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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatattgtctaatcaattcagccatcatagttgctgctgtaatacttgggttcccttcagccatgttattgattatatctattcttattcagGATTTACACCCAAACCCTCCACCTGAGAAGACAAAGGATGATATTTTGCTTTTCTTCAAGCTTTATGATCCTGAGAAGGAAGAGCTAAA

Basic information

species Vitis vinifera
transcript Vv06s0009g00960.t01
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: LOC_Os01g56490.1 (Oryza sativa), 3'ss of exon 17
------------------------------gtaatattgtctaatcaattcagccatcatagttgct--gctgtaatac-------ttgggttcccttcagccatgttattgattatatctattcttattcagGATTTACACCCAAACCCTCCACCTGAGAAGACAAAGGATGATATTTTGCTTTTCTTCAAGCTTTATGATCCTGAGAAGGAAGAGCTAAA
                              |  |  |  |||| ||||||  |   |  || ||| |  ||   | | |       |||| || | |   | ||  |||      ||    |    | | |||||    || || |   ||   |||   |||||||||||||| || ||  | ||||||||||| ||||||||||| ||||||||||||| 
gttaactacttactaaagtgctttttatttgctaagtcatctactcaattgtgttgtgctacttgtttagccaaagttcattgatcttggtttacttgtggacaatttaacccagattatgacatgtgtacagGAAAATCATCCTATTTCTGTGCCTCCAAAGACAAAGGATGACATATTAATATTCTTCAAGCTGTATGATCCTGAAAAGGAAGAGCTAAG

upper sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: LOC_Os11g36470.1 (Oryza sativa), 3'ss of exon 13
----------------------------------------------------------gtaatattgtctaa--tcaattcagccatcatagtt-gctgctgtaatacttgggttcccttcagccatgttattgat-tatatctattcttattcagGATTTACACCCAAACCCTCCACCTGAGAAGACAAAGGATGATATTTTGCTTTTCTTCAAGCTTTATGATCCTGAGAAGGAAGAGCTAAA
                                                          || ||    ||||    ||    |   | | | |||      | | ||||||  | |       |  |  |||||| | | | | |  || | |  ||||||| |  ||   |||||||||||||||||  ||||| |||||| | || |||||||| || ||| |||| || |||||||| ||   
gtaatgatgtgctggagctgctaccatttctttttctgttttttacttattgttgtctgttatggcttctagatgcaggatacttaactttgtttatctgtttgatacttatggttatgcaggatac-ttattgttgtctgttttatcatttatagGATTTGCGGCCTCTCCCTCCACCTGAGAAGAGCAAGGAAGATATTCTTCTGTTCTTCAAACTCTATAATCCCGAAAAGGAAGAACTCTG

upper sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GRMZM2G303655_T01 (Zea mays), 3'ss of exon 7
gtaatattgtctaatcaattcagccatcatagttgctgctgta-atacttgggttcccttcagccatgttattgattatatctattc-ttattcagGATTTACACCCAAACCCTCCACCTGAGAAGACAAAGGATGATATTTTGCTTTTCTTCAAGCTTTATGATCCTGAGAAGGAAGAGCTAAA
|||| || ||    |  |||   |  | ||  |  ||  |||  || | |        || ||     |  ||| || ||  ||||  ||||  |||| |||   ||||  | ||||||||||||||  || || || ||  | |||||||||||||||||| || ||||||||||||||||  |
gtaaaat-gttatttttatttgtcttttattttccctcttgtttatgccttctagattttgagatgcttggttgtttctaattattaattatatagGAGTTATGTCCAATTCGTCCACCTGAGAAGAGCAAAGAAGACATACTTCTTTTCTTCAAGCTTTATAATGCTGAGAAGGAAGAGCTTCA

upper sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GRMZM2G071441_T01 (Zea mays), 3'ss of exon 13
------------------------------------------gtaatattgtctaatcaat-tcagccatcatagttgctgctg--taatacttgggttcccttcag--ccatgttattgattatatctatt--cttattcagGATTTACACCCAAACCCTCCACCTGAGAAGACAAAGGATGATATTTTGCTTTTCTTCAAGCTTTATGATCCTGAGAAGGAAGAGCTAAA
                                          ||   | ||| |||   || | |  |||  || ||  |  |   |  || |||  ||    | |   |  |  | |  |  |||  |  |  |  || |||||    || ||||   ||||   |  ||| || || || ||||| || |||||||||||||| ||||||||||| || ||||| |||| 
gttaagtgcttaaataccttttgattatttcatttacttttggtcccaatgtttaactgatgttattcatt-tacttaatcttacttcttatttgccttttgattatttctttactgtctaacatagtttctggcacatccagGAGAACCAACCAATTGCTCC---TTGGAATACCAAAGAAGATATATTACTTTTCTTCAAGCTCTATGATCCTGAAAAAGAAGACCTAAG

upper sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GLYMA20G11330.1 (Glycine max), 3'ss of exon 9
gtaatattgtc--taatcaattcagccatcatagttgctgctgtaatacttgggttccc--ttca---gccatgttattgattatatctattcttattcagGATTTACACCCAAACCCTCCACCTGAGAAGACAAAGGATGATATTTTGCTTTTCTTCAAGCTTTATGATCCTGAGAAGGAAGAGCTAAA
|||| ||| |   ||   || |     |  | | ||  |    | | ||||   | | |  || |    |  |  | |||   || |  |||| | || |||||| ||  || | | | |||||||| ||||| ||||||||||| || |||||||||||||| ||||||||||| || || |||||   
gtaacatttttattagggaaattgaatacta-atttaatagcatgaaactttaatgctcaattaaaacactgtcctgttggaaatctgcattcatgtttagGATTCACGTCCCATCGCACCACCTGACAAGACCAAGGATGATATATTACTTTTCTTCAAGCTATATGATCCTGAAAAAGAGGAGCTGCG

upper sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GLYMA14G04890.1 (Glycine max), 3'ss of exon 17
gtaatatt---gtctaatcaattcagccatcatagttgctgctgtaatacttgggttcccttcagccatgttattgattatatctattcttattcagGATTTACACCCAAACCCTCCACCTGAGAAGACAAAGGATGATATTTTGCTTTTCTTCAAGCTTTATGATCCTGAGAAGGAAGAGCTAAA
|||| |||    | ||   || |     | |||  |    ||   |||  ||    |||      |  |  | ||||  |  | | || ||||| ||||| ||   || |   | || ||||| ||||||||||||||||| || |||||||||||| | ||||||||||| || || ||||||  
gtaacatttgtatttatggaagttgcataccattttcatagcatgaatcattaatatccaaatttctgtccttttgacaaactatgttgttatttagGATGTATGTCCCATTGCACCGCCTGACAAGACAAAGGATGATATATTACTTTTCTTCAAGTTATATGATCCTGAAAAAGAGGAGCTACG

upper sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GLYMA02G43930.1 (Glycine max), 3'ss of exon 17
---gtaatattgtctaatcaattcagccatcatagttgctgc-tgtaatacttgggttcccttcagccatgttattgattatatctattcttattcagGATTTACACCCAAACCCTCCACCTGAGAAGACAAAGGATGATATTTTGCTTTTCTTCAAGCTTTATGATCCTGAGAAGGAAGAGCTAAA
     | | || | ||   || |     | |||  |    || || |  | |    | |   |   |  |  | ||||  |  |  ||| ||||| |||||||||  || |   | || ||||| ||||||||||||||||| || |||||||||||| | |||||| |||| || || ||||||  
gtaacatttttatttatggaagttgtataccattttcatagcatgaatcattcatatccaaatt--ctgtccttttgacaaactacattgttatttagGATTTACGTCCCATTGCACCGCCTGACAAGACAAAGGATGATATATTACTTTTCTTCAAGTTATATGATACTGAAAAAGAGGAGCTACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtaatacttgggttcccttcagccatgttattgattatatctattcttattcagGATTTACACCCAAACCCTCCACCTGAGAAGACAAAGGATGATATTTTGCTTTTCTTCAAGCTTTATGATCCTGAGAAGGAAGAGCTAAA
                             tattgat  putative branch site (score: 3)
                                        tctattctt  putative PPT
                         atgttattgattatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatattgtctaatcaattcagccatcatagttgctgctgtaatacttgggttcccttcagccatgttattgattatatctattcttattcagGATTTACACCCAAACCCTCCACCTGAGAAGACAAAGGATGATATTTTGCTTTTCTTCAAGCTTTATGATCCTGAGAAGGAAGAGCTAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT