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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgctctaactcaataggaagaattgtagaccttttgtttgatgcatcagaaacaagatggaaatttgagaaaatttccaaggataggaaaattctctccttaaacaaacagtacttataacaattctttttgttggtttcagAAAAGGTATGAGGAAGCAAGTCAAGTAGCCAACGAGGCAGTTGGGAATATTAGAACAGTAGCTTCTTTCTGTGCTGAAGAGAAGGTGATGCAGCTGTACC

Basic information

species Vitis vinifera
transcript Vv05s0020g00900.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g00900.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA13G17890.1 (Glycine max), 3'ss of exon 10
gtttgctctaactcaataggaagaattgtagaccttttgtttgatgcatcagaaacaagatggaaatttgagaaaatttccaaggataggaaaattctctccttaaacaaacagtacttataacaattctttttgttggtttcagAAAAGGTATGAGGAAGCAAGTCAAGTAGCCAACGAGGCAGTTGGGAATATTAGAACAGTAGCTTCTTTCTGTGCTGAAGAGAAGGTGATGCAGCTGTACC------------
                                                  | |   ||   | | || |  |    ||||    | ||   || | ||    | |    | || |     | |  || || | | |      ||||||   ||||||||||||||||||||||| |  || ||||| |||||||| |||||||| ||  |||||||||||||||||||||||||| || | ||||            
------------------------------------------------ctatatttaattagtacatctttg----tttctgtagttaactaa-tgctaatatcatttgagcaatg----tgattatgctctatatgttccacagaaactatatgagGAAGCAAGTCAAGTAGCGAGTGATGCAGTGGGGAATATCAGAACAGTTGCCGCTTTCTGTGCTGAAGAGAAGGTGATGGAGTTATACCAGAAAAAATGTT

upper sequence: Vv05s0020g00900.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA13G17930.1 (Glycine max), 3'ss of exon 8
gtttgctctaactcaataggaagaattgtagaccttttgtttgatgcatcagaaacaagatggaaatttgagaaaatttccaaggataggaaaattctctccttaaacaaacagtacttataa-caattctttttgttggtttcagAAAAGGTATGAGGAAGCAAGTCAAGTAGCCAACGAGGCAGTTGGGAATATTAGAACAGTAGCTTCTTTCTGTGCTGAAGAGAAGGTGATGCAGCTGTACC
                                           ||| ||||  ||    |     || ||        ||  |    |         |  |  ||    |  | |||| |||  |   | || |   ||    ||||||  ||||||||||||||| ||||| || || || || || |||| ||| |||||||| |||||||||||||||||||||||||||||| |  | ||||
---------------------------------------gagcatggatcaataatgttacaagcatatg-------ctcagaatgcatttttgacttagctatatgttatgaatactgatagtctgatattctatatgcccacagAAATTGTATGAGGAAGCAAGCCAAGTGGCAAATGATGCTGTGGGGAGTATAAGAACAGTTGCTTCTTTCTGTGCTGAAGAGAAGGTGATGGAATTATACC

upper sequence: Vv05s0020g00900.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA17G04590.1 (Glycine max), 3'ss of exon 8
gtttgctctaactcaataggaagaattgtagaccttttgtttgatgcatcagaaacaagatggaaatttgagaaaatttccaaggataggaaaattctctccttaaacaaacagtacttataacaattctttttgttggtttcagAAAAGGTATGAGGAAGCAAGTCAAGTAGCCAACGAGGCAGTTGGGAATATTAGAACAGTAGCTTCTTTCTGTGCTGAAGAGAAGGTGATGCAGCTGTACC
                                     ||||  |||     | |  || |  |  | |  || | ||   || | ||      ||| |   ||||   | |   ||   |||   ||  | | | | |    ||||||  |||||||||||| |||||||| || || || || || |||| ||| |||||||| |||||||||||||||||||||||||||||| |  ||||||
------------------------------------atgtt-aatgagcatggatgaaaaatgttact--agcatatgctca-gaatgc----atttttgacttagctatatgatatgaatactgatattctgtat-gcccacagAAATTGTATGAGGAAGCGAGTCAAGTGGCAAATGATGCTGTGGGGAGTATAAGAACAGTTGCTTCTTTCTGTGCTGAAGAGAAGGTGATGGAATTGTACC

upper sequence: Vv05s0020g00900.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA17G04610.1 (Glycine max), 3'ss of exon 9
gtttgctctaactcaataggaagaattgtagaccttttgtttgatgcatcagaaacaagatggaaatttgagaaaatttccaaggataggaaaattctctccttaaacaaacagtacttataacaattctttttgttggtttcagAAAAGGTATGAGGAAGCAAGTCAAGTAGCCAACGAGGCAGTTGGGAATATTAGAACAGTAGCTTCTTTCTGTGCTGAAGAGAAGGTGATGCAGCTGTACC
                                         |  |  || | |   ||   | | || |  |    ||||    | ||   || | ||    | |    | || |  | || |  || || | | |      ||||||   ||||||||||||||||||||||| |  || ||||| |||||||| |||||||| ||  ||||| |||||||||||||||||||| |  | ||||
---------------------------------------catcttcgattatatttaattagtacatctttg----tttctgtagttaattaa-tgctaatatcatttgaccaatg-tgattattatgctctatatgttccgcagAAACTATATGAGGAAGCAAGTCAAGTAGCGAGTGATGCAGTAGGGAATATCAGAACAGTTGCCGCTTTCGGTGCTGAAGAGAAGGTGATGGAATTATACC

upper sequence: Vv05s0020g00900.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA13G17880.1 (Glycine max), 3'ss of exon 4
gtttgctctaactcaataggaagaattgtagaccttttgtttgatgcatcagaaacaagatggaaatttgagaaaatt---tccaaggataggaaaattctctccttaaacaaacagtacttataacaattctttttgttggtttcagAAAAGGTATGAGGAAGCAAGTCAAGTAGCCAACGAGGCAGTTGGGAATATTAGAACAGTAGCTTCTTTCTGTGCTGAAGAGAAGGTGATGCAGCTGTACC
                                             |     | ||  | |||| |  |  || |  ||   || |    ||   |       |    | |  | || || |||       ||| | |||||  | ||||||   ||||||||||||||||||||||| || ||||| || || ||||| ||||||||||   |||||||||| ||||||||||||||| || | ||||
---------------------------------------------gtggtgggaatgatatggtacgtaaaggattttgcctctatatttaattagtactgatatccatatgaccaatatttactgtg-ctctatatgttg--tacagAAACTCTATGAGGAAGCAAGTCAAGTAGCAAATGAGGCGGTAGGTAATATCAGAACAGTAGTCGCTTTCTGTGCAGAAGAGAAGGTGATGGAGTTATACC

upper sequence: Vv05s0020g00900.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA13G17920.1 (Glycine max), 3'ss of exon 8
gtttgctctaactcaataggaagaattgtagaccttttgtttgatgcatcagaaacaagatggaaatttgagaaaatttccaaggataggaaaattctctccttaaacaaacagtacttataacaattctttttgttggtttcagAAAAGGTATGAGGAAGCAAGTCAAGTAGCCAACGAGGCAGTTGGGAATATTAGAACAGTAGCTTCTTTCTGTGCTGAAGAGAAGGTGATGCAGCTGTACC
                                                  ||| ||| |    ||   || |||||          |    |   | |   ||||   | |   ||    ||  |||  | | | |   |  ||||||  ||||||||||||||||||||| || || || || || |||| ||| |||||||| |||||||||||| ||||| ||||||||||| |  | ||||
---------------------------------------------aagatagagacatggatcaacagtgtgaaaaaaatgtgctctgaatatgcttttgtcttatctatatgttatgggtattaatattgtatttacctaacagAAACTGTATGAGGAAGCAAGTCAAGTGGCAAATGATGCTGTAGGGAGTATAAGAACAGTTGCTTCTTTCTGTTCTGAAAAGAAGGTGATGAAATTATACC

upper sequence: Vv05s0020g00900.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA17G04620.1 (Glycine max), 3'ss of exon 9
gtttgctctaactcaataggaagaattgtagaccttttgtttgatgcatcagaaacaagatggaaatttgagaaaatttccaaggataggaaaattctctccttaaacaaacagtacttataacaattctttttgttggtttcagAAAAGGTATGAGGAAGCAAGTCAAGTAGCCAACGAGGCAGTTGGGAATATTAGAACAGTAGCTTCTTTCTGTGCTGAAGAGAAGGTGATGCAGCTGTACC
                                          ||||     ||  ||  | ||||| |        | |       ||| |  ||| ||   || | |||    |  |||     || || | |||||    ||||||   ||||||||||||||||||||||| || || ||||| |||||||| |||||| | ||  |||| ||||||||||||||||| ||| |  | ||||
--------------------------------------aagggatgggaatgatgcagtagggaaagtatttcgtctctgtttaattagtactattatccatttgaccaa----tgtttactgtgat-ctatatgttg--cacagAAACTATATGAGGAAGCAAGTCAAGTAGCGAATGACGCAGTAGGGAATATCAGAACAATTGCCGCTTTTTGTGCTGAAGAGAAGGTAATGAACTTATACC

upper sequence: Vv05s0020g00900.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA13G17910.1 (Glycine max), 3'ss of exon 8
gtttgctctaactcaataggaagaattgtagaccttttgtttgatgcatcagaaacaagatggaaatttgagaaaatttccaaggataggaaaattctctccttaaacaaacagtacttataacaattctttttgttggtttcagAAAAGGTATGAGGAAGCAAGTCAAGTAGCCAACGAGGCAGTTGGGAATATTAGAACAGTAGCTTCTTTCTGTGCTGAAGAGAAGGTGATGCAGCTGTACC
                       ||  | | ||    |  |  ||| |     | ||| |  |   | |||     |||   | | |||  | ||  |           || |||| | |    |||||| |||     | |||||||  ||||||||||||||||||||| || || || ||  | |||| ||| |||||||| |||||||||||||||||| ||||||| ||| |    ||| 
-----------------------aagagaaaac----tactatatggacatagatcaacagtgtgctctgaatgtgtttttgacg-tagctatatgtt-----------aaaagtattaa----aattctatttacc--tatcagAAACTGTATGAGGAAGCAAGTCAAGTGGCGAATGATGCTCTAGGGAGTATAAGAACAGTTGCTTCTTTCTGTGCTGAAAAGAAGGTAATGAAATCATACG

upper sequence: Vv05s0020g00900.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA17G04600.1 (Glycine max), 3'ss of exon 16
gtttgctctaactcaataggaagaattgtagaccttttgtttgatgcatcagaaacaagatggaaatttgagaaaatttccaaggataggaaaattctctccttaaacaaacagtacttataacaattctttttgttggtttcagAAAAGGTATGAGGAAGCAAGTCAAGTAGCCAACGAGGCAGTTGGGAATATTAGAACAGTAGCTTCTTTCTGTGCTGAAGAGAAGGTGATGCAGCTGTACC
                                           |   |    | | |       | | ||| ||   |        |    |  || |   ||||   | |   ||    ||  |||  | | | |   |  ||||||  |||||||||| ||||| |||| || || || ||||| |||| | | |||||||| |||||||||||||||||| ||||||||||| |  |     
-------------------------------------------aaaaaatgaacatagatcaacagtgtgacaagcatgt--gctctgaatatgtttttgacttagctatatgttaaaagtattaatattctatttacctgacagAAACTGTATGAGGAAACAAGTAAAGTGGCAAATGATGCAGTAGGGAGTTTAAGAACAGTTGCTTCTTTCTGTGCTGAAAAGAAGGTGATGGAATT-----


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaattctctccttaaacaaacagtacttataacaattctttttgttggtttcagAAAAGGTATGAGGAAGCAAGTCAAGTAGCCAACGAGGCAGTTGGGAATATTAGAACAGTAGCTTCTTTCTGTGCTGAAGAGAAGGTGATGCAGCTGTACC
                           ttataac  putative branch site (score: 2)
                                    ttctttttgtt  putative PPT
                           ttataacaattctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgctctaactcaataggaagaattgtagaccttttgtttgatgcatcagaaacaagatggaaatttgagaaaatttccaaggataggaaaattctctccttaaacaaacagtacttataacaattctttttgttggtttcagAAAAGGTATGAGGAAGCAAGTCAAGTAGCCAACGAGGCAGTTGGGAATATTAGAACAGTAGCTTCTTTCTGTGCTGAAGAGAAGGTGATGCAGCTGTACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG