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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cccatcattctattataattgaagacttggagtatccatttgactctttaatttctccttttggcattcaagttttagttttccataaaaccttgtgcagGTGTTCTGGGGTTTGGACAAAAAGCTTGCTCAGAGGAAACATTTCCCATCTGTAAACTGGCTTATTTCTTACTCTAAGTACTCAACC

Basic information

species Vitis vinifera
transcript Vv04s0008g02580.t01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g02580.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: LOC_Os06g45120.1 (Oryza sativa), 3'ss of exon 13
---cccatcattctattataattgaagacttggagtatccatttga--ctctttaatttc-tccttttggcattcaagttttagttttccataaaaccttgtgcagGTGTTCTGGGGTTTGGACAAAAAGCTTGCTCAGAGGAAACATTTCCCATCTGTAAACTGGCTTATTTCTTACTCTAAGTACTCAACC
      |   | |||   ||||  ||   ||| | ||    ||  |  || | ||| | | |  |  | |  |   | | |||  |   |  ||       ||||||| || ||||| ||||| || ||||| ||||| || || |||||||||||||| || ||||| || |||||||| || |||||||  
gtaaggaaactgctagattaatccaacctttgaattaaattttcaaacctttctaactgcatgttcattgtttgataatcttaactcctctcaat------tgcagGTCTTTTGGGGATTGGATAAGAAGCTGGCTCAAAGAAAGCATTTCCCATCTGTCAATTGGCTCATCTCTTACTCAAAATACTCAAAG

upper sequence: Vv04s0008g02580.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: LOC_Os02g07870.1 (Oryza sativa), 3'ss of exon 13
cccatcattctattataattgaagacttggagtatccatttgactctttaatttctccttttggcattcaagttttagttttccataaaaccttg--tgcagGTGTTCTGGGGTTTGGACAAAAAGCTTGCTCAGAGGAAACATTTCCCATCTGTAAACTGGCTTATTTCTTACTCTAAGTACTCAACC
                       |    | || | | |  |   || | | |       |||  | ||  ||| ||  |   ||| |    ||||  || |||| |||||||| || || ||||||||||| |||||||| ||||||||||| || || ||||| || ||||| || || || || |  
-----------------------gtaaggaagcagctaagtctgtcatgattaataatgtttatcgtttcagtgttgttaaaccacatgttcttgtttgtagGTCTTCTGGGGATTAGATAAAAAGCTTGCCCAGAGGAAGCATTTCCCATCAGTGAATTGGCTCATATCTTATTCGAAATATTCTAAG

upper sequence: Vv04s0008g02580.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GRMZM2G128877_T02 (Zea mays), 3'ss of exon 13
------------cccatcattctattataattgaagacttggagtat----ccatttgactctttaatttctccttttggcattcaagttttagttttccataaaaccttgtgcagGTGTTCTGGGGTTTGGACAAAAAGCTTGCTCAGAGGAAACATTTCCCATCTGTAAACTGGCTTATTTCTTACTCTAAGTACTCAACC
            || || | |  |  ||| || |   |    |  ||    ||||     | |  | | | |  | ||   ||  |   || | |  |          || ||||||| ||||||||||| || |||||||| ||||| ||||| |||||||||||||| || ||||| ||||| || || || ||||| |  
gtaagacggctgccaattacttca--atacttcagtcccccaatcattggtccatcctgatttacagtgtttgttgtttcaatatattgttaaatcatgtgctgcttttt-tgcagGTCTTCTGGGGTTTAGATAAAAAGCTCGCTCAAAGGAAGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAG

upper sequence: Vv04s0008g02580.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GRMZM2G421857_T02 (Zea mays), 3'ss of exon 13
-------------cccatcattctattataattgaagacttggagtatccatttgactc--ttta----atttctccttttggcat-tcaagttttagttttccataaaaccttgtgcagGTGTTCTGGGGTTTGGACAAAAAGCTTGCTCAGAGGAAACATTTCCCATCTGTAAACTGGCTTATTTCTTACTCTAAGTACTCAACC
             |  || | |  | |||| || |   ||  ||  ||   |    |    ||||     ||| |  |||    || | || |  ||   | |  |      || ||||||| ||||||||||| || |||||||| ||||| ||||| |||||||||||||| || ||||| ||||| || || || ||||| |  
gtaagaaggctgccaaattacttcaatatacttcagtcctctgatcattagtccagcctgatttacagcgtttgttgtttcaatatattaaatcatatgctgctcttt--ttttttgcagGTCTTCTGGGGTTTAGATAAAAAGCTCGCTCAAAGGAAGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAG

upper sequence: Vv04s0008g02580.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA08G23990.1 (Glycine max), 3'ss of exon 14
cccatcattctattataattgaagacttggagtatccatttgactctttaatttctcct--tttggcattcaagtttta-gttttccataaaaccttgtgcagGTGTTCTGGGGTTTGGACAAAAAGCTTGCTCAGAGGAAACATTTCCCATCTGTAAACTGGCTTATTTCTTACTCTAAGTACTCAACC
   |   |   ||||| |   |   ||  |  |||   ||    | | ||   |    |   ||   |||||  || || ||||    |       |  |||||| ||||||||||||||||||||||||||||||||||| || || || ||||||||||||||||||||||| || || |||||||| 
---agattatcattatgaaatacccctctggttatttcttcttttatctatccttctataactttcaattcattttgtaagtttatttttgcttaattggcagGTTTTCTGGGGTTTGGACAAAAAGCTTGCTCAGAGGAAGCACTTTCCTTCTGTAAACTGGCTTATTTCTTATTCAAAATACTCAACG

upper sequence: Vv04s0008g02580.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA07G00430.1 (Glycine max), 3'ss of exon 14
cccatcattctattataattgaagacttggagtatccatttgactctttaatttctccttttggcattcaagttttagttttccataaaacct------tgtgcagGTGTTCTGGGGTTTGGACAAAAAGCTTGCTCAGAGGAAACATTTCCCATCTGTAAACTGGCTTATTTCTTACTCTAAGTACTCAACC
      |   ||| |  ||  ||  |        |   ||   || ||   | ||    | |  | ||||| |  | || |    | |    |      |  |||||| |||||||| ||||||||||||||||| |||||||| || || || ||||||||||||||||||||||| || || |||||||| 
------agattatcactatgaaatgcccctctggttatttcttcttttatctatccttctataactttcaattcattgtgtaagttgatttttgcttaattggcagGTTTTCTGGGGGTTGGACAAAAAGCTTGCCCAGAGGAAGCACTTTCCTTCTGTAAACTGGCTTATTTCTTATTCAAAATACTCAACG

upper sequence: Vv04s0008g02580.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 14
-----------------------------------------------------------------------------------cccatcattctattataattgaagacttggagtatcca-----tttgactctttaatttctccttttggcattcaagttttagttttccataaaaccttgtgcagGTGTTCTGGGGTTTGGACAAAAAGCTTGCTCAGAGGAAACATTTCCCATCTGTAAACTGGCTTATTTCTTACTCTAAGTACTCAACC
                                                                                       |  || ||        | ||||| | | |||  |     |||   |||  | |||    |  |  |  |    || | ||| |   |     ||| ||||||| |||||||||||||||||||||||||| ||||| |||||||| || ||||| || ||| | ||||||||||| ||||| ||||| 
gtgattatttggttcatgtctgcttccctatcttccattgtagattacatagtcgtatatgttggttgagatgaaccagatggtgtttagttttagatctgccgcagactcgta-tatttaagcattttttttctccactttgaaatgcttactcttccattctggttgtttctcttttcttctgcagGTCTTCTGGGGTTTGGACAAAAAGCTTGCCCAGAGAAAACATTTTCCCTCTGTTAATTGGTTGATTTCTTACTCAAAGTATTCAACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttaatttctccttttggcattcaagttttagttttccataaaaccttgtgcagGTGTTCTGGGGTTTGGACAAAAAGCTTGCTCAGAGGAAACATTTCCCATCTGTAAACTGGCTTATTTCTTACTCTAAGTACTCAACC
 ctttaat  putative branch site (score: 4)
                           ttttagtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cccatcattctattataattgaagacttggagtatccatttgactctttaatttctccttttggcattcaagttttagttttccataaaaccttgtgcagGTGTTCTGGGGTTTGGACAAAAAGCTTGCTCAGAGGAAACATTTCCCATCTGTAAACTGGCTTATTTCTTACTCTAAGTACTCAACC

cccatca
- - - - - - - - aattgaa
- - - - - - - - - - - - - - - -gtatcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcattca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccataaa