LOCUS       NM_031050               1728 bp    mRNA    linear   ROD 21-NOV-2023
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 AJ 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 SK, Zoccarato A, Kitazume-Taneike R,
            Fava M, Yin X, Werner T, Hirt MN, Zampetaki A, Viviano A, Chong M,
            Bern M, Kourliouros A, Domenech N, Willeit P, Shah AM, Jahangiri M,
            Schaefer L, Fischer JW, Iozzo RV, 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 DN, Albadawi H, Jahangiri M, Porter KE, Watkins
            MT, 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 AA, Mayr U, Barallobre-Barreiro J, Dong X,
            Cuello F, Sur S, Drozdov I, Langley SR, Lu R, Stathopoulou K,
            Didangelos A, Yin X, Zimmermann WH, Shah AM, 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 AM, 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 PJ, Kay CJ, McQuillan DJ, Beales MP and Hassell JR.
  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 NB and Gressner AM.
  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
            JACYVU010000185.1.
            
            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
                                           SAMEA5756307, SAMEA5760384
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on single protein-coding transcript
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-24                JACYVU010000185.1  14989370-14989393
            25-907              JACYVU010000185.1  14991746-14992628
            908-1728            JACYVU010000185.1  14995354-14996174
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:4.0"
     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    <175..>771
                     /gene="Lum"
                     /note="type III secretion system effector E3 ubiquitin
                     transferase SlrP; Region: PRK15370"
                     /db_xref="CDD:185268"
     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    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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