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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttactttcatcatgtagactaatctatttacccttttttttgtactgaaatatcatctatcattattttcagattctgattattttatttgtacttcgttaaatagTATGGGCGACCATTGTATGGAGATGTTTTTGGTGTTCAGCAACAAGAACAACCAAACTATGAG

Basic information

species Vitis vinifera
transcript Vv00s0818g00010.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0818g00010.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA13G31550.2 (Glycine max), 3'ss of exon 10
-----------------------------gtgagttactttcatcatgtagactaatctatttacccttttttttgtactgaaatatcatctatcattattttc-----agattctgattattttattt--gtacttcgt-taaatagTATGGGCGACCATTGTATGGAGATGTTTTTGGTGTTCAGCAACAAGAACAACCAAACTATGAG
                              |   | | |||  | |  | ||    |   || |  ||| |||||  | ||||   ||  | ||  || | |       | ||  || ||| ||   ||   | |||| | | || |||||||||| ||| ||||||||||||||||||||||||| |||||||| || || |||||||||
gtatatatttttttacatattcactgtttttttatcattttttttaaattgataggttccttaattcttcttttt-cagtgaagagtcccccattcttttatctcactgacatgttgtttacttgtcttcaattcttcatgtgaacagTATGGGCGTCCACTGTATGGAGATGTTTTTGGTGTTCAACAACAAGATCAGCCTAACTATGAG

upper sequence: Vv00s0818g00010.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA15G07760.1 (Glycine max), 3'ss of exon 10
gtgagttactttcatcatgtagactaatctatttacccttttttttgtactgaaatatca--tctatcattattttcagattctgattattttatttgtacttcgttaaatagTATGGGCGACCATTGTATGGAGATGTTTTTGGTGTTCAGCAACAAGAACAACCAAACTATGAG
|| ||  | |||   ||| |  |||  |   |||| | ||| || | |    || |   |  ||| |   | ||||      ||||    |||| ||||  |      || |||||||||| ||| ||||||||||||||||||||||||| |||||||| || || |||||||||
gt-agaaattttttacatattcactgtttattttatcatttattattttaaaaattgataggtctctggctcttttatctcactgacatgtttacttgtcttcacgcgaacagTATGGGCGTCCACTGTATGGAGATGTTTTTGGTGTTCAACAACAAGATCAGCCCAACTATGAG

upper sequence: Vv00s0818g00010.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA13G25110.2 (Glycine max), 3'ss of exon 10
-------------------------gtgagttactttcatcatgtagactaatctatttacccttttt--tttgtactgaaatatcatctatcattattttcagattctgattattttatttgtacttcgttaaatagTATGGGCGACCATTGTATGGAGATGTTTTTGGTGTTCAGCAACAAGAACAACCAAACTATGAG
                          |   | | ||   |  || |   | ||   |||     ||||  ||| || | ||      ||   |    |||        |||  | |||  ||||       |||| ||||||| || ||| | ||||||||||||||||||||||| |||||||| || || || ||||||
gtacattttttatattcactcttcttttcatcatttgatttttgaattattatgggtttctgaattttcatttttattaaagggctctcccaccccttttcacctcattgaccacttttcttgtctgcacctaaacagTATGGCCGTCCACTTTATGGAGATGTTTTTGGTGTTCATCAACAAGATCAGCCTAATTATGAG

upper sequence: Vv00s0818g00010.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA07G31350.1 (Glycine max), 3'ss of exon 6
gtgagttactttcatcatgtagactaatctatttacccttttttttgtactgaaatatcatctatcattattttcagattctgattattttatttgtacttcgttaaatagTATGGGCGACCATTGTATGGAGATGTTTTTGGTGTTCAGCAACAAGAACAACCAAACTATGAG
   |  ||||||        | |  |||  ||| |     | |      |     |  |   | |||    ||| |   ||   || | || | || || |    ||| |||||||  | ||| | ||||||||||||||||||||||| |||||||| || || || ||||||
--tatatacttttgctgataaaaaaaataaattaaagtgctctcccaccccct--tcccccttttcacctctttga---tcactttttcttgtctgcacct----aaacagTATGGCAGTCCACTTTATGGAGATGTTTTTGGTGTTCATCAACAAGACCAGCCTAATTATGAG

upper sequence: Vv00s0818g00010.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT4G21660.2 (Arabidopsis thaliana), 3'ss of exon 10
gtgagttactttcatcatgtagactaatctatttacccttttttttgtactgaaatatcatctatcattattttcagattctgattattttatttgtacttcgttaaatagTATGGGCGACCATTGTATGGAGATGTTTTTGGTGTTCAGCAACAAGAACAACCAAACTATGAG
           | | ||| |    | |||||  | |   ||||||  || |   ||  ||||||  |  | ||| |  || |     || |  | ||  |  |||| |||||||||||| |||||||||||||||||||||||||| ||||||||||| || || ||||| |||
----------gtaagcatttttttttatctacattcttcttttttattatttctatgccatctacta--acttttatttttttcccgttcttatcgt-ttgtgttacatagTATGGGCGTCCATTGTATGGAGATGTTTTTGGTGTCCAGCAACAAGATCAGCCTAACTACGAG

upper sequence: Vv00s0818g00010.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S98_7V6.1 (Physcomitrella patens), 3'ss of exon 10
--gtgagttactttcatcatgtagactaatctatttacccttttttttgtactgaaatatcatctatcattattttcagattctgattattttatttgtacttcgttaaatagTATGGGCGACCATTGTATGGAGATGTTTTTGGTGTTCAGCAACAAGAACAACCAAACTATGAG
   | |  | | |   |  || |  |||||||   || |       ||  ||   || ||    |  ||   ||    |||||  ||| || |  | ||   | |      ||||||||||||| || ||||||||||| |||||||||||||||  |||       |  ||||||
gtctaatatgcgtatgttctggatcctaatctgcctaac-------ttagac---aacatttggtgccaaagttcagcgattcacattgttatgatcgt---ttgggctgcagTATGGGCGACCTTTATATGGAGATGTATTTGGTGTTCAGCAAGCAGAGACTGAGACATATGAG

upper sequence: Vv00s0818g00010.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S505_13V6.1 (Physcomitrella patens), 3'ss of exon 10
gtgagttactttcatcatgtagac---taatctatttacccttttttttgtactgaaatatcatctatcattattttcagattctgattattttatttgtacttcgttaaatagTATGGGCGACCATTGTATGGAGATGTTTTTGGTGTTCAGCAACAAGAACAACCAAACTATGAG
 |||||    ||    ||  ||     | ||  |||| |   | ||| | |||    | ||    |   ||  | || |    |  |||| | | | ||    |        ||||||||||||| |||||||||||||| ||||||||||||||    || |     | || ||||
-tgagtctggttggcaatacagttgtgttatagattttcatctatttctatacgctgaaat----tgggatcttgtttaa---ccaattagtatctgtggggct------gcagTATGGGCGACCCTTGTATGGAGATGTATTTGGTGTTCAGCACGTGGAGCTTGATACCTTTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcatctatcattattttcagattctgattattttatttgtacttcgttaaatagTATGGGCGACCATTGTATGGAGATGTTTTTGGTGTTCAGCAACAAGAACAACCAAACTATGAG
                      ttctgat  putative branch site (score: 3)
                                          cttcgtt  putative PPT
          attattttcagattct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttactttcatcatgtagactaatctatttacccttttttttgtactgaaatatcatctatcattattttcagattctgattattttatttgtacttcgttaaatagTATGGGCGACCATTGTATGGAGATGTTTTTGGTGTTCAGCAACAAGAACAACCAAACTATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC