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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggtaacactcctcacttcccggttatttcatcatttgaaatgaattcttagattcactaaggcccttcaaaacttcatgttagGTGATGTATGAAGAAGCAAGTCAAGTTGCAAATGATGCAGTTGGCAGCATCAGAACTGTTGCATCATTTTGTGCGGAAAAGAAGGTGATGGATATGTATC

Basic information

species Vitis vinifera
transcript Vv10s0003g02540.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0003g02540.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os01g34970.1 (Oryza sativa), 3'ss of exon 9
gttggtaacactcctcacttcccgg--ttatttcatcatttgaaatgaattct-------tagattcactaaggcccttcaaaacttcatgttagGTGATGTATGAAGAAGCAAGTCAAGTTGCAAATGATGCAGTTGGCAGCATCAGAACTGTTGCATCATTTTGTGCGGAAAAGAAGGTGATGGATATGTATC
||   ||  |    | | |     |  || |   | | ||  | |||  ||||        |  ||   | | |   |||     |  |    || ||| ||||||||||||||||||||| |||| ||||||||||||  ||||||||||||| |||||||||||||| ||  |||| ||||| ||    ||| 
gtacatacaatggattaatcatgagcattgtgctacccttacagatgctttctcatgcaacacgttgtttgatgttattctttgttgtaatgcagCTGAAGTATGAAGAAGCAAGTCAAGTAGCAACTGATGCAGTTGGAGGCATCAGAACTGTGGCATCATTTTGTGCTGAGCAGAAAGTGATAGAAGCATATG

upper sequence: Vv10s0003g02540.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os05g47500.1 (Oryza sativa), 3'ss of exon 10
gttggtaacactcctcacttcccggttatttcatcatt-------tgaaatgaattcttagattcactaaggccc--------ttcaaaacttcatgttagGTGATGTATGAAGAAGCAAGTCAAGTTGCAAATGATGCAGTTGGCAGCATCAGAACTGTTGCATCATTTTGTGCGGAAAAGAAGGTGATGGATATGTATC
    |  | | |  |   ||| |  |  ||||||| ||       ||| |   ||| ||| | |   |      |        ||  | |  | |   ||| | ||||||||||||||||| |||||||||| |||||||||||| ||||||||||| || ||||| | |||||| || ||||| ||||||   |  ||  
-cacgatatatttgtgcattctctttcctttcatccttatggatgtgacagtcatttttaaagttgtttgttttccatttatgtttgatatgtgactgtagATCATGTATGAAGAAGCAAGCCAAGTTGCAACTGATGCAGTTGGTAGCATCAGAACAGTAGCATCTTATTGTGCTGAGAAGAAAGTGATGACAAAATACA

upper sequence: Vv10s0003g02540.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os01g50080.1 (Oryza sativa), 3'ss of exon 7
--------------gttggtaacactcctcacttcccggttatttcatcatttgaaatgaattcttagattcactaaggcccttcaaaacttcatgttagGTGATGTATGAAGAAGCAAGTCAAGTTGCAAATGATGCAGTTGGCAGCATCAGAACTGTTGCATCATTTTGTGCGGAAAAGAAGGTGATGGATATGTATC
               |   | |   |   ||   |    | | ||  |   ||| |||        | |||   |      || | |    |      |||||||||||||||| ||||||||||||| || ||| ||| |||| ||||| || ||||| || || || ||||| || ||||  |||||  | |  ||  
gtattacaactgacatatttcatgattggcatcgcataatgaatttttttcttgcaatattagtaaatattgttttgctaactgctagcgatttctacagGTGATGTATGAAGATGCAAGTCAAGTTGTAACTGAAGCAATTGGTAGCATTAGGACTGTAGCGTCTTTCTGTGCAGAGAAGAGAGTGATTAAAACATACA

upper sequence: Vv10s0003g02540.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os01g50160.1 (Oryza sativa), 3'ss of exon 9
-gttggtaacactcctcac---ttcccggttatttcat-catttgaaatgaattctt---agattcactaaggcccttcaa--aacttcatgtt----agGTGATGTATGAAGAAGCAAGTCAAGTTGCAAATGATGCAGTTGGCAGCATCAGAACTGTTGCATCATTTTGTGCGGAAAAGAAGGTGATGGATATGTATC
 |||  |||   || | ||   |     |  |   ||| || |  | ||  ||| ||   |  ||   |||       |||  || | |  |||    || || |||||||||| ||||||||||| || | |||||||||  |||||||||| ||||| || || |||||| | || || |  ||||||   |||||| 
agtttctaaatttcatgacgaataatgagaaacaacattcactctagatacatttttcacaacttgcttaaattgtgacaatgaattcctggtttggcagATGTTGTATGAAGATGCAAGTCAAGTGGCTACTGATGCAGTAAGCAGCATCAGGACTGTAGCTTCCTTTTGTTCTGAGAAAAGAGTGATGACAATGTATG

upper sequence: Vv10s0003g02540.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA15G09680.1 (Glycine max), 3'ss of exon 9
gttggtaacactcctcacttcccggttatttcatcatttgaa--atgaattcttagattcactaaggcccttcaaaacttcatgttagGTGATGTATGAAGAAGCAAGTCAAGTTGCAAATGATGCAGTTGGCAGCATCAGAACTGTTGCATCATTTTGTGCGGAAAAGAAGGTGATGGATATGTATC
||| |    |||    ||||   |   ||| ||| | |  ||  ||| ||| |     |||  |      ||     || |    ||||  | ||||||||| ||||||||||| ||||||||||| ||||| |||||||||||  |||||||||| ||||| |||   |||||||||||||||||  
gttagccttacttgcaacttt--gtcaattccattaatgaaattatgcattatggacatcatgagaatattttgt--ctgctgtgtagGCAAAGTATGAAGAGGCAAGTCAAGTGGCAAATGATGCTGTTGGTAGCATCAGAACCATTGCATCATTCTGTGCCGAATCAAAGGTGATGGATATGTACA

upper sequence: Vv10s0003g02540.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA13G29380.1 (Glycine max), 3'ss of exon 9
gttggtaacactcctcacttcccggttatttcatcat---ttgaaatgaattcttagattcactaaggcccttcaaaacttcatgttagGTGATGTATGAAGAAGCAAGTCAAGTTGCAAATGATGCAGTTGGCAGCATCAGAACTGTTGCATCATTTTGTGCGGAAAAGAAGGTGATGGATATGTATC
||||||   | |       | | | ||   |||  |    ||  || | |  | ||  || || |  | ||||      |   |  |||||||||||||| || |||||||| || |||| |||||| ||||| ||||| ||||||||||||||||| ||||| ||    ||||||||||| |||||  
gttggtctaaatttagttatgctgattccatcaatagaaattagaaagtaagcatatgttgacaagagtcctttg----tcttttatagGTGATGTATGAGGAGGCAAGTCAGGTGGCAACTGATGCTGTTGGTAGCATTAGAACTGTTGCATCATTCTGTGCTGAGCCAAAGGTGATGGAAATGTACA

upper sequence: Vv10s0003g02540.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT4G18050.1 (Arabidopsis thaliana), 3'ss of exon 9
----------gttggtaacactcctcacttcccggttatttcatcatttgaaatgaattcttagattcactaaggcccttcaaaacttcatgttagGTGATGTATGAAGAAGCAAGTCAAGTTGCAAATGATGCAGTTGGCAGCATCAGAACTGTTGCATCATTTTGTGCGGAAAAGAAGGTGATGGATATGTATC
            |||| |||    |   ||   |  ||| ||    ||| |   |   | |  | || ||| |     ||      |     ||||| ||||||||||||||| |||||||| || |||||||||||  ||||||| ||||| |||||||| || ||||| ||  |||| ||||||||| | || |
gttttaatatagtggttacaacatt---tttttgaatatatcccggttt-agtcgcgatttcgggtttactgatcgatttttt--ttctggtttagGCGATGTATGAAGAAGCGAGTCAAGTGGCGAATGATGCAGTGAGCAGCATAAGAACGGTTGCATCTTTCTGTGCAGAGGAGAAAGTGATGGATTTATACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catcatttgaaatgaattcttagattcactaaggcccttcaaaacttcatgttagGTGATGTATGAAGAAGCAAGTCAAGTTGCAAATGATGCAGTTGGCAGCATCAGAACTGTTGCATCATTTTGTGCGGAAAAGAAGGTGATGGATATGTATC
         aaatgaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggtaacactcctcacttcccggttatttcatcatttgaaatgaattcttagattcactaaggcccttcaaaacttcatgttagGTGATGTATGAAGAAGCAAGTCAAGTTGCAAATGATGCAGTTGGCAGCATCAGAACTGTTGCATCATTTTGTGCGGAAAAGAAGGTGATGGATATGTATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA