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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cacctttgtttactgaaacaggatatcagagagtactaatgaatggcttgaaagcagaaaaatgatttccatcctaataattttccacttttcttgtcagAGCTTGGGTGCTGAGAAAGACAGTCTCGACATAGTTCAGCATGAATGGGCCCTACCCAAATTCGAGCAGCGAGCTGAAGCAGTGTTGAGAAAACTCGTCA

Basic information

species Vitis vinifera
transcript Vv00s0187g00170.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0187g00170.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA08G44410.1 (Glycine max), 3'ss of exon 8
cacctttgtttactgaaacaggatatcagagagtactaatgaatggcttg--aaagcag----aaaaatgatttccatcctaataattttccacttttcttgtcagAGCTTGGGTGCTGAGAAAGACAGTCTCGACATAGTTCAGCATGAATGGGCCCTACCCAAATTCGAGCAGCGAGCTGAAGCAGTGTTGAGAAAACTCGTCA
      |    ||  |||   ||    |  || | ||| || ||    |   |||| |     |||  | | |   |         | ||  | | |  || |||| |  |  ||||||||||||||| ||| ||||||   |||||||| |||||| |||| || || |||||||| |||||||| |||||||| ||| ||||||
------taaagacataaatttgactcaaatgaatcctagtgtattctctaacaaagtaatctcaaatctcaatcttacttctgctgtcttttaatatatttttcagGGTCTAAGTGCTGAGAAAGACAATCTTGACATAACCCAGCATGACTGGGCCTTACCGAATTTTGAGCAGCGGGCTGAAGCTGTGTTGAGGAAAGTCGTCA

upper sequence: Vv00s0187g00170.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA18G08370.1 (Glycine max), 3'ss of exon 5
cacctttgtttactgaaacaggatatcagagagtactaatgaatggc--ttgaaagcagaa--aaatgatttccatcctaataattttccacttttcttgtcagAGCTTGGGTGCTGAGAAAGACAGTCTCGACATAGTTCAGCATGAATGGGCCCTACCCAAATTCGAGCAGCGAGCTGAAGCAGTGTTGAGAAAACTCGTCA
  |     || | |     | | | | |  || | | |||||||     | |      |||  || | | | |    || |   | |  |  | ||||| |||| |  || ||||||||||||||| ||| ||||||   |||||||| |||||| |||| || || |||||||| |||||||| |||||||| ||| | | | 
-ccagaaattgagtaggtaaaggtgtaactgact-caaatgaatcatagtcgggtcttgaacaaagtaaatcctgatcttactttctgtcg-tcttcttttcaGGGTCTGAGTGCTGAGAAAGACAATCTTGACATAACCCAGCATGACTGGGCCTTACCAAATTTTGAGCAGCGTGCTGAAGCTGTGTTGAGGAAAGTTGCC-
















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|30136299|gb|CB921637.1|CB921637
EST:     ATACCCAGCGTATGATGCAAATGAGTGGGTTCGGCGTTGATCCTACAAAG                         AGCTTGGGTGCTG
genomic: ATACCCAGCGTATGATGCAAATGAGTGGGTTCGGCGTTGATCCTACAAAGgtatattatt ... ttcttgtcagAGCTTGGGTGCTG
EST: gi|294966792|gb|GW837811.1|GW837811
EST:     ATACCCAGCGTATGATGCAAATGGGTGGGTTCGGCGTTGATCCTACAAAG                         AGCTTGGGTGCT
genomic: ATACCCAGCGTATGATGCAAATGAGTGGGTTCGGCGTTGATCCTACAAAGgtatattatt ... ttcttgtcagAGCTTGGGTGCT
EST: gi|32250235|gb|CD716054.1|CD716054
EST:     ATACCCAGCGTATGATGCAAATGAGTGGGTTCGGCGTTGATCCTACAAAG                         AGCTTGGGTGCTGAGAAAGACAGTCTCGACATAGTTCAGCATGAATG
genomic: ATACCCAGCGTATGATGCAAATGAGTGGGTTCGGCGTTGATCCTACAAAGgtatattatt ... ttcttgtcagAGCTTGGGTGCTGAGAAAGACAGTCTCGACATAGTTCAGCATGAATG
EST: gi|110407602|gb|EC973208.1|EC973208
EST:     ATACCCAGCGTATGATGCAAATGAGTGGGTTCGGCGTTGATCCTACAAAG                         AGCTTGGGTGCTGAGAAAGACAGTCTCGACATAGTTCAGCATGAATGGGCC
genomic: ATACCCAGCGTATGATGCAAATGAGTGGGTTCGGCGTTGATCCTACAAAGgtatattatt ... ttcttgtcagAGCTTGGGTGCTGAGAAAGACAGTCTCGACATAGTTCAGCATGAATGGGCC
EST: gi|110428045|gb|EC994506.1|EC994506
EST:     ATACCCAGCGTATGATGCAAATGAGTGGGTTCGGCGTTGATCCTACAAAG                         AGCTTGGGTGCTGAGAAAGACAGTCTCGACATAGTTCAGCATGAATGGGCC
genomic: ATACCCAGCGTATGATGCAAATGAGTGGGTTCGGCGTTGATCCTACAAAGgtatattatt ... ttcttgtcagAGCTTGGGTGCTGAGAAAGACAGTCTCGACATAGTTCAGCATGAATGGGCC
EST: gi|32456961|gb|CD798135.1|CD798135
EST:     ATACCCAGCGTATGATGCAAATGAGTGGGTTCGGCGTTGATCCTACAAAG                         AGCTTGGGTGCTGAGAAAGACAGTCTCGACATAGTTCAGCATGAATGGGCC
genomic: ATACCCAGCGTATGATGCAAATGAGTGGGTTCGGCGTTGATCCTACAAAGgtatattatt ... ttcttgtcagAGCTTGGGTGCTGAGAAAGACAGTCTCGACATAGTTCAGCATGAATGGGCC
EST: gi|110417816|gb|EC983901.1|EC983901
EST:     ATACCCAGCGTATGATGCAAATGAGTGGGTTCGGCGTTGATCCTACAAAG                         AGCTTGGGTGCTGAGAAAGACAGTCTCGACATAGTTCAGCATGAATGGGCC
genomic: ATACCCAGCGTATGATGCAAATGAGTGGGTTCGGCGTTGATCCTACAAAGgtatattatt ... ttcttgtcagAGCTTGGGTGCTGAGAAAGACAGTCTCGACATAGTTCAGCATGAATGGGCC
EST: gi|110712100|gb|EE089333.1|EE089333
EST:     ATACCCAGCGTATGATGCAAATGAGTGGGTTCGGCGTTGATCCTACAAAG                         AGCTTGGGTGCTGAGAAAGACAGTCTCGACATAGTTCAGCATGAATGGGGC
genomic: ATACCCAGCGTATGATGCAAATGAGTGGGTTCGGCGTTGATCCTACAAAGgtatattatt ... ttcttgtcagAGCTTGGGTGCTGAGAAAGACAGTCTCGACATAGTTCAGCATGAATGGG-C
EST: gi|110423024|gb|EC989359.1|EC989359
EST:     GCAAATGAGTGGGTTCGGCGTTGATCCTACAAAG                         AGCTTGGGTGCTGAGAAAGACAGTCTCGACATAGTTCAGCATGAATGGGCC
genomic: GCAAATGAGTGGGTTCGGCGTTGATCCTACAAAGgtatattatt ... ttcttgtcagAGCTTGGGTGCTGAGAAAGACAGTCTCGACATAGTTCAGCATGAATGGGCC
EST: gi|32457083|gb|CD798257.1|CD798257
EST:     ATACCCAGCGTATGATGCAAATGAGTGGGTTCGGCGTTGATCCTACAAAG                         AGCTTGGGTGCTGAGAAAGACAGTCTCGACATAGTTCAGCATGAATGGGCC
genomic: ATACCCAGCGTATGATGCAAATGAGTGGGTTCGGCGTTGATCCTACAAAGgtatattatt ... ttcttgtcagAGCTTGGGTGCTGAGAAAGACAGTCTCGACATAGTTCAGCATGAATGGGCC
EST: gi|110428615|gb|EC995092.1|EC995092
EST:     ATACCCAGCGTATGATGCAAATGAGTGGGTTCGGCGTTGATCCTACAAAG                         AGCTTGGGTGCTGAGAAAGACAGTCTCGACATAGTTCAGCATGAATGGGCC
genomic: ATACCCAGCGTATGATGCAAATGAGTGGGTTCGGCGTTGATCCTACAAAGgtatattatt ... ttcttgtcagAGCTTGGGTGCTGAGAAAGACAGTCTCGACATAGTTCAGCATGAATGGGCC
EST: gi|27582229|gb|CB004924.1|CB004924
EST:     ATACCCAGCGTATGATGCAAATGAGTGGGTTCGGCGTTGATCCTACAAAG                         AGCTTGGGTGCTGAGAAAGACAGTCTCGACATAGTTCAGCATGAATGGGCC
genomic: ATACCCAGCGTATGATGCAAATGAGTGGGTTCGGCGTTGATCCTACAAAGgtatattatt ... ttcttgtcagAGCTTGGGTGCTGAGAAAGACAGTCTCGACATAGTTCAGCATGAATGGGCC
EST: gi|352764273|gb|FQ471253.1|FQ471253
EST:     ATACCCAGCGTATGATGCAAATGAGTGGGTTCGGCGTTGATCCTACAAAG                         AGCTTGGGTGCTGAGAAAGACAGTCTCGACATAGTTCAGCATGAATGGGCC
genomic: ATACCCAGCGTATGATGCAAATGAGTGGGTTCGGCGTTGATCCTACAAAGgtatattatt ... ttcttgtcagAGCTTGGGTGCTGAGAAAGACAGTCTCGACATAGTTCAGCATGAATGGGCC
EST: gi|110429192|gb|EC995681.1|EC995681
EST:     ATACCCAGCGTATGATGCAAATGAGTGGGTTCGGCGTTGATCCTACAAAG                         AGCTTGGGTGCTGAGAAAGACAGTCTCGACATAGTTCAGCATGAATGGGCC
genomic: ATACCCAGCGTATGATGCAAATGAGTGGGTTCGGCGTTGATCCTACAAAGgtatattatt ... ttcttgtcagAGCTTGGGTGCTGAGAAAGACAGTCTCGACATAGTTCAGCATGAATGGGCC
EST: gi|27580483|gb|CB003178.1|CB003178
EST:     ATACCCAGCGTATGATGCAAATGAGTGGGTTCGGCGTTGATCCTACAAAG                         AGCTTGGGTGCTGAGAAAGACAGTCTCGACATAGTTCAGCATGAATGGGCC
genomic: ATACCCAGCGTATGATGCAAATGAGTGGGTTCGGCGTTGATCCTACAAAGgtatattatt ... ttcttgtcagAGCTTGGGTGCTGAGAAAGACAGTCTCGACATAGTTCAGCATGAATGGGCC
EST: gi|110411782|gb|EC977505.1|EC977505
EST:     GTTGATCCTACAAAG                         AGCTTGGGTGCTGAGAAAGACAGTCTCGACATAGTTCAGCATGAATGGGCC
genomic: GTTGATCCTACAAAGgtatattatt ... ttcttgtcagAGCTTGGGTGCTGAGAAAGACAGTCTCGACATAGTTCAGCATGAATGGGCC
EST: gi|110728851|gb|EE104791.1|EE104791
EST:     ATACCCAACGTATGATGCAAATGAGTGGGTTCGGCGTTGATCCTACAAAG                         AGCTTGGGTGCTGAAAAAGA-AGTCTCGACATATTTAA-CATGAATGGGCC
genomic: ATACCCAGCGTATGATGCAAATGAGTGGGTTCGGCGTTGATCCTACAAAGgtatattatt ... ttcttgtcagAGCTTGGGTGCTGAGAAAGACAGTCTCGACATAGTTCAGCATGAATGGGCC
EST: gi|30125541|gb|CB910880.1|CB910880
EST:     ATACCCAGCGTATGATGCAAATGAGTGGGTTCGGCGTTGATCCTACAAAG                         AGCTTGGGTGCTGAGAAAGACAGTCTCGACATAGTTCAGCATGAATGGGCC
genomic: ATACCCAGCGTATGATGCAAATGAGTGGGTTCGGCGTTGATCCTACAAAGgtatattatt ... ttcttgtcagAGCTTGGGTGCTGAGAAAGACAGTCTCGACATAGTTCAGCATGAATGGGCC
EST: gi|30136533|gb|CB921871.1|CB921871
EST:     ATACCCAGCGTATGATGCAAATGAGTGGGTTCGGCGTTGATCCTACAAAG                         AGCTTGGGTGCTGAGAAAGACAGTCTCGACATAGTTCAGCATGAATGGGCC
genomic: ATACCCAGCGTATGATGCAAATGAGTGGGTTCGGCGTTGATCCTACAAAGgtatattatt ... ttcttgtcagAGCTTGGGTGCTGAGAAAGACAGTCTCGACATAGTTCAGCATGAATGGGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttgaaagcagaaaaatgatttccatcctaataattttccacttttcttgtcagAGCTTGGGTGCTGAGAAAGACAGTCTCGACATAGTTCAGCATGAATGGGCCCTACCCAAATTCGAGCAGCGAGCTGAAGCAGTGTTGAGAAAACTCGTCA
                          tcctaat  putative branch site (score: 2)
                                   ttttccacttttcttg  putative PPT
                         atcctaataatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cacctttgtttactgaaacaggatatcagagagtactaatgaatggcttgaaagcagaaaaatgatttccatcctaataattttccacttttcttgtcagAGCTTGGGTGCTGAGAAAGACAGTCTCGACATAGTTCAGCATGAATGGGCCCTACCCAAATTCGAGCAGCGAGCTGAAGCAGTGTTGAGAAAACTCGTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC