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2024-03-29 23:41:10, GGRNA : RefSeq release 60 (20130726)

LOCUS       NM_004079               4107 bp    mRNA    linear   PRI 15-JUN-2013
DEFINITION  Homo sapiens cathepsin S (CTSS), transcript variant 1, mRNA.
ACCESSION   NM_004079
VERSION     NM_004079.4  GI:315075312
KEYWORDS    RefSeq.
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 4107)
  AUTHORS   Jobs,E., Riserus,U., Ingelsson,E., Sundstrom,J., Jobs,M.,
            Nerpin,E., Iggman,D., Basu,S., Larsson,A., Lind,L. and Arnlov,J.
  TITLE     Serum cathepsin S is associated with decreased insulin sensitivity
            and the development of type 2 diabetes in a community-based cohort
            of elderly men
  JOURNAL   Diabetes Care 36 (1), 163-165 (2013)
   PUBMED   22923671
  REMARK    GeneRIF: Cathepsin S activity appears to be involved in the early
            dysregulation of glucose and insulin metabolism.
REFERENCE   2  (bases 1 to 4107)
  AUTHORS   Fan,Q., Wang,X., Zhang,H., Li,C., Fan,J. and Xu,J.
  TITLE     Silencing cathepsin S gene expression inhibits growth, invasion and
            angiogenesis of human hepatocellular carcinoma in vitro
  JOURNAL   Biochem. Biophys. Res. Commun. 425 (4), 703-710 (2012)
   PUBMED   22796222
  REMARK    GeneRIF: The present study was designed to determine the role of
            Cat S in human hepatocellular carcinoma cell growth, invasion and
            angiogenesis, using RNA interference technology.
REFERENCE   3  (bases 1 to 4107)
  AUTHORS   Sage,J., Leblanc-Noblesse,E., Nizard,C., Sasaki,T., Schnebert,S.,
            Perrier,E., Kurfurst,R., Bromme,D., Lalmanach,G. and Lecaille,F.
  TITLE     Cleavage of nidogen-1 by cathepsin S impairs its binding to
            basement membrane partners
  JOURNAL   PLoS ONE 7 (8), E43494 (2012)
   PUBMED   22952693
  REMARK    GeneRIF: Cleavage of nidogen-1 by cathepsin S impairs its binding
            to basement membrane partners
REFERENCE   4  (bases 1 to 4107)
  AUTHORS   Lv,B.J., Lindholt,J.S., Cheng,X., Wang,J. and Shi,G.P.
  TITLE     Plasma cathepsin S and cystatin C levels and risk of abdominal
            aortic aneurysm: a randomized population-based study
  JOURNAL   PLoS ONE 7 (7), E41813 (2012)
   PUBMED   22844527
  REMARK    GeneRIF: Correlation of plasma CatS and cystatin C with aortic
            diameter
REFERENCE   5  (bases 1 to 4107)
  AUTHORS   Hooton,H., Angquist,L., Holst,C., Hager,J., Rousseau,F.,
            Hansen,R.D., Tjonneland,A., Roswall,N., van der A,D.L., Overvad,K.,
            Jakobsen,M.U., Boeing,H., Meidtner,K., Palli,D., Masala,G.,
            Bouatia-Naji,N., Saris,W.H., Feskens,E.J., Wareham,N.J.,
            Vimaleswaran,K.S., Langin,D., Loos,R.J., Sorensen,T.I. and
            Clement,K.
  TITLE     Dietary factors impact on the association between CTSS variants and
            obesity related traits
  JOURNAL   PLoS ONE 7 (7), E40394 (2012)
   PUBMED   22844403
  REMARK    GeneRIF: CTSS variants seem to be nominally associated to obesity
            related traits and this association may be modified by dietary
            protein intake
REFERENCE   6  (bases 1 to 4107)
  AUTHORS   Munger,J.S., Haass,C., Lemere,C.A., Shi,G.P., Wong,W.S.,
            Teplow,D.B., Selkoe,D.J. and Chapman,H.A.
  TITLE     Lysosomal processing of amyloid precursor protein to A beta
            peptides: a distinct role for cathepsin S
  JOURNAL   Biochem. J. 311 (PT 1), 299-305 (1995)
   PUBMED   7575468
REFERENCE   7  (bases 1 to 4107)
  AUTHORS   Lemere,C.A., Munger,J.S., Shi,G.P., Natkin,L., Haass,C.,
            Chapman,H.A. and Selkoe,D.J.
  TITLE     The lysosomal cysteine protease, cathepsin S, is increased in
            Alzheimer's disease and Down syndrome brain. An immunocytochemical
            study
  JOURNAL   Am. J. Pathol. 146 (4), 848-860 (1995)
   PUBMED   7717452
REFERENCE   8  (bases 1 to 4107)
  AUTHORS   Wiederanders,B., Bromme,D., Kirschke,H., von Figura,K., Schmidt,B.
            and Peters,C.
  TITLE     Phylogenetic conservation of cysteine proteinases. Cloning and
            expression of a cDNA coding for human cathepsin S
  JOURNAL   J. Biol. Chem. 267 (19), 13708-13713 (1992)
   PUBMED   1377692
REFERENCE   9  (bases 1 to 4107)
  AUTHORS   Shi,G.P., Munger,J.S., Meara,J.P., Rich,D.H. and Chapman,H.A.
  TITLE     Molecular cloning and expression of human alveolar macrophage
            cathepsin S, an elastinolytic cysteine protease
  JOURNAL   J. Biol. Chem. 267 (11), 7258-7262 (1992)
   PUBMED   1373132
REFERENCE   10 (bases 1 to 4107)
  AUTHORS   Ritonja,A., Colic,A., Dolenc,I., Ogrinc,T., Podobnik,M. and Turk,V.
  TITLE     The complete amino acid sequence of bovine cathepsin S and a
            partial sequence of bovine cathepsin L
  JOURNAL   FEBS Lett. 283 (2), 329-331 (1991)
   PUBMED   2044774
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AL356292.21, M90696.1 and
            BC002642.2.
            On Dec 15, 2010 this sequence version replaced gi:23110961.
            
            Summary: The protein encoded by this gene, a member of the
            peptidase C1 family, is a lysosomal cysteine proteinase that may
            participate in the degradation of antigenic proteins to peptides
            for presentation on MHC class II molecules. The encoded protein can
            function as an elastase over a broad pH range in alveolar
            macrophages. Alternatively spliced transcript variants encoding
            distinct isoforms have been found for this gene. [provided by
            RefSeq, Dec 2010].
            
            Transcript Variant: This variant (1) encodes a longer isoform (1).
            
            Sequence Note: This RefSeq record was created from transcript and
            genomic sequence data to make the sequence consistent with the
            reference genome assembly. The genomic coordinates used for the
            transcript record were based on transcript alignments.
            
            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 :: AK226095.1, BC002642.2 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           ERS025084 [ECO:0000348]
            ##Evidence-Data-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-237               AL356292.21        118433-118669       c
            238-892             M90696.1           113-767
            893-1851            BC002642.2         694-1652
            1852-4107           AL356292.21        82908-85163         c
FEATURES             Location/Qualifiers
     source          1..4107
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="1"
                     /map="1q21"
     gene            1..4107
                     /gene="CTSS"
                     /note="cathepsin S"
                     /db_xref="GeneID:1520"
                     /db_xref="HGNC:2545"
                     /db_xref="HPRD:00292"
                     /db_xref="MIM:116845"
     exon            1..260
                     /gene="CTSS"
                     /inference="alignment:Splign:1.39.8"
     misc_feature    193..195
                     /gene="CTSS"
                     /note="upstream in-frame stop codon"
     variation       234
                     /gene="CTSS"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:3754212"
     variation       237
                     /gene="CTSS"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:1136774"
     exon            261..387
                     /gene="CTSS"
                     /inference="alignment:Splign:1.39.8"
     CDS             262..1257
                     /gene="CTSS"
                     /EC_number="3.4.22.27"
                     /note="isoform 1 preproprotein is encoded by transcript
                     variant 1"
                     /codon_start=1
                     /product="cathepsin S isoform 1 preproprotein"
                     /protein_id="NP_004070.3"
                     /db_xref="GI:23110962"
                     /db_xref="CCDS:CCDS968.1"
                     /db_xref="GeneID:1520"
                     /db_xref="HGNC:2545"
                     /db_xref="HPRD:00292"
                     /db_xref="MIM:116845"
                     /translation="
MKRLVCVLLVCSSAVAQLHKDPTLDHHWHLWKKTYGKQYKEKNEEAVRRLIWEKNLKFVMLHNLEHSMGMHSYDLGMNHLGDMTSEEVMSLMSSLRVPSQWQRNITYKSNPNRILPDSVDWREKGCVTEVKYQGSCGACWAFSAVGALEAQLKLKTGKLVSLSAQNLVDCSTEKYGNKGCNGGFMTTAFQYIIDNKGIDSDASYPYKAMDQKCQYDSKYRAATCSKYTELPYGREDVLKEAVANKGPVSVGVDARHPSFFLYRSGVYYEPSCTQNVNHGVLVVGYGDLNGKEYWLVKNSWGHNFGEEGYIRMARNKGNHCGIASFPSYPEI
"
     sig_peptide     262..309
                     /gene="CTSS"
                     /inference="COORDINATES: ab initio prediction:SignalP:4.0"
     proprotein      310..1254
                     /gene="CTSS"
                     /product="cathepsin S isoform 1 proprotein"
     misc_feature    343..522
                     /gene="CTSS"
                     /note="Cathepsin propeptide inhibitor domain (I29);
                     Region: Inhibitor_I29; smart00848"
                     /db_xref="CDD:197916"
     misc_feature    526..528
                     /gene="CTSS"
                     /experiment="experimental evidence, no additional details
                     recorded"
                     /note="proteolytic cleavage site; modified site"
                     /db_xref="HPRD:05056"
     misc_feature    538..540
                     /gene="CTSS"
                     /experiment="experimental evidence, no additional details
                     recorded"
                     /note="proteolytic cleavage site; modified site"
                     /db_xref="HPRD:05056"
     mat_peptide     604..1254
                     /gene="CTSS"
                     /product="cathepsin S isoform 1"
     misc_feature    607..1248
                     /gene="CTSS"
                     /note="Peptidase C1A subfamily (MEROPS database
                     nomenclature); composed of cysteine peptidases (CPs)
                     similar to papain, including the mammalian CPs (cathepsins
                     B, C, F, H, L, K, O, S, V, X and W). Papain is an
                     endopeptidase with specific substrate preferences; Region:
                     Peptidase_C1A; cd02248"
                     /db_xref="CDD:30292"
     misc_feature    order(658..660,676..678,1093..1095,1153..1155)
                     /gene="CTSS"
                     /note="active site"
                     /db_xref="CDD:30292"
     misc_feature    order(811..816,1012..1014,1087..1089,1096..1098,
                     1234..1236)
                     /gene="CTSS"
                     /note="S2 subsite; other site"
                     /db_xref="CDD:30292"
     exon            388..510
                     /gene="CTSS"
                     /inference="alignment:Splign:1.39.8"
     exon            511..660
                     /gene="CTSS"
                     /inference="alignment:Splign:1.39.8"
     variation       536
                     /gene="CTSS"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:1059603"
     variation       598
                     /gene="CTSS"
                     /replace="c"
                     /replace="g"
                     /replace="t"
                     /db_xref="dbSNP:2230061"
     exon            661..888
                     /gene="CTSS"
                     /inference="alignment:Splign:1.39.8"
     variation       742
                     /gene="CTSS"
                     /replace="a"
                     /replace="t"
                     /db_xref="dbSNP:1059604"
     exon            889..1054
                     /gene="CTSS"
                     /inference="alignment:Splign:1.39.8"
     variation       960
                     /gene="CTSS"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:1059605"
     exon            1055..1157
                     /gene="CTSS"
                     /inference="alignment:Splign:1.39.8"
     exon            1158..4107
                     /gene="CTSS"
                     /inference="alignment:Splign:1.39.8"
     STS             1274..1454
                     /gene="CTSS"
                     /standard_name="SHGC-35262"
                     /db_xref="UniSTS:60387"
     STS             1286..2042
                     /gene="CTSS"
                     /standard_name="CTSS_573"
                     /db_xref="UniSTS:277137"
     variation       1405
                     /gene="CTSS"
                     /replace="g"
                     /replace="t"
                     /db_xref="dbSNP:1141835"
     variation       1501
                     /gene="CTSS"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:3208233"
     variation       1563
                     /gene="CTSS"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:11542002"
     STS             1651..1887
                     /gene="CTSS"
                     /standard_name="RH44919"
                     /db_xref="UniSTS:4239"
     STS             1727..1887
                     /gene="CTSS"
                     /standard_name="RH80467"
                     /db_xref="UniSTS:84094"
     STS             3961..4087
                     /gene="CTSS"
                     /standard_name="WI-18164"
                     /db_xref="UniSTS:17808"
     variation       4062
                     /gene="CTSS"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:1136808"
     polyA_signal    4086..4091
                     /gene="CTSS"
     polyA_signal    4090..4095
                     /gene="CTSS"
     polyA_site      4107
                     /gene="CTSS"
ORIGIN      
gacaagggctcttcttgatggcttactgtatccactttgtccccaagaccatagggaaatgactagaggtgactgtactagctagattttaaatgaaactgaaatgaaagttcacttcctcattttgagtacctcatgtgacaagttccaatttcttttcaagtcaattgaactgaaatctccttgttgctttgaaatcttagaagagagcccactaattcaaggactcttactgtgggagcaactgctggttctatcacaatgaaacggctggtttgtgtgctcttggtgtgctcctctgcagtggcacagttgcataaagatcctaccctggatcaccactggcatctctggaagaaaacctatggcaaacaatacaaggaaaagaatgaagaagcagtacgacgtctcatctgggaaaagaatctaaagtttgtgatgcttcacaacctggagcattcaatgggaatgcactcatacgatctgggcatgaaccacctgggagacatgaccagtgaagaagtgatgtctttgatgagttccctgagagttcccagccagtggcagagaaatatcacatataagtcaaaccctaatcggatattgcctgattctgtggactggagagagaaagggtgtgttactgaagtgaaatatcaaggttcttgtggtgcttgctgggctttcagtgctgtgggggccctggaagcacagctgaagctgaaaacaggaaagctggtgtctctcagtgcccagaacctggtggattgctcaactgaaaaatatggaaacaaaggctgcaatggtggcttcatgacaacggctttccagtacatcattgataacaagggcatcgactcagacgcttcctatccctacaaagccatggatcagaaatgtcaatatgactcaaaatatcgtgctgccacatgttcaaagtacactgaacttccttatggcagagaagatgtcctgaaagaagctgtggccaataaaggcccagtgtctgttggtgtagatgcgcgtcatccttctttcttcctctacagaagtggtgtctactatgaaccatcctgtactcagaatgtgaatcatggtgtacttgtggttggctatggtgatcttaatgggaaagaatactggcttgtgaaaaacagctggggccacaactttggtgaagaaggatatattcggatggcaagaaataaaggaaatcattgtgggattgctagctttccctcttacccagaaatctagaggatctctcctttttataacaaatcaagaaatatgaagcactttctcttaacttaatttttcctgctgtatccagaagaaataattgtgtcatgattaatgtgtatttactgtactaattagaaaatatagtttgaggccgggcacggtggctcacgcctgtaatcccagtacttgggaggccaaggcaggcatatcaacttgaggccaggagttaaagagcagcctggctaacatggtgaaaccccatctctactaaaaatacaaaaaattagccgagcacggtggtgcatgcctgtaatcccagctacttgggaggctgaggcacgagattccttgaacccaagaggttgaggctatgttgagctgagatcacaccactgtactccagcctggatgacagagtggagactctgtttcaaaaaaacagaaaagaaaatatagtttgattcttcatttttttaaatttgcaaatctcaggataaagtttgctaagtaaattagtaatgtactatagatataactgtacaaaaattgttcaacctaaaacaatctgtaattgcttattgttttattgtatactctttgtctttttaagacccctaatagccttttgtaacttgatggcttaaaaatacttaataaatctgccatttcaaatttctatcattgccacataccattcttattcctaggcaactattaataatctatcctgagaatattaattgtggtattctggtgatggggtttagcaactttgatggaagaaaatattaggctataaatgtcctaaggactcagattgtatctttgtacagaagaggattcaaaacgccacgtgtagtggctcatgcctgtaatcccaacactttgggaggctgaagtaggaggatcgtcttgagcccaggagttcaagaccagcctggacaacatagtgagaccttgtctccacaaaaataaaaaagaaactatccaggagtggtggtgtgtgcctgtggtccctgctatgcagatgtctaagacaggaggatcacaagagcccaggaggttgagaatgcagtgagcttgtaattgcaccactgcactccagcctgggtgacagagcaagaccctgtcttaaaaaaagaggattcaacacatatttttatattatgttaaagtaaagaaatgcataaaagacaagcactttggaagaattattttaatgatcaacaatttaatgtattagtccaaattatttttacgtagtcatcaacaatttgaccagggcctttatttggcaaataactgagccaaccagaataaaataaccaatactccactgctcatatttttatctaattcagatggatcttccttacaactgctctagattagtagatgcatctaagcaggcagcaggaactttaaattttttaagttcatgtctatgacatgaacaatgtgtgggataatgtcattaatatatcctaaattaacctaaacgtatttcactaactctggctccttctccataaagcacattttaaggaacaagaattgctaaatataaaaacataaataataccataatacatggctatcatcaaaagtgtatagaatattatagtttaaaagtatttagttgattacttttcagttttgttttgttttttgagacggagtctcactctgttgcccaggctggagtgcagtggcaccatctcagttcactgcaacttctgcctcccgagttcaagcgattctcctgcctcagcctcccgagtagctggaattataggcgtgcaccaccacgcccagctaatttttgtatttttagtaaagacagggttttgccacattagccaggctggtctcaaactcctgacctcaggtgatccacccaccccagcctcccaaagtgctaagattacaggcgtgagccactgagcccagcctacttttcagtttttaacataatttttgttttatccacaacttttcaagtattgaaagtagaataaaaacatgggttcttagtctttagctatctgttaaagcctatgaatgccttcttaaaatcatgtttttaaatgcataaaatatataggattacaaaggaatctaattatatcgaaatacagttattaaaatgttaaaagataagtttgttatatattaatatgcatgcttctttataaatgcattaaataagagttaatagctatcctaaatttgaaatagtgataagcataatgaaaatagatgcaaaaaactaatgtgatatgaaaatatctgggtttttcttttgatgatgaagtattgctaatattaccgtggtttatgaactatgttcagaattgaagaaaatcctaactttcagttagaggttagtgacggggttcaggacaccctacacaaaatacagcactttgacatattgaatattttaagctgaaggcatttgaggaaattgcagaagcaggaaggtgactctgaccttctgcctgctgttctccccagaagcagccataaaacctgggaaggattttctgaccttcccctgaagtagatcataagactgtcatgtaagaggtgctctcctggcacccagagaaaaggagcatccttacctccaaaagcacagggacacaaagaggaatctaaacaaacaggcctctcagtttcccccagtttattacatttagcttgttcacactttgccctatgacatttctacatcactggctgctcttcatcaaacctactataaaaaacattcaagttcaactgtttctttgggcctttatttccttatggagcccctcgtgtcgtgtaaaacttatattaaataaatgtgcatgcttt
//

Annotations:

ANNOTATIONS from NCBI Entrez Gene (20130726):
            GeneID:1520 -> Molecular function: GO:0004197 [cysteine-type endopeptidase activity] evidence: TAS
            GeneID:1520 -> Biological process: GO:0002224 [toll-like receptor signaling pathway] evidence: TAS
            GeneID:1520 -> Biological process: GO:0002250 [adaptive immune response] evidence: IEP
            GeneID:1520 -> Biological process: GO:0002474 [antigen processing and presentation of peptide antigen via MHC class I] evidence: TAS
            GeneID:1520 -> Biological process: GO:0002480 [antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent] evidence: TAS
            GeneID:1520 -> Biological process: GO:0006508 [proteolysis] evidence: IEA
            GeneID:1520 -> Biological process: GO:0006955 [immune response] evidence: TAS
            GeneID:1520 -> Biological process: GO:0019882 [antigen processing and presentation] evidence: TAS
            GeneID:1520 -> Biological process: GO:0019886 [antigen processing and presentation of exogenous peptide antigen via MHC class II] evidence: TAS
            GeneID:1520 -> Biological process: GO:0042590 [antigen processing and presentation of exogenous peptide antigen via MHC class I] evidence: TAS
            GeneID:1520 -> Biological process: GO:0045087 [innate immune response] evidence: TAS
            GeneID:1520 -> Biological process: GO:0097067 [cellular response to thyroid hormone stimulus] evidence: IEP
            GeneID:1520 -> Cellular component: GO:0005576 [extracellular region] evidence: NAS
            GeneID:1520 -> Cellular component: GO:0005764 [lysosome] evidence: IDA
            GeneID:1520 -> Cellular component: GO:0005764 [lysosome] evidence: NAS
            GeneID:1520 -> Cellular component: GO:0016020 [membrane] evidence: IEA
            GeneID:1520 -> Cellular component: GO:0036021 [endolysosome lumen] evidence: TAS
            GeneID:1520 -> Cellular component: GO:0043202 [lysosomal lumen] evidence: TAS
            GeneID:1520 -> Cellular component: GO:0043231 [intracellular membrane-bounded organelle] evidence: IDA
ANNOTATIONS from NCBI Entrez Gene (20130726):
            NP_004070 -> EC 3.4.22.27

by @meso_cacase at DBCLS
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