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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAGATGCTTTATGGCCGTACTCCTTTCAGAGGAAAGAATAGGCAGAAGACATTTTCCAACATCTTGCACAAAGATCTGACTTTTCCCAGTAGCATTCCGgtaaaatcatcactttctaatgcattaccactgtcttaagataatttctctttgatcattcacttatgtacttaaaagtgttgagcagtacagcagagga...

Basic information

species Vitis vinifera
transcript Vv03s0038g04210.t01
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0038g04210.t01 (Vitis vinifera), 5'ss of exon 20
lower sequence: LOC_Os04g23890.1 (Oryza sativa), 5'ss of exon 20
TGAGATGCTTTATGGCCGTACTCCTTTCAGAGGAAAGAATAGGCAGAAGACATTTTCCAACATCTTGCACAAAGATCTGACTTTTCCCAGTAGCATTCCGgtaaaatcatcactttctaatgcattaccactgtcttaagataatttctctttgatcattcacttatgtacttaaaagtgttgagcagtacagcagagga-
||||||||| ||||| ||||| |||||| |||||||||| ||| | ||||||||||  |||||  |||||||||| || || |||||||||||||||||||||| | | ||  |||   |   ||  ||| ||   |    |    |       |  |||   ||   ||||  |     ||    | ||||   |  || 
TGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGAACAGGAAAAAGACATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCGgtaagaacttcttttttagagaaatggccagtgaagtttcctgtcatgcaggccaatattt-tttgcatactgtattcaatttgcaactacaaaggttgag

upper sequence: Vv03s0038g04210.t01 (Vitis vinifera), 5'ss of exon 20
lower sequence: GRMZM2G032351_T01 (Zea mays), 5'ss of exon 19
TGAGATGCTTTATGGCCGTACTCCTTTCAGAGGAAAGAATAGGCAGAAGACATTTTCCAACATCTTGCACAAAGATCTGACTTTTCCCAGTAGCATTCCGgtaaaa----tcatcact-ttctaatgcattaccactgtcttaagat-------aatttctctttgatcattcacttatgtacttaaaagtgttgagcagtacagcagagga---------------------------------------------------------------------
||| ||| | ||||| ||||| |||||  |||||||||| ||| | | |||||||   || ||| |||||||||| || || ||||| |||||||||||||||| |    |||||  | || |  |    ||| | ||  |  | ||       |||||  || || |  | || |||   | || |  || | ||            |                                                                        
TGAAATGTTGTATGGACGTACACCTTTTCGAGGAAAGAACAGGAAAAGGACATTTCATAATATCCTGCACAAAGACCTTACATTTCCAAGTAGCATTCCGgtaagaaatttcatccttatttttgttacctacaattgcatgtaaatctggtcaaatttgcctgtgtttgtgcagtta-acatttgatggtatagaaataagttttgaaactatctacaatgttttgtaccacatacaacgttgtttattctgttcacctattaacaaatgtttactccag

upper sequence: Vv03s0038g04210.t01 (Vitis vinifera), 5'ss of exon 20
lower sequence: GLYMA16G19560.1 (Glycine max), 5'ss of exon 22
TGAGATGCTTTATGGCCGTACTCCTTTCAGAGGAAAGAATAGGCAGAAGACATTTTCCAACATCTTGCACAAAGATCTGACTTTTCCCAGTAGCATTCCGgtaaaatcatcactttctaatgc-attaccactgtcttaagataatt---tctctttgatcattcacttatgtacttaaaagtgttgagcagtacagcagagga
||||||||| ||||| ||||| || ||||||||||||||||| ||||||||||||||||||||||| ||||| ||||| || ||||| || ||||| ||||||||   |  | |   | ||   | ||        | || || |||   | |  ||   ||| || ||   |    |||      |     | ||  |     
TGAGATGCTCTATGGTCGTACACCATTCAGAGGAAAGAATAGACAGAAGACATTTTCCAACATCTTACACAAGGATCTTACCTTTCCAAGCAGCATCCCGgtaaacaaaatagtgcttgatattagtagttgaacttgaaaattattgaatgttgtttgccatccaattcattttccaaagagaaggtcttattcaagaa----

upper sequence: Vv03s0038g04210.t01 (Vitis vinifera), 5'ss of exon 20
lower sequence: GLYMA08G33520.1 (Glycine max), 5'ss of exon 3
TGAGATGCTTTATGGCCGTACTCCTTTCAGAGGAAAGAATAGGCAGAAGACATTTTCCAACATCTTGCACAAAGATCTGACTTTTCCCAGTAGCATTCCGgtaaaatcatcactttctaatgcattaccactgtcttaagataatttc--tctttgatcattcacttatgtacttaaaagtgttgagcagtacagcagagga----
||||||||| ||||| ||||| || ||||||||||||||||| ||||||||||||||||| || || ||||| ||||| || ||||| || |||||||||||||| | |  |  |  || |   | | |      |||| ||| ||    |  ||   ||| || ||   |    |||      |     ||   |||| |     
TGAGATGCTCTATGGTCGTACACCATTCAGAGGAAAGAATAGACAGAAGACATTTTCCAATATTTTACACAAGGATCTTACCTTTCCAAGCAGCATTCCGgtaaa-taacaaaatattagtagttgaac-----tttaaaatatttatagttgtttgccatccaattcattttccaaagagaggggttcctatttcagaagttttt

upper sequence: Vv03s0038g04210.t01 (Vitis vinifera), 5'ss of exon 20
lower sequence: AT5G58140.3 (Arabidopsis thaliana), 5'ss of exon 20
TGAGATGCTTTATGGCCGTACTCCTTTCAGAGGAAAGAATAGGCAGAAGACATTTTCCAACATCTTGCACAAAGATCTGACTTTTCCCAGTAGCATTCCGgtaaaatcatcactttctaatgcattaccactgtcttaagataatttctctttgatcattcacttatgtacttaaaagtgtt-gagcagtacagcagagga
||||||||||||||| || || |||||||| || ||||||||||| ||||||||| |||||||||||||||||||||| ||||| ||||| || || || || |  |    || || |||   |  |||  ||| |     |         |  |  |   ||| || ||   | | ||||| | ||||            
TGAGATGCTTTATGGTCGCACACCTTTCAGGGGTAAGAATAGGCAAAAGACATTTGCCAACATCTTGCACAAAGATCTCACTTTCCCCAGCAGTATCCCTgtgagct----accttgtaaca-acaacctgtgtgtc----tttcccaaagtaaaaaaaatactaatctaaccatatgtgtttgtgcag------------

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAGATGCTTTATGGCCGTACTCCTTTCAGAGGAAAGAATAGGCAGAAGACATTTTCCAACATCTTGCACAAAGATCTGACTTTTCCCAGTAGCATTCCGgtaaaatcatcactttctaatgcattaccactgtcttaagataatttctctttgatcattcacttatgtacttaaaagtgttgagcagtacagcagagga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agcagagg