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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctctcatgctcttgttccttctcttgatctttgccatcctatcctttgtcaccagatcttaataattggcttctctaattataaactgctcctagtgcagGAGGTGCTGCAAGGCCTGGAAAGGTTGTTGGTTCAGTGTTGCGTTACAACAACTGTGGAGCAGCTGCAGCAGCAGAGGTTCTTGAACAGCGGAGAATGGT

Basic information

species Vitis vinifera
transcript Vv05s0020g02530.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g02530.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA13G28120.1 (Glycine max), 3'ss of exon 9
ctctcatgctcttgttccttctcttgatctttgccatcctat---cctttgtcaccagatcttaataattggcttctctaattataaactgctcctagtgcagGAGGTGCTGCAAGGCCTGGAAAGGTTGTTGGTTCAGTGTTGCGTTACAACAACTGTGGAGCAGCTGCAGCAGCAGAGGTTCTTGAACAGCGGAGAATGGT---
   |   | | |   |   |    |    |||  |||||||      |     ||||       || ||   |   | ||  | |    | | | |  || ||| | |||||||||||||||||||||||| ||||| ||  ||||||||||||||||||| | ||| |   | || |||| |   ||||||||  |  ||||   
---tatagatttaacttggtacaatataatttttcatcctacagatttaaagtaccatgatgctattatcatccaatgtacatttgtggttccctttctgtagGTGTTGCTGCAAGGCCTGGAAAGGTTGTGGGTTCGGTAATGCGTTACAACAACTGTGGGGTAGCCGGGACGGCCGAGGCT---GAACAGCGTCGGGTGGTCAG

upper sequence: Vv05s0020g02530.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA15G10940.2 (Glycine max), 3'ss of exon 9
--ctctcatgctcttgttccttctcttgatctttgccatcctatcctttgtcaccagatcttaata-attggcttctctaattataaactgctcctagtgcagGAGGTGCTGCAAGGCCTGGAAAGGTTGTTGGTTCAGTGTTGCGTTACAACAACTGTGGAGCAGCTGCAGCAGCAGAGGTTCTTGAACAGCGGAGAATGGT---
   |   ||    || | |  |    | | || |   ||   |    |  | |    ||  ||||  | ||     |  | || |      ||     || ||| | ||||||||||||  |||||||||||||||||||  ||||||||||||||||||| | ||| |   | || |||| |   |||||||||||  ||||   
tagtacaatataattctcctctaatattacctatag-atttaaagtatcataatgctattgtaatccaatgtacattacatttgtggctcactttc--tgtagGTGTTGCTGCAAGGCCCCGAAAGGTTGTTGGTTCAGTAATGCGTTACAACAACTGTGGGGTAGCAGTGACGGCCGAGGCT---GAACAGCGGAGGGTGGTCAG
















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|33408065|gb|CF213692.1|CF213692
EST:     TGGAATCCCCATGGCAAGGCTTCCTCTCCAAGTTCCTCAAAGTACCCAAGTGCAG                     
genomic: TGGAATCCCCATGGCAAGGCTTCCTCTCCAAGTTCCTCAAAGTACCC-A----AGgtgggacttt ... cctagt
EST: gi|33407978|gb|CF213605.1|CF213605
EST:     TGGAATCCCCATGGCAAGGCTTCCTCTCCAAGTTCCTCAAAGTACCCAAGTGCAG                     
genomic: TGGAATCCCCATGGCAAGGCTTCCTCTCCAAGTTCCTCAAAGTACCC-A----AGgtgggacttt ... cctagt
EST: gi|110690752|gb|EE068184.1|EE068184
EST:     TGGAATCCCCATGGCAAGGCTTCCTCTCCAAGTTCCTCAAAGTACCCAAG                         GAGGTGCTGGCA-GGCCTGAAAAAGTTGTTGGTTCAGTGTTGCGTTACAAC
genomic: TGGAATCCCCATGGCAAGGCTTCCTCTCCAAGTTCCTCAAAGTACCCAAGgtgggacttt ... cctagtgcagGAGGTGCTG-CAAGGCCTGGAAAGGTTGTTGGTTCAGTGTTGCGTTACAAC
EST: gi|161719505|gb|FC067398.1|FC067398
EST:     TGGAATCCCCATGGCAAGGCTTCCTCTCCAAGTTCCTCAAAGTACCCAAG                         GAGGTGCTGCAAGGCCTGGAAAGGT-GTTGGTTCAGTGTTGCGTTACAACA
genomic: TGGAATCCCCATGGCAAGGCTTCCTCTCCAAGTTCCTCAAAGTACCCAAGgtgggacttt ... cctagtgcagGAGGTGCTGCAAGGCCTGGAAAGGTTGTTGGTTCAGTGTTGCGTTACAACA
EST: gi|33404616|gb|CF210243.1|CF210243
EST:     TGGAATCCCCATGGCAAGGCTTCCTCTCCAAGTTCCTCAAAGTACCCAAG                         GAGGTGCTGCAAGGCCTGGAAAGGTTGTTGGTTCAGTGTTGCGTTACAACA
genomic: TGGAATCCCCATGGCAAGGCTTCCTCTCCAAGTTCCTCAAAGTACCCAAGgtgggacttt ... cctagtgcagGAGGTGCTGCAAGGCCTGGAAAGGTTGTTGGTTCAGTGTTGCGTTACAACA
EST: gi|156735426|gb|EV239547.1|EV239547
EST:     TGGAATCCCCATGGCAAGGCTTCCTCTCCAAGTTCCTCAAAGTACCCAAG                         GAGGTGCTGCAAGGCCTGGAAAGGTTGTTGGTTCAGTGTTGCGTTACAACA
genomic: TGGAATCCCCATGGCAAGGCTTCCTCTCCAAGTTCCTCAAAGTACCCAAGgtgggacttt ... cctagtgcagGAGGTGCTGCAAGGCCTGGAAAGGTTGTTGGTTCAGTGTTGCGTTACAACA
EST: gi|71860512|gb|DT009567.1|DT009567
EST:     TGGAATCCCCATGGCAAGGCTTCCTCTCCAAGTTCCTCAAAGTACCCAAG                         GAGGTGCTGCAAGGCCT
genomic: TGGAATCCCCATGGCAAGGCTTCCTCTCCAAGTTCCTCAAAGTACCCAAGgtgggacttt ... cctagtgcagGAGGTGCTGCAAGGCCT
EST: gi|161706097|gb|FC056247.1|FC056247
EST:     TGGAATCCCCATGGCAAGGCTTCCTCTCCAAGTTCCTCAAAGTACCCAAG                         GAGGTGCTGCAAGGCCTGGAAAGGTTGTTGGTTCAGTGTTGCGTTACAACA
genomic: TGGAATCCCCATGGCAAGGCTTCCTCTCCAAGTTCCTCAAAGTACCCAAGgtgggacttt ... cctagtgcagGAGGTGCTGCAAGGCCTGGAAAGGTTGTTGGTTCAGTGTTGCGTTACAACA
EST: gi|110730439|gb|EE107523.1|EE107523
EST:     TGGAATCCCCATGGCAAGGCTTCCCCTCCAAGTTCCTCAAAGTACCCAAG                         GAGGTGCTGCAAGGCCTGNAAAGGTTGTTGGTTCAGTGTTGCGTTANCA-C
genomic: TGGAATCCCCATGGCAAGGCTTCCTCTCCAAGTTCCTCAAAGTACCCAAGgtgggacttt ... cctagtgcagGAGGTGCTGCAAGGCCTGGAAAGGTTGTTGGTTCAGTGTTGCGTTA-CAAC
EST: gi|110387017|gb|EC951656.1|EC951656
EST:     TGGAATCCCCATGGCAAGGCTTCCTCTCCAAGTTCCTCAAAGTACCCAAG                         GAGGTGCTGCAAGGCCTGGAAAGGTTGTTGGTTCAGTGTTGCGTTACAACA
genomic: TGGAATCCCCATGGCAAGGCTTCCTCTCCAAGTTCCTCAAAGTACCCAAGgtgggacttt ... cctagtgcagGAGGTGCTGCAAGGCCTGGAAAGGTTGTTGGTTCAGTGTTGCGTTACAACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtcaccagatcttaataattggcttctctaattataaactgctcctagtgcagGAGGTGCTGCAAGGCCTGGAAAGGTTGTTGGTTCAGTGTTGCGTTACAACAACTGTGGAGCAGCTGCAGCAGCAGAGGTTCTTGAACAGCGGAGAATGGT
                           ctctaat  putative branch site (score: 3)
                                        ctgctcct  putative PPT
                         ttctctaattataaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctctcatgctcttgttccttctcttgatctttgccatcctatcctttgtcaccagatcttaataattggcttctctaattataaactgctcctagtgcagGAGGTGCTGCAAGGCCTGGAAAGGTTGTTGGTTCAGTGTTGCGTTACAACAACTGTGGAGCAGCTGCAGCAGCAGAGGTTCTTGAACAGCGGAGAATGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- ctcatgc
- - - - - - - - ccttctc
- - - - - - - - - - - - - - - - -ccatcct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggcttc