Subject: RE: update question
Beverley,
Attached is a Word file containing the cDNA sequence of cranky with splice
sites, ORF, and terminator codon listed (fastA format sequence also included
at bottom). The sequence is from the genomic sequence AC008210, and not the
cDNA clone sequence, which was derived by RT-PCR from y w embryos \- there
were no substantial differences. It is likely that both the 5'-end and
3'-end of the sequence are shorter than the full-length mRNA. In
particular, when we primed cDNA with oligo(dT), we seemed to be priming from
an internal genomic poly(A) stretch. 5'-RACE has not been successful.
As you will see, cranky includes CG14554, CG12561 exon 2 (but not 1 and 3),
CG14553 exon 2 (but not 1 and 3), and CG14552 exons 1-4. Cranky exons 3-4
were not predicted by Genie.
..
Steve
\------------------------------------------------
Stephen Crews
Professor
The University of North Carolina at Chapel Hill
Department of Biochemistry/PMBB
CB#3280 Fordham Hall
Chapel Hill, NC 27599-3280
\-------------------------------------------------------------------------------
LOCUS Cranky cDNA 2710 bp DNA 5-JAN-2002
COMMENTS 5'-end and 3'-ends are likely to be incomplete (oligo(dT)-primed
cDNA seems to be primed from genomic poly(A) stretch); position of initiator
methionine (if present) is unknown. The sequence below is derived from (and
identical to) genomic sequence AC008210.
ORGANISM Drosophila melanogaster
COMMENT AUTHORNAME|Lan Jiang, Stephen Crews|
COMMENT AUTHORAD1|UNC-Chapel Hill|
FEATURES Location/Qualifiers
exon 1..357
exon 358..539
exon 540..610
exon 611..700
exon 701..1000
exon 1001..1185
exon 1186..1292
exon 1293..1446
exon 1447..2710
terminator 2660..2662
ORF 2..2659
BASE COUNT 707 a 812 c 642 g 549 t
ORIGIN
1 acgtgcgatc gacgatatgt atgcggataa taaacgtggc ctagacaagg tgacggcagc
61 aaccccgccc acccacgccc tccagcagca gcagcagcag caacatcccc accagcagca
121 gcagcatctg cagcatgtcc tgcaactgca gcagcaacag cagcaacacc ttcagcagca
181 gcaacatcac ttgcagcacc agatgcatac gcatcataac ttccagcagc atgaaacgtc
241 gccaacagtg tcgcagcagc agcacatgca acagcagcag ccgcagacga cacaacagca
301 acatgcaaca cagcaacagc agcagcaaca gcaacagaca gccggcatgt ttacaagatt
361 cgatgcaaac aaatcgacga agggcgcctc gaagatgcga cgcgatctca taaatgcgga
421 gatagccaat ctgagggatc tcctgccgct gccccaatcg acgcgccagc gcctctcgca
481 actgcaactg atggccctcg tttgtgtcta tgtgcggaaa gccaactact tccagcaagt
541 tttcaaacgt cacaatgcga tgcatcatct ccatcatcag acagcaacac caaatattgg
601 cttctcaaag gcactctccg gcttcttgat gatgctcaca caaaatggca aattgcttta
661 tatatcggat aatgctgcgg agtacttggg ccattccatg gaggatctgc tgatacacgg
721 tgactccgtt tacgatatca ttgacaaaca ggatcacgca aacatccagg ccgagctgaa
781 taggaacgtg ccaccgcagc cgggtggctc gagtcaggcg agcagcggtg gtgccggtgg
841 tgctggcggt gccggcgact caacgtccag caatggaagt gccgctggtg ccggtggtgc
901 tggtggcgcc tccagtctcg agggcgagca tcgcatgttc ctctgtcgca tgaatgttag
961 ccgcaatgcg cgacggcaaa tgcgtttcgg cgatcagaag gttgtcttgg tccagggtca
1021 ctatttgtca ttcctgccgc tttgcagtcg caacgagccc gtctttttgg ccacctgcac
1081 tccgattgcc atgcccgaaa ccagggagtg tgttgtacaa ggtgccacca acgtcttcac
1141 caccatccat tcaatggaca tgaaaatagc ccatatcgat aaaaatggcg aatttcattt
1201 gggctatgat aagtcgactc tgcaaggcac atcctggtac aatctgatcc acagcgataa
1261 tctgacggag gcgcaaaaaa aacacagttt aattatccaa tcggaacaag atcgcagttg
1321 tatccttcta gtacgaatgc agagatctag tggggaatac acgtgggtac acgtggtttt
1381 acaagtgcga gatagtcccg actccacgca acaacctgtt atcgtgtgca caaaccaagt
1441 actcaacgat cgagaggcct caattatgct ggccaactcc tggctgtatc actactatac
1501 cgtccagtcg aagatccagt tcggcatgcc gctggacagt ggtatccgtg tcccaccggg
1561 aactccctcc agcggctact acagtcccca ttcatcccat ccaccggcca ctccaggtgg
1621 tgcaacaccc aatttgggca tagccagtag ctttggcccg caccatcatc cacaccactc
1681 gcaccacccg caccaccatc atcaccatca ccatccggcg actgcttacc atcaccatcc
1741 gcatatggga acctatggtg gagtctatca tgcgaaggca gcaatcgagc ttaaggagga
1801 tcaaccgctg ttttgctttc aagagcccgt ggactatagc caagtaaata gccacgttaa
1861 tcctccgaat gcaacaagta ctcccaatcc gcctatctcc aaatcgtcca cgcccccacc
1921 gcccaagaag cgggctcgaa aactggaacc actctactta cacgccgaac gctctccggc
1981 ggcggcgata actccggaac cggattgcta tgccatccat actcatccgg ctgctgccta
2041 tgccacctca tcggtggtca gtagtgatgc ttcagttata tatgccacaa tagtgccgac
2101 gagaccgagg ttacccaata aatcactgcc tccggatcct gcggatttta tagagcaatg
2161 gaaccccagt ccaccctggt cggaatcggc gcaaaaggct tcgttggata gttttggatc
2221 ctcccacgag ctgagtccct gcatcacgac cacgcccccc acgcccacaa gtgctacacc
2281 gcatcaaagt ggcttgggca ccacccagac cataggacct gctttcagtt ttgaatggat
2341 gtcagatcct ttggtaccgg tcacgtacca gcagtggcca ccaactggtg accatcatca
2401 gcatctttcg cagcacttaa gccagagtca aaaccaccaa aatcccctcc agcagcagca
2461 gaacgagcag cttctacttg gacaacagcc gcatctccac cagcagcacc agcacttagc
2521 acttcatcat ggacgtgggg agcactccct ggagggggaa agtcaggggg tggtggtagt
2581 gccaccgata cccatttcga taccgatacc aacggccacg ggccatgggg atgccggcga
2641 accggttgag gatagaggtt agtattaagt gtgtattgtt ttttaagttt ctggcacgat
2701 ttccaaaaaa
//
fastA
>cranky.cDNA
acgtgcgatcgacgatatgtatgcggataataaacgtggcctagacaaggtgacggcagcaaccccgccc
acccacgccctccagcagcagcagcagcagcaacatccccaccagcagcagcagcatctgcagcatgtcc
tgcaactgcagcagcaacagcagcaacaccttcagcagcagcaacatcacttgcagcaccagatgcatac
gcatcataacttccagcagcatgaaacgtcgccaacagtgtcgcagcagcagcacatgcaacagcagcag
ccgcagacgacacaacagcaacatgcaacacagcaacagcagcagcaacagcaacagacagccggcatgt
ttacaagattcgatgcaaacaaatcgacgaagggcgcctcgaagatgcgacgcgatctcataaatgcgga
gatagccaatctgagggatctcctgccgctgccccaatcgacgcgccagcgcctctcgcaactgcaactg
atggccctcgtttgtgtctatgtgcggaaagccaactacttccagcaagttttcaaacgtcacaatgcga
tgcatcatctccatcatcagacagcaacaccaaatattggcttctcaaaggcactctccggcttcttgat
gatgctcacacaaaatggcaaattgctttatatatcggataatgctgcggagtacttgggccattccatg
gaggatctgctgatacacggtgactccgtttacgatatcattgacaaacaggatcacgcaaacatccagg
ccgagctgaataggaacgtgccaccgcagccgggtggctcgagtcaggcgagcagcggtggtgccggtgg
tgctggcggtgccggcgactcaacgtccagcaatggaagtgccgctggtgccggtggtgctggtggcgcc
tccagtctcgagggcgagcatcgcatgttcctctgtcgcatgaatgttagccgcaatgcgcgacggcaaa
tgcgtttcggcgatcagaaggttgtcttggtccagggtcactatttgtcattcctgccgctttgcagtcg
caacgagcccgtctttttggccacctgcactccgattgccatgcccgaaaccagggagtgtgttgtacaa
ggtgccaccaacgtcttcaccaccatccattcaatggacatgaaaatagcccatatcgataaaaatggcg
aatttcatttgggctatgataagtcgactctgcaaggcacatcctggtacaatctgatccacagcgataa
tctgacggaggcgcaaaaaaaacacagtttaattatccaatcggaacaagatcgcagttgtatccttcta
gtacgaatgcagagatctagtggggaatacacgtgggtacacgtggttttacaagtgcgagatagtcccg
actccacgcaacaacctgttatcgtgtgcacaaaccaagtactcaacgatcgagaggcctcaattatgct
ggccaactcctggctgtatcactactataccgtccagtcgaagatccagttcggcatgccgctggacagt
ggtatccgtgtcccaccgggaactccctccagcggctactacagtccccattcatcccatccaccggcca
ctccaggtggtgcaacacccaatttgggcatagccagtagctttggcccgcaccatcatccacaccactc
gcaccacccgcaccaccatcatcaccatcaccatccggcgactgcttaccatcaccatccgcatatggga
acctatggtggagtctatcatgcgaaggcagcaatcgagcttaaggaggatcaaccgctgttttgctttc
aagagcccgtggactatagccaagtaaatagccacgttaatcctccgaatgcaacaagtactcccaatcc
gcctatctccaaatcgtccacgcccccaccgcccaagaagcgggctcgaaaactggaaccactctactta
cacgccgaacgctctccggcggcggcgataactccggaaccggattgctatgccatccatactcatccgg
ctgctgcctatgccacctcatcggtggtcagtagtgatgcttcagttatatatgccacaatagtgccgac
gagaccgaggttacccaataaatcactgcctccggatcctgcggattttatagagcaatggaaccccagt
ccaccctggtcggaatcggcgcaaaaggcttcgttggatagttttggatcctcccacgagctgagtccct
gcatcacgaccacgccccccacgcccacaagtgctacaccgcatcaaagtggcttgggcaccacccagac
cataggacctgctttcagttttgaatggatgtcagatcctttggtaccggtcacgtaccagcagtggcca
ccaactggtgaccatcatcagcatctttcgcagcacttaagccagagtcaaaaccaccaaaatcccctcc
agcagcagcagaacgagcagcttctacttggacaacagccgcatctccaccagcagcaccagcacttagc
acttcatcatggacgtggggagcactccctggagggggaaagtcagggggtggtggtagtgccaccgata
cccatttcgataccgataccaacggccacgggccatggggatgccggcgaaccggttgaggatagaggtt
agtattaagtgtgtattgttttttaagtttctggcacgatttccaaaaaa
\-------------------------------------------------------------------------------