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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggagcttctgcaaaggattatttttgaacagaagtttcactttttctggtaggtttcaataagctatggtctgttttattcttttaacttcattctttgcaattttgtcctagGTGGTATGCCAAAAGGTTTCTGCATCCTGACATTGTGGCGCCATATGACTATATATTTATCTGGGATGAAGATCTAGGAGTTGAGCATTTTAATGCAGAA

Basic information

species Vitis vinifera
transcript Vv01s0137g00770.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0137g00770.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA11G37770.1 (Glycine max), 3'ss of exon 7
gtaaggagct--------------tctgcaaaggattatttttgaacagaagtttcactttttctggtaggtttcaataagctatggtctgttttattcttttaacttcattctttgcaattttgtcctagGTGGTATGCCAAAAGGTTTCTGCATCCTGACATTGTGGCGCCATATGACTATATATTTATCTGGGATGAAGATCTAGGAGTTGAGCATTTTAATGCAGAA
||||||||||              | |  | ||||| | |||| |    |  |||  |  ||  | ||   |     | | |||   ||  || | |   |  |    || | || |   ||   || |||||||||||||||  ||||||||||||||||||||||||| ||||||||||||||||| || ||||||||||| || || |||||||||||||||||||||
gtaaggagctaagatgttcattattttttagaggataaattttcattgtagtttttgcaattaatagtgtttagtgcttacctaatttcaattatgtcaatacattgacaattttagtttttccctcttagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATATTCATATGGGATGAAGACCTGGGTGTTGAGCATTTTAATGCAGAA

upper sequence: Vv01s0137g00770.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA05G30830.1 (Glycine max), 3'ss of exon 7
-----------------------gtaaggagcttctgcaaaggattatttttgaacagaagtttcact-ttttctggtaggtttcaataagctatggtctgttttattcttttaactt----catt-----ctttgcaatttt--gtcctagGTGGTATGCCAAAAGGTTTCTGCATCCTGACATTGTGGCGCCATATGACTATATATTTATCTGGGATGAAGATCTAGGAGTTGAGCATTTTAATGCAGAA
                       ||||  |     ||  ||   ||  ||   |     |   | | | || | ||      |  ||| |    || |||| || |||| | ||  ||     |||      ||    |||||   ||||||||||||||||||  ||||||||||||||||||||||||| |||||||||||||| ||||| ||||||||||| || || ||||| |||||||||||||||
gtaagaatccattgcgctcgatcgtaaatattggatgacaaattttccttgcaacttttaccattattattgtttgcctaactaaaatcaaaagtgttctgctt-attcatctatgttatgatattaagcatttaattattttccctcctagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATTTTTATATGGGATGAAGACCTGGGTGTTGAACATTTTAATGCAGAA

upper sequence: Vv01s0137g00770.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA08G14040.1 (Glycine max), 3'ss of exon 7
gtaaggagcttctgcaaaggattat---ttttgaacagaagtttc--------actttttct---ggtaggtttcaataagctatggtctgttttattcttttaact---tcattctttg------------caattttgt-----cctagGTGGTATGCCAAAAGGTTTCTGCATCCTGACATTGTGGCGCCATATGACTATATATTTATCTGGGATGAAGATCTAGGAGTTGAGCATTTTAATGCAGAA
||||| | |   |||    ||| ||   | ||| |    |  ||         ||| || |      ||   ||     | |||  |||     | ||||  ||| |   ||||  | ||             |||||| |     |||||||||||||||||  ||||||||||||||||||||||||| |||||||||||||| ||||| ||||||||||| || || ||||| |||||||||||||| 
gtaagaatccattgcgctcgatcataaatattggatgacatattttccttgcaactcttaccatcattattgtttgcctaactaaagtcaaaagtgttctgctaattcaatcatgttatgatattaagcatttaatttttttccctcctagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATTTTTATATGGGATGAAGACCTGGGTGTTGAACATTTTAATGCAGAG

upper sequence: Vv01s0137g00770.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA18G01710.1 (Glycine max), 3'ss of exon 7
gtaaggagcttctgcaaaggattattttt--gaacagaagtt-tcacttt--ttctggtaggt-------ttcaata---agctatggtctgttttattcttttaacttcattctttgcaattttgtcctagGTGGTATGCCAAAAGGTTTCTGCATCCTGACATTGTGGCGCCATATGACTATATATTTATCTGGGATGAAGATCTAGGAGTTGAGCATTTTAATGCAGAA
|| |||||||   ||     |||||||||  ||  | || || ||  | |  || | | | ||       ||||||    | |||   ||  || | || || ||    || | || |   ||   || |||||||||||||||  ||||||||||||||||||||||||| ||||||||||||||||| || ||||||||||| || || ||||||||||||||||| |||
gttaggagctaa-gcggttaattattttttagataataaattatcgttgtagtttttgcaagtattagtgttcaatgcttacctaatttcaattatgttattatattgacaattttggtttttccctcttagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATATTCATATGGGATGAAGACCTGGGTGTTGAGCATTTTAATGCGGAA

upper sequence: Vv01s0137g00770.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA08G14050.1 (Glycine max), 3'ss of exon 5
gtaaggagcttctgcaaaggattatttttgaacagaagtttcactttttctggtaggtttcaataagctatggtctgttttattcttttaacttcattctttgcaattttgtcctagGTGGTATGCCAAAAGGTTTCTGCATCCTGACATTGTGGCGCCATATGACTATATATTTATCTGGGATGAAGATCTAGGAGTTGAGCATTTTAATGCAGAA
             | |||  |   || |       || | ||| | | ||       || || | |  ||| || ||    | |        ||  || ||| |  |||  ||  |||||||||||||| |||||||| ||||| ||||||||||| |||||||||||||| || || ||||||||||| || || |||||| |||| |||||||||
-------------gtaaaaaa--gttctctgcttaaattctcattgtgtc-----atttccagttaa-tattgtttgccaaacttaaaatggtttgttattt-ctttttcctctcagGTGGTATGCCAAGAGGTTTCTACATCCAGACATTGTGGCACCATATGACTATATTTTCATGTGGGATGAAGACCTGGGGGTTGAGAATTTCAATGCAGAA

upper sequence: Vv01s0137g00770.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA05G30850.1 (Glycine max), 3'ss of exon 5
gtaaggagcttctgcaaaggattatttttgaacagaagtttcactttttctggtaggtttcaataagctatggtctgttttattcttttaacttcattctttgcaattttgtcctagGTGGTATGCCAAAAGGTTTCTGCATCCTGACATTGTGGCGCCATATGACTATATATTTATCTGGGATGAAGATCTAGGAGTTGAGCATTTTAATGCAGAA
                  | |  | || |   |  || |||   |  || ||| |  |||  |     ||| || |     | |        ||  || ||| |  |    || ||||||||||||||| |||||||| ||||| ||||||||||  |||||||||||||| || || ||||||||||| || || |||||| |||| ||||| |||
------------------gtaaaaattctatgcttaaattt---tcattgtggcatattttcagttaatattgtttaccaaacttaaaatggtttgttattt-ctttcgcctcttagGTGGTATGCCAAGAGGTTTCTACATCCAGACATTGTGGTACCATATGACTATATTTTCATGTGGGATGAAGACCTGGGGGTTGAGAATTTCAATGCTGAA

upper sequence: Vv01s0137g00770.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT1G13000.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaaggagcttctgcaaaggattatttttgaacagaagtttcactttttctggtaggtttcaataagctatggtctgttttatt--cttttaacttcat----tctttgcaattttgtccta-gGTGGTATGCCAAAAGGTTTCTGCATCCTGACATTGTGGCGCCATATGACTATATATTTATCTGGGATGAAGATCTAGGAGTTGAGCATTTTAATGCAGAA
                            | |||| || |||   ||  ||| |    |   |     ||  ||   | ||  ||  |  ||||||   |    |  ||| |  | | |  || |||||||||| ||||||||||||||||||||||||||||| || ||||||||| |||| |||||||||||||| || ||  ||||  | ||  ||| ||||
---------------------------gtaaacataactttactttgctctagctactccaatcttcctgaggctagcttgtttaaccattaactctctctggttattgtatatatattttaagGTGGTATGCTAAAAGGTTTCTGCATCCTGACATTGTGGCACCTTATGACTATGTATTCATCTGGGATGAAGACCTCGGCCTTGAAAACTTCGATGTAGAA

upper sequence: Vv01s0137g00770.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT3G26440.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaaggagcttctgcaaaggattatttttgaacagaagtttcactttttctggtaggtttcaataagctatggtctgttttattcttttaacttcattctttgcaattttgtcctagGTGGTATGCCAAAAGGTTTCTGCATCCTGACATTGTGGCGCCATATGACTATATATTTATCTGGGATGAAGATCTAGGAGTTGAGCATTTTAATGCAGAA
                              |||| ||    |||||||| |  ||  | ||| |   |  || |||      ||   | ||     ||   |    || | |   ||||||||||| |||||||||||||||||||| ||  | || |||||||| |||||||| || |||||||||||||| || |||||  | ||  | ||||||
----------------------------gtaacaaaacaaacactttttttt-tatctctcagtttccattgatctaaagctttaaataaaacgttttgaatatgtttctattgaagGTGGTATGCTAAAAGGTTTCTGCATCCTGATATCATAGCACCATATGAATATATATTCATTTGGGATGAAGATCTTGGCGTTGAAAACTTCGACGCAGAA

upper sequence: Vv01s0137g00770.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT1G67850.2 (Arabidopsis thaliana), 3'ss of exon 7
gtaaggagcttctgcaaaggattatttttgaacagaagtttcactttttctggtaggtttcaataagctatggtctgttttattcttttaacttcattc---tttgcaattttgtcctagGTGGTATGCCAAAAGGTTTCTGCATCCTGACATTGTGGCGCCATATGACTATATATTTATCTGGGATGAAGATCTAGGAGTTGAGCATTTTAATGCAGAA
                         |    |||      || | | ||| ||||||     || |   | |||| |||||    ||  | ||| | ||      || || | | |  |||||||||||| || |||||| |||| ||||| ||||| ||   |||||| ||||| ||  ||||||||||||| || || || ||||||||||| ||||||
------------------------gtaccaaacgct--ctttattctttatggtag-----aaaatagtttggtgtgtttatgactactgactcccttggcacctggaaatatat--tagGTGGTATGCAAAGAGGTTTTTGCACCCTGATATTGTAGCAAGATATGATTATATCTTCGTCTGGGATGAAGACCTGGGTGTCGAGCATTTTAACGCAGAA

upper sequence: Vv01s0137g00770.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT1G24570.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaaggagcttctgcaaaggattatttttgaacagaagtttcactttttctggtaggtttcaataagctatggtctgttttattcttttaacttcattctttgcaattttgtcctagGTGGTATGCCAAAAGGTTTCTGCATCCTGACATTGTGGCGCCATATGACTATATATTTATCTGGGATGAAGATCTAGGAGTTGAGCATTTTAATGCAGAA
                                     || ||| | | | ||      || ||  | || |  | | | |  ||  || |   ||     |||  |   |     ||||||||||| || || ||  |||| || |||||||| || | ||| || |||||||| || |||||||| ||||| |||||||| || ||||||||||||
-------------------------------------gtatcaatatctttg-----ctttaacca-cttttttttatctggtttcttgactctctcatattgtgaacata----agGTGGTATGCAAAGAGATTCTTGCACCCGGACATTGTAGCACGATACGATTATATATTCATATGGGATGAGGATCTTGGAGTTGATCACTTTAATGCAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataagctatggtctgttttattcttttaacttcattctttgcaattttgtcctagGTGGTATGCCAAAAGGTTTCTGCATCCTGACATTGTGGCGCCATATGACTATATATTTATCTGGGATGAAGATCTAGGAGTTGAGCATTTTAATGCAGAA
                       ttttaac  putative branch site (score: 2)
                                            ttttgtcct  putative PPT
               ttttattcttttaact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggagcttctgcaaaggattatttttgaacagaagtttcactttttctggtaggtttcaataagctatggtctgttttattcttttaacttcattctttgcaattttgtcctagGTGGTATGCCAAAAGGTTTCTGCATCCTGACATTGTGGCGCCATATGACTATATATTTATCTGGGATGAAGATCTAGGAGTTGAGCATTTTAATGCAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA