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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgctaggaggaattccattaatgaaaaatttcatgctacttcatttgatattgtttttgtattccagtgctttttctaagcaagctttaacttggtgcagATCCATTGGTTCTCAATCTTCAATTCATTCATGATGGTTATTTTCCTCACTGGATTGGTGTCTATGATATTAATGCGAACTCTTCGAAATGATTATGCCA

Basic information

species Vitis vinifera
transcript Vv18s0041g00680.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0041g00680.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os11g07910.1 (Oryza sativa), 3'ss of exon 6
----------------------------------------------------------------------tgctaggaggaattccattaatgaaaaatttcatgctacttcatttgatattgtttttgtattccagtgctttttctaagcaagcttt-----aacttg----gtgcagATCCATTGGTTCTCAATCTTCAATTCATTCATGATGGTTATTTTCCTCACTGGATTGGTGTCTATGATATTAATGCGAACTCTTCGAAATGATTATGCCA
                                                                      ||||  | ||   |   || |  ||    |  |   || ||  ||| | | | |    | |||  | |         ||  ||| | |     ||| |     || ||||||||||||||||| ||||||||||| |||||||||||||||||| | ||||||||||| || |||||||| ||| | || ||  ||||||||||||| |
gtaatctttgttcgaaccaacattactttttatgtcttttgctggacagtttttgtgctataatttactttgctctgtggtggtt--ttgacaaagtggtagactttattttctttaaaactctcgaggaattgaaatttacaagaaaactaagttctgctgcaaccttccatgttcagATCCATTGGTTCTCCATCTTCAATTCGTTCATGATGGTTATTTTCTTGACTGGATTGGTATCAATGATATTGATGAGGACGCTGAGAAATGATTATGCGA

upper sequence: Vv18s0041g00680.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os02g34690.1 (Oryza sativa), 3'ss of exon 6
-------------------------------------------------------tgctaggaggaattccattaatgaaaaatttcatgctacttcatttgatattgtttttgtattccagtgctttttctaagca----agctttaacttggtgcagATCCATTGGTTCTCAATCTTCAATTCATTCATGATGGTTATTTTCCTCACTGGATTGGTGTCTATGATATTAATGCGAACTCTTCGAAATGATTATGCCA
                                                       |  |      ||||      || |||||||      |  |||      |    | | | | || |||   ||  ||| | ||       |  |  ||   |||||||||||||||||||||||||||||| |||||||||||||| || ||||||||  | ||||| ||||| || ||||| |||||  ||||||| ||||| |
gtaagaactcagtttctgcaattaaagcctggttctgcaccttggttcttatgtattttgttgccaattttccacataaaaaattatgccttgattctcaatttcccatgtatatcttgcagcatttcctctgaccacagataatccattttatggcagATCCATTGGTTCTCAATCTTCAATTCTTTCATGATGGTTATCTTTCTCACTGGGCTAGTGTCAATGATTTTGATGCGCACTCTAAGAAATGACTATGCAA

upper sequence: Vv18s0041g00680.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os12g07670.1 (Oryza sativa), 3'ss of exon 6
-------------------------------------------------------------------tgctag-gaggaattccattaatg--aaaaatttcatgctacttcatttgatattgtttttg-----tattccagtgcttt---ttctaagcaagctttaacttggtgcagATCCATTGGTTCTCAATCTTCAATTCATTCATGATGGTTATTTTCCTCACTGGATTGGTGTCTATGATATTAATGCGAACTCTTCGAAATGATTATGCCA
                                                                   ||  |  ||| ||     |||||   || ||      |||   || | |  | || ||||||     | ||| |  | | |   ||||| ||||  ||  | |  || ||||| ||||||||||| || |||||||| |||||||||||||||||||||||||| ||||| || |||||||| ||||| ||  |  ||||||| ||||| |
gtaatattttcccactccaaagaaaaaaaaactatgcgtaacatgcagctctcagcttgcttacttatgtgaaagagaaaaaatgttaattgtaacaacagggagctgaatcgtct--tgttctttttgaaagttgttcaaaggttctgacttctatgcaaatttctaat--gttcagATTCATTGGTTCTCCATTTTCAATTCTTTCATGATGGTTATTTTCCTCACTGGTTTGGTTTCAATGATATTGATGCGGACATTGAGAAATGACTATGCAA

upper sequence: Vv18s0041g00680.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G165631_T01 (Zea mays), 3'ss of exon 5
----------------------------------------------tgctaggaggaattccattaatgaaa-aatttcatgctacttcatttgatattgtttttgtattccagtgc------------tttttctaa--gcaagctttaacttgg---tgcagATCCATTGGTTCTCAATCTTCAATTCATTCATGATGGTTATTTTCCTCACTGGATTGGTGTCTATGATATTAATGCGAACTCTTCGAAATGATTATGCCA
                                               |||    | |||| || ||  |||  | | | ||       |||| | |    | |   | ||  |  |             | ||  |||   | || | |  ||||    ||||||| |||||||||||||| |||||||| |||||||||||||| || ||||||||| | ||||| |||||| | ||||| |||||  ||||||||||||| |
gtaatataggtatatatttttgcaattaaggagatctttgcagcttggctcctcgtaattacaatacagaaccagtataattacttcccattagctgcgttctacatgtttgaaagagcctgaatcatatcttcttaatttctagttatttcttgtacttgcagATTCATTGGTTCTCAATTTTCAATTCTTTCATGATGGTTATCTTTCTCACTGGACTAGTGTCAATGATACTGATGCGGACTCTAAGAAATGATTATGCAA

upper sequence: Vv18s0041g00680.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G087212_T01 (Zea mays), 3'ss of exon 6
tgctaggaggaattccattaatgaaaaatttcatgctacttcatttgatattg---tttttgtattccagtgctttttctaagcaagct-------ttaacttggtgcagATCCATTGGTTCTCAATCTTCAATTCATTCATGATGGTTATTTTCCTCACTGGATTGGTGTCTATGATATTAATGCGAACTCTTCGAAATGATTATGCCA
           | |     | |      |||| | |  ||     | || | |   ||  | | |  | |   |  ||  |||   |||       ||  |   ||  |||| ||||||||||| |||||||||||||||||||||||||||||| | ||||| || ||||| |||||||| ||| | || ||  ||||||||||||| |
---------acactttgccactttggtctttcct-cggctctgactaatgtggaccttgctatctgtctgaagtaattacaagatggctgacccttttttccatgtttagATTCATTGGTTCTCCATCTTCAATTCATTCATGATGGTTATTTTCTTGACTGGTTTAGTGTCAATGATATTGATGAGGACACTAAGAAATGATTATGCAA

upper sequence: Vv18s0041g00680.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G026231_T01 (Zea mays), 3'ss of exon 6
-tgctaggaggaattccattaatgaaaaatttcatg----ctacttcatttgatattgtttttgtatt--ccagtgctttttctaagcaagctttaacttg-----gtgcagATCCATTGGTTCTCAATCTTCAATTCATTCATGATGGTTATTTTCCTCACTGGATTGGTGTCTATGATATTAATGCGAACTCTTCGAAATGATTATGCCA
 || ||    |  | |    ||  | ||| ||  |     ||| |    |  || ||   |||  | |  | | |     | ||||||    || |  ||       | ||||| || |||||||| || ||||| || |||||||||||||||||||| ||||| ||||| || |||||||| ||||| ||| |  |||||||||||||||
gtgatactttgtttgcagacaaccagaaactttctagtttctattcagctgtatcttcccttttaactaactattagaaatcctaagctctgttcatatttctcattttcagATTCACTGGTTCTCCATTTTCAACTCTTTCATGATGGTTATTTTCCTAACTGGTTTGGTTTCGATGATATTGATGCGGACTTTGAGAAATGATTATGCCA

upper sequence: Vv18s0041g00680.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G420310_T01 (Zea mays), 3'ss of exon 6
---------tgctaggaggaattccattaatgaaaaatttc-atgctacttcatttgatattgtttttgtattccagtgctttt----tctaagcaagctttaacttggtgcagATCCATTGGTTCTCAATCTTCAATTCATTCATGATGGTTATTTTCCTCACTGGATTGGTGTCTATGATATTAATGCGAACTCTTCGAAATGATTATGCCA
         || | | ||  |  | |  | |    | ||||  | |  ||  |  |    || |   |   |   ||   |  |    |||   ||   ||    ||  | ||||| || |||||||| || ||||| || |||||||||||||||||||| ||||| ||||| || |||||||| ||||| ||| |  |||| ||||||||||
gtgatactttgtttgtagacaaccgacaacttcctagtttctgttcagctgtaccttcccttttaactagctattagaagtcctaagctctgttcatatttctcatt--tccagATTCACTGGTTCTCCATTTTCAACTCTTTCATGATGGTTATTTTCCTAACTGGTTTGGTTTCGATGATATTGATGCGGACTTTGAGAAACGATTATGCCA

upper sequence: Vv18s0041g00680.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA08G13370.1 (Glycine max), 3'ss of exon 6
---------------------tgctaggaggaattcca----ttaatgaaaaatttcatgctacttcat-ttgat---attgtttttgtattccagtgctttttctaagcaagctttaacttggtgcagATCCATTGGTTCTCAATCTTCAATTCATTCATGATGGTTATTTTCCTCACTGGATTGGTGTCTATGATATTAATGCGAACTCTTCGAAATGATTATGCCA
                     ||  | |  |   |  |    ||  ||||    |   |  |  | ||| ||| |   |   | | | | |  | | |  ||||        | |||   ||     |||| ||||||||||| || || || || ||||||||||| || ||||| |||||||||||||| |||||||| |||||||||||  ||||||| ||||| |
gtacaactttgcttttaaaattgaaatggtgttgtttatggtttggtgaattgctatgtattcatccatgttggtcctaccatatctctgtcactgagtattttgctcctttgttttctttttccctagATTCATTGGTTCTCCATTTTTAACTCTTTCATGATGGTCATCTTCCTTACTGGATTGGTGTCAATGATATTGATGCGAACTCTGAGAAATGACTATGCAA

upper sequence: Vv18s0041g00680.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA05G30210.1 (Glycine max), 3'ss of exon 6
---------------------tgctaggaggaattcca----ttaatgaaaaatttcatgctacttcat-ttgatattgtttttg---tattccagtgctttttctaagcaagctttaacttggtgcagATCCATTGGTTCTCAATCTTCAATTCATTCATGATGGTTATTTTCCTCACTGGATTGGTGTCTATGATATTAATGCGAACTCTTCGAAATGATTATGCCA
                     ||  | |  |   |  |    ||  ||||    |   |  |  | ||| ||| |  |    | |   |    | | |  ||||        | |||   ||     |||| ||||||||||| || || || || ||||||||||| || ||||| ||||| |||||||| |||||||| |||||||||||  ||||||| ||||| |
gtacagctttgcttttaaaattgaaatggtgttgtttatggtttggtgaattgctatgtattcatccatgttggtcctaccatagctctgccactgagaattttgctcctttgttttctttttccctagATTCATTGGTTCTCCATTTTTAACTCTTTCATGATGGTCATCTTCCTTACTGGTTTGGTGTCAATGATATTGATGCGAACTCTGAGAAATGACTATGCAA

upper sequence: Vv18s0041g00680.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA12G29120.1 (Glycine max), 3'ss of exon 6
---------------------------tgctagga-ggaattccattaatgaaaaatttcatgctacttcatttgatattgtttttgtattccagtgctttttctaagcaagctttaa--------cttggtgcagATCCATTGGTTCTCAATCTTCAATTCATTCATGATGGTTATTTTCCTCACTGGATTGGTGTCTATGATATTAATGCGAACTCTTCGAAATGATTATGCCA
                           |  |||   | |      || ||      || | |||||| |  |     ||     |  |||   ||   | |  || ||| | |||| |        |||  || |||| || |||||||| || || ||||| || |||||||| || ||||| |||||||||||||| |||||||||||||||||  |  ||||||| ||||| |
gtgaaaatcattgctgctagatttgtattttagattgaagaggtgtttattgttggttacctgctacgtgttcattcatgtggatcctatcttagccatgtcactgagcgaactttgatcatttttctttctgtagATTCACTGGTTCTCCATTTTTAATTCTTTTATGATGGTCATCTTCCTTACTGGATTGGTGTCAATGATATTAATGCGAACGTTGAGAAATGACTATGCAA

upper sequence: Vv18s0041g00680.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 6
---------------------------tgctagga-ggaattccattaatgaaaaatttcatgctacttcatttgatattgtttttgtattccagtgctttttctaagcaagctttaa--------cttggtgcagATCCATTGGTTCTCAATCTTCAATTCATTCATGATGGTTATTTTCCTCACTGGATTGGTGTCTATGATATTAATGCGAACTCTTCGAAATGATTATGCCA
                           |  |||   | |      || ||      || | |||||  |  |  |  ||     |  |||   ||   | |  || ||  | |||| |        |||  || |||| || |||||||| || || ||||| || |||||||| || ||||| |||||||||||||| |||||||||||||||||  |  ||||||| ||||| |
gtgaaaatcattgctgctagctttgtattttagattgaagaggtgtttattgttggttacctgctatgtgttcagtcatgtggatcctatcttagccatgtcactgagagaactttgatccgttttctttctgtagATTCACTGGTTCTCCATTTTTAATTCTTTTATGATGGTCATCTTCCTTACTGGATTGGTGTCAATGATATTAATGCGAACATTGAGAAATGACTATGCAA

upper sequence: Vv18s0041g00680.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 6
tgctaggaggaattccattaatga---aaaatttcatgctacttca-tttgatattgtttttgtattccagtgctttttctaagcaagctttaacttggtgcagATCCATTGGTTCTCAATCTTCAATTCATTCATGATGGTTATTTTCCTCACTGGATTGGTGTCTATGATATTAATGCGAACTCTTCGAAATGATTATGCCA
   ||       |||||  |||     ||| ||  ||  | | ||  ||  | |||  | ||  |      |     |||| ||  || ||   |||  |||||||||| |||||||| ||||| || || ||||||||||||||||||||||| || ||||| || |||||||| ||| | |||||  ||||||||||||| |
--ataattattcttccaagaatctaccaaagttctatattccatctcttcaagatttctgttcaagctttataagccttctgag--agtttgttctttttgcagATCCACTGGTTCTCCATCTTTAACTCGTTCATGATGGTTATTTTCCTCACCGGTTTGGTCTCAATGATATTGATGAGGACTCTCAGAAATGATTATGCGA

upper sequence: Vv18s0041g00680.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: PP1S438_26V6.1 (Physcomitrella patens), 3'ss of exon 6
-------------------------------------------------------------------------------------------tgctagga-ggaattccatta-atgaaaaatttcatgctacttcatttgatattgtttttgtattccagtgctttttctaagcaagctttaact-tggtg-cagATCCATTGGTTCTCAATCTTCAATTCATTCATGATGGTTATTTTCCTCACTGGATTGGTGTCTATGATATTAATGCGAACTCTTCGAAATGATTATGCCA
                                                                                           || |  |  |||  | |||   |||   |||   | |   |   | ||     |||    || ||    |  |  ||        |      |   | || ||||| ||||||||||| |||||||| || ||||||||||| || || || || ||  |||| || |||||  | ||||| || || || || |||||||| |
gtgggtgtgaggagggagcggagggctgagttgcaagatttgtgtagcgagtgtgggtggagacgggagcttgaagctacatgcgagttagtggtgtgttggaggttcatgggatggtgaatgggacgagtcgcgagtttgacgtgtgggggtgtttggtttgtggttgatgttgggtggcggccgcgatgacagATACATTGGTTCTCTATCTTCAACTCGTTCATGATGGTGATATTTCTGACGGGGCTGGTATCGATGATTCTGATGCGCACCCTCCGCAACGATTATGCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatattgtttttgtattccagtgctttttctaagcaagctttaacttggtgcagATCCATTGGTTCTCAATCTTCAATTCATTCATGATGGTTATTTTCCTCACTGGATTGGTGTCTATGATATTAATGCGAACTCTTCGAAATGATTATGCCA
                                       ctttaac  putative branch site (score: 3)
        tttttgtatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgctaggaggaattccattaatgaaaaatttcatgctacttcatttgatattgtttttgtattccagtgctttttctaagcaagctttaacttggtgcagATCCATTGGTTCTCAATCTTCAATTCATTCATGATGGTTATTTTCCTCACTGGATTGGTGTCTATGATATTAATGCGAACTCTTCGAAATGATTATGCCA

- - - - - - - ccattaa
- - - - - - - - - - -tgaaaaa
- - - - - - - - - - - - - - - tcatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcaagct