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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtttattgtcaaagtatatataactagacactgaatacagcattctaattgggattttgaaatcaaatctcctataagtaaattctttatttgctaaaggtgcaatttctcttcttcttagatctcttactgtttttctttgtcatctactctctctcccccctttcctcctctccatttcagGGCCGATTTGCAGAAGCATTACTACGAGAGCTTGCAGGAGTGACAATACCATCTGAAAGAATCTATGGTCTGGGAACAGG

Basic information

species Vitis vinifera
transcript Vv15s0046g02330.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0046g02330.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA18G46830.1 (Glycine max), 3'ss of exon 5
-gtgtgtttattgtcaaagta-tatataactagacactgaatac--agcattctaattgggattttgaaatcaaatctcctataagtaaattctttatttgctaaaggtgcaatttctcttcttcttagatctcttactgtttttctttgtcatctactctct-----ctcccccctttcctcctctccatttcagGGCCGATTTGCAGAAGCATTACTACGAGAGCTTGCAGGAGTGACAATACCATCTGAAAGAATCTATGGTCTGGGAACAGG
 ||    || || ||   |   || ||   |  ||  | | ||   ||||   |||| |||      ||   ||        |  |  | ||  | || | |   |     |  || |     | |   ||| |||  ||| ||| |||||  |||||  | |     | |  |||  |  |       ||||||| |||| ||||| || || ||||| ||||||||||| |||||||| |||||| |||||||||| ||||| || ||||| | 
ggtaacctttttctctttgccctagattgttttactttcattattaagcaaaataataggggac--aaagataa--------tgggccattttctcatctccatgaaaaaaacgttttaccaatttctcatccctttttgtctttttttgttttctacaattttagaacccaacccccttatttctgttatttcaGAGCCGCTTTGCTGATGCTTTACTCCGAGAGCTTGCCGGAGTGACCATACCACCTGAAAGAATATATGGCCTTGGAACTG-
















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|351014417|gb|FQ437419.1|FQ437419
EST:     ATGCTTTGAAGTTTGCAAGCTCAAAGGTCTACATCGTTACCACAAAACAG                         GGCCGATTTGCAGAAGCATTACTACGAGAGCTTGCAGGAGTGACAATACCA
genomic: ATGCTTTGAAGTTTGCAAGCTCAAAGGTCTACATCGTTACCACAAAACAGgtgtgtttat ... tccatttcagGGCCGATTTGCAGAAGCATTACTACGAGAGCTTGCAGGAGTGACAATACCA
EST: gi|349812531|gb|FQ407150.1|FQ407150
EST:     ATGCTTTGAAGTTTGCAAGCTCAAAGGTCTACATCGTTACCACAAAACAG                         GGCCGATTTGCAGAAGCATTACTACGAGAGCTTGCAGGAGTGACAATACCA
genomic: ATGCTTTGAAGTTTGCAAGCTCAAAGGTCTACATCGTTACCACAAAACAGgtgtgtttat ... tccatttcagGGCCGATTTGCAGAAGCATTACTACGAGAGCTTGCAGGAGTGACAATACCA
EST: gi|32268405|gb|CD717564.1|CD717564
EST:     ATGCTTTGAAGTTTGCAAGCTCAAAGGTCTACATCGTTACCACAAAACAG                         GGCCGATTTGCAGAAGCATTACTACGAGAGCTTGCAGGAGTGACAATACCA
genomic: ATGCTTTGAAGTTTGCAAGCTCAAAGGTCTACATCGTTACCACAAAACAGgtgtgtttat ... tccatttcagGGCCGATTTGCAGAAGCATTACTACGAGAGCTTGCAGGAGTGACAATACCA
EST: gi|71856100|gb|DT005155.1|DT005155
EST:     ATGCTTTGAAGTTTGCAAGCTCAAAGGTCTACATCGTTACCACAAAACAG                         GGCCGATTTGCAGAAGCATTACTACGAGAGC
genomic: ATGCTTTGAAGTTTGCAAGCTCAAAGGTCTACATCGTTACCACAAAACAGgtgtgtttat ... tccatttcagGGCCGATTTGCAGAAGCATTACTACGAGAGC
EST: gi|110425155|gb|EC991534.1|EC991534
EST:     ATGCTTTGAAGTTTGCAAGCTCAAAGGTCTACATCGTTACCACAAAACAG                         GGCCGATTTGCAGAAGCATTACTACGAGAGCTTGCAGGAGTGACAATACCA
genomic: ATGCTTTGAAGTTTGCAAGCTCAAAGGTCTACATCGTTACCACAAAACAGgtgtgtttat ... tccatttcagGGCCGATTTGCAGAAGCATTACTACGAGAGCTTGCAGGAGTGACAATACCA
EST: gi|26257481|gb|CA808544.1|CA808544
EST:     ATGCTTTGAAGTTTGCAAGCTCAAAGGTCTACATCGTTACCACAAAACAG                         GGCCGATTTGCAGAAGCATTACTACGAGAGCTTGCAGGAGTGACAATACCA
genomic: ATGCTTTGAAGTTTGCAAGCTCAAAGGTCTACATCGTTACCACAAAACAGgtgtgtttat ... tccatttcagGGCCGATTTGCAGAAGCATTACTACGAGAGCTTGCAGGAGTGACAATACCA
EST: gi|26258266|gb|CA809329.1|CA809329
EST:     ATGCTTTGAAGTTTGCAAGCTCAAAGGTCTACATCGTTACCACAAAACAG                         GGCCGATTTGCAGAAGCATTACTACGAGAGCTTGCAGGAGTGACAATACCA
genomic: ATGCTTTGAAGTTTGCAAGCTCAAAGGTCTACATCGTTACCACAAAACAGgtgtgtttat ... tccatttcagGGCCGATTTGCAGAAGCATTACTACGAGAGCTTGCAGGAGTGACAATACCA
EST: gi|30328156|gb|CD011418.1|CD011418
EST:     ATGCTTTGAAGTTTGCAAGCTCAAAGGTCTACATCGTTACCACAAAACAG                         GGCCGATTTGCAGAAGCATTACTACGAGAGCTTGCAGGAGTGACAATACCA
genomic: ATGCTTTGAAGTTTGCAAGCTCAAAGGTCTACATCGTTACCACAAAACAGgtgtgtttat ... tccatttcagGGCCGATTTGCAGAAGCATTACTACGAGAGCTTGCAGGAGTGACAATACCA
EST: gi|32247310|gb|CD713129.1|CD713129
EST:     ATGCTTTGAAGTTTGCAAGCTCAAAGGTCTACATCGTTACCACAAAACAG                         GGCCGATTTGCAGAAGCATTACTACGAGAGCTTGCAGGAGTGACAATACCA
genomic: ATGCTTTGAAGTTTGCAAGCTCAAAGGTCTACATCGTTACCACAAAACAGgtgtgtttat ... tccatttcagGGCCGATTTGCAGAAGCATTACTACGAGAGCTTGCAGGAGTGACAATACCA
EST: gi|32248082|gb|CD713901.1|CD713901
EST:     ATGCTTTGAAGTTTGCAAGCTCAAAGGTCTACATCGTTACCACAAAACAG                         GGCCGATTTGCAGAAGCATTACTACGAGAGCTTGCAGGAGTGACAATACCA
genomic: ATGCTTTGAAGTTTGCAAGCTCAAAGGTCTACATCGTTACCACAAAACAGgtgtgtttat ... tccatttcagGGCCGATTTGCAGAAGCATTACTACGAGAGCTTGCAGGAGTGACAATACCA
EST: gi|26265908|gb|CA816971.1|CA816971
EST:     ATGCTTTGAAGTTTGCAAGCTCAAAGGTCTACATCGTTACCACAAAACAG                         GGCCGATTTGCAGAAGCATTACTACGAGAGCTTGCAGGAGTGACAATACCA
genomic: ATGCTTTGAAGTTTGCAAGCTCAAAGGTCTACATCGTTACCACAAAACAGgtgtgtttat ... tccatttcagGGCCGATTTGCAGAAGCATTACTACGAGAGCTTGCAGGAGTGACAATACCA
EST: gi|26263928|gb|CA814991.1|CA814991
EST:     ATGCTTTGAAGTTTGCAAGCTCAAAGGTCTACATCGTTACCACAAAACAG                         GGCCGATTTGCAGAAGCATTACTACGAGAGCTTGCAGGAGTGACAATACCA
genomic: ATGCTTTGAAGTTTGCAAGCTCAAAGGTCTACATCGTTACCACAAAACAGgtgtgtttat ... tccatttcagGGCCGATTTGCAGAAGCATTACTACGAGAGCTTGCAGGAGTGACAATACCA
EST: gi|110387546|gb|EC952223.1|EC952223
EST:     ATGCTTTGAAGTTTGCAAGCTCAAAGGTCTACATCGTTACCACAAAACAG                         GGCCGATTTGCAGAAGCATTACTACGAGAGCTTGCAGGAGTGACAATACCA
genomic: ATGCTTTGAAGTTTGCAAGCTCAAAGGTCTACATCGTTACCACAAAACAGgtgtgtttat ... tccatttcagGGCCGATTTGCAGAAGCATTACTACGAGAGCTTGCAGGAGTGACAATACCA
EST: gi|32271023|gb|CD720182.1|CD720182
EST:     ATGCTTTGAAGTTTGCAAGCTCAAAGGTCTACATCGTTACCACAAAACAG                         GGCCGATTTGCAGAAGCATTACTACGAGAGCTTGCAGGAGTGACAATACCA
genomic: ATGCTTTGAAGTTTGCAAGCTCAAAGGTCTACATCGTTACCACAAAACAGgtgtgtttat ... tccatttcagGGCCGATTTGCAGAAGCATTACTACGAGAGCTTGCAGGAGTGACAATACCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actgtttttctttgtcatctactctctctcccccctttcctcctctccatttcagGGCCGATTTGCAGAAGCATTACTACGAGAGCTTGCAGGAGTGACAATACCATCTGAAAGAATCTATGGTCTGGGAACAGG
 ctcttac  putative branch site (score: 3)
       ttctttgtcatctact  putative PPT
     ttttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgtttattgtcaaagtatatataactagacactgaatacagcattctaattgggattttgaaatcaaatctcctataagtaaattctttatttgctaaaggtgcaatttctcttcttcttagatctcttactgtttttctttgtcatctactctctctcccccctttcctcctctccatttcagGGCCGATTTGCAGAAGCATTACTACGAGAGCTTGCAGGAGTGACAATACCATCTGAAAGAATCTATGGTCTGGGAACAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA