Subject: gene merge
Hi Gillian,
I thought I should send you this merge sooner rather than have it come
down the apollo pipeline.
Trfp has already been merged with CG18267 which is fine (I guess). It
turns out there is a duplicate annotation (same transcript, same
location) in GadFly under the gene symbol CG18780. Please merge them
all under Trfp. I don't know how the same gene got two different CG
names in the first place. It's only has a single exon. Anyway, there
you have it.
Bev
Here's the alignment of Trfp and CG18780 from GadFly
Sequence 1
lcl|tmpseq_0 GO:<up></up> located on: 2L 28E3-28E3; |cDNA sequence
Length 835(1 .. 835)
Sequence 2
lcl|tmpseq_1 GO:<up></up> located on: 2L 28E3-28E3; |cDNA sequence
Length 835(1 .. 835
Query: 1 cactggacgcttttagcttgcaagacttgtaaacaaaattaataaaactaaaaagctgac 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1 cactggacgcttttagcttgcaagacttgtaaacaaaattaataaaactaaaaagctgac 60
Query: 61 attattgcataaactatgggagtaactatccttcaaccgtatcccttacccgaaggcaaa 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61 attattgcataaactatgggagtaactatccttcaaccgtatcccttacccgaaggcaaa 120
Query: 121 tcgggtgcccacataatcgatcagctgagcaagcgtctgctcgccctgggcgccacacat 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 121 tcgggtgcccacataatcgatcagctgagcaagcgtctgctcgccctgggcgccacacat 180
Query: 181 gccggtcaatttctggtggactgcgaaacgttcatctcgacgccacagccgcacaatgga 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 181 gccggtcaatttctggtggactgcgaaacgttcatctcgacgccacagccgcacaatgga 240
Query: 241 gcacctggacgcgcagtccacgtcctgcacaactccgagtatcccgcctccacgttctcg 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 241 gcacctggacgcgcagtccacgtcctgcacaactccgagtatcccgcctccacgttctcg 300
Query: 301 atcatcgacaatggcaccggcaaacaagtggccattgtcgccgacaatatcttcgatctg 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 301 atcatcgacaatggcaccggcaaacaagtggccattgtcgccgacaatatcttcgatctg 360
Query: 361 ctcatgctcaagatgaccaacaccttcacctccaaaaagcagaccaaaatcgagtcccgt 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 361 ctcatgctcaagatgaccaacaccttcacctccaaaaagcagaccaaaatcgagtcccgt 420
Query: 421 ggcgctcgtttcgagtatggtgactttgttatcaaactcggttccgtcaccatgatggag 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 421 ggcgctcgtttcgagtatggtgactttgttatcaaactcggttccgtcaccatgatggag 480
Query: 481 cacttcaagggcatcctcatcgaaatcgagtacaagtcatgcgtgattctggcctactgc 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 481 cacttcaagggcatcctcatcgaaatcgagtacaagtcatgcgtgattctggcctactgc 540
Query: 541 tgggaaatgatacgcgaaatgctgcagggattcctcggcattgctgtgaataaggacttt 600
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 541 tgggaaatgatacgcgaaatgctgcagggattcctcggcattgctgtgaataaggacttt 600
Query: 601 ccctcctatttcgctccacagacaataatgacggcaatggggcaacagcagctgcatgcc 660
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 601 ccctcctatttcgctccacagacaataatgacggcaatggggcaacagcagctgcatgcc 660
Query: 661 aagcacaacgacatctttgagccaatggacaccgtgaaacaatacctggagcagttcacc 720
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 661 aagcacaacgacatctttgagccaatggacaccgtgaaacaatacctggagcagttcacc 720
Query: 721 aactataggaagcatgtgactcttatgggcggtatgggcagtggaccgggtagccaacag 780
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 721 aactataggaagcatgtgactcttatgggcggtatgggcagtggaccgggtagccaacag 780
Query: 781 gttggtccgaacgtgcatatgtcgccggcggtggcgggaatacatcgatcctgat 835
|||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 781 gttggtccgaacgtgcatatgtcgccggcggtggcgggaatacatcgatcctgat 835
CPU time: 0.02 user secs. 0.06 sys. secs 0.08 total secs.
Gapped
Lambda K H
1.33 0.621 1.12
Gapped
Lambda K H
1.33 0.621 1.12
Matrix: blastn  matrix:1  \-2
Gap Penalties: Existence: 5, Extension: 2
Number of Hits to DB: 1
Number of Sequences: 0
Number of extensions: 1
Number of successful extensions: 1
Number of sequences better than 10.0: 1
length of query: 835
length of database: 433,807,876
effective HSP length: 23
effective length of query: 812
effective length of database: 421,858,686
effective search space: 342549253032
effective search space used: 342549253032
T: 0
A: 30
X1: 6 (11.5 bits)
X2: 26 (50.0 bits)
S1: 12 (23.8 bits)
S2: 18 (35.3 bits)