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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacagcccctaccctacatcacttcacttggtagctgattgtcatcgagtctaagcatttttggtatgtaatttgcagTGGATATACGGGTTTTTAGTATTCTTCTACCCAGGAGGCACGCTTGGTCTGAGAAGTGCGTCGTTGCCATGGCACGTACTGTTTGGGCTACTGGTGTATG

Basic information

species Vitis vinifera
transcript Vv16s0050g00090.t01
intron # 3
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|351019197|gb|FQ429357.1|FQ429357
EST:     GCCTCCACTCCTGGCTTGGAATCGTCCTTATCTCACTCTATGGCATTCAG                         TGGATATACGGGTTTTTAGTATTCTTCTACCCAGGAGGCACGCTTGGTCTG
genomic: GCCTCCACTCCTGGCTTGGAATCGTCCTTATCTCACTCTATGGCATTCAGgtacagcccc ... taatttgcagTGGATATACGGGTTTTTAGTATTCTTCTACCCAGGAGGCACGCTTGGTCTG
EST: gi|349825799|gb|FQ423094.1|FQ423094
EST:     GCCTCCACTCCTGGCTTGGAATCGTCCTTATCTCACTCTATGGCATTCAG                         TGGATATACGGGTTTTTAGTATTCTTCTACCCAGGAGGCACGCTTGGTCTG
genomic: GCCTCCACTCCTGGCTTGGAATCGTCCTTATCTCACTCTATGGCATTCAGgtacagcccc ... taatttgcagTGGATATACGGGTTTTTAGTATTCTTCTACCCAGGAGGCACGCTTGGTCTG
EST: gi|351022337|gb|FQ445112.1|FQ445112
EST:     GCCTCCACTCCTGGCTTGGAATCGTCCTTATCTCACTCTATGGCATTCAG                         TGGATATACGGGTTTTTAGTATTCTTCTACCCAGGGGGCACGCTTGGTCTG
genomic: GCCTCCACTCCTGGCTTGGAATCGTCCTTATCTCACTCTATGGCATTCAGgtacagcccc ... taatttgcagTGGATATACGGGTTTTTAGTATTCTTCTACCCAGGAGGCACGCTTGGTCTG
EST: gi|351012490|gb|FQ427091.1|FQ427091
EST:     GCCTCCACTCCTGGCTTGGAATCGTCCTTATCTCACTCCATGGCATTCAG                         TGGATATACGGGTTTTTAGTATTCTTCTACCCAGGAGGCACGCTTGGTCTG
genomic: GCCTCCACTCCTGGCTTGGAATCGTCCTTATCTCACTCTATGGCATTCAGgtacagcccc ... taatttgcagTGGATATACGGGTTTTTAGTATTCTTCTACCCAGGAGGCACGCTTGGTCTG
EST: gi|110688305|gb|EE066705.1|EE066705
EST:     GCCTCCACTCCTGGCTTGGAATCGTCCTTATCTCACTCTATGGCATTCAG                         TGGATATACGGGTTTTTAATATTCTTCTACCCGGGAGGCACGCTTGGTCTG
genomic: GCCTCCACTCCTGGCTTGGAATCGTCCTTATCTCACTCTATGGCATTCAGgtacagcccc ... taatttgcagTGGATATACGGGTTTTTAGTATTCTTCTACCCAGGAGGCACGCTTGGTCTG
EST: gi|110691007|gb|EE068613.1|EE068613
EST:     GCCTCCACTCCTGGCTTGGAATCGTCCTTATCTCACTCTATGGCATTCAG                         TGGATATACGGGTTTTTAGTATTCTTCTACCCAGGAGGCACGCTTGGTCTG
genomic: GCCTCCACTCCTGGCTTGGAATCGTCCTTATCTCACTCTATGGCATTCAGgtacagcccc ... taatttgcagTGGATATACGGGTTTTTAGTATTCTTCTACCCAGGAGGCACGCTTGGTCTG
EST: gi|110692555|gb|EE071937.1|EE071937
EST:     GCCTCCACTCCTGGCTTGGAATCGTCCTTATCTCACTCTATGGCATTCAG                         TGGATATACGGGTTTTTAGTATTCTTCTACCCAGGAGGCACGCTTGGTCTG
genomic: GCCTCCACTCCTGGCTTGGAATCGTCCTTATCTCACTCTATGGCATTCAGgtacagcccc ... taatttgcagTGGATATACGGGTTTTTAGTATTCTTCTACCCAGGAGGCACGCTTGGTCTG
EST: gi|29785323|gb|CB342199.2|CB342199
EST:     GCCTCCACTCCTGGCTTGGAATCGTCCTTATCTCACTCTATGGCATTCAG                         TGGATATACGGGTTTTTAGTATTCTTCTACCCAGGAGGCACGCTTGGTCTG
genomic: GCCTCCACTCCTGGCTTGGAATCGTCCTTATCTCACTCTATGGCATTCAGgtacagcccc ... taatttgcagTGGATATACGGGTTTTTAGTATTCTTCTACCCAGGAGGCACGCTTGGTCTG
EST: gi|351024296|gb|FQ423719.1|FQ423719
EST:     GCCTCCACTCCTGGCTTGGAATCGTCCTTATCTCACTCTATGGCATTCAG                         TGGATATACGGGTTTTTAGTATTCTTCTACCCAGGAGGCACGCTTGGTCTG
genomic: GCCTCCACTCCTGGCTTGGAATCGTCCTTATCTCACTCTATGGCATTCAGgtacagcccc ... taatttgcagTGGATATACGGGTTTTTAGTATTCTTCTACCCAGGAGGCACGCTTGGTCTG
EST: gi|110694899|gb|EE072300.1|EE072300
EST:     GCCTCCACTCCTGGCTTGGAATCGTCCTTATCTCACTCTATGGCATTCAG                         TGGATATACGGGTTTTTAGTATTCTTCTACCCAGGAGGCACGCTTGGTCTG
genomic: GCCTCCACTCCTGGCTTGGAATCGTCCTTATCTCACTCTATGGCATTCAGgtacagcccc ... taatttgcagTGGATATACGGGTTTTTAGTATTCTTCTACCCAGGAGGCACGCTTGGTCTG
EST: gi|351030555|gb|FQ436981.1|FQ436981
EST:     GCCTCCACTCCTGGCTTGGAATCGTCCTTATCTCACTCTATGGCATTCAG                         TGGATATACGGGTTTTTAGTATTCTTCTACCCAGGAGGCACGCTTGGTCTG
genomic: GCCTCCACTCCTGGCTTGGAATCGTCCTTATCTCACTCTATGGCATTCAGgtacagcccc ... taatttgcagTGGATATACGGGTTTTTAGTATTCTTCTACCCAGGAGGCACGCTTGGTCTG
EST: gi|28963233|gb|CB342266.1|CB342266
EST:     GCCTCCACTCCTGGCTTGGAATCGTCCTTATCTCACTCTATGGCATTCAG                         TGGATATACGGGTTTTTAGTATTCTTCTACCCAGGAGGCACGCTTGGTCTG
genomic: GCCTCCACTCCTGGCTTGGAATCGTCCTTATCTCACTCTATGGCATTCAGgtacagcccc ... taatttgcagTGGATATACGGGTTTTTAGTATTCTTCTACCCAGGAGGCACGCTTGGTCTG
EST: gi|110376372|gb|EC941432.1|EC941432
EST:     GCCTCCACTCCTGGCTTGGAATCGTCCTTATCTCACTCTATGGCATTCAG                         TGGATATACGGGTTTTTAGTATTCTTCTACCCAGGAGGCACGCTTGGTCTG
genomic: GCCTCCACTCCTGGCTTGGAATCGTCCTTATCTCACTCTATGGCATTCAGgtacagcccc ... taatttgcagTGGATATACGGGTTTTTAGTATTCTTCTACCCAGGAGGCACGCTTGGTCTG
EST: gi|110689320|gb|EE065439.1|EE065439
EST:     GCCTCCACTCCTGGCTTGGAATCGTCCTTATCTCACTCTATGGCATTCAG                         TGGATATACGGGTTTTTAGTATTCTTCTACCCAGGAGGCACGCTTGGTCTG
genomic: GCCTCCACTCCTGGCTTGGAATCGTCCTTATCTCACTCTATGGCATTCAGgtacagcccc ... taatttgcagTGGATATACGGGTTTTTAGTATTCTTCTACCCAGGAGGCACGCTTGGTCTG
EST: gi|351019127|gb|FQ429287.1|FQ429287
EST:     GCCTCCACTCCTGGCTTGGAATCGTCCTTATCTCACTCTATGGCATTCAG                         TGGATATACGGGTTTTTAGTATTCTTCTACCCAGGAGGCACGCTTGGTCTG
genomic: GCCTCCACTCCTGGCTTGGAATCGTCCTTATCTCACTCTATGGCATTCAGgtacagcccc ... taatttgcagTGGATATACGGGTTTTTAGTATTCTTCTACCCAGGAGGCACGCTTGGTCTG
EST: gi|349814124|gb|FQ414358.1|FQ414358
EST:     GCCTCCACTCCTGGCTTGGAATCGTCCTTATCTCACTCTATGGCATTCAG                         TGGATATACGGGTTTTTAGTATTCTTCTACCCAGGAGGCACGCTTGGTCTG
genomic: GCCTCCACTCCTGGCTTGGAATCGTCCTTATCTCACTCTATGGCATTCAGgtacagcccc ... taatttgcagTGGATATACGGGTTTTTAGTATTCTTCTACCCAGGAGGCACGCTTGGTCTG
EST: gi|28963070|gb|CB342103.1|CB342103
EST:     GCCTCCACTCCTGGCTTGGAATCGTCCTTATCTCACTCTATGGCATTCAG                         TGGATATACGGGTTTTTAGTATTCTTCTACCCAGGAGGCACGCTTGGTCTG
genomic: GCCTCCACTCCTGGCTTGGAATCGTCCTTATCTCACTCTATGGCATTCAGgtacagcccc ... taatttgcagTGGATATACGGGTTTTTAGTATTCTTCTACCCAGGAGGCACGCTTGGTCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcacttggtagctgattgtcatcgagtctaagcatttttggtatgtaatttgcagTGGATATACGGGTTTTTAGTATTCTTCTACCCAGGAGGCACGCTTGGTCTGAGAAGTGCGTCGTTGCCATGGCACGTACTGTTTGGGCTACTGGTGTATG
         agctgat  putative branch site (score: 4)
                                         tatgtaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacagcccctaccctacatcacttcacttggtagctgattgtcatcgagtctaagcatttttggtatgtaatttgcagTGGATATACGGGTTTTTAGTATTCTTCTACCCAGGAGGCACGCTTGGTCTGAGAAGTGCGTCGTTGCCATGGCACGTACTGTTTGGGCTACTGGTGTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT