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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattatattgtgttcatctcatgctttgttcccccccctaagattccctttttgtgggaaccttctaatcgtttccttatatctgtctcttgaagTGCCTCTCCTGCCCGGCGTAGCCCCAGTCCTCGAGGGAGCCCCTCTCCACGCAGAACACCACCTTCCAGGGAAGAAAGTCCTGTTGGACGCAAGAGAAAT

Basic information

species Vitis vinifera
transcript Vv18s0001g05550.t01
intron # 6
splice site 3'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|351026523|gb|FQ428535.1|FQ428535
EST:     AGAGGCAGATATGATGATGAGCGGCGTAGTCGCAGCCGGTCATATGGAAG                         TGCCTCTCCTGCCCGGCGTAGCCCCAGTCCTCGAGGGAGCCCCTCTCCACG
genomic: AGAGGCAGATATGATGATGAGCGGCGTAGTCGCAGCCGGTCATATGGAAGgtattatatt ... tctcttgaagTGCCTCTCCTGCCCGGCGTAGCCCCAGTCCTCGAGGGAGCCCCTCTCCACG
EST: gi|110416281|gb|EC982251.1|EC982251
EST:     AGAGGCAGATATGATGATGAGCGCCGTAGTCGCAGCCGGTCATATGGAAG                         TGCCTCTCCTGCCCGGCGTAGCCCCAGT
genomic: AGAGGCAGATATGATGATGAGCGGCGTAGTCGCAGCCGGTCATATGGAAGgtattatatt ... tctcttgaagTGCCTCTCCTGCCCGGCGTAGCCCCAGT
EST: gi|351015878|gb|FQ431833.1|FQ431833
EST:     AGAGGCAGATATGATGATGAGCGGCGTAGTCGCAGCCGGTCATATGGAAG                         TGCCTCTCCTGCCCGGCGTAGCCCCAGTCCTCGAGGGAGCCCCTCTCCACG
genomic: AGAGGCAGATATGATGATGAGCGGCGTAGTCGCAGCCGGTCATATGGAAGgtattatatt ... tctcttgaagTGCCTCTCCTGCCCGGCGTAGCCCCAGTCCTCGAGGGAGCCCCTCTCCACG
EST: gi|32265216|gb|CD716805.1|CD716805
EST:     AGAGGCAGATATGATGATGAGCGGCGTAGTCGCAGCCGGTCATATGGAAG                         TGCCTCTCCTGCCCGGCGTAGCCCCAGTC
genomic: AGAGGCAGATATGATGATGAGCGGCGTAGTCGCAGCCGGTCATATGGAAGgtattatatt ... tctcttgaagTGCCTCTCCTGCCCGGCGTAGCCCCAGTC
EST: gi|351056154|gb|FQ453616.1|FQ453616
EST:     AGAGGCAGATATGATGATGAGCGGCGTAGTCGCAGCCGGTCATATGGAAG                         AGCCTCTCCTGCCCGGCGTAGCCCCAGTCCTCGAGGGAGCCCCTCTCCACG
genomic: AGAGGCAGATATGATGATGAGCGGCGTAGTCGCAGCCGGTCATATGGAAGgtattatatt ... tctcttgaagTGCCTCTCCTGCCCGGCGTAGCCCCAGTCCTCGAGGGAGCCCCTCTCCACG
EST: gi|110715132|gb|EE092829.1|EE092829
EST:     AGAGGCAGATATGATGATGAGCGGCGTAGTCGCAGCCGGTCATATGGAAG                         TGCCTCTCCTGCCCGGCGTAGCCCCAGTCCTCGAGGGAGCCCCTCTCCACG
genomic: AGAGGCAGATATGATGATGAGCGGCGTAGTCGCAGCCGGTCATATGGAAGgtattatatt ... tctcttgaagTGCCTCTCCTGCCCGGCGTAGCCCCAGTCCTCGAGGGAGCCCCTCTCCACG
EST: gi|110409912|gb|EC975586.1|EC975586
EST:     AGAGGCAGATATGATGATGAGCGCCGTAGTCGCAGCCGGTCATATGGAAG                         TGCCTCTCCTGCCCGGCGTAGCCCCAGTCCTCGAGGGAGCCCCTCTCCACG
genomic: AGAGGCAGATATGATGATGAGCGGCGTAGTCGCAGCCGGTCATATGGAAGgtattatatt ... tctcttgaagTGCCTCTCCTGCCCGGCGTAGCCCCAGTCCTCGAGGGAGCCCCTCTCCACG
EST: gi|18459646|gb|BM437924.1|BM437924
EST:     AGAGGCAGATATGATGATGAGCGGCGTAGTCGCAGCCGGTCATATGGAAG                         TGCCTCTCCTGCCCGGCGTAGCCCCAGTCCTCGAGGGAGCCCCTCTCCACG
genomic: AGAGGCAGATATGATGATGAGCGGCGTAGTCGCAGCCGGTCATATGGAAGgtattatatt ... tctcttgaagTGCCTCTCCTGCCCGGCGTAGCCCCAGTCCTCGAGGGAGCCCCTCTCCACG
EST: gi|351027210|gb|FQ444459.1|FQ444459
EST:     AGAGGCAGATATGATGATGAGCGGCGTAGTCGCAGCCGGTCATATGGAAG                         TGCCTCTCCTGCCCGGCGTAGCCCCAGTCCTCGAGGGAGCCCCTCTCCACG
genomic: AGAGGCAGATATGATGATGAGCGGCGTAGTCGCAGCCGGTCATATGGAAGgtattatatt ... tctcttgaagTGCCTCTCCTGCCCGGCGTAGCCCCAGTCCTCGAGGGAGCCCCTCTCCACG
EST: gi|110413030|gb|EC978799.1|EC978799
EST:     AGAGGCAGATATGATGATGAGCGCCGTAGTCGCAGCCGGTCATATGGAAG                         TGCCTCTCCTGCCCGGCGTAGCCCCAGTCCTCGAGGGAGCCCCTCTCCACG
genomic: AGAGGCAGATATGATGATGAGCGGCGTAGTCGCAGCCGGTCATATGGAAGgtattatatt ... tctcttgaagTGCCTCTCCTGCCCGGCGTAGCCCCAGTCCTCGAGGGAGCCCCTCTCCACG
EST: gi|351013557|gb|FQ425588.1|FQ425588
EST:     AGAGGCAGATATGATGATGAGCGGCGTAGTCACAGCCGGTCATATGGAAG                         TGCCTCTCCTGCCCGGCGTAGCCCCAGTCCTCGAGGGAGCCCCTCTCCACG
genomic: AGAGGCAGATATGATGATGAGCGGCGTAGTCGCAGCCGGTCATATGGAAGgtattatatt ... tctcttgaagTGCCTCTCCTGCCCGGCGTAGCCCCAGTCCTCGAGGGAGCCCCTCTCCACG
EST: gi|22012306|gb|BQ797340.1|BQ797340
EST:     AGAGGCAGATATGATGATGAGCGGCGTAGTCGCAGCCGGTCATATGGAAG                         TGCCTCTCCTGCCCGGCGTAGCCCCAGTCCTCGAGGGAGCCCCTCTCCACG
genomic: AGAGGCAGATATGATGATGAGCGGCGTAGTCGCAGCCGGTCATATGGAAGgtattatatt ... tctcttgaagTGCCTCTCCTGCCCGGCGTAGCCCCAGTCCTCGAGGGAGCCCCTCTCCACG
EST: gi|110407464|gb|EC973066.1|EC973066
EST:     AGAGGCAGATATGATGATGAGCGCCGTAGTCGCAGCCGGTCATATGGAAG                         TGCCTCTCCTGCCCGGCGTAGCCCCAGT
genomic: AGAGGCAGATATGATGATGAGCGGCGTAGTCGCAGCCGGTCATATGGAAGgtattatatt ... tctcttgaagTGCCTCTCCTGCCCGGCGTAGCCCCAGT
EST: gi|37184355|gb|CF603709.1|CF603709
EST:     AGAGGCAGATATGATGATGAGCGGCGTAGTCGCAGCCGGTCATATGGAAG                         TGCCTCTCCTGCCCGGCGTAGCCCCAGTCCTCGAGGGAGCCCCTCTCCACG
genomic: AGAGGCAGATATGATGATGAGCGGCGTAGTCGCAGCCGGTCATATGGAAGgtattatatt ... tctcttgaagTGCCTCTCCTGCCCGGCGTAGCCCCAGTCCTCGAGGGAGCCCCTCTCCACG
EST: gi|351026982|gb|FQ436635.1|FQ436635
EST:     GAGGGCAGATATGATGATGAGCGGCGTAGTCGCAGCCGGTCATATGGAAG                         TGCCTCTCCTGCCCGGCGTA
genomic: GAGG-CAGATATGATGATGAGCGGCGTAGTCGCAGCCGGTCATATGGAAGgtattatatt ... tctcttgaagTGCCTCTCCTGCCCGGCGTA
EST: gi|110374026|gb|EC938504.1|EC938504
EST:     AGAGGCAGATATGATGATGAGCGGCGTAGTCGCAGCCGGTCATATGGAAG                         TGCCTCTCCTGCCCGGCGTAGCCCCAGTCCTCGAGGGAGCCCCTCTCCACG
genomic: AGAGGCAGATATGATGATGAGCGGCGTAGTCGCAGCCGGTCATATGGAAGgtattatatt ... tctcttgaagTGCCTCTCCTGCCCGGCGTAGCCCCAGTCCTCGAGGGAGCCCCTCTCCACG
EST: gi|349825188|gb|FQ415735.1|FQ415735
EST:     AGAGGCAGATATGATGATGAGCGGCGTAGTCGCAGCCGGTCATATGGAAG                         TGCCTCTCCTGCCCGGCGTAGCCCCAGTCCTCGAGGGAGCCCCTCTCCACG
genomic: AGAGGCAGATATGATGATGAGCGGCGTAGTCGCAGCCGGTCATATGGAAGgtattatatt ... tctcttgaagTGCCTCTCCTGCCCGGCGTAGCCCCAGTCCTCGAGGGAGCCCCTCTCCACG
EST: gi|30321299|gb|CD004561.1|CD004561
EST:     AGAGGCAGATATGATGATGAGCGGCGTAGTCGCAGCCGGTCATATGGAAG                         TGCCTCTCCTGCCCGGCGTAGCCCCAGTCCTCGAGGGAGCCCCTCTCCACG
genomic: AGAGGCAGATATGATGATGAGCGGCGTAGTCGCAGCCGGTCATATGGAAGgtattatatt ... tctcttgaagTGCCTCTCCTGCCCGGCGTAGCCCCAGTCCTCGAGGGAGCCCCTCTCCACG
EST: gi|351015736|gb|FQ431691.1|FQ431691
EST:     AGAGGCAGATATGATGATGAGCGGCGTAGTCGCAGCCGGTCATATGGAAG                         TGCCTCTCCTGCCCGGCGTAGCCCCAGCCCTCGAGGGAGCCCCTCTCCACG
genomic: AGAGGCAGATATGATGATGAGCGGCGTAGTCGCAGCCGGTCATATGGAAGgtattatatt ... tctcttgaagTGCCTCTCCTGCCCGGCGTAGCCCCAGTCCTCGAGGGAGCCCCTCTCCACG
EST: gi|110733043|gb|EE108857.1|EE108857
EST:     AGAGGCAGATATGATGATGAGCGGCGTAGTCGCAGCCGGTCATATGGAAG                         TGCCTCTCCTGCCCGGCGTAGCCCCAGTCCTCGAGGGAGCCCCTCTCCACG
genomic: AGAGGCAGATATGATGATGAGCGGCGTAGTCGCAGCCGGTCATATGGAAGgtattatatt ... tctcttgaagTGCCTCTCCTGCCCGGCGTAGCCCCAGTCCTCGAGGGAGCCCCTCTCCACG
EST: gi|110381112|gb|EC946429.1|EC946429
EST:     AGAGGCAGATATGATGATGAGCGCCGTAGTCGCAGCCGGTCATATGGAAG                         TGCCTCTCCTGCCCGGCGTAGCCCCAGTCCTCGAGGGAGCCCCTCTCCACG
genomic: AGAGGCAGATATGATGATGAGCGGCGTAGTCGCAGCCGGTCATATGGAAGgtattatatt ... tctcttgaagTGCCTCTCCTGCCCGGCGTAGCCCCAGTCCTCGAGGGAGCCCCTCTCCACG
EST: gi|351039277|gb|FQ461144.1|FQ461144
EST:     AGAGGCAGATATGATGATGAGCGGCGTAGTCGCAGCCGGTCATATGGAAG                         TGCCTCTCCTGCCCGGCGTAGCCCCAGTCCTCGAGGGAGCCCCTCTCCACG
genomic: AGAGGCAGATATGATGATGAGCGGCGTAGTCGCAGCCGGTCATATGGAAGgtattatatt ... tctcttgaagTGCCTCTCCTGCCCGGCGTAGCCCCAGTCCTCGAGGGAGCCCCTCTCCACG
EST: gi|22012365|gb|BQ797399.1|BQ797399
EST:     AGAGGCAGATATGATGATGAGCGGCGTAGTCGCAGCCGGTCATATGGAAG                         TGCCTCTCCTGCCCGGCGTAGCCCCAGTCCTCGAGGGAGCCCCTCTCCACG
genomic: AGAGGCAGATATGATGATGAGCGGCGTAGTCGCAGCCGGTCATATGGAAGgtattatatt ... tctcttgaagTGCCTCTCCTGCCCGGCGTAGCCCCAGTCCTCGAGGGAGCCCCTCTCCACG
EST: gi|110408451|gb|EC974087.1|EC974087
EST:     AGAGGCAGATATGATGATGAGCGGCGTAGTCGCAGCCGGTCATATGGAAG                         TGCCTCTCCTGCCCGGCGTAGCCCCAGTCCTCGAGGGAGCCCCTCTCCACG
genomic: AGAGGCAGATATGATGATGAGCGGCGTAGTCGCAGCCGGTCATATGGAAGgtattatatt ... tctcttgaagTGCCTCTCCTGCCCGGCGTAGCCCCAGTCCTCGAGGGAGCCCCTCTCCACG
EST: gi|349809657|gb|FQ414548.1|FQ414548
EST:     AGAGGCAGATATGATGATGAGCGGCGTAGTCGCAGCCGGTCATATGGAAG                         TGCCTCTCCTGCCCGGCGTAGCCCCAGTCCTCGAGGGAGCACCTCCCCAC
genomic: AGAGGCAGATATGATGATGAGCGGCGTAGTCGCAGCCGGTCATATGGAAGgtattatatt ... tctcttgaagTGCCTCTCCTGCCCGGCGTAGCCCCAGTCCTCGAGGGAGCCCCTCTCCAC
EST: gi|110405318|gb|EC970858.1|EC970858
EST:     AGAGGCAGATATGATGATGAGCGGCGTAGTCGCAGCCGGTCATATGGAAG                         TGCCTCTCCTGCCCGGCGTAGCCCCAGTCCTCGAGGGAGCCCCTCTCCACG
genomic: AGAGGCAGATATGATGATGAGCGGCGTAGTCGCAGCCGGTCATATGGAAGgtattatatt ... tctcttgaagTGCCTCTCCTGCCCGGCGTAGCCCCAGTCCTCGAGGGAGCCCCTCTCCACG
EST: gi|110430375|gb|EC996928.1|EC996928
EST:     AGAGGCAGATATGATGATGAGCGGCGTAGTCGCAGCCGGTCATATGGAAG                         TGCCTCTCCTGCCCGGCGTAGCCCCAGT
genomic: AGAGGCAGATATGATGATGAGCGGCGTAGTCGCAGCCGGTCATATGGAAGgtattatatt ... tctcttgaagTGCCTCTCCTGCCCGGCGTAGCCCCAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agattccctttttgtgggaaccttctaatcgtttccttatatctgtctcttgaagTGCCTCTCCTGCCCGGCGTAGCCCCAGTCCTCGAGGGAGCCCCTCTCCACGCAGAACACCACCTTCCAGGGAAGAAAGTCCTGTTGGACGCAAGAGAAAT
                      ttctaat  putative branch site (score: 2)
                                         tctgtctctt  putative PPT
                                    ttatatct  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattatattgtgttcatctcatgctttgttcccccccctaagattccctttttgtgggaaccttctaatcgtttccttatatctgtctcttgaagTGCCTCTCCTGCCCGGCGTAGCCCCAGTCCTCGAGGGAGCCCCTCTCCACGCAGAACACCACCTTCCAGGGAAGAAAGTCCTGTTGGACGCAAGAGAAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA