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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTCGAGAACACGTTGAATTATGGTCTTGAAAGAGTTTGGGCTGTTGGATACATGAAAGGTTCACGCCGgttagtgtcttctccttcttactactaccactactactactttttttcatttcaatttattggtcttttgaatttttttttctggtttgaactttgaagt...

Basic information

species Vitis vinifera
transcript Vv09s0002g04810.t01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: LOC_Os06g05180.2 (Oryza sativa), 5'ss of exon 9
GCTCGAGAACACGTTGAATTATGGTCTTGAAAGAGTTTGGGCTGTTGGATACATGAAAGGTTCACGCCGgttagtg-----tcttctccttcttactactac----cactactactactttttttcatttcaattt------attggtcttttgaatttttttttctggtttga-actttgaagt------
 || ||||||||| | || |||||||||||| |||| |||||||||||||||||||| |||||| |  ||| |        || | | | |  | ||  |      || |   |  | ||  ||| | | |  ||       | |  || ||| ||||||||       || || | |||    |      
ACTTGAGAACACGCTAAACTATGGTCTTGAACGAGTCTGGGCTGTTGGATACATGAAGGGTTCAAGAAGgtaaacagaagatcctttgcattctgcttttgtgttgcattgtaatcaattgcttttactactgttctgcgtcactcctcctttcaattttttaacaccattcgacattttatgatatgtag

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GRMZM2G000645_T03 (Zea mays), 5'ss of exon 9
GCTCGAGAACACGTTGAATTATGGTCTTGAAAGAGTTTGGGCTGTTGGATACATGAAAGGTTCACGCCGgttagtgtcttctccttcttactac-taccactactactactttttttcatttcaatttattggtcttttgaatttttttttctggtttgaactttgaagt
 || ||||||||  | || ||||| ||||| ||||| |||||||||||||||||||| || ||  |  ||| ||    ||  | ||||   |   |  || || | ||  |  || | ||    | |   |  |  | |    |||   || ||  | |||||  |||| 
ACTTGAGAACACACTAAACTATGGCCTTGAGAGAGTCTGGGCTGTTGGATACATGAAGGGGTCTAGAAGgtaagatcatttgcattctctttttgtttcagtagtgctgttagttgtaatggacactagctattaatatagcatttcacttttgagtagaacta-gaagc

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GRMZM2G095348_T02 (Zea mays), 5'ss of exon 8
GCTCGAGAACACGTTGAATTATGGTCTTGAAAGAGTTTGGGCTGTTGGATACATGAAAGGTTCACGCCGgttagtgtcttctccttcttactactac--cactactactactttttttcatttcaatttattggtcttttgaatttttttttctggtttgaactttgaagt
 || ||||||||  | || ||||| ||||| ||||| |||||||||||||||||||| || ||| |  ||| ||  || ||| | |  | ||  |    || || | ||     || | ||    | | | |  |  | |    | |   || ||  | |||||  |||| 
ACTTGAGAACACACTAAACTATGGCCTTGAGAGAGTCTGGGCTGTTGGATACATGAAGGGATCAAGAAGgtaag-atcatctacattctgcttttgtttcagtagtgctgtcagttattatggacactaactattaatatatcatctcacttttgagtagaacta-gaagc

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA07G03890.1 (Glycine max), 5'ss of exon 9
GCTCGAGAACACGTTGAATTATGGTCTTGAAAGAGTTTGGGCTGTTGGATACATGAAAGGTTCACGCCGgttagtgtcttctccttcttactactaccactactactactttttttcatttcaatttattggtcttttgaatttttttttctggtttga-actttgaagt-----
||| |||||||| ||||| |||||||||||||||||||||||| |||||||  |||| ||||||||||||| ||| |  | |     ||   | |   | |   | | ||   | ||||    || | | || | |  ||||  | ||   |||    | | | | ||       
GCTTGAGAACACATTGAACTATGGTCTTGAAAGAGTTTGGGCTATTGGATATCTGAAGGGTTCACGCCGgtgagttttgtttttggattga-attgtgaatgtaatttctgagtctcat----atctgtaggccctg-gaatcatgttgagtgggacaatagtgtcaaactgtca

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA08G22140.1 (Glycine max), 5'ss of exon 9
GCTCGAGAACACGTTGAATTATGGTCTTGAAAGAGTTTGGGCTGTTGGATACATGAAAGGTTCACGCCGgttagtgtcttctccttcttactactaccactactactactttttttcatttcaatttattggtcttttgaatttttttttctggt-ttgaactttgaagt---
||| |||||||| ||||| ||| |||||||||||||||||||| |||||||| |||| |||||||| |||| ||| |  | |     |||     |     |     | ||||  |   |  |    ||||     |      |       | || |  ||||   || |   
GCTTGAGAACACATTGAACTATAGTCTTGAAAGAGTTTGGGCTATTGGATACCTGAAGGGTTCACGTCGgtgagttttgtttttggattaa----attgtgaaagtaatttttgatatctgtaggccattgaatcatgatgagtgggacaatagtgtcaaactgccaactaat

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA13G43680.2 (Glycine max), 5'ss of exon 9
GCTCGAGAACACGTTGAATTATGGTCTTGAAAGAGTTTGGGCTGTTGGATACATGAAAGGTTCACGCCGgttagtgtcttctccttcttactactaccacta-----ctactactttttttcatttcaatttattggtct---tttgaatttttttt---tctggtttgaactttgaagt---------------------------------------------
||| |||||||| || || ||||||||||||||||| |||||| |||||||| ||||  |||| || |||| ||| | || |   |   | |  | | | ||      || ||   ||||| |   |  |  || |  ||   |  |||  | |      |   |  |||| | |||| |                                             
GCTTGAGAACACATTAAACTATGGTCTTGAAAGAGTCTGGGCTATTGGATACTTGAAGAGTTCTCGTCGgtaagttttttgtggatagaatttttgcaattaatttcttaatataattttttaagcccttgaatagtgctgagtgggaagctgtgccaaattgtgcctgaattatgaaattttcttatccttaactcttttctcgtatcgggtgcattcaaacag

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA15G01680.1 (Glycine max), 5'ss of exon 9
GCTCGAGAACACGTTGAATTATGGTCTTGAAAGAGTTTGGGCTGTTGGATACATGAAAGGTTCACGCCGgttagtgtcttctccttcttactactaccactactactactttttttcatttcaatttattggtcttttgaatttttttttctggtttgaactttgaagt-------------------------------------------------------
||| |||||||| || || ||||||||||||||||| |||||| |||||||| ||||  |||| || |||| ||| | ||||   |   | |  |   | || |           |    | |  | | |||     ||  |    || |   |  |||| | |||| |                                                       
GCTTGAGAACACATTAAACTATGGTCTTGAAAGAGTCTGGGCTATTGGATACTTGAAGAGTTCTCGTCGgtaagttttttctggatagaaattttgtaagtaatttcttaggccgttgaataatctgagtgggaaactgtgtcaaattgt---gcctgaattatgaaattttcttatctttaactcttttctcataatcaaaattttcgggtgcattcaaacag

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 5'ss of exon 13
GCTCGAGAACACGTTGAATTATGGTCTTGAAAGAGTTTGGGCTGTTGGATACATGAAAGGTTCACGCCGgttagtgtcttctccttc------ttactacta--ccactactac-----tactttttttcatttcaatttattggtcttttgaatttttttttctggtttgaactttgaagt-----------------------
||| ||||| || ||||| ||||| ||||| || ||||||||| ||||| |||| |||||||||||||||| ||| |||  || ||       | | || |    | ||| ||      ||  | ||  |||   ||||  ||  |  | | ||||| | ||||     | |  |  ||  |                       
GCTTGAGAATACATTGAACTATGGCCTTGAGAGGGTTTGGGCTATTGGACACATTAAAGGTTCACGCCGgtaagtttctgatcttttactatgtcaatatttattccctattaaagatatatatcttcacatcataattatttctttgtgtaaatttatgtttccttcataacttacgagatggcaataccttgtctttttccag

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: AT1G52360.1 (Arabidopsis thaliana), 5'ss of exon 9
GCTCGAGAACACGTTGAATTATGGTCTTGAAAGAGTTTGGGCTGTTGGATACATGAAAGGTTCACGCCGgttagtgtcttctcctt--cttactactaccactactactactttttttcatttcaat--ttattggtcttttgaatttttttttctggtttgaactttgaagt
||| |||||||| ||||||||||| ||||| ||||| |||||  |||| ||||| ||| |||||||||||| |||   |  |  ||  ||  || ||   | || ||  | |  |  |  |   ||   ||||  |    ||||  | ||   |||  |||||    |||| |
GCTAGAGAACACATTGAATTATGGCCTTGAGAGAGTCTGGGCAATTGGTTACATTAAAAGTTCACGCCGgtgagttattagtttttggctcccttctcttattaataa-attgatgcttgtccgaactgttatccgggagttga--tgttccctctcatttga-tagtgaaat

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTCGAGAACACGTTGAATTATGGTCTTGAAAGAGTTTGGGCTGTTGGATACATGAAAGGTTCACGCCGgttagtgtcttctccttcttactactaccactactactactttttttcatttcaatttattggtcttttgaatttttttttctggtttgaactttgaagt

- - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctccttc