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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccacccaagaactttgaattagtacatgcttatcagtacagtttggctcaaggaatttttcacacccatttatctaattatactgatgttaaatcagGTCTGGAGCAACGATACTTATGAGAGTGTGGAGCACAGGGTGATGGTGAATTCAGAGAGGGAAAGGTTTTCGATTCCGTTCTTTTTCAATCCCGGGCACC

Basic information

species Vitis vinifera
transcript Vv03s0063g01150.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0063g01150.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA02G15360.1 (Glycine max), 3'ss of exon 2
gtaccacccaagaactttgaattagtacatgcttatcagtacagtttggctcaaggaatttttcacacccat-ttatctaattatactgat--gttaaatcagGTCTGGAGCAACGATACTTATGAGAGTGTGGAGCACAGGGTGATGGTGAATTCAGAGAGGGAAAGGTTTTCGATTCCGTTCTTTTTCAATCCCGGGCACC
    |      |     |    || |   || | || |    | ||| | |  |    |||  |  |    | |||   |||     |  |  ||  || ||||| |||||||| ||| ||||||||||||| || |||||||| |||||||| || |||| ||| |||||||| ||||| |||||| | || || |  | | 
---acgttgtggttgcatagtctattttctgataatgaagttaattttgttttaatgctttggcctatagttattacagaatggcttttgtttgtgcaagcagGTTTGGAGCAATGATGCTTATGAGAGTGTAGAACACAGGGTTATGGTGAACTCTGAGAAGGATAGGTTTTCAATTCCATTCTTTCTGAAACCAGCACTCT
















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|30130374|gb|CB915713.1|CB915713
EST:     TTAAGCCCACCCCAGATGCTTATATTATCAATGTTGGGGATATAATTCAG                         GTCTGGAGCAACGATACTTATGAGAGTGTGGAGCACAGGGTGATGGTGAAT
genomic: TTAAGCCCACCCCAGATGCTTATATTATCAATGTTGGGGATATAATTCAGgtaccaccca ... gttaaatcagGTCTGGAGCAACGATACTTATGAGAGTGTGGAGCACAGGGTGATGGTGAAT
EST: gi|32246320|gb|CD712139.1|CD712139
EST:     TTAAGCCCACCCCAGATGCTTATATTATCAATGTTGGGGATATAATTCAG                         GTCTGGAGCAACGATACTTATGAGAGTGTGGAGCACAGGGTGATGGTGAAT
genomic: TTAAGCCCACCCCAGATGCTTATATTATCAATGTTGGGGATATAATTCAGgtaccaccca ... gttaaatcagGTCTGGAGCAACGATACTTATGAGAGTGTGGAGCACAGGGTGATGGTGAAT
EST: gi|110379220|gb|EC944400.1|EC944400
EST:     TTAAGCCCACCCCAGATGCTTATATTATCAATGTTGGGGATATAATTCAG                         GTCTGGAGCAACGATACTTATGAGAGTGTGGAGCACAGGGTGATGGTGAAT
genomic: TTAAGCCCACCCCAGATGCTTATATTATCAATGTTGGGGATATAATTCAGgtaccaccca ... gttaaatcagGTCTGGAGCAACGATACTTATGAGAGTGTGGAGCACAGGGTGATGGTGAAT
EST: gi|30129770|gb|CB915109.1|CB915109
EST:     TTAAGCCCACCCCAGATGCTTATATTATCAATGTTGGGGATATAATTCAG                         GTCTGGAGCAACGATACTTATGAGAGTGTGGAGCACAGGGTGATGGTGAAT
genomic: TTAAGCCCACCCCAGATGCTTATATTATCAATGTTGGGGATATAATTCAGgtaccaccca ... gttaaatcagGTCTGGAGCAACGATACTTATGAGAGTGTGGAGCACAGGGTGATGGTGAAT
EST: gi|110373027|gb|EC937234.1|EC937234
EST:     TTAAGCCCACCCCAGATGCTTATATTATCAATGTTGGGGATATAATTCAG                         GTCTGGAGCAACGATACTTATGAGAGTGTGGAGCACAGGGTGATGGTGAAT
genomic: TTAAGCCCACCCCAGATGCTTATATTATCAATGTTGGGGATATAATTCAGgtaccaccca ... gttaaatcagGTCTGGAGCAACGATACTTATGAGAGTGTGGAGCACAGGGTGATGGTGAAT
EST: gi|27585603|gb|CB008298.1|CB008298
EST:     TTAAGCCCACCCCAGATGCTTATATTATCAATGTTGGGGATATAATTCAG                         GTCTGGAGCAACGATACTTATGAGAGTGTGGAGCACAGGGTGATGGTGAAT
genomic: TTAAGCCCACCCCAGATGCTTATATTATCAATGTTGGGGATATAATTCAGgtaccaccca ... gttaaatcagGTCTGGAGCAACGATACTTATGAGAGTGTGGAGCACAGGGTGATGGTGAAT
EST: gi|27582722|gb|CB005417.1|CB005417
EST:     TTAAGCCCACCCCAGATGCTTATATTATCAATGTTGGGGATATAATTCAG                         GTCTGGAGCAACGATACTTATGAGAGTGTGGAGCACAGGGTGATGGTGAAT
genomic: TTAAGCCCACCCCAGATGCTTATATTATCAATGTTGGGGATATAATTCAGgtaccaccca ... gttaaatcagGTCTGGAGCAACGATACTTATGAGAGTGTGGAGCACAGGGTGATGGTGAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggctcaaggaatttttcacacccatttatctaattatactgatgttaaatcagGTCTGGAGCAACGATACTTATGAGAGTGTGGAGCACAGGGTGATGGTGAATTCAGAGAGGGAAAGGTTTTCGATTCCGTTCTTTTTCAATCCCGGGCACC
                                      tactgat  putative branch site (score: 2)
                         atttatctaattatac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaccacccaagaactttgaattagtacatgcttatcagtacagtttggctcaaggaatttttcacacccatttatctaattatactgatgttaaatcagGTCTGGAGCAACGATACTTATGAGAGTGTGGAGCACAGGGTGATGGTGAATTCAGAGAGGGAAAGGTTTTCGATTCCGTTCTTTTTCAATCCCGGGCACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG