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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatcaactgccttgctgtatacgtggatgcatctttcctctccttacaattgctgtaacatggctttactactgctcacagATTCGTGATGCATATATGCTTAAAATCTTTGAGAACAACCAATCACGTCTGCCAAGTTGGTGCGGCGATGAAGATGGTCGGCTCCAGTTCTGCCAGATCC

Basic information

species Vitis vinifera
transcript Vv01s0026g00920.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0026g00920.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA02G03160.1 (Glycine max), 3'ss of exon 6
gtaagtatcaactgccttgctgtatacgtggatgcatctttcctctccttacaattgc----tgtaacatggctttactactgctcacagATTCGTGATGCATATATGCTTAAAATCTTTGAGAACAACCAATCACGTCTGCCAAGTTGGTGCGGCGATGAAGATGGTCGGCTCCAGTTCTGCCAGATCC
|||||    | || ||||  ||  ||        |     ||   || ||| ||||||    | | |  |  || |  |        ||||||||||||||||| |||||||  || |||||| | |||||| ||||||| ||||| ||||||  | ||||  | | |||||  |  ||||||||||| |
gtaagc-caagcttccttagtgcttata-----accaacctctgatcgttataattgccttttcttatgtttctatgttgtaatctgcagATTCGTGATGCATACATGCTTAGGATTTTTGAGGATAACCAAACACGTCTACCAAGATGGTGCAACAATGAGAACGATCGGCATCCATTCTGCCAGATTC

upper sequence: Vv01s0026g00920.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA01G04400.1 (Glycine max), 3'ss of exon 6
gtaagtatcaactgccttgctgtatacgtggatgcatctttcctctccttacaattgctgtaacatggctttactactgctcacagATTCGTGATGCATATATGCTTAAAATCTTTGAGAACAACCAATCACGTCTGCCAAGTTGGTGCGGCGATGAAGATGGTCGGCTCCAGTTCTGCCAGATCC
|||||    | || ||||  ||  ||     |  | |||      |        ||  | | |  |  || |     |     ||||||||||||||||| |||||||  || |||||| | |||||| ||||||| ||||| ||||||  | ||||  | | |||||| |  ||||||||||| |
gtaagc-caagcttccttagtgcttataacca-acctctgatagttataattgctttttcttatgtttctatgtcgttatctgcagATTCGTGATGCATACATGCTTAGGATTTTTGAGGATAACCAAACACGTCTACCAAGATGGTGCAACAATGAGAACGATCGGCTTCCATTCTGCCAGATTC

upper sequence: Vv01s0026g00920.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA18G17350.1 (Glycine max), 3'ss of exon 5
-gtaagtatcaactgccttgctgtatacgtggatgcatctttcctctccttacaa--ttgctgtaacatggctttactactgctcacagATTCGTGATGCATATATGCTTAAAATCTTTGAGAACAACCAATCACGTCTGCCAAGTTGGTGCGGCGATGAAGATGGTCGGCTCCAGTTCTGCCAGATCC
 ||||||   ||   |  |||     |  || ||| | |||||  |    || ||  ||  | |||      | |  |  |  |  |||||||| |||||||| ||||| | ||| || ||| |||||||| |||| || ||||||||||||  | ||||  |||  ||| | |  ||||| |||||  
cgtaagtcgtaatgtctctgc-----aaatgcatgaacctttcaccattataaaaactttttctaatgcttatatcttgttatttgcaGATTCGCGATGCATACATGCTCAGAATTTTCGAGGACAACCAAACACGCCTACCAAGTTGGTGCAACAATGAGAATGACCGGATTCCATTCTGTCAGATT-

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|110721434|gb|EE098424.1|EE098424
EST:     CAGGAATCTTTGGTCCCGCTTCTAGCTCTATTCAAGTAACTGAGTTCACT                         ATTCGTGATGCATATATGCTTAAAATCTTTGAGAACAACCAATCACGTCTG
genomic: CAGGAATCTTTGGTCCCGCTTCTAGCTCTATTCAAGTAACTGAGTTCACTgtaagtatca ... ctgctcacagATTCGTGATGCATATATGCTTAAAATCTTTGAGAACAACCAATCACGTCTG
EST: gi|27579647|gb|CB002342.1|CB002342
EST:     CAGGAATCTTTGGTCCCGCTTCTAGCTCTATTCAAGTAACTGAGTTCACT                         ATTCGTGATGCATATATGCTTAAAATC
genomic: CAGGAATCTTTGGTCCCGCTTCTAGCTCTATTCAAGTAACTGAGTTCACTgtaagtatca ... ctgctcacagATTCGTGATGCATATATGCTTAAAATC
EST: gi|22008704|gb|BQ793738.1|BQ793738
EST:     CAGGAATCTTTGGTCCCGCTTCTAGCTCTATTCAAGTAACTGAGTTCACT                         ATTCGTGATGCATATATGCTTAAAATCTTTGAGAACAACCAATCACGTCTG
genomic: CAGGAATCTTTGGTCCCGCTTCTAGCTCTATTCAAGTAACTGAGTTCACTgtaagtatca ... ctgctcacagATTCGTGATGCATATATGCTTAAAATCTTTGAGAACAACCAATCACGTCTG
EST: gi|27579589|gb|CB002284.1|CB002284
EST:     CAGGAATCTTTGGTCCCGCTTCTAGCTCTATTCAAGTAACTGAGTTCACT                         ATTCGTGATGCATATATGCTTAAAATCTTTGAGAACAACCAATCACGTCTG
genomic: CAGGAATCTTTGGTCCCGCTTCTAGCTCTATTCAAGTAACTGAGTTCACTgtaagtatca ... ctgctcacagATTCGTGATGCATATATGCTTAAAATCTTTGAGAACAACCAATCACGTCTG
EST: gi|32244938|gb|CD710757.1|CD710757
EST:     CAGGAATCTTTGGTCCCGCTTCTAGCTTTATTCAAGTAACTGAGTTCACT                         ATTCGTGATGCATATATGCTTAAAATCTTGGAGAACAACCAATCACGTCTG
genomic: CAGGAATCTTTGGTCCCGCTTCTAGCTCTATTCAAGTAACTGAGTTCACTgtaagtatca ... ctgctcacagATTCGTGATGCATATATGCTTAAAATCTTTGAGAACAACCAATCACGTCTG
EST: gi|110425597|gb|EC991986.1|EC991986
EST:     CAGGAATCTTTGGTCCCGCTTCTAGCTCTATTCAAGTAACTGAGTTCACT                         ATTCGTGATGCATATATGCTTAAAATCTTTGAGAACAACCAATCACGTCTG
genomic: CAGGAATCTTTGGTCCCGCTTCTAGCTCTATTCAAGTAACTGAGTTCACTgtaagtatca ... ctgctcacagATTCGTGATGCATATATGCTTAAAATCTTTGAGAACAACCAATCACGTCTG
EST: gi|32245156|gb|CD710975.1|CD710975
EST:     CAGGAATCTTTGGTCCCGCTTCTAGCTCTATTCAAGTAACTGAGTTCACT                         ATTCGTGATGCATATATGCTTAAAATCTTTGAGAACAACCAATCACGTCTG
genomic: CAGGAATCTTTGGTCCCGCTTCTAGCTCTATTCAAGTAACTGAGTTCACTgtaagtatca ... ctgctcacagATTCGTGATGCATATATGCTTAAAATCTTTGAGAACAACCAATCACGTCTG
EST: gi|110419714|gb|EC985963.1|EC985963
EST:     CAGGAATCTTTGGTCCCGCTTCTAGCTCTATTCAAGTAACTGAGTTCACT                         ATTCGTGATGCATATATGCTTAAAATCTTTGAGAACAACCAATCACGTCTG
genomic: CAGGAATCTTTGGTCCCGCTTCTAGCTCTATTCAAGTAACTGAGTTCACTgtaagtatca ... ctgctcacagATTCGTGATGCATATATGCTTAAAATCTTTGAGAACAACCAATCACGTCTG
EST: gi|161711722|gb|FC058291.1|FC058291
EST:     CAGGAATCTTTGGTCCCGCTTCTAGCTCTATTCAAGTAACTGAGTTCACT                         ATTCGTGATGCATATATGCTTAAAATCTTTGAGAACAACCAATCACGTCTG
genomic: CAGGAATCTTTGGTCCCGCTTCTAGCTCTATTCAAGTAACTGAGTTCACTgtaagtatca ... ctgctcacagATTCGTGATGCATATATGCTTAAAATCTTTGAGAACAACCAATCACGTCTG
EST: gi|34362044|gb|CF403629.1|CF403629
EST:     CCGCTTCTAGCTCTATTCAAGTAACTGAGTTCACT                         ATTCGTGATGCATATATGCTTAAAATCTTTGAGAACAACCAATCACGTCTG
genomic: CCGCTTCTAGCTCTATTCAAGTAACTGAGTTCACTgtaagtatca ... ctgctcacagATTCGTGATGCATATATGCTTAAAATCTTTGAGAACAACCAATCACGTCTG
EST: gi|27578697|gb|CB001392.1|CB001392
EST:     CAGGAATCTTTGGTCCCGCTTCTAGCTCTATTCAAGTAACTGAGTTCACT                         ATTCGTGATGCATATATGCTTAAAATCTTTGAGAACAACCAATCACGTCTG
genomic: CAGGAATCTTTGGTCCCGCTTCTAGCTCTATTCAAGTAACTGAGTTCACTgtaagtatca ... ctgctcacagATTCGTGATGCATATATGCTTAAAATCTTTGAGAACAACCAATCACGTCTG
EST: gi|27581381|gb|CB004076.1|CB004076
EST:     CAGGAATCTTTGGTCCCGCTTCTAGCTCTATTCAAGTAACTGAGTTCACT                         ATTCGTGATGCATATATGCTTAAAATCTTTGAGAACA-CCAATCACGTCTG
genomic: CAGGAATCTTTGGTCCCGCTTCTAGCTCTATTCAAGTAACTGAGTTCACTgtaagtatca ... ctgctcacagATTCGTGATGCATATATGCTTAAAATCTTTGAGAACAACCAATCACGTCTG
EST: gi|34545798|gb|CF514030.1|CF514030
EST:     CAGGAATCTTTGGTCCCGCTTCTAGCTCTATTCAAGTAACTGAGTTCACT                         ATTCGTGATGCATATATGCTTAAAATCTTTGAGAACAACCAATCACGTCTG
genomic: CAGGAATCTTTGGTCCCGCTTCTAGCTCTATTCAAGTAACTGAGTTCACTgtaagtatca ... ctgctcacagATTCGTGATGCATATATGCTTAAAATCTTTGAGAACAACCAATCACGTCTG
EST: gi|34545878|gb|CF514110.1|CF514110
EST:     CAGGAATCTTTGGTCCCGCTTCTAGCTCTATTCAAGTAACTGAGTTCACT                         ATTCGTGATGCATATATGCTTAAAATCTTTGAGAACAACCAATCACGTCTG
genomic: CAGGAATCTTTGGTCCCGCTTCTAGCTCTATTCAAGTAACTGAGTTCACTgtaagtatca ... ctgctcacagATTCGTGATGCATATATGCTTAAAATCTTTGAGAACAACCAATCACGTCTG
EST: gi|28970697|gb|CB349730.1|CB349730
EST:     CAGGAATCTTTGGTCCCGCTTCTAGCTCTATTCAAGTAACTGAGTTCACT                         ATTCGTGATGCATATATGCTTAAAAT
genomic: CAGGAATCTTTGGTCCCGCTTCTAGCTCTATTCAAGTAACTGAGTTCACTgtaagtatca ... ctgctcacagATTCGTGATGCATATATGCTTAAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgcatctttcctctccttacaattgctgtaacatggctttactactgctcacagATTCGTGATGCATATATGCTTAAAATCTTTGAGAACAACCAATCACGTCTGCCAAGTTGGTGCGGCGATGAAGATGGTCGGCTCCAGTTCTGCCAGATCC
                 ttacaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtatcaactgccttgctgtatacgtggatgcatctttcctctccttacaattgctgtaacatggctttactactgctcacagATTCGTGATGCATATATGCTTAAAATCTTTGAGAACAACCAATCACGTCTGCCAAGTTGGTGCGGCGATGAAGATGGTCGGCTCCAGTTCTGCCAGATCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG