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Tumor Endothelial Marker Report: TEM23, TEM38 (alpha1(I) collagen)

TEM domain structure

site-guide


TEM Sequence Analysis
name from to source/E description
SIGNALP 1 23    
VWC 40 95 Smart, E=5.8e-23 The VWC domain has a proposed function in complex formation.
18x Collagen triple helical repeats 107 1198 Pfam, E = 3.3e-288 The region is invoved in triple helix formation.
COLFI 1245 1463 Pfam, E= 2e-220 The COLFI domain is typically found in the C terminus of fibrillar collagens.
1466        

Remarks



Sequence Information
TEM TEM23 (TEM38)
Reliability of Gen2Tag mapping
Cid->tag (Hs.172928) frequency:
     : CATG-ACCAAAAACC=132/208
tem38: CATG-TGGAAATGAC=30/208
tem23: CATG-TTAAATAGCA=11/208
tag occurrence in N-EC/T-ECs/HMVEC:
     : CATG-ACCAAAAACC=--
tem38: CATG-TGGAAATGAC=15/179/40
tem23: CATG-TTAAATAGCA=2/33/4
  • CATG-ACCAAAAACC could not be found neither as a PEM nor as TEM
  • TEM23 can be annotated as COL1A1 if it is assumed that not only Poly-A tags
    but also the 20 nt poly-T stretch located upstream of the TEM23 tag lead to an amplification and selection via Poly-T.
  • The relation of Cid->tag frequency of tem38:tem23 tags is similar to the relation
    of the tag occurence in T-EC.
    This supports the assumption that both (TEM23 and 38) tags are derived from the same transcript
Analysis
  • Output Created by a Suite of Single Sequence Analysis Techniques
  • Protein Description
    SEQ.SOURCE: sp|P02452|CA11_HUMAN COLLAGEN ALPHA 1(I) CHAIN PRECURSOR
    Homo sapiens (Human).
     
    PROPEP 23 161 AMINO-TERMINAL PROPEPTIDE.
    CHAIN 162 1218 COLLAGEN ALPHA 1(III)CHAIN.
    PROPEP 1219 1464 CARBOXYL-TERMINAL PROPEPTIDE.
    Protein Sequence
    MFSFVDLRLLLLLAATALLTHGQEEGQVEGQDEDIPPITCVQNGLRYHDRDVWKPEPCRICVCDNGKVLC
    DDVICDETKNCPGAEVPEGECCPVCPDGSESPTDQETTGVEGPKGDTGPRGPRGPAGPPGRDGIPGQPGL
    PGPPGPPGPPGPPGLGGNFAPQLSYGYDEKSTGGISVPGPMGPSGPRGLPGPPGAPGPQGFQGPPGEPGE
    PGASGPMGPRGPPGPPGKNGDDGEAGKPGRPGERGPPGPQGARGLPGTAGLPGMKGHRGFSGLDGAKGDA
    GPAGPKGEPGSPGENGAPGQMGPRGLPGERGRPGAPGPAGARGNDGATGAAGPPGPTGPAGPPGFPGAVG
    AKGEAGPQGPRGSEGPQGVRGEPGPPGPAGAAGPAGNPGADGQPGAKGANGAPGIAGAPGFPGARGPSGP
    QGPGGPPGPKGNSGEPGAPGSKGDTGAKGEPGPVGVQGPPGPAGEEGKRGARGEPGPTGLPGPPGERGGP
    GSRGFPGADGVAGPKGPAGERGSPGPAGPKGSPGEAGRPGEAGLPGAKGLTGSPGSPGPDGKTGPPGPAG
    QDGRPGPPGPPGARGQAGVMGFPGPKGAAGEPGKAGERGVPGPPGAVGPAGKDGEAGAQGPPGPAGPAGE
    RGEQGPAGSPGFQGLPGPAGPPGEAGKPGEQGVPGDLGAPGPSGARGERGFPGERGVQGPPGPAGPRGAN
    GAPGNDGAKGDAGAPGAPGSQGAPGLQGMPGERGAAGLPGPKGDRGDAGPKGADGSPGKDGVRGLTGPIG
    PPGPAGAPGDKGESGPSGPAGPTGARGAPGDRGEPGPPGPAGFAGPPGADGQPGAKGEPGDAGAKGDAGP
    PGPAGPAGPPGPIGNVGAPGAKGARGSAGPPGATGFPGAAGRVGPPGPSGNAGPPGPPGPAGKEGGKGPR
    GETGPAGRPGEVGPPGPPGPAGEKGSPGADGPAGAPGTPGPQGIAGQRGVVGLPGQRGERGFPGLPGPSG
    EPGKQGPSGASGERGPPGPMGPPGLAGPPGESGREGAPAAEGSPGRDGSPGAKGDRGETGPAGPPGAPGA
    PGAPGPVGPAGKSGDRGETGPAGPAGPVGPVGARGPAGPQGPRGDKGETGEQGDRGIKGHRGFSGLQGPP
    GPPGSPGEQGPSGASGPAGPRGPPGSAGAPGKDGLNGLPGPIGPPGPRGRTGDAGPVGPPGPPGPPGPPG
    PPSAGFDFSFLPQPPQEKAHDGGRYYRADDANVVRDRDLEVDTTLKSLSQQIENIRSPEGSRKNPARTCR
    DLKMCHSDWKSGEYWIDPNQGCNLDAIKVFCNMETGETCVYPTQPSVAQKNWYISKNPKDKRHVWFGESM
    TDGFQFEYGGQGSDPADVAIQLTFLRLMSTEASQNITYHCKNSVAYMDQQTGNLKKALLLKGSNEIEIRA
    EGNSRFTYSVTVDGCTSHTGAWGKTVIEYKTTKSSRLPIIDVAPLDVGAPDQEFGFDVGPVCFL
    SAGE-Tag CATG-TTAAATAGCAC  
    EST/cluster Description
    UNIGEN CLUSTER: Hs.172928
    SEQ.SOURCE:gi|4502944|ref|NM_000088.1| Homo sapiens collagen, type I, alpha 1 (COL1A1)
    ANALYSIS:blastn against EST_human of the marked sequence
    -> as a proof of the tag localization relativ to the 3 end of the mRNA
    MARKINGS: CATG-ACCAAAAACC tag in firebrick
    TEM23 tag marked in mediumvioletred
    TEM38 tag marked in red
    EST/cluster Sequence
         1  AGCAGACGGGAGTTTCTCCTCGGGGTCGGAGCAGGAGGCACGCGGAGTGTGAGGCCACGC
        61  ATGAGCGGACGCTAACCCCCTCCCCAGCCACAAAGAGTCTACATGTCTAGGGTCTAGACA
       121  TGTTCAGCTTTGTGGACCTCCGGCTCCTGCTCCTCTTAGCGGCCACCGCCCTCCTGACGC
       181  ACGGCCAAGAGGAAGGCCAAGTCGAGGGCCAAGACGAAGACATCCCACCAATCACCTGCG
       241  TACAGAACGGCCTCAGGTACCATGACCGAGACGTGTGGAAACCCGAGCCCTGCCGGATCT
       301  GCGTCTGCGACAACGGCAAGGTGTTGTGCGATGACGTGATCTGTGACGAGACCAAGAACT
       361  GCCCCGGCGCCGAAGTCCCCGAGGGCGAGTGCTGTCCCGTCTGCCCCGACGGCTCAGAGT
       421  CACCCACCGACCAAGAAACCACCGGCGTCGAGGGACCCAAGGGAGACACTGGCCCCCGAG
       481  GCCCAAGGGGACCCGCAGGCCCCCCTGGCCGAGATGGCATCCCTGGACAGCCTGGACTTC
       541  CCGGACCCCCCGGACCCCCCGGACCTCCCGGACCCCCTGGCCTCGGAGGAAACTTTGCTC
       601  CCCAGCTGTCTTATGGCTATGATGAGAAATCAACCGGAGGAATTTCCGTGCCTGGCCCCA
       661  TGGGTCCCTCTGGTCCTCGTGGTCTCCCTGGCCCCCCTGGTGCACCTGGTCCCCAAGGCT
       721  TCCAAGGTCCCCCTGGTGAGCCTGGCGAGCCTGGAGCTTCAGGTCCCATGGGTCCCCGAG
       781  GTCCCCCAGGTCCCCCTGGAAAGAATGGAGATGATGGGGAAGCTGGAAAACCTGGTCGTC
       841  CTGGTGAGCGTGGGCCTCCTGGGCCTCAGGGTGCTCGAGGATTGCCCGGAACAGCTGGCC
       901  TCCCTGGAATGAAGGGACACAGAGGTTTCAGTGGTTTGGATGGTGCCAAGGGAGATGCTG
       961  GTCCTGCTGGTCCTAAGGGTGAGCCTGGCAGCCCTGGTGAAAATGGAGCTCCTGGTCAGA
      1021  TGGGCCCCCGTGGCCTGCCTGGTGAGAGAGGTCGCCCTGGAGCCCCTGGCCCTGCTGGTG
      1081  CTCGTGGAAATGATGGTGCTACTGGTGCTGCCGGGCCCCCTGGTCCCACCGGCCCCGCTG
      1141  GTCCTCCTGGCTTCCCTGGTGCTGTTGGTGCTAAGGGTGAAGCTGGTCCCCAAGGGCCCC
      1201  GAGGCTCTGAAGGTCCCCAGGGTGTGCGTGGTGAGCCTGGCCCCCCTGGCCCTGCTGGTG
      1261  CTGCTGGCCCTGCTGGAAACCCTGGTGCTGATGGACAGCCTGGTGCTAAAGGTGCCAATG
      1321  GTGCTCCTGGTATTGCTGGTGCTCCTGGCTTCCCTGGTGCCCGAGGCCCCTCTGGACCCC
      1381  AGGGCCCCGGCGGCCCTCCTGGTCCCAAGGGTAACAGCGGTGAACCTGGTGCTCCTGGCA
      1441  GCAAAGGAGACACTGGTGCTAAGGGAGAGCCTGGCCCTGTTGGTGTTCAAGGACCCCCTG
      1501  GCCCTGCTGGAGAGGAAGGAAAGCGAGGAGCTCGAGGTGAACCCGGACCCACTGGCCTGC
      1561  CCGGACCCCCTGGCGAGCGTGGTGGACCTGGTAGCCGTGGTTTCCCTGGCGCAGATGGTG
      1621  TTGCTGGTCCCAAGGGTCCCGCTGGTGAACGTGGTTCTCCTGGCCCCGCTGGCCCCAAAG
      1681  GATCTCCTGGTGAAGCTGGTCGTCCCGGTGAAGCTGGTCTGCCTGGTGCCAAGGGTCTGA
      1741  CTGGAAGCCCTGGCAGCCCTGGTCCTGATGGCAAAACTGGCCCCCCTGGTCCCGCCGGTC
      1801  AAGATGGTCGCCCCGGACCCCCAGGCCCACCTGGTGCCCGTGGTCAGGCTGGTGTGATGG
      1861  GATTCCCTGGACCTAAAGGTGCTGCTGGAGAGCCCGGCAAGGCTGGAGAGCGAGGTGTTC
      1921  CCGGACCCCCTGGCGCTGTCGGTCCTGCTGGCAAAGATGGAGAGGCTGGAGCTCAGGGAC
      1981  CCCCTGGCCCTGCTGGTCCCGCTGGCGAGAGAGGTGAACAAGGCCCTGCTGGCTCCCCCG
      2041  GATTCCAGGGTCTCCCTGGTCCTGCTGGTCCTCCAGGTGAAGCAGGCAAACCTGGTGAAC
      2101  AGGGTGTTCCTGGAGACCTTGGCGCCCCTGGCCCCTCTGGAGCAAGAGGCGAGAGAGGTT
      2161  TCCCTGGCGAGCGTGGTGTGCAAGGTCCCCCTGGTCCTGCTGGACCCCGAGGGGCCAACG
      2221  GTGCTCCCGGCAACGATGGTGCTAAGGGTGATGCTGGTGCCCCTGGAGCTCCCGGTAGCC
      2281  AGGGCGCCCCTGGCCTTCAGGGAATGCCTGGTGAACGTGGTGCAGCTGGTCTTCCAGGGC
      2341  CTAAGGGTGACAGAGGTGATGCTGGTCCCAAAGGTGCTGATGGCTCTCCTGGCAAAGATG
      2401  GCGTCCGTGGTCTGACCGGCCCCATTGGTCCTCCTGGCCCTGCTGGTGCCCCTGGTGACA
      2461  AGGGTGAAAGTGGTCCCAGCGGCCCTGCTGGTCCCACTGGAGCTCGTGGTGCCCCCGGAG
      2521  ACCGTGGTGAGCCTGGTCCCCCCGGCCCTGCTGGCTTTGCTGGCCCCCCTGGTGCTGACG
      2581  GCCAACCTGGTGCTAAAGGCGAACCTGGTGATGCTGGTGCCAAAGGCGATGCTGGTCCCC
      2641  CTGGGCCTGCCGGACCCGCTGGACCCCCTGGCCCCATTGGTAATGTTGGTGCTCCTGGAG
      2701  CCAAAGGTGCTCGCGGCAGCGCTGGTCCCCCTGGTGCTACTGGTTTCCCTGGTGCTGCTG
      2761  GCCGAGTCGGTCCTCCTGGCCCCTCTGGAAATGCTGGACCCCCTGGCCCTCCTGGTCCTG
      2821  CTGGCAAAGAAGGCGGCAAAGGTCCCCGTGGTGAGACTGGCCCTGCTGGACGTCCTGGTG
      2881  AAGTTGGTCCCCCTGGTCCCCCTGGCCCTGCTGGCGAGAAAGGATCCCCTGGTGCTGATG
      2941  GTCCTGCTGGTGCTCCTGGTACTCCCGGGCCTCAAGGTATTGCTGGACAGCGTGGTGTGG
      3001  TCGGCCTGCCTGGTCAGAGAGGAGAGAGAGGCTTCCCTGGTCTTCCTGGCCCCTCTGGTG
      3061  AACCTGGCAAACAAGGTCCCTCTGGAGCAAGTGGTGAACGTGGTCCCCCCGGTCCCATGG
      3121  GCCCCCCTGGATTGGCTGGACCCCCTGGTGAATCTGGACGTGAGGGGGCTCCTGCTGCCG
      3181  AAGGTTCCCCTGGACGAGACGGTTCTCCTGGCGCCAAGGGTGACCGTGGTGAGACCGGCC
      3241  CCGCTGGACCCCCTGGTGCTCCTGGTGCTCCTGGTGCCCCTGGCCCCGTTGGCCCTGCTG
      3301  GCAAGAGTGGTGATCGTGGTGAGACTGGTCCTGCTGGTCCCGCCGGTCCCGTCGGCCCCG
      3361  TCGGCGCCCGTGGCCCCGCCGGACCCCAAGGCCCCCGTGGTGACAAGGGTGAGACAGGCG
      3421  AACAGGGCGACAGAGGCATAAAGGGTCACCGTGGCTTCTCTGGCCTCCAGGGTCCCCCTG
      3481  GCCCTCCTGGCTCTCCTGGTGAACAAGGTCCCTCTGGAGCCTCTGGTCCTGCTGGTCCCC
      3541  GAGGTCCCCCTGGCTCTGCTGGTGCTCCTGGCAAAGATGGACTCAACGGTCTCCCTGGCC
      3601  CCATTGGGCCCCCTGGTCCTCGCGGTCGCACTGGTGATGCTGGTCCTGTTGGTCCCCCCG
      3661  GCCCTCCTGGACCTCCTGGTCCCCCTGGTCCTCCCAGCGCTGGTTTCGACTTCAGCTTCC
      3721  TGCCCCAGCCACCTCAAGAGAAGGCTCACGATGGTGGCCGCTACTACCGGGCTGATGATG
      3781  CCAATGTGGTTCGTGACCGTGACCTCGAGGTGGACACCACCCTCAAGAGCCTGAGCCAGC
      3841  AGATCGAGAACATCCGGAGCCCAGAGGGAAGCCGCAAGAACCCCGCCCGCACCTGCCGTG
      3901  ACCTCAAGATGTGCCACTCTGACTGGAAGAGTGGAGAGTACTGGATTGACCCCAACCAAG
      3961  GCTGCAACCTGGATGCCATCAAAGTCTTCTGCAACATGGAGACTGGTGAGACCTGCGTGT
      4021  ACCCCACTCAGCCCAGTGTGGCCCAGAAGAACTGGTACATCAGCAAGAACCCCAAGGACA
      4081  AGAGGCATGTCTGGTTCGGCGAGAGCATGACCGATGGATTCCAGTTCGAGTATGGCGGCC
      4141  AGGGCTCCGACCCTGCCGATGTGGCCATCCAGCTGACCTTCCTGCGCCTGATGTCCACCG
      4201  AGGCCTCCCAGAACATCACCTACCACTGCAAGAACAGCGTGGCCTACATGGACCAGCAGA
      4261  CTGGCAACCTCAAGAAGGCCCTGCTCCTCAAGGGCTCCAACGAGATCGAGATCCGCGCCG
      4321  AGGGCAACAGCCGCTTCACCTACAGCGTCACTGTCGATGGCTGCACGAGTCACACCGGAG
      4381  CCTGGGGCAAGACAGTGATTGAATACAAAACCACCAAGTCCTCCCGCCTGCCCATCATCG
      4441  ATGTGGCCCCCTTGGACGTTGGTGCCCCAGACCAGGAATTCGGCTTCGACGTTGGCCCTG
      4501  TCTGCTTCCTGTAAACTCCCTCCATCCCAACCTGGCTCCCTCCCACCCAACCAACTTTCC
      4561  CCCCAACCCGGAAACAGACAAGCAACCCAAACTGAACCCCCCCAAAAGCCAAAAAATGGG
      4621  AGACAATTTCACATGGACTTTGGAAAATATTTTTTTCCTTTGCATTCATCTCTCAAACTT
      4681  AGTTTTTATCTTTGACCAACCGAACATGACCAAAAACCAAAAGTGCATTCAACCTTACCA
      4741  AAAAAAAAAAAAAAAAAAAAAGAATAAATAAATAAGTTTTTAAAAAAGGAAGCTTGGTCC
      4801  ACTTGCTTGAAGACCCATGCGGGGGTAAGTCCCTTTCTGCCCGTTGGGTTATGAAACCCC
      4861  AATGCTGCCCTTTCTGCTCCTTTCTCCACACCCCCCTTGGCCTCCCCTCCACTCCTTCCC
      4921  AAATCTGTCTCCCCAGAAGACACAGGAAACAATGTATTGTCTGCCCAGCAATCAAAGGCA
      4981  ATGCTCAAACACCCAAGTGGCCCCCACCCTCAGCCCGCTCCTGCCCGCCCAGCACCCCCA
      5041  GGCCCTGGGGACCTGGGGTTCTCAGACTGCCAAAGAAGCCTTGCCATCTGGCGCTCCCAT
      5101  GGCTCTTGCAACATCTCCCCTTCGTTTTTGAGGGGGTCATGCCGGGGGAGCCACCAGCCC
      5161  CTCACTGGGTTCGGAGGAGAGTCAGGAAGGGCCACGACAAAGCAGAAACATCGGATTTGG
      5221  GGAACGCGTGTCATCCCTTGTGCCGCAGGCTGGGCGGGAGAGACTGTTCTGTTCTGTTCC
      5281  TTGTGTAACTGTGTTGCTGAAAGACTACCTCGTTCTTGTCTTGATGTGTCACCGGGGCAA
      5341  CTGCCTGGGGGCGGGGATGGGGGCAGGGTGGAAGCGGCTCCCCATTTTTATACCAAAGGT
      5401  GCTACATCTATGTGATGGGTGGGGTGGGGAGGGAATCACTGGTGCTATAGAAATTGAGAT
      5461  GCCCCCCCAGGCCAGCAAATGTTCCTTTTTGTTCAAAGTCTATTTTTATTCCTTGATATT
      5521  TTTTCTTTCTTTTTTTTTTTTTTTGTGGATGGGGACTTGTGAATTTTTCTAAAGGTGCTA
      5581  TTTAACATGGGAGGAGAGCGTGTGCGCTCCAGCCCAGCCCGCTGCTCACTTTCCACCCTC
      5641  TCTCCACCTGCCTCTGGCTTCTCAGGCCTCTGCTCTCCGACCTCTCTCCTCTGAAACCCT
      5701  CCTCCACAGCTGCAGCCCATCCTCCCGGCTCCCTCCTAGTCTGTCCTGCGTCCTCTGTCC
      5761  CCGGGTTTCAGAGACAACTTCCCAAAGCACAAAGCAGTTTTTCCCTAGGGGTGGGAGGAA
      5821  GCAAAAGACTCTGTACCTATTTTGTATGTGTATAATAATTTGAGATGTTTTTAATTATTT
      5881  TGATTGCTGGAATAAAGCATGTGGAAATGACCCAAACATAATCCGCAGTGGCCTCCTAAT
      5941  TTCCTTCTTTGGAGTTGGGGGAGGGGTAGACATGGGGAAGGGGCCTTGGGGTGATGGGCT
      6001  TGCCTTCCATTCCTGCCCTTTCCCTCCCCACTATTCTCTTCTAGATCCCTCCATAACCCC
      6061  ACTCCCCTTTCTCTCACCCTTCTTATACCGCAAACCTTTCTACTTCCTCTTTCATTTTCT
      6121  ATTCTTGCAATTTCCTTGCACCTTTTCCAAATCCTCTTCTCCCCTGCAATACCATACAGG
      6181  CAATCCACGTGCACAACACACACACACACTCTTCACATCTGGGGTTGTCCAAACCTCATA
      6241  CCCACTCCCCTTCAAGCCCATCCACTCTCCACCCCCTGGATGCCCTGCACTTGGTGGCGG
      6301  TGGGATGCTCATGGATACTGGGAGGGTGAGGGGAGTGGAACCCGTGAGGAGGACCTGGGG
      6361  GCCTCTCCTTGAACTGACATGAAGGGTCATCTGGCCTCTGCTCCCTTCTCACCCACGCTG
      6421  ACCTCCTGCCGAAGGAGCAACGCAACAGGAGAGGGGTCTGCTGAGCCTGGCGAGGGTCTG
      6481  GGAGGGACCAGGAGGAAGGCGTGCTCCCTGCTCGCTGTCCTGGCCCTGGGGGAGTGAGGG
      6541  AGACAGACACCTGGGAGAGCTGTGGGGAAGGCACTCGCACCGTGCTCTTGGGAAGGAAGG
      6601  AGACCTGGCCCTGCTCACCACGGACTGGGTGCCTCGACCTCCTGAATCCCCAGAACACAA
      6661  CCCCCCTGGGCTGGGGTGGTCTGGGGAACCATCGTGCCCCCGCCTCCCGCCTACTCCTTT
      6721  TTAAGCTT
    Genomic Sequence Description  
    Genomic Sequence
    
          


    Literature

    PubMed:6467375 Embryonic lethal mutation in mouse collagen I gene causes rupture of blood vessels and is associated with erythropoietic and mesenchymal cell death.
    Löhler J, Timpl R, Jaenisch R
    Cell 1984 Sep 38:2 597-607
    PubMed:9050868
    PCNA:94/5/1852
    Type III collagen is crucial for collagen I fibrillogenesis and for normal cardiovascular development.
    Liu X, Wu H, Byrne M, Krane S, Jaenisch R
    Proc Natl Acad Sci U S A 1997 Mar 4;94(5):1852-6


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