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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctatttctcagaaagctgcattgttctctttaaaaagtattgtatcttgattaattgcatttctatcaccactttttttcacatctttgcctggtttttcagGACTGTTGTTTACAAAGGGCAGTTAAAGCCTGATCAAGTGAAGGGATACTACTATGCAGATCTTGGCAATGAAAGGTTTACGAGCTACATGGCCCTG

Basic information

species Vitis vinifera
transcript Vv16s0098g00290.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0098g00290.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA04G41540.1 (Glycine max), 3'ss of exon 6
gtctatttctcagaaagctgcattgttctctttaaaaagtattgtatcttgattaattgcatttctatcaccactttttttcacatctttgcctggttttt--cagGACTGTTGTTTACAAAGGGCAGTTAAAGCCTGATCAAGTGAAGGGATACTACTATGCAGATCTTGGCAATGAAAGGTTTACGAGCTACATGGCCCTG
||   ||| |||  | |   |||   ||| ||| | || ||   |||  | | |     | | |  ||||        ||||| ||||||  |   ||||   ||||||||||||||||||||| |||||||  || | |||  ||||||  ||||| | |||||| ||||||||||||||||||||||||||||||||||||
gtgc-tttgtcaagatgggacatc--tctttttgagaactaaattatggttactctcaacgtctaaatcagtttccaatttcaaatctttatccaattttgtacagGACTGTTGTTTACAAAGGTCAGTTAACACCAGCTCAGTTGAAGGATTACTATTTTGCAGACCTTGGCAATGAAAGGTTTACGAGCTACATGGCCCTG

upper sequence: Vv16s0098g00290.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA19G16450.1 (Glycine max), 3'ss of exon 2
gtctatttctcagaaagctgcattgttctctttaaaaagtattgtatcttgattaattgcatttctatca--ccactttt---tttcacatctttgcctggttt--ttcagGACTGTTGTTTACAAAGGGCAGTTAAAGCCTGATCAAGTGAAGGGATACTACTATGCAGATCTTGGCAATGAAAGGTTTACGAGCTACATGGCCCTG
|| | || ||||  | ||  | |  || |||| | ||     |  ||  || ||| |  || |  |||||   || |||    ||||  ||  ||  |   |||  ||||||||||||||||||||||| ||| |||  || | |||  ||| ||  || |||| |||||||||||||||||||||||||||||||||||||||||||
gtgtgtt-ctcaagaggcaacctcattttcttgagaag----taaattatggttactgtcactgttatcagatcaatttcaaatttctgatggttatccaattttgttcagGACTGTTGTTTACAAAGGTCAGCTAACACCAGCTCAGTTGAGGGATTATTACTTTGCAGATCTTGGCAATGAAAGGTTTACGAGCTACATGGCCCTG

upper sequence: Vv16s0098g00290.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA06G13280.1 (Glycine max), 3'ss of exon 6
gtctatttctcagaaagctgcattgttctctttaaaaagtattgtatcttgattaattgcatttctatcaccactttttttcacatctttgcctggttttt--cagGACTGTTGTTTACAAAGGGCAGTTAAAGCCTGATCAAGTGAAGGGATACTACTATGCAGATCTTGGCAATGAAAGGTTTACGAGCTACATGGCCCTG
                   |   | ||  |   |  |   ||    | ||||  || |  |||    | ||        |  | |||  |  |   ||||   ||||||  ||||||||||||| |||||||  || | |||  ||||||  ||||| | |||||||||||||||||||||||||||||||||||||||||||
-------------------gtgct-ttgccaagatgagacatctctttttgag-aactaaattatggttactctcaacgtctaaatcagtttccaattttgtacagGACCATTGTTTACAAAGGTCAGTTAACACCAGCTCAGTTGAAGGATTACTATTTTGCAGATCTTGGCAATGAAAGGTTTACGAGCTACATGGCCCTG

upper sequence: Vv16s0098g00290.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA14G32500.1 (Glycine max), 3'ss of exon 6
gtctatttctcagaaagctgcattgttctctttaaaaa-gtattgtatcttgattaattgcatttctatcaccactttttttcacatctttgcctggttt-ttcagGACTGTTGTTTACAAAGGGCAGTTAAAGCCTGATCAAGTGAAGGGATACTACTATGCAGATCTTGGCAATGAAAGGTTTACGAGCTACATGGCCCTG
|| | || ||||  | ||  |    || |||| | ||    ||| |   |    | | ||  ||   ||||        ||||  ||     ||   ||| ||||||||||||||||||||||| ||| |||  || | |||  ||| ||  || |||| ||||||| |||||||||||||||||||||||||||||||||||
gtgtgtt-ctcaagaggcaaccacattttcttgagaagtaaattatggttactgtcactgttttcaaatcaatttcaaatttctgataacatccaattttgttcagGACTGTTGTTTACAAAGGTCAGCTAACACCAGCTCAGCTGAGGGATTATTACTTTGCAGATATTGGCAATGAAAGGTTTACGAGCTACATGGCCCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgattaattgcatttctatcaccactttttttcacatctttgcctggtttttcagGACTGTTGTTTACAAAGGGCAGTTAAAGCCTGATCAAGTGAAGGGATACTACTATGCAGATCTTGGCAATGAAAGGTTTACGAGCTACATGGCCCTG
 gattaat  putative branch site (score: 3)
                                               tttttc  putative PPT
                       acttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctatttctcagaaagctgcattgttctctttaaaaagtattgtatcttgattaattgcatttctatcaccactttttttcacatctttgcctggtttttcagGACTGTTGTTTACAAAGGGCAGTTAAAGCCTGATCAAGTGAAGGGATACTACTATGCAGATCTTGGCAATGAAAGGTTTACGAGCTACATGGCCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT