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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTGCATCTGGTGGAATTATGTGGAACTGGTGAATACTTTGCCATGAAAGCTATGGATAAAAATGTCATGCTCAACCGCAACAAGgtattcaaattaaattgctgggttacttttctagttaatttagcagccagataagctcttagaattcctattgtttacatgtatgactactacagctatg...

Basic information

species Vitis vinifera
transcript Vv06s0004g03700.t01
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g03700.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: LOC_Os12g01140.5 (Oryza sativa), 5'ss of exon 10
TGTGCATCTGGTGGAATTATGTGGAACTGGTGAATACTTTGCCATGAAAGCTATGGATAAAAATGTCATGCTCAACCGCAACAAGgtat-----tcaaattaaattgctgggt---tacttttctagttaatttagca-gccagataagctcttaga-attcctattgt-ttacatgtatgactactacagctatg-------
||| ||  |||| || || |     || || |||||||||||||||||||||||||||||||   ||||||| |||||||| ||||| |     |    | |  ||      |   ||| ||| | || |||  |  |       ||  ||  |||  ||  ||||||  ||| || | ||| ||| |     |||       
TGTACACTTGGTAGAGTTGTTGAATACAGGAGAATACTTTGCCATGAAAGCTATGGATAAAAGCATCATGCTTAACCGCAATAAGgtttgatgcttgtttcaccttttaaaatgtatacattttttgtgaataaaagacattgtttatacttctagttatgtctattgcattatatctctgagtac-attataatgtctctag

upper sequence: Vv06s0004g03700.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: GRMZM2G001457_T02 (Zea mays), 5'ss of exon 13
TGTGCATCTGGTGGAATTATGTGGAACTGGTGAATACTTTGCCATGAAAGCTATGGATAAAAATGTCATGCTCAACCGCAACAAGgtattcaaattaaatt---gctgggttacttttctagttaatttagcagccagataagctcttagaattcctattgtttacatgtatgactactacagctatg
||| ||  ||||||| ||   ||| || |||||||||||||||||||||||||||||||||| ||||||||| ||||| ||||||||||    |  |||||    |     ||   || |||||| ||        |   |   | |    ||     |||| || |  ||   |||           
TGTCCACTTGGTGGAGTTGCTTGGCACAGGTGAATACTTTGCCATGAAAGCTATGGATAAAAGTGTCATGCTTAACCGAAACAAGgtatgagtaacaaatttgatcacaaataacattttagttacttccatttttaatgattttttccacatctgatttgtctata-atacctctag----------

upper sequence: Vv06s0004g03700.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: GLYMA15G04850.1 (Glycine max), 5'ss of exon 14
TGTGCATCTGGTGGAATTATGTGGAACTGGTGAATACTTTGCCATGAAAGCTATGGATAAAAATGTCATGCTCAACCGCAACAAGgtattcaaattaaattgctgggttacttttctagttaattta-gcagccagataagctcttagaattcctattgtttacatgtatgactactacagctatg---
 ||||||||||||||  || ||||||||||| |||| ||||||||||| |||||||||||   ||| |||||||| || ||||||||  | |   | || | |  |  |  |||| ||  || |  | | |  |   | |  ||| |  ||    ||  ||          |  | || |  ||     
CGTGCATCTGGTGGAGCTACGTGGAACTGGTCAATATTTTGCCATGAAGGCTATGGATAAGGGTGTTATGCTCAATCGTAACAAGgttgtgattgtgaactacaagactttttttttacatattgcatgtattc---tcaattctcaacatgaaaat-attagttcactgaaacagtatatttacatag

upper sequence: Vv06s0004g03700.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: GLYMA13G40550.1 (Glycine max), 5'ss of exon 13
TGTGCATCTGGTGGAATTATGTGGAACTGGTGAATACTTTGCCATGAAAGCTATGGATAAAAATGTCATGCTCAACCGCAACAAGgtattcaaattaaattgctgggttacttttctagttaatttagcagccagataagctcttagaattcctattgtttacatgtatgactact-acagctatg----
|||||||||||||||  || ||||||||||| |||| ||||| |||||||||||||||||   ||| |||||||| || || |||||  |  ||||||  ||     ||  ||  | || |  |||     |    |    ||| | | |||  |   |  | || |  |   |||   | |  |     
TGTGCATCTGGTGGAGCTACGTGGAACTGGTCAATATTTTGCGATGAAAGCTATGGATAAGGGTGTTATGCTCAATCGTAATAAGgtgatttaattaacgtg--aatttttttccccaggt--tttcattacatattgtattctca-atttctcaacatggaaatattagttcacttgaaacagtatatt

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|30324849|gb|CD008111.1|CD008111
EST:     ACTTTGCCATGAAAGCTATGGATAAAAATGTCATGCTCAACCGCAACAAG                         GTGCATAGAGCTTGTGCTGAAAGAGAAATTCTTGACATGTTGGATCACCCT
genomic: ACTTTGCCATGAAAGCTATGGATAAAAATGTCATGCTCAACCGCAACAAGgtattcaaat ... ttttctgcagGTGCATAGAGCTTGTGCTGAAAGAGAAATTCTTGACATGTTGGATCACCCT
EST: gi|32267450|gb|CD716413.1|CD716413
EST:     ACTTTGCCATGAAAGCTATGGATAAAAATGTCATGCTCAACCGCAACAAG                         GTGCATAGAGCTTGTGCTGAAAGAGAAATTCTTGACATGTTGGATCACCCT
genomic: ACTTTGCCATGAAAGCTATGGATAAAAATGTCATGCTCAACCGCAACAAGgtattcaaat ... ttttctgcagGTGCATAGAGCTTGTGCTGAAAGAGAAATTCTTGACATGTTGGATCACCCT
EST: gi|30325883|gb|CD009145.1|CD009145
EST:     ACTTTGTCATGAAAGCTATGGATAAAAATGTCATGCTCAACCGCAACAAG                         GTGCATAGAGCTTGTGCTGAAAGAGAAATTCTTGACATGTTGGATCACCCT
genomic: ACTTTGCCATGAAAGCTATGGATAAAAATGTCATGCTCAACCGCAACAAGgtattcaaat ... ttttctgcagGTGCATAGAGCTTGTGCTGAAAGAGAAATTCTTGACATGTTGGATCACCCT
EST: gi|30325043|gb|CD008305.1|CD008305
EST:     ACTTTGCCATGAAAGCTATGGATAAAAATGTCATGCTCAACCGCAACAAG                         GTGCATAGAGCTTGTGCTGAAAGAGAAATTCTTGACATGTTGGATCACCCT
genomic: ACTTTGCCATGAAAGCTATGGATAAAAATGTCATGCTCAACCGCAACAAGgtattcaaat ... ttttctgcagGTGCATAGAGCTTGTGCTGAAAGAGAAATTCTTGACATGTTGGATCACCCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTGCATCTGGTGGAATTATGTGGAACTGGTGAATACTTTGCCATGAAAGCTATGGATAAAAATGTCATGCTCAACCGCAACAAGgtattcaaattaaattgctgggttacttttctagttaatttagcagccagataagctcttagaattcctattgtttacatgtatgactactacagctatg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aattaaa