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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgctagttgtttttataggatctcagaagtttttaatctttgatccatttggcctgctttaaatttaacatgtgtaatatctgtttctatctgcctgaagTACTGCAAGTCGGACGTCTATACAGTGAACTGTGGCACGGCATATGGTCAAGCAGCAATGCTTCTATCAGTTGGAGCCAAGGGTTACCGTGGTCTACAGC

Basic information

species Vitis vinifera
transcript Vv03s0091g00700.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0091g00700.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA20G26950.1 (Glycine max), 3'ss of exon 6
------------tgctagttgtttttataggatctcagaagtttttaatctttgatccatttggcctg---ctttaaatttaacatgtgtaat--atctgttt-ctatctgcctgaagTACTGCAAGTCGGACGTCTATACAGTGAACTGTGGCACGGCATATGGTCAAGCAGCAATGCTTCTATCAGTTGGAGCCAAGGGTTACCGTGGTCTACAGC
                | |  |   |||   | || |    |     ||   | |||  ||||  ||     ||| ||  |      | ||||  |||| ||| || ||| |||||||||   |||  | || |||||||| ||||| ||||||| ||||| ||||||||||||||||||||| ||  ||||| | ||||| || |||| | ||||||
gtaagtttttatcatgaatcctgcctatcccaccttaagcctggaatatggcttatctctttgaactaatctttttaaactcttgcttttaattaatcttttttctttcttcctgaagTATGTCAAAGCAGATGTCTATACTGTGAATTGTGGCATGGCATTTGGTCAAGCAGCAATGCTTCTGTCGCTTGGAACAAAGGGCTATCGTGCTGTACAGC

upper sequence: Vv03s0091g00700.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA10G40390.1 (Glycine max), 3'ss of exon 5
tgctagttgtttttataggatctcagaagttttta----atctttgatcc---atttggcctg---ctttaaatttaacatgtgtaat--atctgttt-ctatctgcctgaagTACTGCAAGTCGGACGTCTATACAGTGAACTGTGGCACGGCATATGGTCAAGCAGCAATGCTTCTATCAGTTGGAGCCAAGGGTTACCGTGGTCTACAGC
 |  |||| || | ||      |  |    |  ||    | ||     |    || | || |    |||| || | | | | | ||||  |||| ||| || |||||||||||||   |||  | || || ||||| ||||| ||||||| ||||| ||||||||||||||||||||| ||  ||||| | |||||||| |||| | ||||||
-gtaagtttttatcatgaatcatgtgccactcctatcccacctcaagcctggaatattgcttatctctttgaactaatcttttttaattaatcttttttctttctgcctgaagTATGTCAAAGCAGATGTTTATACTGTGAATTGTGGCATGGCATTTGGTCAAGCAGCAATGCTTCTGTCGCTTGGAACAAAGGGTTATCGTGCTGTACAGC
















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|26266206|gb|CA817269.1|CA817269
EST:     GACT-TTGGGATCTGAAACTGAGGCATATGCTATTGCTGATTCCATGGCG                         TACTGCAAGTCGGACGTCTATACAGTGAACTGTGGCACGGGCATATGGTCA
genomic: GACTGTT-GGATCTGAAACTGAGGCATATGCTATTGCTGATTCCATGGCGgtaagtatta ... ctgcctgaagTACTGCAAGTCGGACGTCTATACAGTGAACTGTGGCAC-GGCATATGGTCA
EST: gi|110396404|gb|EC962089.1|EC962089
EST:     AGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCTGATTCCATGGCG                         TACTGCAAGTCGGACGTCTATACAGTGAACTGTGGCACGGCATATGGTCAA
genomic: AGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCTGATTCCATGGCGgtaagtatta ... ctgcctgaagTACTGCAAGTCGGACGTCTATACAGTGAACTGTGGCACGGCATATGGTCAA
EST: gi|27579693|gb|CB002388.1|CB002388
EST:     AGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCTGATTCCATGGCG                         TACTGCAAGTCGGACGTCTATACAGTGAACTGTGGCACGGCATATGGTCAA
genomic: AGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCTGATTCCATGGCGgtaagtatta ... ctgcctgaagTACTGCAAGTCGGACGTCTATACAGTGAACTGTGGCACGGCATATGGTCAA
EST: gi|110713462|gb|EE089402.1|EE089402
EST:     GACTGGTTGGATCTGAA-CTGANGCATATGCTATTGCTGATTCCATGGCG                         TACTGCAAGTCGGACGTCTATACAGTGAACTGTGGC
genomic: GACTG-TTGGATCTGAAACTGAGGCATATGCTATTGCTGATTCCATGGCGgtaagtatta ... ctgcctgaagTACTGCAAGTCGGACGTCTATACAGTGAACTGTGGC
EST: gi|26267312|gb|CA818375.1|CA818375
EST:     AGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCTGATTCCATGGCG                         TACTGCAAGTCGGACGTCTATACAGTGAACTGTGGCACGGCATATGGTCAA
genomic: AGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCTGATTCCATGGCGgtaagtatta ... ctgcctgaagTACTGCAAGTCGGACGTCTATACAGTGAACTGTGGCACGGCATATGGTCAA
EST: gi|30321875|gb|CD005137.1|CD005137
EST:     AGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCTGATTCCATGGCG                         TACTGCAAGTCGGACGTCTATACAGTGAACTGTGGCACGGCATATGGTCAA
genomic: AGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCTGATTCCATGGCGgtaagtatta ... ctgcctgaagTACTGCAAGTCGGACGTCTATACAGTGAACTGTGGCACGGCATATGGTCAA
EST: gi|110686908|gb|EE063865.1|EE063865
EST:     AGACTGTTGGATCTGAAACTGANGCATATGCTATTGCTGATTCCATGGCG                         TACTGCAAGTCAGACGT
genomic: AGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCTGATTCCATGGCGgtaagtatta ... ctgcctgaagTACTGCAAGTCGGACGT
EST: gi|28968092|gb|CB347125.1|CB347125
EST:     AGACTGTTGGATTTGAAACTGAGGCATATGCTATTGCTGATTCCATGGCG                         TTCTGCAAGTCGGACGTTTATACAGTGAACTGTGGCACGGCATATGGTCAA
genomic: AGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCTGATTCCATGGCGgtaagtatta ... ctgcctgaagTACTGCAAGTCGGACGTCTATACAGTGAACTGTGGCACGGCATATGGTCAA
EST: gi|110391380|gb|EC956351.1|EC956351
EST:     AGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCTGATTCCATGGCG                         TACTGCAAGTCGGACGTCTATACAGTGAACTGTGGCACGGCATATGGTCAA
genomic: AGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCTGATTCCATGGCGgtaagtatta ... ctgcctgaagTACTGCAAGTCGGACGTCTATACAGTGAACTGTGGCACGGCATATGGTCAA
EST: gi|26264295|gb|CA815358.1|CA815358
EST:     AGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCTGATTCCATGGCG                         TACTGCAAGTCGGACGTCTATACAGTGAACTGTGGCACGGCATATGGTCAA
genomic: AGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCTGATTCCATGGCGgtaagtatta ... ctgcctgaagTACTGCAAGTCGGACGTCTATACAGTGAACTGTGGCACGGCATATGGTCAA
EST: gi|30321951|gb|CD005213.1|CD005213
EST:     AGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCTGATTCCATGGCG                         TACTGCAAGTCGGACGTCTATACAGTGAACTGTGGCACGGCATATGGTCAA
genomic: AGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCTGATTCCATGGCGgtaagtatta ... ctgcctgaagTACTGCAAGTCGGACGTCTATACAGTGAACTGTGGCACGGCATATGGTCAA
EST: gi|351025662|gb|FQ426676.1|FQ426676
EST:     AGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCTGATTCCATGGCG                         TACTGCAAGTCGGACGTCTATACAGTGAACTGTGGCACGGCATATGGTCAA
genomic: AGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCTGATTCCATGGCGgtaagtatta ... ctgcctgaagTACTGCAAGTCGGACGTCTATACAGTGAACTGTGGCACGGCATATGGTCAA
EST: gi|351030338|gb|FQ432276.1|FQ432276
EST:     AGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCTGATTCCATGGCG                         TACTGCAAGTCGGACGTCTATACAGTGAACTGTGGCACGGCATATGGTCAA
genomic: AGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCTGATTCCATGGCGgtaagtatta ... ctgcctgaagTACTGCAAGTCGGACGTCTATACAGTGAACTGTGGCACGGCATATGGTCAA
EST: gi|110361742|gb|EC925238.1|EC925238
EST:     AGACTGTTGGATCTGAAATTGAGGCATATGCTATTGCTGATTCCATGGCG                         TACTGCAAGTCGGACGTCTATACAGTGAACTGTGGCACGGCATATGGTCAA
genomic: AGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCTGATTCCATGGCGgtaagtatta ... ctgcctgaagTACTGCAAGTCGGACGTCTATACAGTGAACTGTGGCACGGCATATGGTCAA
EST: gi|22007314|gb|BQ792348.1|BQ792348
EST:     AGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCTGATTCCATGGCG                         TACTGCAAGTCGGACGTCTATACAGTGAACTGTGGCACGGCATATGGTCAA
genomic: AGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCTGATTCCATGGCGgtaagtatta ... ctgcctgaagTACTGCAAGTCGGACGTCTATACAGTGAACTGTGGCACGGCATATGGTCAA
EST: gi|27578583|gb|CB001278.1|CB001278
EST:     AGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCTGATTCCATGGCG                         TACTGCAAGTCGGACGTCTATACAGTGAACTGTGGCACGGCATATGGTCAA
genomic: AGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCTGATTCCATGGCGgtaagtatta ... ctgcctgaagTACTGCAAGTCGGACGTCTATACAGTGAACTGTGGCACGGCATATGGTCAA
EST: gi|26257779|gb|CA808842.1|CA808842
EST:     AGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCTGATTCCATGGCG                         TACTGCAAGTCGGACGTCTATACAGTGAACTGTGGCACGGCATATGGTCAA
genomic: AGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCTGATTCCATGGCGgtaagtatta ... ctgcctgaagTACTGCAAGTCGGACGTCTATACAGTGAACTGTGGCACGGCATATGGTCAA
EST: gi|110685602|gb|EE062466.1|EE062466
EST:     AGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCTGATTCCATGGCG                         TACTGCAAGTCGGACGTCTATACAGTGAACTGTGGCACGGCATATGGTCAA
genomic: AGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCTGATTCCATGGCGgtaagtatta ... ctgcctgaagTACTGCAAGTCGGACGTCTATACAGTGAACTGTGGCACGGCATATGGTCAA
EST: gi|26264973|gb|CA816036.1|CA816036
EST:     TGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCTGATTCCATGGCG                         TACTGCAAGTCGGACGTCTATACAGTGAACTGTGGCACGGCATATGGTCAA
genomic: AGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCTGATTCCATGGCGgtaagtatta ... ctgcctgaagTACTGCAAGTCGGACGTCTATACAGTGAACTGTGGCACGGCATATGGTCAA
EST: gi|26258048|gb|CA809111.1|CA809111
EST:     AGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCTGATTCCATGGCG                         TACTGCAAGTCGGACGTCTATACAGTGAACTGTGGCACGGCATATGGTCAA
genomic: AGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCTGATTCCATGGCGgtaagtatta ... ctgcctgaagTACTGCAAGTCGGACGTCTATACAGTGAACTGTGGCACGGCATATGGTCAA
EST: gi|26267206|gb|CA818269.1|CA818269
EST:     TGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCTGATTCCATGGCG                         TACTGCAAGTCGCACGTCTATACAGTGAACTGTGGCACGGCATATG
genomic: AGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCTGATTCCATGGCGgtaagtatta ... ctgcctgaagTACTGCAAGTCGGACGTCTATACAGTGAACTGTGGCACGGCATATG
EST: gi|110388571|gb|EC953335.1|EC953335
EST:     AGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCTGATTCCATGGCG                         TACTGCAAGTCGGACGTCTATACAGTGAACTGTGGCACGGCATATGGTCAA
genomic: AGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCTGATTCCATGGCGgtaagtatta ... ctgcctgaagTACTGCAAGTCGGACGTCTATACAGTGAACTGTGGCACGGCATATGGTCAA
EST: gi|110395310|gb|EC960968.1|EC960968
EST:     AGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCTGATTCCATGGCG                         TACTGCAAGTCGGACGTCTATACAGTGAACTGTGGCACGGCATATGGTCAA
genomic: AGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCTGATTCCATGGCGgtaagtatta ... ctgcctgaagTACTGCAAGTCGGACGTCTATACAGTGAACTGTGGCACGGCATATGGTCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttggcctgctttaaatttaacatgtgtaatatctgtttctatctgcctgaagTACTGCAAGTCGGACGTCTATACAGTGAACTGTGGCACGGCATATGGTCAAGCAGCAATGCTTCTATCAGTTGGAGCCAAGGGTTACCGTGGTCTACAGC
                 atttaac  putative branch site (score: 3)
                                      tttctatct  putative PPT
            tttaaatttaacatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgctagttgtttttataggatctcagaagtttttaatctttgatccatttggcctgctttaaatttaacatgtgtaatatctgtttctatctgcctgaagTACTGCAAGTCGGACGTCTATACAGTGAACTGTGGCACGGCATATGGTCAAGCAGCAATGCTTCTATCAGTTGGAGCCAAGGGTTACCGTGGTCTACAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - ccatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - cctgctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgtgt