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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTCTGTTTCACGAGGTACATGTGATGCTGTTCTAGCTTGCCATGCTGGTCCAATTTTATGTGTTGAGTATTTGATGTCAGACAGAGGAATAATAACAGgttaacaccttgtcttttgcatttttctgtagtctttcatcttttttactttggcacttcaaagacatttctgttcagtggcagatttatccctggtgctaatgtgagcaattttataaatagtgtctgaataaggatatccttcttttcag

Basic information

species Vitis vinifera
transcript Vv17s0000g03950.t01
intron # 28
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g03950.t01 (Vitis vinifera), 5'ss of exon 28
lower sequence: GLYMA05G35210.1 (Glycine max), 5'ss of exon 12
TGGTCTGTTTCACGAGGTACATGTGATGCTGTTCTAGCTTGCCATGCTGGTCCAATTTTATGTGTTGAGTATTTGATGTCAGACAGAGGAATAATAACAGgt-taacaccttgtcttttgcatttttctgtagtctttcatcttttttactttggcacttcaaagacatttctgttcagtggcagatttatccctggtgctaatgtgagcaattttataaatagtgtctg--aataaggatatccttcttttcag
||||||||||| ||||| ||||||||| ||||  |||| ||||||||||| ||||| ||||||||||||||||     | ||| ||||||||||| ||||||    || ||    ||||    | | |||   |  || || | ||||| ||||    |||   |||     || |    |  | ||||   ||   ||||           |||||||   ||||  |   || | |   |   | | || |||
TGGTCTGTTTCTCGAGGAACATGTGATACTGTCTTAGCATGCCATGCTGGACCAATATTATGTGTTGAGTATTCTTCTTTAGATAGAGGAATAATTACAGgtgcttcatctccaattttttgctatgctgccat--ttgatatcttttattttgttggttcttggac----ttgcttgaagagaaatttccgcc--atgct-----------ttttatatccagtgcttactaaaatgttaaatttccattccag

upper sequence: Vv17s0000g03950.t01 (Vitis vinifera), 5'ss of exon 28
lower sequence: GLYMA08G04510.1 (Glycine max), 5'ss of exon 28
TGGTCTGTTTCACGAGGTACATGTGATGCTGTTCTAGCTTGCCATGCTGGTCCAATTTTATGTGTTGAGTATTTGATGTCAGACAGAGGAATAATAACAGgt-taacaccttgtcttttgcatttttctgtagtctttcatcttttttactttggcacttcaaagacatttctgttcagtggcagatttatccctggtgctaatgtgagcaattttataaatagtgtctgaataaggatatccttcttttcag
||||||||||| ||||| |||   ||||||||  |||||||||||||||| ||||| ||||||||||||||||     | ||||||||||||||| ||||||    || ||    ||||    | | |||   | |   |||||||  | ||||    |||   | |     || |    |  | ||||  ||   |||||  | |   || |  |    | | ||| | |||          | | ||  ||
TGGTCTGTTTCCCGAGGAACAATGGATGCTGTCTTAGCTTGCCATGCTGGGCCAATATTATGTGTTGAGTATTCTTCTTTAGACAGAGGAATAATTACAGgtgcgtcatctccaattttttgctatgctgccatttggtatctttt--attttgttggttcttgggc----ttgcttgaagagaaattt--ccactgtgcttttatatccagtgcttactaaaatgt-taaat---------ttccattctag
















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|29783106|gb|CB349051.2|CB349051
EST:     CCAATTTTTATGTGTTGAGTATTTGATGTCAGACAGAGGAATAATAACAG                         GTTCAACTGATGGGCTGCTTCGATTTTGGGAAAATGAAGAGG
genomic: CCAA-TTTTATGTGTTGAGTATTTGATGTCAGACAGAGGAATAATAACAGgttaacacct ... ttcttttcagGTTCAACTGATGGGCTGCTTCGATTTTGGGAAAATGAAGAGG
EST: gi|29783070|gb|CB348965.2|CB348965
EST:     TCCAATTTTATGTGTTGAGTATTTGATGTCAGACAGAGGAATAATAACAG                         GTTCAACTGATGGGCTGCTTCGATTTTGGGAAAATGAAGAGG
genomic: TCCAATTTTATGTGTTGAGTATTTGATGTCAGACAGAGGAATAATAACAGgttaacacct ... ttcttttcagGTTCAACTGATGGGCTGCTTCGATTTTGGGAAAATGAAGAGG
EST: gi|30132304|gb|CB917643.1|CB917643
EST:     TCCAATTTTATGTGTTGAGTATTTGATGTCAGACAGAGGAATAATAACAG                         GTTCAACTGATGGGCTGCTTCGATTTTGGGAAAATGAAGAGG
genomic: TCCAATTTTATGTGTTGAGTATTTGATGTCAGACAGAGGAATAATAACAGgttaacacct ... ttcttttcagGTTCAACTGATGGGCTGCTTCGATTTTGGGAAAATGAAGAGG
EST: gi|32250254|gb|CD716073.1|CD716073
EST:     TCCAATTTTATGTGTTGAGTATTTGATGTCAGACAGAGGAATAATAACAG                         GTTCAACTGATGGGCTGCTTCGATTTTGGGAAAATGAAGAGG
genomic: TCCAATTTTATGTGTTGAGTATTTGATGTCAGACAGAGGAATAATAACAGgttaacacct ... ttcttttcagGTTCAACTGATGGGCTGCTTCGATTTTGGGAAAATGAAGAGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGTCTGTTTCACGAGGTACATGTGATGCTGTTCTAGCTTGCCATGCTGGTCCAATTTTATGTGTTGAGTATTTGATGTCAGACAGAGGAATAATAACAGgttaacaccttgtcttttgcatttttctgtagtctttcatcttttttactttggcacttcaaagacatttctgttcagtggcagatttatccctggtgctaatgtgagcaattttataaatagtgtctgaataaggatatccttcttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA