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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catttttccatcctgcaatctcaacgaactcagttatgttttagatgattatgtgttggacaaaatatagcaaattttaaccctttactttgtatcttagCTACGAGAGTCAAAGGGCATGACTACTATCAAATTCCGTCCACATTCTGGGGAG

Basic information

species Vitis vinifera
transcript Vv08s0105g00570.t01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0105g00570.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GRMZM2G416667_T01 (Zea mays), 3'ss of exon 13
catttttccatcctgcaatctcaacgaactcagttatgttttagatgattatgtgttggacaaaatatagcaaattttaaccctttactttgtatcttagCTACGAGAGTCAAAGGGCATGACTACTATCAAATTCCGTCCACATTCTGGGGAG
              |  |||  | |   |||     |   | |  |   |    |||   || | |       ||| |     || | |||     | |||| || ||||||||||| ||||| ||||||||||||||||||||| |||| |||
--------------gtgatcatatcttcctc--cccttcctcaattttctccacgtttctcagagtggtaatgattctg----ttcaattt-----tcagCTGCGTGAGTCAAAGGGAATGACCACTATCAAATTCCGTCCACATGCTGGAGAG

upper sequence: Vv08s0105g00570.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA03G07460.1 (Glycine max), 3'ss of exon 13
catttttccatcc--tgcaatctcaacgaactcagttatgttttagatgattatgtgttggacaaaatatagcaaattttaaccctttact-ttgtatcttagCTACGAGAGTCAAAGGGCATGACTACTATCAAATTCCGTCCACATTCTGGGGAG
 | |  |  || |   | | | ||  | |  |||     | | | || | || || | |       | | | |||| || |||||| ||   || | | | |||| ||||| |||||||| ||||| || ||||||||||||||||||||||| |||
-agtaatgtattcaaagaattttctgcaacttcataatcggtgttga-gtttttgagctttgtttgacacaccaaagtt-aaccctatataattatttttcagCTTCGAGAATCAAAGGGAATGACGACAATCAAATTCCGTCCACATTCTGGAGAG

upper sequence: Vv08s0105g00570.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA01G29470.2 (Glycine max), 3'ss of exon 14
catttttccatcctgcaatctcaacgaactcagttat--gttttagatgattatgtgttggacaaaatatagcaaattttaaccctttactttgtatcttagCTACGAGAGTCAAAGGGCATGACTACTATCAAATTCCGTCCACATTCTGGGGAG
  |  |    |||   ||| |     ||||   | ||  || || ||   ||     || |     | | | |||| || | |   |    || | ||| |||| ||||| |||||||| ||||| || ||||||||||||||||||||||| |||
--taatgtattccaataattttctgcaacttcatcatcagtgtttgaatttttgagctttgttttgacacaccaaagttaacctaatataattatttctcagCTTCGAGAATCAAAGGGAATGACAACAATCAAATTCCGTCCACATTCTGGAGAG

upper sequence: Vv08s0105g00570.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: AT2G38280.1 (Arabidopsis thaliana), 3'ss of exon 13
catttttccatcctgcaatctcaacgaactcagttatgttt-tagatgattatgtgttggacaaaatatagcaaattttaaccctttactttgtatcttagCTACGAGAGTCAAAGGGCATGACTACTATCAAATTCCGTCCACATTCTGGGGAG
                  |  ||     || |||    | | ||  | | |  |||||    ||| | |    ||| |  |     || |||   ||  |||| ||||||||||||||||||||||||||||   | || ||||||||||| |||
-----------------gtaccattcctcttagtcgcttctgtaactaacttggtgttctcaaaactgtgt--aatatggagtaactatttttcttc--agCTTCGAGAGTCAAAGGGCATGACTACTATCACGCTACGACCACATTCTGGAGAG

upper sequence: Vv08s0105g00570.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: EFJ17267 (Selaginella moellendorffii), 3'ss of exon 12
catttttccatcctgcaatctcaacgaactcagttatgttttagatgattatgtgttggacaaaatatagcaaattttaaccctttactttgtatcttagCTACGAGAGTCAAAGGGCATGACTACTATCAAATTCCGTCCACATTCTGGGGAG
                                  || | |||   |  || | | ||           |  |  ||  |||  |        | |  |||||||||||||| || || ||| |||| |||||||||||||| ||  |||| |||
---------------------------------gtaagcttttcttagttttctctt----------caatacgttcgaactgtgc------tgttgtagCTACGAGAGTCGAAAGGAATGTCTACGATCAAATTCCGTCCTCACGCTGGCGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgattatgtgttggacaaaatatagcaaattttaaccctttactttgtatcttagCTACGAGAGTCAAAGGGCATGACTACTATCAAATTCCGTCCACATTCTGGGGAG
                             ttttaac  putative branch site (score: 2)
                                   ccctttacttt  CT-rich tract
              acaaaatatagcaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catttttccatcctgcaatctcaacgaactcagttatgttttagatgattatgtgttggacaaaatatagcaaattttaaccctttactttgtatcttagCTACGAGAGTCAAAGGGCATGACTACTATCAAATTCCGTCCACATTCTGGGGAG

- - - -ccatcct
- - - - - - - -caatctc
- - - - - - - - - - - - -gaactca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atagcaaa