Subject: annotation of ph-d
Dear Dr. Brock,
I am a curator for FlyBase and am working on the annotation of the
Drosophila genomic sequence from information in GenBank and the
literature. I am currently working on ph-p and ph-d and would like to
mark the exon/intron structure of ph-d on the sequence. Unfortunately,
I have not found that information in GenBank or in the literature. I
see from the Hodgson et. al. 1997 Mechanisms of Development paper that
you have a cDNA sequence. I was wondering if you would send me the cDNA
sequence so I can use it to locate the exon boundaries on the sequence.
If the sites of introns are marked that would be even better. 
Any information that you send will be kept as a personal communication
to FlyBase and used as a reference for the annotation.
Thanks for your help.
Sincerely,
Beverley Matthews
Subject: ph-d
Dear Beverley,
        I'm attaching the ph-d cDNA sequence , which is 5536 bp long. We
mapped the translational start site to nucleotide residue 678. The exon
junctions are located at the following nucleotide residues:
1) exon 2.......334/335
2) exon 3.......1896/1897
3) exon 4......2347/2348
4) exon 5......4161/4162
Let me know if you need any further help.
Cheers, Jacob
Subject: text file
Dear Beverley,
        Here a text file of the ph-d cDNA (5.536 kb):
TTTGAAACTTAACTTGGCGGCGTGCGGTTCTTGCGCTCTGCTCTCTTTGCGTTCGTGTTGGTGTGGTGTCGATGTG
TCGCATACCGCATGTGTATTGAACGGGGGAAAAAAAAAGCGCCGACGCGACGCACACACACCCTACCACCGTTTCG
TAGTATTTATTTATATATTTATTTTTGGCGATCAATGCAAATCGGTGCTGACTATAAGTGATTAGTGAAAACAATT
AATGCTGTGCGGCGTCTAAAGTTGCGTCGTTTTGAATGTTAGGCATGTACAGGTGCCTCCAAATATACAATAATAC
AGTACAGCAAGGAAAGCAAAAATGAAAACGCAGTGGGGACACCGAAAGTGAATCAGCAACAACAATACGTACACCA
CCACCTTCCCCGGAAGCCACCACATCTGTAAAGGTCAACTCCACCACTCGCGTGGACCCCCAGCGGCCACTAAGGT
GCCTGGAAACACTCGCCCAGAAGGCAGGCATCAGCTTCGACGAGGACTTTGCCAAGAGTCCATCCCAATCGCCCAG
CTCTAAGGCAGCACGTGGGTCAGTCGGAACGCCATCAATCAGACGGCGCCACCCACTACTACCGCTCAGCAGCAGA
TCGCCAAGCGCACCCGACTCAAAGACAACCGGCCGCAAACTGGAGAAGTCACAGAGTCCAGCTCAACCGATGGCGG
CCGCCACCAATGTGCCGCTGCAGATCTCCCCCGAGCAGCTGCAGCAGTTATATGCAAACAATCCCTACGCCATTCA
GGTGAAGCAAGAGTTTCCCACGCACACGACCAGTGGCAGTGGAACTGAACTAAAGCATGCAACCAACATTATGGAA
GTTCAGCAGCAGTTGCACGTGCAGCAGCAGCTGTCGGAAGCCAACGGTGGAGGAGCAGCCTCGGCCGGAGCCGGAG
GAGCAGCTAGTCCGGCCAACTCGCAGCAAAGCCAGCAACAGCAGCACTCCACAGCCATCAGCACCATGTCGCCGAT
GCAATTGGCAGGGCCCACTGGAGGAGTTGGCGGGGATTGGACACAGGGAAGGACGGTGCAGCTAATGCAACCCTCC
ACCAGTTTCCTGTATCCCCAAATGATTGTGTCGGGAAATCTGTTGCATCCAGGAGGCCTCGGTCAGCAGCCAATCC
AGGTGATCACCGCCGGCAAGCCATTCCAAGGCAACGGCCCCCAGATGCTTACCACCACGACTCAAAACGCCAAGCA
AATGATCGGTGGCCAAGCGGGATTCGCTGGCGGAAATTACGCGACCTGCATTCCTTCGAACCACAATCAGTCGCCT
CAGACGGTGCTCATCTCGCCGGTGAATGTCATCTCCCACTCGCCACAGCAGCAGCAAAACCTTCTGCAATCAATGG
CCGCCGCAGCTCAACAACAGCAACTTACCCAACAGCAGCAGCAACAGCTTAACCAGCAGCAACAGCAGCTCAACCA
GCAGCAGCAACAGCAACAGCTGACTGCCGCTCTGGCCAAGGTGGGAGTGGATGCGCAGGGCAAGCTGGCCCAGAAA
GTGGTTCAGAAGGTGACCACCACCAGCAGCACGGTGCAGGCGGCGACGGGTCCTGGATCTACTGGGTCAACACAGA
CCCAGCAGGTGCAGCAGGTTCAGCAACAGCAGCAGCAGACCACCCAAACCACTCAGCAGTGCGTGCAGGTTTCACA
GTCGACTTTGCCAGTCGGTGTGGGTGGACAGTCTGTTCAGACTGCCCAACTTTTGAACGCTGGCCAAGCGCAACAA
ATGCAGATCCCTTGGTTCTGGCAGAATGCGGCGGGCCTGCAACCCTTCGGCTCCAATCAGATCATCCTGCGAAACC
AGCCAGACGGAACCCAAGGCATGTTCATTCAACAGCAACCGGCGACGCAGACTTTGCAGACCCAGCAAAACCAGAT
TATTCAATGCAACGTGACGCAGACGCCCACTAAGGCACGCACTCAACTGGATGCACTTGCTCCCAAGCAGCAACAG
CAGCAGCAGCAGGTTGGCACTACCAACCAGACGCAGCAGCAGCAACTAGCGGTGGCTACTGCCCAGTTGCAGCAAC
AGCAGCAGCAACTCACTGCAGCAGCTCTGCAGCGACCAGGAGCCCCTGTCATGCCCCACAATGGAACTCAAGTGCG
TCCGGCCAGTTCCGTATCCACACAGACTGCCCAGAACCAGAGCCTGCTGAAGGCCAAAATGCGCAACAAGCAGCAG
CCGGTGCGCCCCGCTTTAGCCACATTGAAAACCGAAATCGGTCAAGTCGCAGGACAAAATAAGGTAGTAGGCCACC
TGACCACCGTGCAGCAGCAGCAACAGGCGACGAATCTCCAGCAGGTGGTTAATGCGGCGGGCAACAAAATGGTTGT
GATGAGCACAACGGGCACTCCGATCACCCTGCAGAATGGACAGACCCTTCATGCAGCCACTGCGGCAGGAGTCGAC
AAGCAGCAACAGCAGCTACAACTGTTTCAGAAACAGCAAATCCTGCAACAACAACAAATGTTGCAACAGCAGATTG
CTGCCATTCAAATGCAGCAGCAGCAAGCGGCTGTTCAGGCCCAGCAACAACAGCAGCAACAGGTCTCTCAGCAGCA
GCAGGTTAACGCCCAGCAACAGCAAGCGGTGGCGCAACAACAACAGGCAGTCGCGCAGGCTCAGCAACAGCAGAGG
GAGCAACAGCAGCAAGTTGCCCAAGCCCAGGCGCAGCATCAACAGGCTCTCGCGAATGCCACTCAGCAAATCCTTC
AGGTGGCGCCAAATCAATTCATCACGTCCCACCAGCAACAGCAGCAGCAGCAACTTCACAACCAACTGATACAGCA
GCAGCTACAGCAACAGGCGCAGGCACAAGTTCAAGCCCAAGTGCAGGCTCAAGCGCAACAGCAACAACAGCAGCGA
GAGCAGCAGCAGAATATTATCCAGCAGATTGTGGTGCAACAGTCAACTGGAGCGACTTCTCAACAGCAGCAGCAGC
AACCGCAACAGCAGTCTGGACAGTTGCAGCTTAGCAGCGTGCCGTTTTCGGTTTCACCATCGATGACGGCGGAAGA
TATTGCCGGAATAACATCCAGTGCCCTACAAGAAGCTCTCTCGGTGTCTGGCGCCATCTTTCAGACAACCAAACCG
ATTACTTGCAGTTCCTCTACGCTCCCCACAAGCAGTGTGGTCACAATTACCAGCCAGAGCAGCACTCCTCTGGTCA
CCAGCAGTACGGTGGCCAGTATGCAGCAGGCTCAGACGCAAGGTACTCAGATCCATCAACATCAGCAGCTAATCAG
CGCCACTATTGCCGGAGGGTCTCAACAGCAGCAGCAGCAGCAGCAACTGGGACTACCTTCACTTACACCCACCACG
CCCTCACCTACAACAAATCCCATTCTGGCCATGACCTCGATGATGAATGCCACCGTGGGTCACCTATCCACTGCCC
CACCCGTTAGTGTTTCTAGCACCGCTGTCACTCCATCGTCTGGACAGCTGGTCACACTAAGCAGTGCTAGTAGCGG
TGGAGGAGCAGGCTTTCCAGCCACGCCCACCAAAGAGACACCTTCAAAAGGGCCCACCGCAACCCTGGTGCCCATT
GATTCGCCCAAGACTCCTGTATCAGGAAAGGACACCTGCACTACCCCCAAATCATCTACTCCTGCCACTGTTAGCG
CATCCGTAGAGGCCAGTAGTTCCACAGGCGAAGCCCTGTCCAATGGAGATGCCTCAGATAGGTCTTCCACGCCGTC
AAAGGGCGCTACCACTCCCACCAGCAAGCAAAGCAATGCAGCAGTGCAGCCACCGAGTAGCACCATTCCCAACAGT
GTCAGTGGGAAAGAAGAGCCGAAGCTGCACAACTGCGGCAGTTTAACGTCCGCAACATCAACATCAACCACGACAA
CGATCACCAATGGGATTGGAGTAGCCAGAACGACAGCCAGCACGGCTGTCTCAACCGCTAGCACAACCACTACCAG
TTCTGGCACCTTTACCACAAGTTGCACCAGCACAACCACAACCACCACGTCGAGTATCAGTAATGGATCGAAGGAT
CTCCCCAAGGCGATGATTAAGCCGAACGTCTTAACTCACGTCATCGATGGCTTCATCATCCAGGAGGCCAACGAGC
CATTTCCCGTCACCAGACAGCGATATGCAGACAAAGACGTCAGCGATGAGCCGCCAAAGAAAAAGGCAACCATGCA
GGAGGACATCAAGCTAAGTGGAATAGCATCAGCTCCAGGCTCGGATATGGTTGCTTGCGAGCAGTGTGGAAAGATG
GAGCACAAAGCAAAGCTGAAACGGAAGCGCTACTGTTCGCCAGGATGCTCGAGGCAGGCAAAGAACGGCATCGGTG
GAGTTGGATCAGGAGAGACGAACGGCCTGGGGACAGGTGGTATAGTTGGGGTGGACGCAATGGCATTGGTGGACAG
ACTGGATGAAGCCATGGCTGAGGAGAAGATGCAGACAGAATCATACCAGACAGTATCGGACGCTTTGCCAATTCAA
GCGGCTACGCCGGAGGTCCCACCGATTTCGATGCCAGTGCTGGCGGCTATGTCGACATCTTCACCACTTTCGTTGC
CCCTGACATTGCCCTTGCCAATTGCAATAGCTCCCACTGTGTCACTGCCAGTGGTTTCAGCTGGAGTGGTTGCGCC
GGTCCTAGCAATACCATCCTCGAATATAAATGGATCCGATCGCCCTCCCATCAGCAGTTGGAGTGTGGAAGAAGTT
AGCAATTTCATCCGAGAACTGCCTGGTTGCCAGGACTACGTGGACGACTTTATACAGCAGGAGATCGACGGCCAAG
CGCTGCTGCTGCTCAAAGAAAACCATTTGGTTAACGCCATGGGCATGAAGCTGGGTCCAGCTCTCAAAATTGTGGC
CAAGGTGGAGTCCATTAAGGAGGTCCCGCCAGGCGATGTAAAGGATTAAAAACACGCAACAAAGTCAAGGTTTCAA
AAGACCGCTTTCTTTAGTTTCCCGCGTTTCACCTAAATGTAACGACATTTACTTCGTGAGCGAATGTGATCAGACA
GAACAAAGTGAATCACGTTCCGACTCACCACTTCTCACACGACGTACACCCTAATCATCAGCTACATGCACCTAAT
CTACAAAGGGAACTCCCCAGAGAGCAACCGGTGCCTGGAATCACTGACTCTGTTGCGAGGCCCATCCCATCCAGAA
TCTATGCGAGAAATCCATAATTAGGTGATGTAGTTGTTTTTCCGAGAGCAACCGGTGCCTGGAATCACTGACTCTG
TTGCGAGGCCCATCCCATCCAGAATCTATGCGAGAAATCCATAATTAGGTGATGTAGTTGTTTTTCCCGCACATGA
CGAAAGCAAGGAATATGACCCTCCTTCGGCGCCGAAGCTGCAGCTAGTTTAAGCACCCCGATCAGACCCCAAGATT
GTGGCAATAGTAGAGTCCATGACTCTGTGCGACGAAAAGGACGGGGAGGTTATAGGACCGCTGGCGCCTCCGCGTT
GGATCAACAGTCTTCAGCAGTCTACCAGAGTCTGAGGATAGGAGCGGGCAGTATCTGAGCTCTA
Cheers, Jacob
Dept. of Zoology, UBC,
6270 University Blvd.
Vancouver, BC, V6T 1Z4