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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttaattctttgccattccaactgtttctttgtgttttggttttggcttctttcttgaattctcgtcatgggagaggcgtgtggtgagtgttggggggggattagatatgttcttggtgaagctgggttggtgtttgtttaattcttatttctgcctgttctagaaaatcataattaccatgtgtcttacctgcagAATACTACCACAAAAGAAAATGAAACACTTTTGGCCATTGGGACTGCTTACGTACAAGGGGAGGATGTTGCTGCAAGGGGACGGGTGCTTTTATTTTCTG

Basic information

species Vitis vinifera
transcript Vv16s0022g01860.t01
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0022g01860.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: LOC_Os04g18010.1 (Oryza sativa), 3'ss of exon 21
gtgagttaattctttgccattccaactgtttctttgtgttttggttttggcttctttcttgaattctcgtcatgggagaggcgtgtggtgagtgttggggggggattagatatgttcttggtgaagctgggttggtgtttgtttaattcttatttctgcctgttctagaaaatcat------aattaccatgtgtcttacctgcagAATACTACCACAAAAGAAAATGAAACACTTTTGGCCATTGGGACTGCTTACGTACAAGGGGAGGATGTTGCTGCAAGGGGACGGGTGCTTTTATTTTCTG
                                                                                                      |  | |||| | |  |   ||||  |   ||  || |       | |  || ||||   |||  |  | || ||      ||     |||  | ||  || |||||||| ||||| || |||||||| || || |||||||||||||||||||| || |  ||||||||||| ||||| || ||||| |||||| | || ||| 
------------------------------------------------------------------------------------------------------gcttgagatttatcttgtttgaaaat---ttaatgatcaaa-ggtacacatgtctgtaggtttaattatattattcactgaacagttatgcatttttacttcagAATACAACCACCAAGGAAAATGAGACCCTGTTGGCCATTGGGACTGCTTATGTTCTTGGGGAGGATGTAGCTGCTAGAGGACGTGTGCTTCTGTTCTCTT

upper sequence: Vv16s0022g01860.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: GRMZM2G453879_T02 (Zea mays), 3'ss of exon 6
gtgagttaattctttgccattccaactgtttctttgtgttttggttttggcttctttcttgaattctcgtcatgggagaggcgtgtggtgagtgttggggggggattagatatgttcttggtgaagctgggttggtgtt-tgtttaattcttatttctgcctgttctagaaaatcataattaccatgtgtcttacctgcagAATACTACCACAAAAGAAAATGAAACACTTTTGGCCATTGGGACTGCTTACGTACAAGGGGAGGATGTTGCTGCAAGGGGACGGGTGCTTTTATTTTCTG
                                                                                                          ||  |||||  |   |  |  ||  | | |  |    | ||     | || |   |   | |||| || ||        ||  | |  ||| ||||| ||  | || || ||||||||||| ||  |||||||||| |||||||| || |||||||||||||||||||| || |||||||||||| | || ||| 
---------------------------------------------------------------------------------------------------------gtatgtatgtcttc--tacacttgtatggatactgcactcaaactaaaattttattta--ccagaatattat--------tgattttcgcct-cagAACACATCTACGAAGGAAAATGAAACCCTGATGGCCATTGGAACTGCTTATGTTCAAGGGGAGGATGTTGCTGCTAGAGGACGGGTGCTTCTGTTCTCTT

upper sequence: Vv16s0022g01860.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: GRMZM2G453879_T01 (Zea mays), 3'ss of exon 6
gtgagttaattctttgccattccaactgtttctttgtgttttggttttggcttctttcttgaattctcgtcatgggagaggcgtgtggtgagtgttggggggggattagatatgttcttggtgaagctgggttggtgtt-tgtttaattcttatttctgcctgttctagaaaatcataattaccatgtgtcttacctgcagAATACTACCACAAAAGAAAATGAAACACTTTTGGCCATTGGGACTGCTTACGTACAAGGGGAGGATGTTGCTGCAAGGGGACGGGTGCTTTTATTTTCTG
                                                                                                          ||  |||||  |   |  |  ||  | | |  |    | ||     | || |   |   | |||| || ||        ||  | |  ||| ||||| ||  | || || ||||||||||| ||  |||||||||| |||||||| || |||||||||||||||||||| ||                       
---------------------------------------------------------------------------------------------------------gtatgtatgtcttc--tacacttgtatggatactgcactcaaactaaaattttattta--ccagAATATTAT--------TGATTTTCGCCT-CAGAACACATCTACGAAGGAAAATGAAACCCTGATGGCCATTGGAACTGCTTATGTTCAAGGGGAGGATGTTGCTGCTAG-----------------------

upper sequence: Vv16s0022g01860.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: GLYMA09G28030.1 (Glycine max), 3'ss of exon 21
gtgagttaattctttgccattccaactgtttctttgtgttttggttttggcttctttcttgaattctcgtcatgggagaggcgtgtggtgagtgttggggggggattagatatgttcttggtgaagctgggttggtgtttgtttaattcttatttctgcctgttctagaaaatcataattaccatgtgtcttacctgcagAATACTACCACAAAAGAAAATGAAACACTTTTGGCCATTGGGACTGCTTACGTACAAGGGGAGGATGTTGCTGCAAGGGGACGGGTGCTTTTATTTTCTG
                                                                                                            |  ||||| ||        ||  ||||  ||||   |||| |   | |||  | ||   |||  | |||| |   |    ||||   |||||||||| ||| |||||||||||||||||||||| |||||||| |||||||| || ||||| ||||||||||||||||| |||||  | || || || ||| 
------------------------------------------------------------------------------------------------------------gtaatgttttt--------tgctttggcttttg---aattgtggatgctgattattgctgaaccttataaatgaaaatgatctttattgcagAATACAACCTCAAAAGAAAATGAAACACTTTTAGCCATTGGTACTGCTTATGTGCAAGGAGAGGATGTTGCTGCAAGAGGACGTATCCTCTTGTTCTCTT

upper sequence: Vv16s0022g01860.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: GLYMA16G32890.1 (Glycine max), 3'ss of exon 21
gtgagttaattctttgccattccaactgtttctttgtgttttggttttggcttctttcttgaattctcgtcatgggagaggcgtgtggtgagtgttggggggggattagatatgttcttggtgaagctgggttggtgtttgtttaattcttatttctgcctgttctagaaaatcataattaccatgtgtcttacctgcagAATACTACCACAAAAGAAAATGAAACACTTTTGGCCATTGGGACTGCTTACGTACAAGGGGAGGATGTTGCTGCAAGGGGACGGGTGCTTTTATTTTCTG
                                                                                                                |  | || ||     ||| ||     |||     | || |||  |||     ||   ||||  |       || | ||||   |||||||||| ||| |||||||||||||||||||||| |||||||| |||||||| || ||||| ||||||||||||||||| |||||  | || || || ||| 
---------------------------------------------------------------------------------------------------------------gtaatgtttgttcctttggtttacaaattgag-gttgctgattgttgctgaaccttataaatt-tctcagaaatttatctttattgcagAATACAACCTCAAAAGAAAATGAAACACTTTTAGCCATTGGTACTGCTTATGTGCAAGGAGAGGATGTTGCTGCAAGAGGACGTATCCTATTGTTCTCTT

upper sequence: Vv16s0022g01860.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: AT5G51660.1 (Arabidopsis thaliana), 3'ss of exon 21
gtgagttaattctttgccattccaactgtttctttgtgttttggttttggcttctttcttgaattctcgtcatgggagaggcgtgtggtgagtgttggggggggattagatatgttcttggtgaagctgggttggtgtttgtttaattcttatttctgcctgttctagaaaatcataattaccatgtgtcttacctgcagAATACTACCACAAAAGAAAATGAAACACTTTTGGCCATTGGGACTGCTTACGTACAAGGGGAGGATGTTGCTGCAAGGGGACGGGTGCTTTTATTTTCTG
                                                                                             ||  |   |  | ||       |  ||    |  ||| |  |  | | | |  || | ||| |    |   | ||  |       ||||    ||   |   | |||||| | | ||||   || |||||||||||| | ||  |||||||||| || || |||||||||||||||||||||||||| || |||||| | || ||| 
---------------------------------------------------------------------------------------------gtaagttagctactaacccgcctaatgtcatatttggatcag-atctctctg-ttttaattgcaa--taaccaagccacattctcttactccctggggtgttt-cagAATGCAAGCACAGGGGAGAATGAAACACTTCTTGCTGTTGGGACTGCGTATGTCCAAGGGGAGGATGTTGCTGCAAGGGGCCGTGTGCTTCTTTTCTCTT

upper sequence: Vv16s0022g01860.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: PP1S61_42V6.1 (Physcomitrella patens), 3'ss of exon 23
gtgagttaattctttgccattccaactgtttctttgtgttttggttttggcttctttcttgaattctcgtcatgggagaggcgtgtggtgagtgttggggggggattagatatgttcttggtgaagctgggttggtgtttgtttaattcttatttctgcctgttctagaaaatcataattaccatgtgtcttacctgcagAATACTACCACAAAAGAAAATGAAACACTTTTGGCCATTGGGACTGCTTACGTACAAGGGGAGGATGTTGCTGCAAGGGGACGGGTGCTTTTATTTTCTG
                                                                                         || | ||    |     |  |||  || |||  |        |||  |   |||| | | | || ||   |  ||  ||    || || | |   | ||   |  | |||||| |  || ||| |  | |   | ||  |  | || ||||| ||  | || |||||||||||||||||||||||||  || ||| |  |  |  | ||||
-----------------------------------------------------------------------------------------gattctttcaag----ctccata-atttttgaggtgctctaattgaggc--gtttgaat-taatatcaatcatttgcagtg--tcttattaattgtttgggatgtc-gcagAACATCACAACAGATCAGACACAGACCTTACTTGCTATTGGTACATCGTATGTACAAGGGGAGGATGTTGCTGCAAAAGGTCGGATTATACTTGTCTCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcttatttctgcctgttctagaaaatcataattaccatgtgtcttacctgcagAATACTACCACAAAAGAAAATGAAACACTTTTGGCCATTGGGACTGCTTACGTACAAGGGGAGGATGTTGCTGCAAGGGGACGGGTGCTTTTATTTTCTG
                                          gtcttac  putative branch site (score: 3)
                                           tcttacct  CT-rich tract
                    tagaaaatcataatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttaattctttgccattccaactgtttctttgtgttttggttttggcttctttcttgaattctcgtcatgggagaggcgtgtggtgagtgttggggggggattagatatgttcttggtgaagctgggttggtgtttgtttaattcttatttctgcctgttctagaaaatcataattaccatgtgtcttacctgcagAATACTACCACAAAAGAAAATGAAACACTTTTGGCCATTGGGACTGCTTACGTACAAGGGGAGGATGTTGCTGCAAGGGGACGGGTGCTTTTATTTTCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC