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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtcggtaatttattttaaaattatgtttattatttgtgaagttttgattctatgtaattttcttcttttgcttactgagatgaatggttatggtttgcagCTGCTTGTGAATCAGTTGGAGCCTCTGACCGAACAGCAACTGTTGGGCATCGGAAACTTGCAACAGTCCTCCCAACAGGCAGAGGATGCATTATCACAAG

Basic information

species Vitis vinifera
transcript Vv13s0084g00660.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0084g00660.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA15G37220.1 (Glycine max), 3'ss of exon 6
gtcggtaatt---tattttaaaattatgtttattatttgtgaagttttgattctatgtaattttcttcttttgctt-actgagatgaatggttatggtttgcagCTGCTTGTGAATCAGTTGGAGCCTCTGACCGAACAGCAACTGTTGGGCATCGGAAACTTGCAACAGTCCTCCCAACAGGCAGAGGATGCATTATCACAAG
 |   |||||     |  | |  || | |||   || |||| |||    ||| |||    |  |   ||||  ||| | |    |||||     ||  ||||||||||| || | ||| ||||||||||| || || ||||| ||| |||| ||    |||||||| || ||||||||||| ||||| ||||||||||| || |
-ttcataattgtggctactgaggttttatttcggatatgtggagtc---attttataatttccttgactttgactttagtcctgtgaatttggttgcattgcagCTGCTGGTTAGTCAATTGGAGCCTCTCACAGAGCAGCAGCTGATGGGTATTACCAACTTGCAGCAATCCTCCCAACAAGCAGAAGATGCATTATCTCAGG
















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|156737550|gb|EV241663.1|EV241663
EST:     AGAGGTGTTTTTTGTGGCTTGGTGGTTTCCGTTCATCTGAACTCCTAAAG                         CTGCTTGTGAATCAGTTGGAGCCTCTGACCGAACAGCAACTGTTGGGCATC
genomic: AGAGGTGTTTTTTGTGGCTTGGTGGTTTCCGTTCATCTGAACTCCTAAAGgtatgaccct ... tggtttgcagCTGCTTGTGAATCAGTTGGAGCCTCTGACCGAACAGCAACTGTTGGGCATC
EST: gi|110358202|gb|EC922250.1|EC922250
EST:     AGAGGTGTTTTTTGTGGCTTGGTGGTTTCCGTTCATCTGAACTCCTAAAG                         CTGCTTGTGAATCAGTTGGAGCCTCTGACCGAACAGCAACTGTTGGGCATC
genomic: AGAGGTGTTTTTTGTGGCTTGGTGGTTTCCGTTCATCTGAACTCCTAAAGgtatgaccct ... tggtttgcagCTGCTTGTGAATCAGTTGGAGCCTCTGACCGAACAGCAACTGTTGGGCATC
EST: gi|110393937|gb|EC959530.1|EC959530
EST:     AGAGGTGTTTTTTGTGGCTTGGTGGTTTCCGTTCATCTGAACTCCTAAAG                         CTGCTTGTGAATCAGTTGGAGCCTCTGACCGAACAGCAACTGTTGGGCATC
genomic: AGAGGTGTTTTTTGTGGCTTGGTGGTTTCCGTTCATCTGAACTCCTAAAGgtatgaccct ... tggtttgcagCTGCTTGTGAATCAGTTGGAGCCTCTGACCGAACAGCAACTGTTGGGCATC
EST: gi|110687850|gb|EE065730.1|EE065730
EST:     AGAGGTGTTTTTTGTGGCTTGGTGGTTTCCGTTCATCTGAACTCCTAAAG                         CTGCTTGTGAATCAGTTGGAGCCTCTGACCGAACAGCAACTGTTGGGCATC
genomic: AGAGGTGTTTTTTGTGGCTTGGTGGTTTCCGTTCATCTGAACTCCTAAAGgtatgaccct ... tggtttgcagCTGCTTGTGAATCAGTTGGAGCCTCTGACCGAACAGCAACTGTTGGGCATC
EST: gi|110697733|gb|EE074978.1|EE074978
EST:     AGAGGTGTTTTTTGTGGCTTGGTGGTTTCCGTTCATCTGAACTCCTAAAG                         CTGCTTGTGAATCAGTTGGAGCCTCTGACCGAACAGCAACTGTTGGGCATC
genomic: AGAGGTGTTTTTTGTGGCTTGGTGGTTTCCGTTCATCTGAACTCCTAAAGgtatgaccct ... tggtttgcagCTGCTTGTGAATCAGTTGGAGCCTCTGACCGAACAGCAACTGTTGGGCATC
EST: gi|110360089|gb|EC922696.1|EC922696
EST:     AGAGGTGTTTTTTGTGGCTTGGTGGTTTCCGTTCATCTGAACTCCTAAAG                         CTGCTTGTGAATCAGTTGGAGCCTCTGACCGAACAGCAACTGTTGGGCATC
genomic: AGAGGTGTTTTTTGTGGCTTGGTGGTTTCCGTTCATCTGAACTCCTAAAGgtatgaccct ... tggtttgcagCTGCTTGTGAATCAGTTGGAGCCTCTGACCGAACAGCAACTGTTGGGCATC
EST: gi|110685242|gb|EE063437.1|EE063437
EST:     AGAGGTGTTTTTTGTGGCTTGGTGGTTTCCGTTCATCTGAACTCCTAAAG                         CTGCTTGTGAATCAGTTGGAGCCTCTGACCGAACAGCAACTGTTGGGCATC
genomic: AGAGGTGTTTTTTGTGGCTTGGTGGTTTCCGTTCATCTGAACTCCTAAAGgtatgaccct ... tggtttgcagCTGCTTGTGAATCAGTTGGAGCCTCTGACCGAACAGCAACTGTTGGGCATC
EST: gi|110383071|gb|EC947420.1|EC947420
EST:     AGAGGTGTTTTTTGTGGCTTGGTGGTTTCCGTTCATCTGAACTCCTAAAG                         CTGCTTGTGAATCAGTTGGAGCCTCTGACCGAACAGCAACTGTTGGGCATC
genomic: AGAGGTGTTTTTTGTGGCTTGGTGGTTTCCGTTCATCTGAACTCCTAAAGgtatgaccct ... tggtttgcagCTGCTTGTGAATCAGTTGGAGCCTCTGACCGAACAGCAACTGTTGGGCATC
EST: gi|18458746|gb|BM437024.1|BM437024
EST:     AGAGGTGTTTTTTGTGGCTTGGTGGTTTCCGTTCATCTGAACTCCTAAAG                         CTGCTTGTGAATCAGTTGGAGCCTCTGACCGAACAGCAACTGTTGGGCATC
genomic: AGAGGTGTTTTTTGTGGCTTGGTGGTTTCCGTTCATCTGAACTCCTAAAGgtatgaccct ... tggtttgcagCTGCTTGTGAATCAGTTGGAGCCTCTGACCGAACAGCAACTGTTGGGCATC
EST: gi|110428204|gb|EC994669.1|EC994669
EST:     AGAGGTGTTTTTTGTGGCTTGGTGGTTTCCGTTCATCTGAACTCCTAAAG                         CTGCTTGTGAATCAGTTGGAGCCTCTGACCGAACAGCAACTGTTGGGCATC
genomic: AGAGGTGTTTTTTGTGGCTTGGTGGTTTCCGTTCATCTGAACTCCTAAAGgtatgaccct ... tggtttgcagCTGCTTGTGAATCAGTTGGAGCCTCTGACCGAACAGCAACTGTTGGGCATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattctatgtaattttcttcttttgcttactgagatgaatggttatggtttgcagCTGCTTGTGAATCAGTTGGAGCCTCTGACCGAACAGCAACTGTTGGGCATCGGAAACTTGCAACAGTCCTCCCAACAGGCAGAGGATGCATTATCACAAG
                       tgcttac  putative branch site (score: 2)
         taattttcttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcggtaatttattttaaaattatgtttattatttgtgaagttttgattctatgtaattttcttcttttgcttactgagatgaatggttatggtttgcagCTGCTTGTGAATCAGTTGGAGCCTCTGACCGAACAGCAACTGTTGGGCATCGGAAACTTGCAACAGTCCTCCCAACAGGCAGAGGATGCATTATCACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - aaaatta
- - - - - - - - - - - - - - - - - - - - - - - - -ctatgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgaatgg