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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgcaactccaccatgattaagaaaaaattaattgtaatttaccaacacactacttatttattaatttttaactgtagAGATCGGTATTCTTATCGGAAAGGGAGGACTACATGGAAATGTCTTCAGAATAAAGCCACCTATGTGTTTCACCAAAGATGATGCTG

Basic information

species Vitis vinifera
transcript Vv07s0031g01330.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0031g01330.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA11G36000.2 (Glycine max), 3'ss of exon 7
-----------gtttgcaactccaccat-gattaagaaaaaattaattgtaa----tttaccaa-cacactacttatttattaatttttaactgtagAGATCGGTATTCTTATCGGAAAGGGAGGACTACATGGAAATGTCTTCAGAATAAAGCCACCTATGTGTTTCACCAAAGATGATGCTG-------------
           | ||| |     |  || |  || |||    |   ||  ||    | ||| || || | ||  | |||| |   | | || ||||||| ||||||||||  | ||||| ||||| || ||||||||||| || || || |||||||| ||||||||||||||||||||||| |             
gtaagaaatttggttgaataaaaagaattgcatatgaagctttcttttccaaaatttctacaaaacatagtaactgtttactc-ctataaattgtagAGCTCGGTATTCTAGTTGGAAAAGGAGGGCTGCATGGAAATGTTTTTAGGATCAAGCCACCAATGTGTTTCACCAAAGATGATGCAGGTATATAAATAAA

upper sequence: Vv07s0031g01330.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA11G36000.3 (Glycine max), 3'ss of exon 7
-----------gtttgcaactccaccat-gattaagaaaaaattaattgtaa----tttaccaa-cacactacttatttattaatttttaactgtagAGATCGGTATTCTTATCGGAAAGGGAGGACTACATGGAAATGTCTTCAGAATAAAGCCACCTATGTGTTTCACCAAAGATGATGCTG
           | ||| |     |  || |  || |||    |   ||  ||    | ||| || || | ||  | |||| |   | | || ||||||| ||||||||||  | ||||| ||||| || ||||||||||| || || || |||||||| ||||||||||||||||||||||| |
gtaagaaatttggttgaataaaaagaattgcatatgaagctttcttttccaaaatttctacaaaacatagtaactgtttactc-ctataaattgtagAGCTCGGTATTCTAGTTGGAAAAGGAGGGCTGCATGGAAATGTTTTTAGGATCAAGCCACCAATGTGTTTCACCAAAGATGATGCAG

upper sequence: Vv07s0031g01330.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA18G02440.1 (Glycine max), 3'ss of exon 9
------------gtttgcaactccaccatgattaagaaaaaattaattgtaa----tttaccaa-cacactacttatttattaatttttaactgtagAGATCGGTATTCTTATCGGAAAGGGAGGACTACATGGAAATGTCTTCAGAATAAAGCCACCTATGTGTTTCACCAAAGATGATGCTG
            |||    |    |   ||  || |||    |   ||  ||    | ||| || ||   ||  | |||| |   | | || | ||||| ||||||||||  | || || ||||| || ||||||||||| || || || |||||||| ||||||||||||||||||||||| |
gtaagaaatttggttgaataaaaaaaattgcatatgaagctttcttttccaaaatttctacaaaacatggtaactgtttactc-ctataaattttagAGCTCGGTATTCTAGTTGGGAAAGGAGGGCTGCATGGAAATGTTTTTAGGATCAAGCCACCAATGTGTTTCACCAAAGATGATGCAG

upper sequence: Vv07s0031g01330.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA05G31630.1 (Glycine max), 3'ss of exon 7
-------gtttgcaactccaccatgattaagaaaaaattaatt-------gtaatttaccaacacact-acttatttattaattttta-actgtagAGATCGGTATTCTTATCGGAAAGGGAGGACTACATGGAAATGTCTTCAGAATAAAGCCACCTATGTGTTTCACCAAAGATGATGCTG
            | | |  |   |    | |  ||   | |||        ||| || | ||||  || |   |||||||  | | |  | || |||  ||||| | ||  | || || |||||||| ||||| ||||| ||||| || |||||||| ||||||||| ||||||||||||| |
gttacacaagaaccattttattctatgcatgtgaagccttattttccaaaataacttccaaacagtcttaacaatttatttgtatatgcattgaagAACTCGGTGTGCTAGTTGGGAAAGGAGGACTTCATGGCAATGTTTTCAGGATCAAGCCACCAATGTGTTTCTCCAAAGATGATGCAG

upper sequence: Vv07s0031g01330.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA08G14850.2 (Glycine max), 3'ss of exon 7
-----------------------gtttgcaactccaccatgattaagaaaaaattaattgtaatttaccaacacactacttatttattaatttttaactgtagAGATCGGTATTCTTATCGGAAAGGGAGGACTACATGGAAATGTCTTCAGAATAAAGCCACCTATGTGTTTCACCAAAGATGATGCTG
                        | |||| |   | | |  ||    |||||| | ||  ||   |||  |  || | |||||| |  |||    | || |||| | ||| | ||  | || || |||||||| ||||| ||||| ||||| || |||||||| ||||||||| ||||||||||||| |
gttagacaaggaaccattttattttatgcatccgaagccttcttttccaaaaataacttccaa---accgtctaacgaattatttgtatattc---attgaagAGCTTGGTGTGCTAGTTGGGAAAGGAGGACTTCATGGCAATGTTTTCAGGATCAAGCCACCAATGTGTTTCTCCAAAGATGATGCAG

upper sequence: Vv07s0031g01330.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT4G39660.1 (Arabidopsis thaliana), 3'ss of exon 7
---------gtttgcaactccaccat-gattaagaaaaaattaattgtaatttaccaacacactacttatttattaatttttaactgtagAGATCGGTATTCTTATCGGAAAGGGAGGACTACATGGAAATGTCTTCAGAATAAAGCCACCTATGTGTTTCACCAAAGATGATGCTG
          ||     |   | ||| ||||    ||  || | |||   || ||||| |   |  ||  |  ||  | | | | || |||  | || |||||  ||||||| |||||||| ||||| || || ||||| ||||||||||| ||||||||||| ||||||||||| |
gtaaacaacattaaagccaaaagcatcgatttgataagcatcagttg--gttaaccaaaatgtt--ttgctcctt--tctcttaatgaagAACTTGGCATTCTCGTCGGAAAAGGAGGACTTCATGGGAACGTTTTCAGGATAAAGCCACCAATGTGTTTCACTAAAGATGATGCAG

upper sequence: Vv07s0031g01330.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: PP1S32_198V6.1 (Physcomitrella patens), 3'ss of exon 7
---------------------------------------------------gtttgcaactccaccatgattaagaaaaaattaa--ttgtaatttaccaacacactacttatttattaatttttaa----ctgtagAGATCGGTATTCTTATCGGAAAGGGAGGACTACATGGAAATGTCTTCAGAATAAAGCCACCTATGTGTTTCACCAAAGATGATGCTG
                                                   ||||   ||| | || |||    |    || |     |||      || ||     |||||   ||    ||||       || |||  ||||  || |  | || ||||| || || |||||||||||||| ||||| ||||| |||||||||||| | |  || ||||| |
gtgatgctgcacttcacctagggctggcctagttctgtgtatcactagcaagttttgtactgctccttgacatggtggcaagtggggctgtgcaactcctaccattcacttacgcataggctttttggatgttgcagACCTCGGAGTTTTAGTTGGGAAGGGCGGGCTTCATGGAAATGTCTTTAGAATCAAGCCTCCTATGTGTTTCTCAATGGAAGATGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaaattaattgtaatttaccaacacactacttatttattaatttttaactgtagAGATCGGTATTCTTATCGGAAAGGGAGGACTACATGGAAATGTCTTCAGAATAAAGCCACCTATGTGTTTCACCAAAGATGATGCTG
                                           ttttaac  putative branch site (score: 2)
                                          ttttt  CT-rich tract
                     aacacactacttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgcaactccaccatgattaagaaaaaattaattgtaatttaccaacacactacttatttattaatttttaactgtagAGATCGGTATTCTTATCGGAAAGGGAGGACTACATGGAAATGTCTTCAGAATAAAGCCACCTATGTGTTTCACCAAAGATGATGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG