Thread View: bionet.molbio.seqnet
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Started by MJB1
Thu, 18 Feb 1988 14:03
SEQNET Bulletin
Author: MJB1
Date: Thu, 18 Feb 1988 14:03
Date: Thu, 18 Feb 1988 14:03
150 lines
7902 bytes
7902 bytes
From: MJB1@VMS-SUPP.CAM.AC.UK
Bulletin_# 83 <ATTIMONELLI%VAXBA1.INFNET@EARN.IBOINFN> 17-FEB-1988 15:21 GenB
From: <ATTIMONELLI%VAXBA1.INFNET@EARN.IBOINFN>
Date: 17-FEB-1988 15:21
To: SEQNET
Subject: GenBank changes
Via: UK.AC.RL.EARN; Wed, 17 Feb 88 15:20:28 GMT
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Date: Wed, 17 Feb 88 13:31 N
From: <ATTIMONELLI%VAXBA1.INFNET@EARN.IBOINFN>
Reply-To: <ATTIMONELLI%VAXBA1.INFNET@EARN.IBOINFN>
Subject: GenBank changes
To: MJB1@UK.AC.CAM.VMS-SUPP
X-Original-To: "MJB1@VMS-SUPP.CAM.AC.UK"
Message-id: <6589>
Date: WED, 17-FEB-88 13:31 N
From: <ATTIMONELLI@VAXBA1.INFNET>
Reply-To: <ATTIMONELLI%VAXBA1.INFNET@IBOINFN.BITNET> (alternate reply)
Subject: GenBank changes
To: <MJB1@VMS-SUPP.CAM.AC.UK>
X-Original-To: mjb1@vms-supp.cam.ac.uk, ATTIMONELLI
Christian Burks:
we refer to our previous communication about GenBank changes and your answer
dated 6-Feb-1988.
We still believe that it is very important to have the collections structured
in such a way to maintain the maximum information in a machine readable form
allowing a selective retrieval.
You stated in your message that since you "are not able to automatically
translate" EMBL features into GenBank format "you decided to adopt" the
use of COMMENT field for parking EMBL feature.
This, together with the lost of the SITES field, is in our opinion a great
devaluation of the GenBank collection and in particular makes the GenBank
unusable for our software ACNUC.
We have the software TRANSFORM which automatically convert in all its part
the EMBL collection into the "old" GenBank format.
An example is reported below refering to the EMBL entry PTAGGLOG already
mentioned in our previous message.
If you are interested in the software TRANSFORM please contact us at your
earlier convenience.
Dr. Marcella Attimonelli
>>>>>>>>>>
EMBL PTAGGLOG entry converted into GenBank format by TRANSFORM program
LOCUS PTAGGLOG 1815 bp DNA entered 02/16/87
DEFINITION Chimpanzee fetal A-gamma-globin gene
ACCESSION X03110
KEYWORDS gamma-globin; A-gamma-globin; direct repeat; tandem repeat.
SOURCE
ORGANISM Pan troglodytes ;(chimpanzee, chimpanze, Chimpanse)
Eukaryota; Metazoa; Chordata; Vertebrata; Tetrapoda; Mammalia;
Eutheria; Primates.
REFERENCE 1 (bases 1 to 1815)
AUTHORS Slightom,J.L., Chang,L.-Y.E., Koop,B.F. and Goodman,M.
TITLE Chimpanzee fetal G-gamma and A-gamma globin gene nucleotide
sequences provide further evidence of gene conversions in hominine
evolution
JOURNAL Mol. Biol. Evol. 2, 370-389 (1985)
COMMENT History:
17-JAN-1986 (annotation)
Data kindly reviewed (07-JUL-1986) by Slightom J.L.
FEATURES from to/span description
pept 55 199 put. exon 1
matp 108 199 A-gamma-globin (aa 1-31)
(199 is 2nd base in codon)
322 544 A-gamma-globin (aa 32-105)
(322 is 3rd base in codon)
1432 1557 A-gamma-globin (aa 106-147)
pept 1431 1647 put. exon 3
RNA 55 1647 put. primary transcript
SITES
->prm 24 1 put. TATA-box start
prm<- 28 1 put. TATA-box end
cap 55 0 put. cap site
->pept 55 1 put. exon 1 start
->RNA 55 1 put. primary transcript start
->matp 108 1 A-gamma-globin (aa 1-31)
(199 is 2nd base in codon) start
matp/ivs 199 0 A-gamma-globin (aa 1-31)
(199 is 2nd base in codon) end/intron
start
pept<- 199 1 put. exon 1 end
ivs/matp 322 0 intron end /A-gamma-globin (aa 32-105)
(322 is 3rd base in codon) start
matp/ivs 544 0 A-gamma-globin (aa 32-105)
(322 is 3rd base in codon) end/intron
start
->rpt 1123 1 TG(14) repeat (hot spot sequence start
rpt<- 1162 1 TG(14) repeat (hot spot sequence end
->pept 1431 1 put. exon 3 start
ivs/matp 1432 0 intron end /A-gamma-globin (aa 106-147
) start
matp<- 1557 1 A-gamma-globin (aa 106-147) end
->site 1621 1 put. polyadenylation signal start
site<- 1626 1 put. polyadenylation signal end
polya 1647 0 put. polyadenylation site
pept<- 1647 1 put. exon 3 end
RNA<- 1647 1 put. primary transcript end
BASE COUNT 471 A 357 C 474 G 513 T
ORIGIN
1 CCGGCGGCTG GCTAGGGATG AAGAATAAAA GGAAGCACCC TCCAGCAGTT CCACACACTC
61 GCTTCTGGAA CGTCTGAGGT TATCAATAAG CTCCTAGTCC AGACGCCATG GGTCATTTCA
121 CAGAGGAGGA CAAGGCTACT ATCACAAGCC TGTGGGGCAA GGTGAATGTG GAAGATGCTG
181 GAGGAGAAAC CCTGGGAAGG TAGGCTCTGG TGACCAGGAC AAGGGAGGGA AGGAAGGACC
241 CTGTGCCTGG CAAAAGTCCA GGTCACTTCT CAGGATTTGT GGCACCTTCT GACTGTCAAA
301 CTGTTCTTGT CAATCTTACA GGCTCCTGGT TGTCTACCCA TGGACCCAGA GGTTCTTTGA
361 CAGCTTTGGC AACCTGTCCT CTGCCTCTGC CATCATGGGC AACCCCAAGG TCAAGGCACA
421 TGGCAAGAAG GTGCTGACTT CCTTGGGAGA TGCCATAAAG CACCTGGATG ACCTCAAGGG
481 CACCTTTGCC CAGCTGAGTG AACTGCACTG TGACAAGCTG CATGTGGATC CTGAGAACTT
541 CAAGGTGAGT CCAGGAGATG TTTCAGCCCT GTTGCCTTTA GTCTGGAGGC AACTTAGACA
601 ACTGAGTATT AATCTGAGCA CAGCTGAATC TACCCACAGG GTGTAAACTA TTTGAAGATA
661 TTGGGGTTGG GAGTGAAGGA ACTGCAGAGG ACTAACTGGG CTGAGACCCA GTGGTAATGT
721 TTTAGGGCCT AAGGAGTGCC TCTAAAAATC TAGATGGACA ATTTTGACTT TGAGAATAGA
781 GAGGTGGAAA TGAGGAAAAT GACTTTTCTT TATTAGATTC CAGTAGAAAG AACTTTCATC
841 TTTCCCTCAT TTTTGTTGTT TTAAAACATC TATCTGGAGG CAGGACAAGT ATGGTCATTA
901 AAAAGATGCA GGCAGAAGGC ATATATTGGC TCAGTCAAAG TGGGGAACTT TGGTGGCCAA
961 ACATATATTG CTAAGGCTAT TCCTATGTCA TCTGGACACA TATAAAATGC TGCTAATGCT
1021 TCATTACAAA CTTATATCCT TTAATTCCAG ATGGGGGCAA AGTATGTCCA GGGGTGAGGA
1081 ACAATTGGAA CATTTGGGCT GGAGTAGATT TTGAAAGTCA GCTGTGAGTT TGTGTGTGTG
1141 TGTGTGTGTG TGTGTGTGCG TGTCAGCGTG TGTTTCTTTT AACGTCTTCA GCCTACAACA
1201 TACAGGGTTC ATGGTGGCAA GAAGATAGCA AGATTTAAAT TATGGCCAGT GACTAGTGCT
1261 GCAAGGGGAA CAACTACCTG CATTTAATGG GAAGGCAAAA TCTCAGGCTT TGAGGGAAGT
1321 TAACATAGGC TTGATTCTGG GTGGAAGCTG GGTGTGTAGT TATCTGGAGG CCAGGCTGGA
1381 GCTCTCAGCT CACTATGGGT TCATCTTTAT TGTCTCCTTT CATCTCAACA GCTCCTGGGA
1441 AATGTGCTGG TGACCGTTTT GGCAATCCAT TTCGGCAAAG AATTCACCCC TGAGGTGCAG
1501 GCTTCCTGGC AGAAGATGGT GACTGCAGTG GCCAGTGCCC TGTCCTCCAG ATACCACTGA
1561 GCCTCTTGCC CATGATTCAG AGCTTTCAAG GATAGGCTTT ATTCTGCAAG CAATACAAAT
1621 AATAAATCTA TTCTGCTGAG AGATCACACA TGATTTTCTT CAGCTCTTTT TTTTACATCT
1681 TTTTAAATAC ATGAGCCACA AAGGGTTTAT ATTGAGGGAA GTGTGTATGT GTATTTCTGC
1741 ATGCCTGTTT GTGTTTGTGG TGTGTGCATG CTCCTCATTT ATTTTTATAT GAGATGTGCA
1801 TTTTGATGAG CAAAT
//
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