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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttttgtcacccatcaaaaaatgaaaaagaactttttttgttacctatttgtcattagttttagcgagctttaagtaattgtttgatgttatctttgcagGGCTCCTGAACTTCTGCTGGGAACAAAACAATACTCAACGGCAATTGACATGTGGTCTGTGGGTTGTATAATGGCTGAACTTTTAGCGAAAGAGCCACTA

Basic information

species Vitis vinifera
transcript Vv17s0000g01810.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g01810.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G179097_T04 (Zea mays), 3'ss of exon 2
-----tttttgtcacccatcaaaaaatgaaaaa------gaacttttttt---gttacctatttgtcattagttttagcgagctttaagtaattgtttgatgttatctttg------cagGGCTCCTGAACTTCTGCTGGGAACAAAACAATACTCAACGGCAATTGACATGTGGTCTGTGGGTTGTATAATGGCTGAACTTTTAGCGAAAGAGCCACTA
     |  | |     ||||| |   | |  |       |   || || |   ||||   | |||  | |  | || |      | ||| | |   ||    |  || |||      |||||| || ||| |  || | ||||||||  | || || || || ||||| |||||||||||||| |||||||||||||| ||| | || ||||| ||  ||
gtaggtcatcggacaacatcagatcctcagcagtgttttggttttcttctaaagttattcagttgagagttctgtttggtcaaatcaaggactcacttttcttgctccttgtggctacagGGCCCCAGAATTGTTGTTAGGAACAAAGGAGTATTCTACTGCTATTGATATGTGGTCTGTGGGCTGTATAATGGCTGAGCTTCTTGCCAAAGAACCGTTA

upper sequence: Vv17s0000g01810.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G179097_T07 (Zea mays), 3'ss of exon 2
tttttgtcacccatcaaaaaatgaaaaagaactttttttgttacctatttgtcattagttttagcgagctttaagtaattgtttgatgttatctttg------cagGGCTCCTGAACTTCTGCTGGGAACAAAACAATACTCAACGGCAATTGACATGTGGTCTGTGGGTTGTATAATGGCTGAACTTTTAGCGAAAGAGCCACTA
        | ||     |   |         ||| |   ||||   | |||  | |  | || |      | ||| | |   ||    |  || |||      |||||| || ||| |  || | ||||||||  | || || || || ||||| |||||||||||||| |||||||||||||| ||| | || ||||| ||  ||
------agatcctcagcagtgttttggttttcttctaaagttattcagttgagagttctgtttggtcaaatcaaggactcacttttcttgctccttgtggctacagGGCCCCAGAATTGTTGTTAGGAACAAAGGAGTATTCTACTGCTATTGATATGTGGTCTGTGGGCTGTATAATGGCTGAGCTTCTTGCCAAAGAACCGTTA

upper sequence: Vv17s0000g01810.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA05G03110.3 (Glycine max), 3'ss of exon 1
--------------------tttttgtcacccatcaaa---aaatgaaaaagaactttttttgttacctatttgtcat-tagttttagcgagctttaagt---aattgtttgatgttatctt------tgcagGGCTCCTGAACTTCTGCTGGGAACAAAACAATACTCAACGGCAATTGACATGTGGTCTGTGGGTTGTATAATGGCTGAACTTTTAGCGAAAGAGCCACTA
                    |||||      |||  ||   |  |  | | | |  |   |||| |  | |   |||| | | |  ||  |  | || ||   || |  ||  |||| | ||      ||||| || ||||||||| |||||||  | ||| |||||||||| ||||||||||||||||| |||||||| |||||||||||| |  | || || || || || 
gtgagtagcattatagtacttttttagttttcattgaagttatctctagatgtatctggcttgtgatttttcaatcatattggtagagaaatgtatatgtcacaactcattattgttgtattggtttgtgcagAGCACCTGAACTTTTGCTGGGTGCTAAAGAATACTCAACTGCAATTGACATGTGGTCAGTGGGTTGCATAATGGCTGAATTAATTGCCAAGGAACCTCTG

upper sequence: Vv17s0000g01810.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA17G13750.1 (Glycine max), 3'ss of exon 2
-------------------tttttgtcacccatcaaaaaatgaaaaagaactttttttgttacctatttgtcattagttt---tagcgagctttaagtaattgtt----------tgatgt---tatctttgcagGGCTCCTGAACTTCTGCTGGGAACAAAACAATACTCAACGGCAATTGACATGTGGTCTGTGGGTTGTATAATGGCTGAACTTTTAGCGAAAGAGCCACTA
                   |||| ||   |  | ||   ||        |  | | | |||    |||| | |||  | |   ||| ||  | ||  ||| | |           || |||     | | ||||| || ||||||||| |||||||  | ||| ||||||||||  |||||||||||||||| |||||||| |||||||||||| |  | |  || ||||| || 
gtgagtagcattattattattttagttttcattgaagttatctctgtagatatatctggtttgtgatttttaatttatattggtagagaaatgtatataagtctcaactcatgaatggtgtattggtttgtgcagAGCACCTGAACTTTTGCTGGGTGCTAAAGAATACTCAACATCAATTGACATGTGGTCAGTGGGTTGCATAATGGCTGAATTAATTGTCAAGGAGCCTCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttgtcattagttttagcgagctttaagtaattgtttgatgttatctttgcagGGCTCCTGAACTTCTGCTGGGAACAAAACAATACTCAACGGCAATTGACATGTGGTCTGTGGGTTGTATAATGGCTGAACTTTTAGCGAAAGAGCCACTA
                                   gtttgat  putative branch site (score: 5)
                                           ttatcttt  CT-rich tract
                        tttaagtaattgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttttgtcacccatcaaaaaatgaaaaagaactttttttgttacctatttgtcattagttttagcgagctttaagtaattgtttgatgttatctttgcagGGCTCCTGAACTTCTGCTGGGAACAAAACAATACTCAACGGCAATTGACATGTGGTCTGTGGGTTGTATAATGGCTGAACTTTTAGCGAAAGAGCCACTA

- - - tcaccca
- - - - - - - -aaaaaat
- - - - - - - - - - - - aaaagaa