trembl and EMBL 45

Jean-Marc Plaza plaza at infobiogen.fr
Thu Dec 28 06:43:50 EST 1995


Sorry, I forgot the subjecty so I post it again:


Hi,
there are several problems with EMBL 45 when you
run trembl (Thure Etzold) on it.
First, in CDS complement , trembl does a core dump when it finds :
        "complememt(>" instead of "complememt("
Secondly, The codon start for HSACTSG7 is /codon_start!29 in EMBL 45
instead of 1, 2 or 3. And trembl does not like it -core dump. :-)
In Genbank the codon start is /codon_start=1 for HUMACTSG7 and
the translated sequence is different.


Any idea to fix that ?


Thanks


Jean-Marc


EMBL 45
ID   HSACTSG7   standard; DNA; PRI; 466 BP.
DE   Human enteric smooth muscle gamma-actin gene, exon 9 and 3' flank.
FT   CDS_pept        join(D00649:2129..2254,D00649:3135..3263,D00650:653..763,
FT                   D00650:1033..1117,D00651:66..227,D00652:55..246,D00653:357
FT                   ..538,89..232)
FT                   /note="gamma-actin precursor"
FT                   /codon_start!29
FT                   /db_xref="PID:e34116"
FT                   /translation="PEWPQTASPWIRVVPWGIRRLLRFASMEYTKGKLPIFLAGNGMPVFT
GEEADLFDDSVRVNYFNWYINEVLKAVKEDL
VDVRSYIVRSLIDGYEGPLGFSQRFGLYFT                   HVNFNDSSRPRTPRKSAYLFTSIIEKNGFSAKKVKRNPLPVRADFTSRARVTDSLPSEVFT
PSK
AKISVEKFSKQPRFERDLFYDGRFRDDFLWGVSSSPYQIEGGWNADGKGPSIWDNFFT
THTPGNGVKDNATGDVACDSYHQLDADLNILRTLKVKSYRFSISWSRIFPTGRNS
TINKFT                   QGVDYYNRLIDSLVDNNIFPMVTLFHWDLPQALQDIGGWENPSLIELFDSYADYCFKTFFT
GDRVKFWMTFNEPWCHVVLGYSSGIFP
PSVQEPGWLPYKVSHIVIKAHARVYHTYDEKYFT                   RSEQKGVISLSLNTHWAEPKDPGLQRDVEAADRMLQFTMGWFAHPIFKNGDYPDVMKWTFT
 VGNRSELQHLASSRLPTFTEEEKNYVRGTADVFCHNTYTSVFVQHSTPRLNPPSYDDDMFT
ELKLIEMNSSTGVMHQDVPWGTRRLLNWIKEEYGNIPIYITENGQGLENPT
LDDTERIFFT                   YHKTYINEALKAYKLDGVDLRGYSAWTLMDDFEWLLGYTMRFGLYYVDFNHVSRPRTARFT
ASARYYPDLIANNGMPLAREDEF
LYGEFPKGFIWSAASASYQVEGAWRADGKGLSIWDTFT                   FSHTPLRIGNDDNGDVACDSYHKIAEDVVALQNLGVSHYRFSIAWSRILPDGTTKFINEFT
     AGLSYYVRFIDALLAAGITPQVTIYHWDLPQALQDVGGWENETIVQRFKEYADVLFQRLFT
GDRVKFWITLNEPFVIAAQGYGTGVSAPGISFRPGTAPYIAGHNLIK
AHAEAWHLYNDVFT                   YRARQGGTISITISSDWGEPRDPTNREHVEAARSYVQFMGGWFAHPIFKNGDYPEVMKTFT
RIRDRSLGAGLNKSRLPEF
TESEKSRIKGTFDFFGFNHNTTVLAYNLDYPAAFSSFDADFT                   RGVASIADSSWPVSGSFWLKVTPFGFRRILNWLKEEYNNPPIYVTENGVSRRGEPELNDFT
         TDRIYYLRSYINEALKAVHDKVDLRGYTVWSIMDNFEWATGFAERFGVHFVNRSDPSLPFT
RIPRASAKFYATIVRCNGFPDPAQGPHPCLQQPEDAAPTASPV
QSEVPFLGLMLGIAEAFT
QTALYVLFALLLLGACSLAFLTYNTGRRSKQGNAQPSQHQLSPISSF"
<H2>ERROR:</H2><P> syntax error, at "129
/db_xref="PID:e34116"
/translation="PEWPQTASPWIRVVPWGIRRLLRFASMEYTKGKLPIFLAGNGM


GENBANK 92
LOCUS       HUMACTSG7     466 bp    DNA             PRI       23-JAN-1992
DEFINITION  Human enteric smooth muscle gamma-actin gene, exon 9 and 3' flank.
ACCESSION   D00654
NID         g219424
KEYWORDS    actin; gamma-actin.
SEGMENT     7 of 7
SOURCE      Human peripheral blood genomic DNA, clone HACTSG-112.
  ORGANISM  Homo sapiens
            Eukaryota; Animalia; Metazoa; Chordata; Vertebrata; Mammalia;
            Theria; Eutheria; Primates; Haplorhini; Catarrhini; Hominidae.
REFERENCE   1  (bases 89 to 309)
  AUTHORS   Miwa,T. and Kamada,S.
  TITLE     The nucleotide sequence of a human smooth muscle (enteric type)
            gamma-actin cDNA
  JOURNAL   Nucleic Acids Res. 18, 4263-4263 (1990)
  MEDLINE   90332437
REFERENCE   2  (bases 1 to 466)
  AUTHORS   Miwa,T., Manabe,Y., Kurokawa,K., Kamada,S., Kanda,N., Bruns,G.,
            Ueyama,H. and Kakunaga,T.
  TITLE     Structure, chromosome location, and expression of the human smooth
            muscle (enteric type) gamma-actin gene: evolution of six human
            actin genes
  JOURNAL   Mol. Cell. Biol. 11, 3296-3306 (1991)
  MEDLINE   91246198
COMMENT     These data kindly submitted in computer readable form by: Takeshi
            Miwa
            Department of Oncogene Research
            Research Institute for Microbial Diseases
            Osaka University
            3-1 Yamadaoka
            Suita
            Osaka 565
            Japan
            Phone:  06-875-2470
            Fax:    06-875-1292.
            

            NCBI gi: 219424
FEATURES             Location/Qualifiers
          1..466
                     /organism="Homo sapiens"
CDS_pept        join(D00649:2129..2254,D00649:3135..3263,D00650:653..763,
                     D00650:1033..1117,D00651:66..227,D00652:55..246,
                     D00653:357..538,89..232)
                     /note="gamma-actin precursor;  NCBI gi: 219426"
                     /codon_start=1
                     /db_xref="PID:g219426"
                     /translation="MCEEETTALVCDNGSGLCKAGFAGDDAPRAVFPSIVGRPRHQGV
                     MVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIITNWDDMEKIWHHSFYNELRVAPEEH
                     PTLLTEAPLNPKANREKMTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGV
                     THNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLC
                     YVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIH
                     ETTYNSIMKCDIDIRKDLYANNVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPP
                     ERKYSVWIGGSILASLSTFQQMWISKPEYDEAGPSIVHRKCF"


---------------------------------------------------
Jean-Marc PLAZA
INFOBIOGEN - CNRS
7, rue Guy Moquet BP8 94801 VILLEJUIF Cedex, France
tel: +33 45 59 52 39  fax: +33 45 59 52 50




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