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
