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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAACACATTTTGCTCTGGCCTTTGAAGTTCCCGGTGGTTGGCATAAGGAGAAGGAAGCAATGACTTTGACAGTTCTTCAGgtattggatttttatttcaggttcctatggtgaatcaatgtgcttgaaataatttcttgttctttctagcattatttacaaaatgtggttagaattgcattctttccaggtcccttagctttcaaatatgtcactcctgttcttatttggtgccaagttaggaagtaataataagtcccactttctgcag

Basic information

species Vitis vinifera
transcript Vv11s0016g02870.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g02870.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA08G03580.1 (Glycine max), 5'ss of exon 5
AAAACACATTTTGCTCTGGCCTTTGAAGTTCCCGGTGGTTGGCATAAGGAGAAGGAAGCAATGACTTTGACAGTTCTTCAGgtattggatttttatttcaggttcctatggtgaatcaatgtgcttgaaataatttcttgttctttctagcattatttacaaaatgt---ggttagaattgcattctttccaggtcccttagctttcaaatatgtc-actcctgttcttatttggtgccaagttaggaagtaataataagtcc-cacttt-ctgcag
|  || ||||||||||| || |||||| |||| ||||| |||||||||  |||||| || |||  |||||| ||||||||||| |||   |  | | | |  ||    || |   |   ||  |||||||| |  | |  ||||||  ||  |   ||| || || |    ||  | | || ||   |    |||  ||||      || |||||  || | |     |||        ||||| | |  |||   ||  ||| || ||| ||  ||
AGGACCCATTTTGCTCTAGCATTTGAACTTCCTGGTGGCTGGCATAAGTTGAAGGATGCTATGGTTTTGACTGTTCTTCAGgttttga--taatgtcttacattttcttgct---tttctgcacttgaaatcacctttccttcttttaag-gtggcttaaaatatatcagagtatggactgtatgtctagttggtttctta------aagtatgtttacactttacaatatgattcattaagtttgtatttaactgtatttcctcattttactatag

upper sequence: Vv11s0016g02870.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA05G36040.1 (Glycine max), 5'ss of exon 6
AAAACACATTTTGCTCTGGCCTTTGAAGTTCCCGGTGGTTGGCATAAGGAGAAGGAAGCAATGACTTTGACAGTTCTTCAGgtattggatttttatttcaggttcctatggtgaatcaatgtgcttgaaataatttcttgttctttctagcattatttacaaaatgtggttagaattgcattctttccaggtcccttagctttcaaatatgtc-actcctgttcttatttggtgccaagttaggaagtaataataagtcccactttc--tgcag
|  || ||||||||||| || |||||| |||| ||||| |||||||||  |||||| || |||  |||||| ||||||||||| |||   |  | | | |  ||    || |   |   ||  ||||||||    | || ||||||  ||  |   ||| || || |   |  ||| | ||   |    |||  ||||      || |||||  |||| |     |||        ||||| | |  | |   ||  | |   ||||  |  ||
AGGACCCATTTTGCTCTAGCATTTGAACTTCCTGGTGGCTGGCATAAGTTGAAGGATGCTATGGTTTTGACTGTTCTTCAGgttttga--taatgtcttatattttcttgct---tttctgcacttgaaatttccttttcttcttttaag-gtggcttaaaatatatcagtgtaat-gtatgtctagttggtttctta------aagtatgtttactctttacaatatgattcattaagtttgtattttactgtattttctcatttcactatag
















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|32247970|gb|CD713789.1|CD713789
EST:     CCGGTGGTTGGCATAAGGAGAAGGAAGCAATGACTTTGACAGTTCTTCAG                         ATGCTAATGGGAGGAGGTGGATCTTTCTCTGCTGGTGGTCCTGGAAAAGGG
genomic: CCGGTGGTTGGCATAAGGAGAAGGAAGCAATGACTTTGACAGTTCTTCAGgtattggatt ... ctttctgcagATGCTAATGGGAGGAGGTGGATCTTTCTCTGCTGGTGGTCCTGGAAAAGGG
EST: gi|110716318|gb|EE091196.1|EE091196
EST:     CCGGTGGTTGGCATAAGGAGAAGGAAGCAATGACTTTGACAGTTCTTCAG                         ATGCTAATGGGAGGAGGTGGATCTTTCTCTGCTGGTGGTCCTGGAAAAGGG
genomic: CCGGTGGTTGGCATAAGGAGAAGGAAGCAATGACTTTGACAGTTCTTCAGgtattggatt ... ctttctgcagATGCTAATGGGAGGAGGTGGATCTTTCTCTGCTGGTGGTCCTGGAAAAGGG
EST: gi|110382252|gb|EC938898.1|EC938898
EST:     CCGGTGGTTGGCATAAGGAGAAGGAAGCAATGACTTTGACAGTTCTTCAG                         ATGCTAATGGGAGGAGGTGGATCTTTCTCTGCTGGTGGTCCTGGAAAAGGG
genomic: CCGGTGGTTGGCATAAGGAGAAGGAAGCAATGACTTTGACAGTTCTTCAGgtattggatt ... ctttctgcagATGCTAATGGGAGGAGGTGGATCTTTCTCTGCTGGTGGTCCTGGAAAAGGG
EST: gi|22014250|gb|BQ799284.1|BQ799284
EST:     CCGGTGGTTGGCATAAGGAGAAGGAAGCAATGACTTTGACAGTTCTTCAG                         ATGCTAATGGGAGGAGGTGGATCTTTCTCTGCTGGTGGTCCTGGAAAAGGG
genomic: CCGGTGGTTGGCATAAGGAGAAGGAAGCAATGACTTTGACAGTTCTTCAGgtattggatt ... ctttctgcagATGCTAATGGGAGGAGGTGGATCTTTCTCTGCTGGTGGTCCTGGAAAAGGG
EST: gi|32268962|gb|CD718121.1|CD718121
EST:     CCGGTGGTTGGCATAAGGAGAAGGAAGCAATGACTTTGACAGTTCTTCAG                         ATGCTAATGGGAGGAGGTGGATCTTTCTCTGCTGGTGGTCCTGGAAAAGGG
genomic: CCGGTGGTTGGCATAAGGAGAAGGAAGCAATGACTTTGACAGTTCTTCAGgtattggatt ... ctttctgcagATGCTAATGGGAGGAGGTGGATCTTTCTCTGCTGGTGGTCCTGGAAAAGGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAACACATTTTGCTCTGGCCTTTGAAGTTCCCGGTGGTTGGCATAAGGAGAAGGAAGCAATGACTTTGACAGTTCTTCAGgtattggatttttatttcaggttcctatggtgaatcaatgtgcttgaaataatttcttgttctttctagcattatttacaaaatgtggttagaattgcattctttccaggtcccttagctttcaaatatgtcactcctgttcttatttggtgccaagttaggaagtaataataagtcccactttctgcag

- - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA