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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacattttagtaattacattctacattgaagtacattgctctggataaaagtgtttttttttttcctttaggttcctacaacaaaaattcatataaacatgtgcattatatgtgtgcatggctgtgaaagaaatatgccttagaatttgaagtattaaactcttttttgcaacacccaactgtttacattgtccagGGTGAGGAATACAAGTTGTTTTGGCCAGAATCATCTGAGTTTATCCGAATGGCGGCTAGATTTGGAGCCAAAATTGTACCCTTTGGGGTGGTTGGAGAAG

Basic information

species Vitis vinifera
transcript Vv14s0068g01440.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0068g01440.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA16G05580.1 (Glycine max), 3'ss of exon 10
gtaacattttagtaattacattctacattgaagtacattgctctggataaaagtgtttttttttttcctttaggttcctacaacaaaaattcatataaacatgtgcattatatgtgtgcatggctgtgaaagaaatatgccttagaatttgaagtattaaactcttttttgcaacacccaactgtttac-attgtccagGGTGAGGAATACAAGTTGTTTTGGCCAGAATCATCTGAGTTTATCCGAATGGCGGCTAGATTTGGAGCCAAAATTGTACCCTTTGGGGTGGTTGGAGAAG
                                                                                    |  || |  | ||  |     || | ||| |||   || || |     |  ||||| ||  |||      ||  | | || |||    ||   |||||  |  |  | |   |||||||| ||||||||||| || ||||| |||  ||| |||||| |  | ||||| || ||||||||||||||||| ||||| ||||| || ||||||||||
-----------------------------------------------------------------------------------tatgaaattttttaggct----cactttatctgtctctgtctct-----atttatgctttgaaat-----ataccagagtcgttt--aaaatctccaacattgcattaattctcagGGTGAAGAATACAAGTTATTCTGGCCTGAACAATCCGAGTTTGTAAGGATGGCAGCAAGATTTGGAGCCAAAATAGTACCTTTTGGTGTAGTTGGAGAAG

upper sequence: Vv14s0068g01440.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA16G05570.1 (Glycine max), 3'ss of exon 12
gtaacattttagtaattacattctacattgaagtacattgctctggataaaagtgtttttttttttcctttaggttcctacaacaaaaattcatataaacatgtgcattatatgtgtgcatggctgtgaaagaaatatgccttagaatttgaagtattaaactcttttttgcaacacccaac-tgtttacattgtccagGGTGAGGAATACAAGTTGTTTTGGCCAGAATCATCTGAGTTTATCCGAATGGCGGCTAGATTTGGAGCCAAAATTGTACCCTTTGGGGTGGTTGGAGAAG
                                                                                         ||  | |  | |    | |||| ||| |   |  ||||     |  | ||| ||  |||       | || | |  |||    ||    || | | || | | | | |||||||| ||||||||||| || |||||  ||  |||||||||| |  | ||||| || ||||||||||||||||||||||| ||||| |  ||||||||||
-------------------------------------------------------------------------------------ttggttattttttagacccactttatttgtctctct--ctgt-----atttgtgctttgaaat-----acactagaatagttt--aaaatcttcagcattttaataattttcagGGTGAAGAATACAAGTTATTCTGGCCTCAACAATCTGAGTTTGTAAGGATGGCAGCAAGATTTGGAGCCAAAATTGTACCTTTTGGTGCAGTTGGAGAAG

upper sequence: Vv14s0068g01440.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT3G26840.1 (Arabidopsis thaliana), 3'ss of exon 10
gtaacattttagtaattacattctacattgaagtacattgctctggataaaagtgtttttttttttcctttaggttcctacaacaaaaattcatataaacatgtgcattatatgtgtgcatggctgtgaaagaaatatgc---cttagaatttgaagtattaaactcttttttgcaacacccaactgtttacattgtccagGGTGAGGAATACAAGTTGTTTTGGCCAGAATCATCTGAGTTTATCCGAATGGCGGCTAGATTTGGAGCCAAAATTGTACCCTTTGGGGTGGTTGGAGAAG
                                                                                                      |||   |||| || || |    | |    |   | |||   |||  || |||   | ||| |  ||||  || ||||  |||        | | | |||||||| ||||||||| ||||||||||||||   || |||||| |  || | ||  ||| |||||||||||||||||| || ||||| || ||||||||||
------------------------------------------------------------------------------------------------------gtgatatata-gtttgtaaactttttccgggtttctgcattcttgaaacttgttattttagaggctttaatg-aacaaacaa--------aatttgcagGGTGAAGAATACAAGCTGTTTTGGCCAGAACGGTCCGAGTTTGTGAGAGTTGCATCTAAATTTGGAGCCAAAATTGTTCCTTTTGGTGTTGTTGGAGAAG

upper sequence: Vv14s0068g01440.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT5G41130.2 (Arabidopsis thaliana), 3'ss of exon 10
gtaacattttagtaattacattctacattgaagtacattgctctggataaaagtgtttttttttttcctttaggttcctacaacaaaaattcatataaacatgtgcattatatgtgtgcatggctgtgaaagaaatatgccttagaatttgaagt--attaaactcttttttgcaacacccaactgtttacattgtccagGGTGAGGAATACAAGTTGTTTTGGCCAGAATCATCTGAGTTTATCCGAATGGCGGCTAGATTTGGAGCCAAAATTGTACCCTTTGGGGTGGTTGGAGAAG
                                                                                                                             || |     | ||  || | | || |   |   || |||| |     |  |||   ||      |  || | |||||||| | ||||||||||||||||||||||   || |||||| |  | |  ||  ||| ||||||| | |||||  | || |||||||| ||||| ||||
-----------------------------------------------------------------------------------------------------------------------------gtaatgattagatatctcatatttggccttcgttttaactttgaagcgttacatagaatgacacat-ttctacagGGTGAAGTATACAAGTTGTTTTGGCCAGAACATTCAGAGTTTGTAAGGACCGCATCTAAATTTGGAACAAAAATCATTCCTTTTGGGGTTGTTGGTGAAG

upper sequence: Vv14s0068g01440.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT3G26820.1 (Arabidopsis thaliana), 3'ss of exon 12
gtaacattttagtaattacattctacattgaagtacattgctctggataaaagtgtttttttttttcctttaggttcctacaacaaaaattcatataaacatgtgcattatatgtgtgcatggctgtgaaagaaatatgcct-tagaatttgaagtattaaactcttttttgc-aacacccaactgtttacattgtccagGGTGAGGAATACAAGTTGTTTTGGCCAGAATCATCTGAGTTTATCCGAATGGCGGCTAGATTTGGAGCCAAAATTGTACCCTTTGGGGTGGTTGGAGAAG
                                                                                          | || | |  ||    | |||||   ||| |||   |||      |  |  | || |||||    |||||   | ||    |  ||||   ||      || |    |||||||| ||||||||| ||||||||||||||  ||| |||||| |  || | ||  ||| ||||||||| ||||| || || || || || ||||||||||
-----------------------------------------------------------------------------------------gttatgttataat---taatatattgttgcgtgg---tgacctttttcggtttctacaattttggatattagtgttttggaggttaacatgtaaagagagacttca--cagGGTGAAGAATACAAGCTGTTTTGGCCAGAACAATCCGAGTTTGTGAGAGTTGCATCTAAATTTGGAGCGAAAATCGTTCCTTTCGGTGTTGTTGGAGAAG

upper sequence: Vv14s0068g01440.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT5G41120.1 (Arabidopsis thaliana), 3'ss of exon 10
gtaacattttagtaattacattctacattgaagtacattgctctggataaaagtgtttttttttttcctttaggttcctacaacaaaaattcatataaacatgtgcattatatgtgtgcatggctgtgaaagaaatatgccttagaatttgaagtattaaactcttttttgcaacacccaactgtttacattgtccagGGTGAGGAATACAAGTTGTTTTGGCCAGAATCATCTGAGTTTATCCGAATGGCGGCTAGATTTGGAGCCAAAATTGTACCCTTTGGGGTGGTTGGAGAAG
                                                                                                                   |||  |   | |     | || | ||||   |||| || | || |    || | |  ||   |  ||  |||| |     |||||||| ||||||||||| ||||||||||||   || |||||| |  | || ||  ||| ||||||||| |||||  | || ||||| || ||||||||||
-------------------------------------------------------------------------------------------------------------------gtgattatgtattttccatattttccttc--attttaatttttgaggctttatatctaaagac--acattttataa----cagGGTGAAGAATACAAGTTATTTTGGCCAGAACATTCGGAGTTTGTAAGGATAGCATCTAAATTTGGAGCAAAAATCATTCCTTTTGGAGTTGTTGGAGAAG

upper sequence: Vv14s0068g01440.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: EFJ23061 (Selaginella moellendorffii), 3'ss of exon 10
gtaacattttagtaattacattctacattgaagtacattgctctggataaaagtgtttttttttttcctttaggttcctacaacaaaaattcatataaacatgtgcattatatgtgtgcatggctgtgaaagaaatatgccttagaatttgaagtattaaactcttttttgcaacac-ccaactgtttacattgtccagGGTGAGGAATACAAGTTGTTTTGGCCAGAATCATCTGAGTTTATCCGAATGGCGGCTAGATTTGGAGCCAAAATTGTACCCTTTGGGGTGGTTGGAGAAG
                                                                                                                                              | | ||||    | |     | | |||  ||||   ||| |||  |   ||  |||||| |||||||||||| | ||||||||||||   || |||||| |||||||||| ||  | || || ||||  ||  | || ||  |    ||||| ||||
-------------------------------------------------------------------------------------------------------------------------------------------gtatggtattt---atctcttcttttctttgtcaacttaccatctggatttttttcccagGGAGAGGAATACAAGCTCTTTTGGCCAGAACAGTCCGAGTTTGTCCGAATGGCTGCGCGTTTCGGTGCCACCATAATTCCTTTCAGCTGCGTTGGCGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaatttgaagtattaaactcttttttgcaacacccaactgtttacattgtccagGGTGAGGAATACAAGTTGTTTTGGCCAGAATCATCTGAGTTTATCCGAATGGCGGCTAGATTTGGAGCCAAAATTGTACCCTTTGGGGTGGTTGGAGAAG
           tattaaactctttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacattttagtaattacattctacattgaagtacattgctctggataaaagtgtttttttttttcctttaggttcctacaacaaaaattcatataaacatgtgcattatatgtgtgcatggctgtgaaagaaatatgccttagaatttgaagtattaaactcttttttgcaacacccaactgtttacattgtccagGGTGAGGAATACAAGTTGTTTTGGCCAGAATCATCTGAGTTTATCCGAATGGCGGCTAGATTTGGAGCCAAAATTGTACCCTTTGGGGTGGTTGGAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA