From: eesnyder@boulder.Colorado.EDU (Eric E. Snyder)
Subject: GenBank error?! (brain damage?)
Organization: University of Colorado, Boulder
Date: 12 Aug 92 20:50:19 GMT

Well, I wrote a program to fish out coding exons from GenBank by looking
at the 'CDS join...' entry in the feature table and came out with this 
interesting entry which appears to contain a 3 bp internal exon (and an intron of 
length zero!)...  

     CDS             join(3455..3511,3512..3515,5060..5092,6258..6333,
                     7025..7166)

What is the point of 'joining' the sig_pep separately?  I would have liked to 
think that the purpose of 'join' was to link segments which are non-contiguous...
Are signal peptides always treated this way or is this just an odd ball case?


LOCUS       HUMMGPA      7734 bp ds-DNA             PRI       03-OCT-1990
DEFINITION  Human matrix Gla protein (MGP) gene, complete cds.
ACCESSION   M55270 J05572
KEYWORDS    matrix Gla protein; vitamin K-dependent protein.
SOURCE      Human leukocyte DNA.
  ORGANISM  Homo sapiens
            Eukaryota; Animalia; Metazoa; Chordata; Vertebrata; Mammalia;
            Theria; Eutheria; Primates; Haplorhini; Catarrhini; Hominidae.
REFERENCE   1  (bases 1 to 7734)
  AUTHORS   Cancela,L., Hsieh,C.-L., Francke,U. and Price,P.A.
  TITLE     Molecular structure, chromosome assignment, and promoter
            organization of the human matrix Gla protein gene
  JOURNAL   J. Biol. Chem. 265, 15040-15048 (1990)
  STANDARD  full staff_review
FEATURES             Location/Qualifiers
     mRNA            join(3399..3515,5060..5092,6258..6333,7025..7166,
                     7167..>7734)
                     /gene="MGP"
                     /partial
     mat_peptide     join(3512..3515,5060..5092,6258..6333,7025..7163)
                     /product="matrix Gla protein"
                     /gene="MGP"
                     /codon_start=1
     CDS             join(3455..3511,3512..3515,5060..5092,6258..6333,
                     7025..7166)
                     /product="matrix Gla protein"
                     /gene="MGP"
                     /codon_start=1
                     /translation="MKSLILLAILAALAVVTLCYESHESMESYELNPFINRRNANTFI
                     SPQQRWRAKVQERIRERSKPVHELNREACDDYRLCERYAMVYGYNAAYNRYFRKRRGT
                     K"
     CAAT_signal     complement(2868..2872)
                     /gene="MGP"
     CAAT_signal     3276..3280
                     /gene="MGP"
     TATA_signal     3358..3366
                     /gene="MGP"
     exon            3399..3515
                     /number=1
                     /gene="MGP"
     sig_peptide     3455..3511
                     /product="matrix Gla protein"
                     /gene="MGP"
                     /codon_start=1
     intron          3516..5059
                     /number=1
                     /gene="MGP"
     exon            5060..5092
                     /number=2
                     /gene="MGP"
     intron          5093..6257
                     /number=2
                     /gene="MGP"
     repeat_unit     complement(5470..5788)
                     /rpt_family="Alu"
                     /gene="MGP"
     exon            6258..6333
                     /number=3
                     /gene="MGP"
     intron          6334..7024
                     /number=3
                     /gene="MGP"
     repeat_unit     complement(6679..6888)
                     /gene="MGP"
     exon            7025..7166
                     /number=4
                     /gene="MGP"
     polyA_signal    7389..7394
                     /gene="MGP"
     repeat_unit     7489..7678
                     /gene="MGP"
BASE COUNT     2303 a   1580 c   1470 g   2381 t
//


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TTGATTGCTAAACACTGGGCGGCGAATCAGGGTTGGGATCTGAACAAAGACGGTCAGATTCAGTTCGTACTGCTG
Eric E. Snyder                            
Department of MCD Biology              ...making feet for childrens' shoes.
University of Colorado, Boulder   
Boulder, Colorado 80309-0347
LeuIleAlaLysHisTrpAlaAlaAsnGlnGlyTrpAspLeuAsnLysAspGlyGlnIleGlnPheValLeuLeu
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