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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atagatttaaatccttgagtttttgtgaatctctatgaggtttaactttgttacaagggaggggtatgtttagtgattgtcctttttgtttgtggaacagATATACCCACCTATTAATGTTCTTCCATCACTCTCTCGACTAATGAAG

Basic information

species Vitis vinifera
transcript Vv18s0001g01020.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g01020.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 11
----------atagatttaaatccttgagttt--ttgtgaa-tctctatgaggtttaactttgttacaagggag-----gggtatgtttagtgattgtcctttttgtttg----------tggaacagATATACCCACCTATTAATGTTCTTCCATCACTCTCTCGACTAATGAAG
           | || ||   | | |   | |  || |||  ||||||  |  |  ||| |    |  |  |           || |  | ||||      || ||| |           |  |||||||||||||||| ||||| || ||||||||||| ||||| || ||||||
gtgcaataagctcgacttttttgcatatatctcattatgagctctctaacacatcaaacataagcaagaaaggtttctcatacatttacaatgatctctgattctgtcttggttcttccctaaaacagATATACCCACCCATTAACGTGCTTCCATCACTTTCTCGGCTGATGAAG

upper sequence: Vv18s0001g01020.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 10
atagatttaa-atccttgagtttttgtgaatctctatgaggttta-actttgttacaagggaggggtatgtttagtgattgtcctttttgtttgtggaacagATATACCCACCTATTAATGTTCTTCCATCACTCTCTCGACTAATGAAG
 | | ||||  |||   |||     | ||        |||    | |    |  | |  ||    ||| ||| | | |||||  |  | | | |||  |||||| ||||| |||||||||||||| ||||| || |||||||| ||||||
ctcgttttattatcaaggagagagagagagagagagagagagagagagagagagatagagggactgta-gttgatttattgttatggt-gctcgtgatacagATCTACCCGCCTATTAATGTTCTGCCATCTCTGTCTCGACTGATGAAG
















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|33402236|gb|CF207863.1|CF207863
EST:     ATATTACTGAGGGCCAGATATACATTGATAGGCAACTCCACAACCGGCAG                         ATATACCCACCTATTAATGTTCTTCCATCACTCTCTCGACTAATGAAG
genomic: ATATTACTGAGGGCCAGATATACATTGATAGGCAACTCCACAACCGGCAGgtgagttgaa ... tgtggaacagATATACCCACCTATTAATGTTCTTCCATCACTCTCTCGACTAATGAAG
EST: gi|37184152|gb|CF603506.1|CF603506
EST:     ATATTACTGAGGGCCAGATATACATTGATAGGCAACTCCACAACCGGCAG                         ATATACCCACCTATTAATGTTCTTCCATCACTCTCTCGACTAATGAAG
genomic: ATATTACTGAGGGCCAGATATACATTGATAGGCAACTCCACAACCGGCAGgtgagttgaa ... tgtggaacagATATACCCACCTATTAATGTTCTTCCATCACTCTCTCGACTAATGAAG
EST: gi|30128132|gb|CB913471.1|CB913471
EST:     ATATTACTGAGGGCCAGATATACATTGATAGGCAACTCCACAACCGGCAG                         ATATACCCACCTATTAATGTTCTTCCATCACTCTCTCGACTAATGAAG
genomic: ATATTACTGAGGGCCAGATATACATTGATAGGCAACTCCACAACCGGCAGgtgagttgaa ... tgtggaacagATATACCCACCTATTAATGTTCTTCCATCACTCTCTCGACTAATGAAG
EST: gi|110421897|gb|EC988201.1|EC988201
EST:     ATATTACTGAGGGCCAGATATACATTGATAGGCAACTCCACAACCGGCAG                         ATATACCCACCTATTAATGTTCTTCCATCACTCTCTCGACTAATGAAG
genomic: ATATTACTGAGGGCCAGATATACATTGATAGGCAACTCCACAACCGGCAGgtgagttgaa ... tgtggaacagATATACCCACCTATTAATGTTCTTCCATCACTCTCTCGACTAATGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttgttacaagggaggggtatgtttagtgattgtcctttttgtttgtggaacagATATACCCACCTATTAATGTTCTTCCATCACTCTCTCGACTAATGAAG
                               ttgtcctttttgttt  CT-rich tract
                                     tttttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atagatttaaatccttgagtttttgtgaatctctatgaggtttaactttgttacaagggaggggtatgtttagtgattgtcctttttgtttgtggaacagATATACCCACCTATTAATGTTCTTCCATCACTCTCTCGACTAATGAAG

- - - - - - ccttgag
- - - - - - - - - - - - - - - ctctatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - gggaggg