swiss-Prot (P51886.1);
                     Region: LRR 1"
     misc_feature    247..318
                     /gene="Lum"
                     /note="leucine-rich repeat [structural motif]; Region:
                     leucine-rich repeat"
                     /db_xref="CDD:275380"
     misc_feature    256..>1008
                     /gene="Lum"
                     /note="Leucine-rich repeat (LRR) protein [Transcription];
                     Region: LRR; COG4886"
                     /db_xref="CDD:443914"
     misc_feature    307..309
                     /gene="Lum"
                     /note="N-linked (GlcNAc...) (keratan sulfate) asparagine.
                     /evidence=ECO:0000255; propagated from
                     UniProtKB/Swiss-Prot (P51886.1); glycosylation site"
     misc_feature    316..387
                     /gene="Lum"
                     /note="propagated from UniProtKB/Swiss-Prot (P51886.1);
                     Region: LRR 2"
     misc_feature    319..396
                     /gene="Lum"
                     /note="leucine-rich repeat [structural motif]; Region:
                     leucine-rich repeat"
                     /db_xref="CDD:275380"
     misc_feature    394..456
                     /gene="Lum"
                     /note="propagated from UniProtKB/Swiss-Prot (P51886.1);
                     Region: LRR 3"
     misc_feature    397..459
                     /gene="Lum"
                     /note="leucine-rich repeat [structural motif]; Region:
                     leucine-rich repeat"
                     /db_xref="CDD:275380"
     misc_feature    424..426
                     /gene="Lum"
                     /note="N-linked (GlcNAc...) (keratan sulfate) asparagine.
                     /evidence=ECO:0000255; propagated from
                     UniProtKB/Swiss-Prot (P51886.1); glycosylation site"
     misc_feature    457..522
                     /gene="Lum"
                     /note="propagated from UniProtKB/Swiss-Prot (P51886.1);
                     Region: LRR 4"
     misc_feature    460..525
                     /gene="Lum"
                     /note="leucine-rich repeat [structural motif]; Region:
                     leucine-rich repeat"
                     /db_xref="CDD:275380"
     misc_feature    523..588
                     /gene="Lum"
                     /note="propagated from UniProtKB/Swiss-Prot (P51886.1);
                     Region: LRR 5"
     misc_feature    523..525
                     /gene="Lum"
                     /note="N-linked (GlcNAc...) (keratan sulfate) asparagine.
                     /evidence=ECO:0000255; propagated from
                     UniProtKB/Swiss-Prot (P51886.1); glycosylation site"
     misc_feature    526..600
                     /gene="Lum"
                     /note="leucine-rich repeat [structural motif]; Region:
                     leucine-rich repeat"
                     /db_xref="CDD:275380"
     misc_feature    598..660
                     /gene="Lum"
                     /note="propagated from UniProtKB/Swiss-Prot (P51886.1);
                     Region: LRR 6"
     misc_feature    601..663
                     /gene="Lum"
                     /note="leucine-rich repeat [structural motif]; Region:
                     leucine-rich repeat"
                     /db_xref="CDD:275380"
     misc_feature    661..726
                     /gene="Lum"
                     /note="propagated from UniProtKB/Swiss-Prot (P51886.1);
                     Region: LRR 7"
     misc_feature    664..735
                     /gene="Lum"
                     /note="leucine-rich repeat [structural motif]; Region:
                     leucine-rich repeat"
                     /db_xref="CDD:275380"
     misc_feature    733..795
                     /gene="Lum"
                     /note="propagated from UniProtKB/Swiss-Prot (P51886.1);
                     Region: LRR 8"
     misc_feature    736..810
                     /gene="Lum"
                     /note="leucine-rich repeat [structural motif]; Region:
                     leucine-rich repeat"
                     /db_xref="CDD:275380"
     misc_feature    799..801
                     /gene="Lum"
                     /note="N-linked (GlcNAc...) (keratan sulfate) asparagine.
                     /evidence=ECO:0000255; propagated from
                     UniProtKB/Swiss-Prot (P51886.1); glycosylation site"
     misc_feature    808..873
                     /gene="Lum"
                     /note="propagated from UniProtKB/Swiss-Prot (P51886.1);
                     Region: LRR 9"
     misc_feature    871..960
                     /gene="Lum"
                     /note="leucine-rich repeat [structural motif]; Region:
                     leucine-rich repeat"
                     /db_xref="CDD:275380"
     misc_feature    874..933
                     /gene="Lum"
                     /note="propagated from UniProtKB/Swiss-Prot (P51886.1);
                     Region: LRR 10"
     misc_feature    955..957
                     /gene="Lum"
                     /note="Phosphoserine.
                     /evidence=ECO:0007744|PubMed:22673903; propagated from
                     UniProtKB/Swiss-Prot (P51886.1); phosphorylation site"
     misc_feature    958..1023
                     /gene="Lum"
                     /note="propagated from UniProtKB/Swiss-Prot (P51886.1);
                     Region: LRR 11"
     misc_feature    961..1032
                     /gene="Lum"
                     /note="leucine-rich repeat [structural motif]; Region:
                     leucine-rich repeat"
                     /db_xref="CDD:275380"
     exon            908..1728
                     /gene="Lum"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

cggaaacagtgtcaagagagtaagggcacagaggacttgctgaaaatgaatgtatgtacgttcactcttgtcttggcattagtcggtagtgtcagtggccaatactatgattatgatgcccctctcttcatgtatggggaactgtcacccaactgtgcaccagaatgtaactgtccccacagctacccaactgccatgtactgtgatgatctcaagttgaaaagtgtgcccatggtgccccctggcatcaagtacctttacctgaggaataaccagatcgaccatattgatgaaaaggcctttgagaatgtaacggatctgcagtggctcattcttgaccacaatcttctagaaaactccaagatcaaaggaaaggtcttctctaagctgaaacaactgaagaagctgcatataaactacaacaatttgaccgagtccgtgggtccgctcccaaagtccctacaagacctgcagctggccaataataagatcagcaagctgggctccttcgacgggctggtaaacctgaccttcatttaccttcaacacaaccagctcaaagaggaggctgtctcggcttctctgaaaggccttaagtcactcgaatacctcgacttgagcttcaatcagatgagcaagctgcccgctggccttccaacatctcttctaactctctacctagacaacaataagatcaccaacattcctgatgagtatttcaatcgcttcaccgggcttcaatacttgcgtttatctcacaatgagctggctgacagtggcgtgcctggaaactcatttaacatatcatctctgctcgagctcgatctctcctacaataagctcaagagtataccaaccgttaatgaaaaccttgaaaactattacctggaggtcaataaactcgaaaagtttgatgtcaagagcttctgtaagatcctgggaccactatcttactccaagatcaagcatttgcgcttggatggcaatcccctcactcaaagcagtctgccccctgacatgtacgagtgtctacgtgtagcaaatgaaatcacggttaattaacctcctctcattctaatacattgaagtatgttccagagcagtacttcatggatgggtatttgctggatgtgttaaagttttcacaatatcctttacattgttattgtcattgttgttgttggtattacttcatggattttaattaataaaggaaatgttttgtgaacatttaccactttttaaataaaagatgaaaagcaggcctatttcatcgtgagaacagacacataaaacccgttaaacttaagtctatttgtgaatttaatgttttctatagctctatgttcaggtgattatgaagcctttttactgattgcttggaagtccaccaggtttctatggttcctcacattttacattagtgacttcgaaaacatgaaacaaacatgcatggatgtttgttatcctaatccaaatttttgtgacatgtcaagtttgttttacagaagtttagatcctatgttttgaaaccagtgatttgcaacataccaaagaaaattactaaagacctgtctacttaaagaaatgtagttagcagtaagaatttgcccagttacttaatgaaacttttcttgagtcattttcctgtcatatctatgtttctttctgattgtttgcatgttatgattaacaagctgatagcaaaataaaacaatgcaaatggta

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