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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctccacttttttttggttctcttaataatctatataactgattaaatacagaatttttttatagccgagtcaccaagctgaccacagcattattgtgcagGTTACATTTGTTGAAGCTTTAGATCAGCTTATGCCTGGCTTTGATCCTGAGATTGGGAAATTGGCTCGGCGGGTTCTAATTAATCCTCGAAAAATTGATT

Basic information

species Vitis vinifera
transcript Vv14s0060g01330.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0060g01330.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 5
ctccacttttttttggttctcttaataatctatataactgattaaatacagaatttttttatagccgagtcacc-aagctgaccacagcatta-ttgtgcagGTTACATTTGTTGAAGCTTTAGATCAGCTTATGCCTGGCTTTGATCCTGAGATTGGGAAATTGGCTCGGCGGGTTCTAATTAATCCTCGAAAAATTGATT
      |   || |  ||  |    ||  || | | | |||||||   | |   |  | |   |     |||||     | |||  |   | | |||  |||||||| |||||||||||  | |||||| | |||||||| ||||||||||||||||  |||||||| |   || |||| || |||||||| |||||||| |
-catgttaaattctaattaaccatctatgctgtttta-tgattaaggcctgttgtcatctgatgatatttcacctgtatttacctaaatttcacttggacagGTTACTTTTGTTGAAGCACTTGATCAGTTGATGCCTGGTTTTGATCCTGAGATTGCAAAATTGGCCCAAAGGATTCTTATCAATCCTCGTAAAATTGACT

upper sequence: Vv14s0060g01330.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os05g06460.1 (Oryza sativa), 3'ss of exon 5
-ctccactttttt--ttggttctcttaataatctatataactgattaaatacagaatttttttatagccgagtcaccaagctgaccacagcattattgtgcagGTTACATTTGTTGAAGCTTTAGATCAGCTTATGCCTGGCTTTGATCCTGAGATTGGGAAATTGGCTCGGCGGGTTCTAATTAATCCTCGAAAAATTGATT
  || ||||       || |||| |||      ||| |   | | |  || | || |||| || |  |     | |  |  ||||       | ||| | |||||||| |||||||||||| | || ||||| |||||||| ||||||||||| ||||  ||||| || | | | || || || || ||||| || || || |
tttcaacttacacaaatgattctattacagtagtat-tgtatcactgcatgctgatttttgttttcacatgccccctgaattgacagt--tttcattcttcagGTTACTTTTGTTGAAGCTCTTGACCAGCTAATGCCTGGTTTTGATCCTGAAATTGCAAAATTAGCCCAGAGAGTCCTTATCAACCCTCGGAATATAGACT

upper sequence: Vv14s0060g01330.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 5
-ctccacttttttttggtt--ctcttaataatctatataactgattaaatacagaatttttttatagccgagtcacc--aagctgaccacagcattattgtgcagGTTACATTTGTTGAAGCTTTAGATCAGCTTATGCCTGGCTTTGATCCTGAGATTGGGAAATTGGCTCGGCGGGTTCTAATTAATCCTCGAAAAATTGATT
 ||  |    || | |  |    ||||   |||| | |  |||||  ||||      || ||   ||   | ||||   ||  |   ||   ||  |||| ||||||||| |||||||||||| | || ||||| |||||||| ||||||||||| ||||  ||||| || | | | ||||| || |||||||| |||||||| |
gctggatgaattctagaatgctccttagacatctgt-tgcctgat-gaatatga---ttgttctcagttaattcacttgaatttactcaattcaaaattgggcagGTTACTTTTGTTGAAGCTCTTGACCAGCTGATGCCTGGATTTGATCCTGAAATTGCAAAATTAGCCCAGAGAGTTCTTATCAATCCTCGGAAAATTGACT

upper sequence: Vv14s0060g01330.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G145595_T02 (Zea mays), 3'ss of exon 4
ctccacttttttttggttctcttaataatctatataactgattaaatacagaatttttttatagccgagtcaccaagctgaccacagcatt-----attgtgcagGTTACATTTGTTGAAGCTTTAGATCAGCTTATGCCTGGCTTTGATCCTGAGATTGGGAAATTGGCTCGGCGGGTTCTAATTAATCCTCGAAAAATTGATT
 |      |   |||| |  | | ||  |||  ||     |||       |    | |  ||||| |      ||     |     |||||     || |  |||||||| |||||||||||| | |||||  | |||||||| |||||||| |||||||  |||||||| | | || |||| |||| |||||| |||||||| |
-tgtttcctgaattggattacatcatc-tcttgatccacaattgggctttg---ctgtcaatagctggagtttcatctgtatttatgcattttttgatcgatcagGTTACTTTTGTTGAAGCTCTTGATCAATTAATGCCTGGGTTTGATCCCGAGATTGCAAAATTGGCGCAGAGGATTCTTATTAGTCCTCGTAAAATTGACT

upper sequence: Vv14s0060g01330.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: EFJ16882 (Selaginella moellendorffii), 3'ss of exon 5
ctccacttttttttggttctcttaataatctatataactgattaaatacagaatttttttatagccgagtcaccaagctgaccacagcattattgtgcagGTTACATTTGTTGAAGCTTTAGATCAGCTTATGCCTGGCTTTGATCCTGAGATTGGGAAATTGGCTCGGCGGGTTCTAATTAATCCTCGAAAAATTGATT
                                              | |    |||| || |  ||   |       | ||  ||   |    ||||||||| || ||||| |||||| | ||||| || ||||| |||||||||||||| || |||||  | |||| | || | || || |||||||||||||||||||
-------------------------------------------gtttgcgagtttttcttctttcc---tttttctacagaatacgcga----tgtgcagGTGACTTTTGTGGAAGCTCTGGATCAACTGATGCCAGGCTTTGATCCTGAAATCGGGAAGCTTGCTCAGAGGCTGCTGATCAATCCTCGAAAAATTGATT

upper sequence: Vv14s0060g01330.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: EFJ06739 (Selaginella moellendorffii), 3'ss of exon 5
ctccacttttttttggttctcttaataatctatataactgattaaatacagaatttttttatagccgagtcaccaagctgaccacagcattattgtgcagGTTACATTTGTTGAAGCTTTAGATCAGCTTATGCCTGGCTTTGATCCTGAGATTGGGAAATTGGCTCGGCGGGTTCTAATTAATCCTCGAAAAATTGATT
                                                   | ||||| |     |   |  | |    ||  ||   |    ||||||||| || |||||||||||| | ||||| || ||||| |||||||||||||| || |||||  | |||| | || | || || || ||||||||||||||||
-----------------------------------------------gtttagtttttcttctttcctttttcta--tagaatacgcga----tgtgcagGTGACTTTTGTTGAAGCTCTGGATCAACTGATGCCAGGCTTTGATCCTGAAATCGGGAAGCTTGCTCAGAGGCTCCTGATCAACCCTCGAAAAATTGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atacagaatttttttatagccgagtcaccaagctgaccacagcattattgtgcagGTTACATTTGTTGAAGCTTTAGATCAGCTTATGCCTGGCTTTGATCCTGAGATTGGGAAATTGGCTCGGCGGGTTCTAATTAATCCTCGAAAAATTGATT
                              agctgac  putative branch site (score: 3)
      aatttttttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctccacttttttttggttctcttaataatctatataactgattaaatacagaatttttttatagccgagtcaccaagctgaccacagcattattgtgcagGTTACATTTGTTGAAGCTTTAGATCAGCTTATGCCTGGCTTTGATCCTGAGATTGGGAAATTGGCTCGGCGGGTTCTAATTAATCCTCGAAAAATTGATT

ctccact
- - - - - - - - - - - - - - - - - - - - - -aaataca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcaccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccacagc