Personal communication to FlyBase, 26 Jan 2007
Susan Celniker, PhD
Berkeley Drosophila Genome Project
Lawrence Berkeley National Laboratory
1 Cyclotron Rd MS 64-0119
Berkeley, CA 94720, USA
FlyBase annotators requested confirmation for sequence extent
on 2L (reverse complement):
>9938588
>gaaacgaaagaggaagccgggaaagtgcacaacgatatatcttttaaaacatgcttaa
>9938531 ^
>
>The indicated "a" (9938567) necessitates that we postulate
>a GA splice donor for the gene Apf. However, in other
>Drosophila species this splice site is either GT or GC, eg:
>
>
>Query: 61 gaaacgaaagaggaagccgggaaagtgcacaacgatatatctt 103
> ||||| ||||||||||||||| |||||| ||||||||||||||
>Sbjct: 534 gaaacaaaagaggaagccgggcaagtgctcaacgatatatctt 492
> ^
>
>
>Query: 61 gaaacgaaagaggaagccgggaaagtgc 88
> ||||| ||||||||||||||| ||||||
>Sbjct: 12629169 gaaacaaaagaggaagccgggtaagtgc 12629142
> ^
>
>Any chance this sequence could be checked?
-----------------------
The sequence is correct. See the attached illustrator file.
I think the strain contains a 4 bp insertion. We now have a cDNA IP04585 (see alignment below) that suggests the genomic sequence is incorrect. I think the CG31713 cds (see below) may also be incorrect. The cDNA is from a pool so may come from another strain.
seq1 = cg31713-ra.fasta, 446 bp
seq2 = ip04585.fasta (Contig1), 562 bp
0 . : . : . : . : . :
1 AAGGCAGCTGGTTTTGTTATTTTTCGCCGCCTTTGTGGGGAAATACAATA
||||||||||||||||||||||||||||||||||||||||||||||||||
13 AAGGCAGCTGGTTTTGTTATTTTTCGCCGCCTTTGTGGGGAAATACAATA
50 . : . : . : . : . :
51 CCTATTGCTGAAGGCTTCCTACGGCTCCTTCCACTGGAGTTCTCCCAAGG
||||||||||||||||||||||||||||||||||||||||||||||||||
63 CCTATTGCTGAAGGCTTCCTACGGCTCCTTCCACTGGAGTTCTCCCAAGG
100 . : . : . : . : . :
101 GACATGTGGACCCAGGCGAGGATGATTTTACCACTGCCCTGCGAGAAACG
||||||||||||||||||||||||||||||||||||||||||||||||||
113 GACATGTGGACCCAGGCGAGGATGATTTTACCACTGCCCTGCGAGAAACG
150 . : . : . : . : . :
151 AAAGAGGAAGCCGGGAAAGTACGACGAGAAGGATCTGATCATATACAAGG
||||||||||||||----||||||||||||||||||||||||||||||||
163 AAAGAGGAAGCCGG GTACGACGAGAAGGATCTGATCATATACAAGG
200 . : . : . : . : . :
201 ACACTCCGCTGACCCTGAATTATCAGGTGCAAGACAAGCCGAAGATTGTT
||||||||||||||||||||||||||||||||||||||||||||||||||
209 ACACTCCGCTGACCCTGAATTATCAGGTGCAAGACAAGCCGAAGATTGTT
250 . : . : . : . : . :
251 ATTTACTGGCTAGCGGAGCTGCGGAATCCCTGCCAGGAGCCCATTCTCTC
||||||||||||||||||||||||||||||||||||||||||||||||||
259 ATTTACTGGCTAGCGGAGCTGCGGAATCCCTGCCAGGAGCCCATTCTCTC
300 . : . : . : . : . :
301 CGAGGAGCACACCGACCTCAAGTGGCTGCCCAAGGAGGAGGCCAAGCAGT
||||||||||||||||||||||||||||||||||||||||||||||||||
309 CGAGGAGCACACCGACCTCAAGTGGCTGCCCAAGGAGGAGGCCAAGCAGT
350 . : . : . : . : . :
351 GCGTCGGCTTTAAGGATAACCAAGTCATGATCGACAAGTTCCACCAAATG
||||||||||||||||||||||||||||||||||||||||||||||||||
359 GCGTCGGCTTTAAGGATAACCAAGTCATGATCGACAAGTTCCACCAAATG
400 . : . : . : . : .
401 ATTTTAGATCAAAACAAACCAATGTGAACTGAAAACAATTGCCGGT
||||||||||||||||||||||||||||||||||||||||||||||
409 ATTTTAGATCAAAACAAACCAATGTGAACTGAAAACAATTGCCGGT
0 . : . : . : . : . :
1
--------------------------------------------------
1 NNMEKAAGFVIFRRLCGEIQYLLLKASYGSFHWSSPKGHVDPGEDDFTTA
50 . : . : . : . : . :
1 MWTQARMILPLPCEKRKRKPGKYDEKDLIIYKDTPLTLNYQVQDKP
--------------------|XXX|-||||||||||||||||||||||||
51 LRET KEEAG YDEKDLIIYKDTPLTLNYQVQDKP
100 . : . : . : . : . :
47 KIVIYWLAELRNPCQEPILSEEHTDLKWLPKEEAKQCVGFKDNQVMIDKF
||||||||||||||||||||||||||||||||||||||||||||||||||
84 KIVIYWLAELRNPCQEPILSEEHTDLKWLPKEEAKQCVGFKDNQVMIDKF
150 . :
97 HQMILDQNKPM
|||||||||||
134 HQMILDQNKPM
seq1=cg31713.pep, length=107
seq2=ip04585.pep, length=144
