Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACAATGCCACTATTTCAGCACCTCATATGCATGCCACATGCCTCGAGCTGTTGCAGGAAAATTTGCAGCCTGGAATGCATGCTCTAGATGTTGGTTCTGgtatattttaattctcatctcttgtgtttctataatttacatgcactacttctatgatgctgctttttaattttagtactaaaagaatataggataacaa...

Basic information

species Vitis vinifera
transcript Vv17s0000g09690.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g09690.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: LOC_Os04g40540.3 (Oryza sativa), 5'ss of exon 1
TACAATGCCACTATTTCAGCACCTCATATGCATGCCACATGCCTCGAGCTGTTGCAGGAAAATTTGCAGCCTGGAATGCATGCTCTAGATGTTGGTTCTGgtatat---tttaattctcatctcttgtgtttctataatttacatgcactacttcta-tgatgctgctttttaattttagtactaaaagaatataggataacaa
|| || || || || || || ||||| |||||||| || ||| | |||||  || ||||  | |||||||| ||||||||||||||||||||||| || |||||     || | | || |       |  | || || |     || ||||   | | ||  | || ||||  | |    |  | |     | |||   |   |
TATAACGCGACGATATCTGCTCCTCACATGCATGCGACCTGCTTGGAGCTACTGAAGGATCACTTGCAGCCAGGAATGCATGCTCTAGATGTTGGATCAGgtattcaggttcattactgaaacaccatactcctgtagtcc---tgtactatagcaaatgcggttgtttttagagtgccctgttgagttt-tctagaccatgca

upper sequence: Vv17s0000g09690.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA04G36430.1 (Glycine max), 5'ss of exon 2
TACAATGCCACTATTTCAGCACCTCATATGCATGCCACATGCCTCGAGCTGTTGCAGGAAAATTTGCAGCCTGGAATGCATGCTCTAGATGTTGGTTCTGgtatat-tttaattctcatctcttgtgtttctataatttacatgcactacttctatgatgctgctttttaattttagtactaaaagaatataggataacaa--
|||||||||||||| || || || |||||||||||||  || ||  || || |  |||| |||||||||||||| ||||||||||| |||||||| ||||||||||  |  ||   | | |  |  |||  ||| |  |  |   | ||||  | ||   ||  ||| || |      ||       ||      |       
TACAATGCCACTATCTCTGCGCCGCATATGCATGCCATGTGTCTTCAGTTGCTTGAGGAGAATTTGCAGCCTGGGATGCATGCTCTGGATGTTGGCTCTGgtatatgctccatgaacctattataagttattattacattaaaagattactgtt-tgt--cttatttgtattccacagaccgcgttcatgcgaagtgggtgct

upper sequence: Vv17s0000g09690.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA06G18460.1 (Glycine max), 5'ss of exon 1
TACAATGCCACTATTTCAGCACCTCATATGCATGCCACATGCCTCG-AGCTGTTGCAGGAAAATTTGCAGCCTGGAATGCATGCTCTAGATGTTGGTTCTGgtatattttaattctcatctcttgtgtttctat-aatttacatgcactacttctatgatgctgctttttaattttagtactaaaagaatataggataacaa---
 |||   |||       ||      ||   ||    |  |||  || |  || || ||||||||||||||||||| ||||||||| | || ||||| | ||||||||  |     ||| | || || ||   || || ||| | | | || |  |    |  |   | ||    |  || | |    | |    | |    |   
GACAGCCCCATGGCCATAGGGTACAATGC-CACTATATCTGCGCCGCATATGCTGGAGGAAAATTTGCAGCCTGGGATGCATGCTTTGGACGTTGGCTATGgtatatgct--ccatcaac-ctcgtattataatcaaattagaag-attattgtttgtctaatttgtattggactgcgttcaagtgaagtgggaggttgttagtt

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|110391868|gb|EC956879.1|EC956879
EST:     GTTGCAGGAAAATTTGCAGCCTGGAATGCATGCTCTAGATGTTGGTTCTG                         GAACGGGGTATTTGACAGCCTGCTTTGCACTGATGGTTGGACCACAAGGTT
genomic: GTTGCAGGAAAATTTGCAGCCTGGAATGCATGCTCTAGATGTTGGTTCTGgtatatttta ... taaattttagGAACGGGGTATTTGACAGCCTGCTTTGCACTGATGGTTGGACCACAAGGTT
EST: gi|30253100|gb|CB970651.1|CB970651
EST:     GTTGCAGGAAAATTTGCAGCCTGGAATGCATGCTCTAGATGTTGGTTCTG                         GAACGGGGTATTTGACAGCCTGCTTTGCACTGATGGTTGGACCACAAGGTT
genomic: GTTGCAGGAAAATTTGCAGCCTGGAATGCATGCTCTAGATGTTGGTTCTGgtatatttta ... taaattttagGAACGGGGTATTTGACAGCCTGCTTTGCACTGATGGTTGGACCACAAGGTT
EST: gi|110380339|gb|EC945595.1|EC945595
EST:     GTTGCAGGAAAATTTGCAGCCTGGAATGCATGCTCTAGATGTTGGTTCTG                         GAACGGGGTATTTGACAGCCTGCTTTGCACTGATGGTTGGACCACAAGGTT
genomic: GTTGCAGGAAAATTTGCAGCCTGGAATGCATGCTCTAGATGTTGGTTCTGgtatatttta ... taaattttagGAACGGGGTATTTGACAGCCTGCTTTGCACTGATGGTTGGACCACAAGGTT
EST: gi|110731607|gb|EE106167.1|EE106167
EST:     GTTGCAGGAAAATTTGCAGCCTGGAATGCATGCTCTAGATGTTGGTTCTG                         GAACGGGGTATTTGACAGCCTGCTTTGCACTGATGGTTGGACCACAAGGTT
genomic: GTTGCAGGAAAATTTGCAGCCTGGAATGCATGCTCTAGATGTTGGTTCTGgtatatttta ... taaattttagGAACGGGGTATTTGACAGCCTGCTTTGCACTGATGGTTGGACCACAAGGTT
EST: gi|22009919|gb|BQ794953.1|BQ794953
EST:     GTTGCAGGAAAATTTGCAGCCTGGAATGCATGCTCTAGATGTTGGTTCTG                         GAACGGGGTATTTGACAGCCTGCTTTGCACTGATGGTTGGACCACAAGGTT
genomic: GTTGCAGGAAAATTTGCAGCCTGGAATGCATGCTCTAGATGTTGGTTCTGgtatatttta ... taaattttagGAACGGGGTATTTGACAGCCTGCTTTGCACTGATGGTTGGACCACAAGGTT
EST: gi|110726896|gb|EE103078.1|EE103078
EST:     GTTGCAAGAAAATTTGCAGCCTGGAATGCATGCTCTAGATGTTGGTTCTG                         GAACGGGGTATTTGACAGCCTGCTTTGCACTGATGGTTGGACCACAAGGTT
genomic: GTTGCAGGAAAATTTGCAGCCTGGAATGCATGCTCTAGATGTTGGTTCTGgtatatttta ... taaattttagGAACGGGGTATTTGACAGCCTGCTTTGCACTGATGGTTGGACCACAAGGTT
EST: gi|110688221|gb|EE066525.1|EE066525
EST:     GTTGCAGGAAAATTTGCAGCCTGGAATGCATGCTCTAGATGTTGGTTCTG                         GAACGGGGTATTTGACAGCCTGCTTTGCACTGATGGTTGGACCACAAGGTT
genomic: GTTGCAGGAAAATTTGCAGCCTGGAATGCATGCTCTAGATGTTGGTTCTGgtatatttta ... taaattttagGAACGGGGTATTTGACAGCCTGCTTTGCACTGATGGTTGGACCACAAGGTT
EST: gi|33407775|gb|CF213402.1|CF213402
EST:     GTTGCAGGAAAATTTGCAGCCTGGAATGCGTGCTCTAGATGTTGGTTCTG                         GAACGGGGTATTTGACAGCCTGCTTTGCACTGATGGTTGGACCACAAGGTT
genomic: GTTGCAGGAAAATTTGCAGCCTGGAATGCATGCTCTAGATGTTGGTTCTGgtatatttta ... taaattttagGAACGGGGTATTTGACAGCCTGCTTTGCACTGATGGTTGGACCACAAGGTT
EST: gi|33410468|gb|CF216095.1|CF216095
EST:     GTTGCAGGAAAATTTGCAGCCTGGAATGCGTGCTCTAGATGTTGGTTCTG                         GAACGGGGTATTTGACAGCCTGCTTTGCACTGATGGTTGGACCACAAGGTT
genomic: GTTGCAGGAAAATTTGCAGCCTGGAATGCATGCTCTAGATGTTGGTTCTGgtatatttta ... taaattttagGAACGGGGTATTTGACAGCCTGCTTTGCACTGATGGTTGGACCACAAGGTT
EST: gi|14580339|gb|BG273781.1|BG273781
EST:     GTTGCAGGAAAATTTGCAGCCTGGAATGCATGCTCTAGATGTTGGTTCTG                         GAACGGGGTATTTGACAGCCTGCTTTGCACTGATGGTTGGACCACAAGGTT
genomic: GTTGCAGGAAAATTTGCAGCCTGGAATGCATGCTCTAGATGTTGGTTCTGgtatatttta ... taaattttagGAACGGGGTATTTGACAGCCTGCTTTGCACTGATGGTTGGACCACAAGGTT
EST: gi|110696639|gb|EE072934.1|EE072934
EST:     CTGGAATGCATGCTCTAGATGTTGGTTCTG                         GAACGGGGTATTTGACAGCCTGCTTTGCACTGATGGTTGGACCACAAGGTT
genomic: CTGGAATGCATGCTCTAGATGTTGGTTCTGgtatatttta ... taaattttagGAACGGGGTATTTGACAGCCTGCTTTGCACTGATGGTTGGACCACAAGGTT
EST: gi|110405103|gb|EC970636.1|EC970636
EST:     GTTGCAGGAAAATTTGCAGCCTGGAATGCATGCTCTAGATGTTGGTTCTG                         GAACGGGGTATTTGACAGCCTGCTTTGCACTGATGGTTGGACCACAAGGTT
genomic: GTTGCAGGAAAATTTGCAGCCTGGAATGCATGCTCTAGATGTTGGTTCTGgtatatttta ... taaattttagGAACGGGGTATTTGACAGCCTGCTTTGCACTGATGGTTGGACCACAAGGTT
EST: gi|161713127|gb|FC062485.1|FC062485
EST:     GTTGCAGGAAAATTTGCAGCCTGGAATGCATGCTCTAGATGTTGGTTCTG                         GAACGGGGTATTTGACAGCCTGCTTTGCACTGATGGTTGGACCACAAGGTT
genomic: GTTGCAGGAAAATTTGCAGCCTGGAATGCATGCTCTAGATGTTGGTTCTGgtatatttta ... taaattttagGAACGGGGTATTTGACAGCCTGCTTTGCACTGATGGTTGGACCACAAGGTT
EST: gi|34549921|gb|CF518153.1|CF518153
EST:     GTTGCAGGAAAATTTGCAGCCTGGAATGCATGCTCTAGATGTTGGTTCTG                         GAACGGGGTATTTGACAGCCTGCTTTGCACTGATGGTTGGACCACAAGGTT
genomic: GTTGCAGGAAAATTTGCAGCCTGGAATGCATGCTCTAGATGTTGGTTCTGgtatatttta ... taaattttagGAACGGGGTATTTGACAGCCTGCTTTGCACTGATGGTTGGACCACAAGGTT
EST: gi|46917806|gb|CN547135.1|CN547135
EST:     GTTGCAGGAAAATTTGCAGCCTGGAATGCATGCTCTAGATGTTGGTTCTG                         GAACGGGGTATTTGACAGCCTGCTTTGCACTGATGGTTGGACCACAAGGTT
genomic: GTTGCAGGAAAATTTGCAGCCTGGAATGCATGCTCTAGATGTTGGTTCTGgtatatttta ... taaattttagGAACGGGGTATTTGACAGCCTGCTTTGCACTGATGGTTGGACCACAAGGTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TACAATGCCACTATTTCAGCACCTCATATGCATGCCACATGCCTCGAGCTGTTGCAGGAAAATTTGCAGCCTGGAATGCATGCTCTAGATGTTGGTTCTGgtatattttaattctcatctcttgtgtttctataatttacatgcactacttctatgatgctgctttttaattttagtactaaaagaatataggataacaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aggataa