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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tacaatagagttgtttttgacttaaattttgaagttttacatagagttcaggttcttaatctcgagaactaagttctatgattcttgggtgtgttttcagTTAAAATTGGTAGGCCCGGGTATCGGGTAACAAAGCAATTTGATCCAGAGACAAAGCAGAGGTCTCTTCTCTTCCAG

Basic information

species Vitis vinifera
transcript Vv08s0007g04710.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g04710.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S318_71V6.1 (Physcomitrella patens), 3'ss of exon 2
tacaatagagttgtttttgacttaaattttgaa-gttttacatagagttcaggtt---cttaatctcgagaactaagttctatgattcttgggtgtgttttcagTTAAAATTGGTAGGCCCGGGTATCGGGTAACAAAGCAATTTGATCCAGAGACAAAGCAGAGGTCTCTTCTCTTCCAG
     |   ||  |||  ||| |   | | |    ||  |   |   ||   |||   || |   ||||   | |  ||   | |       |  |    ||||||||||||||| | || || ||||| ||||| |||||||||||||  ||||| |  ||| | || || || ||||||
----ttctggtgctttaagacatttgtgtggttcattccattcaacattggtgtttgcctgagcatcgatccccagattaattcagctgattgatttccctcagTTAAAATTGGTCGCCCGGGTTATCGAGTAACTAAGCAATTTGATCAGGAGACTAGACAGCGTTCACTACTTTTCCAG
















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|161708910|gb|FC060919.1|FC060919
EST:     GCCTGCGCAGCCACAGCCCCACAAGCGCAAAGTCTCCGTACGCAAGACAG                         TTAAAATTGGTAGGCCCGGGTATCGGGTAACAAAGCAATTTGATCCAGAGA
genomic: GCCTGCGCAGCCACAGCCCCACAAGCGCAAAGTCTCCGTACGCAAGACAGgtaaggtttt ... gtgttttcagTTAAAATTGGTAGGCCCGGGTATCGGGTAACAAAGCAATTTGATCCAGAGA
EST: gi|110713132|gb|EE088784.1|EE088784
EST:     GCCTGCGCAGCCACAGCCCCACAAGCGCAAAGTCTCCGTACGCAAGACAG                         TTAAAATTGGTAGGCCCGGGTATCGGGTAACAAAGCAATTTGATCCAGAGA
genomic: GCCTGCGCAGCCACAGCCCCACAAGCGCAAAGTCTCCGTACGCAAGACAGgtaaggtttt ... gtgttttcagTTAAAATTGGTAGGCCCGGGTATCGGGTAACAAAGCAATTTGATCCAGAGA
EST: gi|30134998|gb|CB920336.1|CB920336
EST:     GCCTGCGCAGCCACAGCCCCACAAGCGCAAAGTCTCCGTACGCAAGACAG                         TTAAAATTGGTAGGCCCGGGTATCGGGTAACAAAGCAATTTGATCCAGAGA
genomic: GCCTGCGCAGCCACAGCCCCACAAGCGCAAAGTCTCCGTACGCAAGACAGgtaaggtttt ... gtgttttcagTTAAAATTGGTAGGCCCGGGTATCGGGTAACAAAGCAATTTGATCCAGAGA
EST: gi|110710951|gb|EE087592.1|EE087592
EST:     GCCTGCGCAGCCACAGCCCCACAAGCGCAAAGTCTCCGTACGCAAGACAG                         TTAAAATTGGTAGGCCCGGGTATCGGGTAACAAAGCAATTTGATCCAGAGA
genomic: GCCTGCGCAGCCACAGCCCCACAAGCGCAAAGTCTCCGTACGCAAGACAGgtaaggtttt ... gtgttttcagTTAAAATTGGTAGGCCCGGGTATCGGGTAACAAAGCAATTTGATCCAGAGA
EST: gi|161711277|gb|FC060365.1|FC060365
EST:     GCCTGCGCAGCCACAGCCCCACAAGCGCAAAGTCTCCGTACGCAAGACAG                         TTAAAATTGGTAGGCCCGGGTATCGGGTAACAAAGCAATTTGATCCAGAGA
genomic: GCCTGCGCAGCCACAGCCCCACAAGCGCAAAGTCTCCGTACGCAAGACAGgtaaggtttt ... gtgttttcagTTAAAATTGGTAGGCCCGGGTATCGGGTAACAAAGCAATTTGATCCAGAGA
EST: gi|30133297|gb|CB918636.1|CB918636
EST:     GCCTGCGCAGCCACAGCCCCACAAGCGCAAAGTCTCCGTACGCAAGACAG                         TTAAAATTGGTAGGCCCGGGTATCGGGTAACAAAGCAATTTGATCCAGAGA
genomic: GCCTGCGCAGCCACAGCCCCACAAGCGCAAAGTCTCCGTACGCAAGACAGgtaaggtttt ... gtgttttcagTTAAAATTGGTAGGCCCGGGTATCGGGTAACAAAGCAATTTGATCCAGAGA
EST: gi|110713768|gb|EE089980.1|EE089980
EST:     GCCTGCGCAGCCACAGCCCCACAAGCGCAAAGTCTCCGTACGCAAGACAG                         TTAAAATTGGTAGGCCCGGGTATCGGGTAACAAAGCAATTTGATCCAGAGA
genomic: GCCTGCGCAGCCACAGCCCCACAAGCGCAAAGTCTCCGTACGCAAGACAGgtaaggtttt ... gtgttttcagTTAAAATTGGTAGGCCCGGGTATCGGGTAACAAAGCAATTTGATCCAGAGA
EST: gi|110686098|gb|EE063396.1|EE063396
EST:     GCCTGCGCAGCCACAGCCCCACAAGCGCAAAGTCTCCGTACGCAAGACAG                         TTAAAATTGGTAGGCCCGGGTATCGGGTAACAAAGCAATTTGATCCAGAGA
genomic: GCCTGCGCAGCCACAGCCCCACAAGCGCAAAGTCTCCGTACGCAAGACAGgtaaggtttt ... gtgttttcagTTAAAATTGGTAGGCCCGGGTATCGGGTAACAAAGCAATTTGATCCAGAGA
EST: gi|156739019|gb|EV243140.1|EV243140
EST:     GCCTGCGCAGCCACAGCCCCACAAGCGCAAAGTCTCCGTACGCAAGACAG                         TTAAAATTGGTAGGCCCGGGTATCGGGTAACAAAGCAATTTGATCCAGAGA
genomic: GCCTGCGCAGCCACAGCCCCACAAGCGCAAAGTCTCCGTACGCAAGACAGgtaaggtttt ... gtgttttcagTTAAAATTGGTAGGCCCGGGTATCGGGTAACAAAGCAATTTGATCCAGAGA
EST: gi|161707166|gb|FC055570.1|FC055570
EST:     GCCTGCGCAGCCACAGCCCCACAAGCGCAAAGTCTCCGTACGCAAGACAG                         TTAAAATTGGTAGGCCCGGGTATCGGGTAACAAAGCAATTTGATCCAGAGA
genomic: GCCTGCGCAGCCACAGCCCCACAAGCGCAAAGTCTCCGTACGCAAGACAGgtaaggtttt ... gtgttttcagTTAAAATTGGTAGGCCCGGGTATCGGGTAACAAAGCAATTTGATCCAGAGA
EST: gi|71872083|gb|DT021138.1|DT021138
EST:     GCCTGCGCAGCCACAGCCCCACAAGCGCAAAGTCTCCGTACGCAAGACAG                         TTAAAATTGGTAGGCCCGGGTATCGGGTAACAAAGCAATTTGATCCAGAGA
genomic: GCCTGCGCAGCCACAGCCCCACAAGCGCAAAGTCTCCGTACGCAAGACAGgtaaggtttt ... gtgttttcagTTAAAATTGGTAGGCCCGGGTATCGGGTAACAAAGCAATTTGATCCAGAGA
EST: gi|71869160|gb|DT018215.1|DT018215
EST:     GCCTGCGCAGCCACAGCCCCACAAGCGCAAAGTCTCCGTACGCAAGACAG                         TTAAAATTGGTAGGCCCGGGTATCGGGTAACAAAGCAATTTGATCCAGAGA
genomic: GCCTGCGCAGCCACAGCCCCACAAGCGCAAAGTCTCCGTACGCAAGACAGgtaaggtttt ... gtgttttcagTTAAAATTGGTAGGCCCGGGTATCGGGTAACAAAGCAATTTGATCCAGAGA
EST: gi|110698196|gb|EE075475.1|EE075475
EST:     GCCTGCGCAGCCACAGCCCCACAAGCGCAAAGTCTCCGTACGCAAGACAG                         TTAAAATTGGTAGGCCCGGGTATCGGGTAACAAAGCAATTTGATCCAGAGA
genomic: GCCTGCGCAGCCACAGCCCCACAAGCGCAAAGTCTCCGTACGCAAGACAGgtaaggtttt ... gtgttttcagTTAAAATTGGTAGGCCCGGGTATCGGGTAACAAAGCAATTTGATCCAGAGA
EST: gi|161714376|gb|FC063217.1|FC063217
EST:     GCCTGCGCAGCCACAGCCCCACAAGCGCAAAGTCTCCGTACGCAAGACAG                         TTAAAATTGGTAGGCCCGGGTATCGGGTAACAAAGCAATTTGATCCAGAGA
genomic: GCCTGCGCAGCCACAGCCCCACAAGCGCAAAGTCTCCGTACGCAAGACAGgtaaggtttt ... gtgttttcagTTAAAATTGGTAGGCCCGGGTATCGGGTAACAAAGCAATTTGATCCAGAGA
EST: gi|71869133|gb|DT018188.1|DT018188
EST:     GCCTGCGCAGCCACAGCCCCACAAGCGCAAAGTCTCCGTACGCAAGACAG                         TTAAAATTGGTAGGCCCGGGTATCGGGTAACAAAGCAATTTGATCCAGAGA
genomic: GCCTGCGCAGCCACAGCCCCACAAGCGCAAAGTCTCCGTACGCAAGACAGgtaaggtttt ... gtgttttcagTTAAAATTGGTAGGCCCGGGTATCGGGTAACAAAGCAATTTGATCCAGAGA
EST: gi|294964013|gb|GW836888.1|GW836888
EST:     GCCTGCGCAGCCACAGCCCCACAAGCGCAAAGTCTCCGTACGCAAGACAG                         TTAAAATTGGTAGGCCTGGGTATCGGGTAACAAAGCAATTTGATCCAGAGA
genomic: GCCTGCGCAGCCACAGCCCCACAAGCGCAAAGTCTCCGTACGCAAGACAGgtaaggtttt ... gtgttttcagTTAAAATTGGTAGGCCCGGGTATCGGGTAACAAAGCAATTTGATCCAGAGA
EST: gi|27584644|gb|CB007339.1|CB007339
EST:     GCCTGCGCAGCCACAGCCCCACAAGCGCAAAGTCTCCGTACGCAAGACAG                         TTAAAATTGGTAGGCCCGGGTATCGGGTAACAAAGCAATTTGATCCAGAGA
genomic: GCCTGCGCAGCCACAGCCCCACAAGCGCAAAGTCTCCGTACGCAAGACAGgtaaggtttt ... gtgttttcagTTAAAATTGGTAGGCCCGGGTATCGGGTAACAAAGCAATTTGATCCAGAGA
EST: gi|161712620|gb|FC061943.1|FC061943
EST:     GCCTGCGCAGCCACAGCCCCACAAGCGCAAAGTCTCCGTACGCAAGACAG                         TTAAAATTGGTAGGCCCGGGTATCGGGTAACAAAGCAATTTGATCCAGAGA
genomic: GCCTGCGCAGCCACAGCCCCACAAGCGCAAAGTCTCCGTACGCAAGACAGgtaaggtttt ... gtgttttcagTTAAAATTGGTAGGCCCGGGTATCGGGTAACAAAGCAATTTGATCCAGAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttcaggttcttaatctcgagaactaagttctatgattcttgggtgtgttttcagTTAAAATTGGTAGGCCCGGGTATCGGGTAACAAAGCAATTTGATCCAGAGACAAAGCAGAGGTCTCTTCTCTTCCAG
        tcttaat  putative branch site (score: 3)
                                              tgttttc  putative PPT
       ttcttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tacaatagagttgtttttgacttaaattttgaagttttacatagagttcaggttcttaatctcgagaactaagttctatgattcttgggtgtgttttcagTTAAAATTGGTAGGCCCGGGTATCGGGTAACAAAGCAATTTGATCCAGAGACAAAGCAGAGGTCTCTTCTCTTCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- -aatagag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttcttgg