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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTCTTATTGCTCATTTCCAAAACTCGAGCTTGATGAATGAGGATAAACGTTGCCGCCCTATTCTATTTCATACTGATGGTCCAAATGCAGGTGATCAGgtaggacatctgacataaagtatgttctctattttgttgttggatctcggatgtaaacctgtttaagaatattctttattctaattggtaatgactatta...

Basic information

species Vitis vinifera
transcript Vv17s0000g00240.t01
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g00240.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: LOC_Os02g31290.1 (Oryza sativa), 5'ss of exon 14
TGCTCTTATTGCTCATTTCCAAAACTCGAGCTTGATGAATGAGGATAAACGTTGCCGCCCTATTCTATTTCATACTGATGGTCCAAATGCAGGTGATCAGgtaggacatctgacataaagtatgttctctattttgttgttggatctcggatgtaaacctgtttaagaatattctttattctaattggtaatg-actatta
 |||||||||||||| ||||| ||||| || |||||||||||||| || || |||||||| || ||||| ||| | |||||||| |||||||| ||||||||| ||  | |  |      | | |       | | |   |   |||||    ||||     ||||         | |  ||       | |   || || 
AGCTCTTATTGCTCACTTCCAGAACTCCAGTTTGATGAATGAGGACAAGCGCTGCCGCCCCATACTATTCCATTCGGATGGTCCTAATGCAGGAGATCAGgtatgatctttctctctctctctctctctctctctctctctctctctcgttgataaatggagttaaagcagcagatgacacttggacacagtttgctgtt-

upper sequence: Vv17s0000g00240.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: GRMZM2G451716_T01 (Zea mays), 5'ss of exon 14
TGCTCTTATTGCTCATTTCCAAAACTCGAGCTTGATGAATGAGGATAAACGTTGCCGCCCTATTCTATTTCATACTGATGGTCCAAATGCAGGTGATCAGgtaggacatctgacataaagtatgttctctattttgttgttggatctcggatgtaaacctgtttaagaatattctttattctaattggtaatgactatta----
 |||||  ||||||||||||| ||||| || |||||||||||||||||||| ||||||||||| || || ||  |||||||||| |||||||| ||||| ||| |   ||| || |         |||||||| |  ||||| |||  || | ||   || | |    |  |  |   | || |    |  ||  |||      
AGCTCTAGTTGCTCATTTCCAGAACTCAAGTTTGATGAATGAGGATAAACGCTGCCGCCCTATACTCTTCCACTCTGATGGTCCGAATGCAGGAGATCAAgtatgctctct-acttgtccatcactctctattat-ctgttgcatcatgg-tatatgactatatggtgac-tagtagttcctgaactctgctgcttatcgcata

upper sequence: Vv17s0000g00240.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: GRMZM2G459746_T01 (Zea mays), 5'ss of exon 14
TGCTCTTATTGCTCATTTCCAAAACTCGAGCTTGATGAATGAGGATAAACGTTGCCGCCCTATTCTATTTCATACTGATGGTCCAAATGCAGGTGATCAGgtaggacatctgacataaagtatgttctctattttgttgttgg-atctcggatgtaaacctgtt------taagaatattctttattctaattggtaatgactatta----
 ||||| |||||||||||||| ||||| || |||||||||||||| |||||||||||||| || || || ||  | |||||||| |||||||| ||||||||| |    || |       | | || | |||||||| ||||| |  |    ||  | | ||||      | | | |||  ||   |  | |      |||| | |     
AGCTCTGATTGCTCATTTCCAGAACTCTAGTTTGATGAATGAGGACAAACGTTGCCGCCCCATACTCTTCCACTCAGATGGTCCTAATGCAGGAGATCAGgtatg----ctta-------tttcttttttattttgtcgttggtactttccctgctatcttgttctccagttacattatgtttcgctgcagtgcactgtgacgagtcttct

upper sequence: Vv17s0000g00240.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: GRMZM5G814700_T01 (Zea mays), 5'ss of exon 4
TGCTCTTATTGCTCATTTCCAAAACTCGAGCTTGATGAATGAGGATAAACGTTGCCGCCCTATTCTATTTCATACTGATGGTCCAAATGCAGGTGATCAGgtaggacatctgacataaagtatgttctctattttgttgttggatctcggatgtaaacctgtttaagaatattctttattctaattggtaatgactatta---
 || || |||||||||||||| ||||| || |||||||||||||| ||||| |||||||| || || || ||  | |||||||| |||||||| ||||||||| | | | |    ||   | |  |   || |||       |   |    |         ||    | | || | |  | | | | || |  | | ||    
AGCCCTGATTGCTCATTTCCAGAACTCTAGTTTGATGAATGAGGACAAACGCTGCCGCCCCATACTTTTCCACTCAGATGGTCCTAATGCAGGAGATCAGgtatg-cttattttgtattttgtcctgggtactttccctcctgtctttttctccggttacattatgtactgttgtct--tgtgagttgtgacaagtcttctct

upper sequence: Vv17s0000g00240.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: GLYMA08G01040.1 (Glycine max), 5'ss of exon 14
TGCTCTTATTGCTCATTTCCAAAACTCGAGCTTGATGAATGAGGATAAACGTTGCCGCCCTATTCTATTTCATACTGATGGTCCAAATGCAGGTGATCAGgtaggaca----tctga-cataaagtatgttctctattttgttgttggatctcggatgtaaacctgtttaagaatattctttattctaattggtaatgactatta
| ||||||||||||||||||| ||||| ||| |||||||||| || ||||||||||| |||||||| || ||||| ||||| |||||||| ||||||| ||||   ||    | ||  | | |  || |  || | | || |       |   ||  || |     || |  |||||| |||  |||     |            
TTCTCTTATTGCTCATTTCCAGAACTCAAGCCTGATGAATGAAGACAAACGTTGCCGTCCTATTCTCTTCCATACAGATGGCCCAAATGCTGGTGATCCGgtaaatcaagcttttgttctttagttaagaactttgtattatctgattcttctggtggtgataaaattgatcaatatttttttgtctctgcag------------

upper sequence: Vv17s0000g00240.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: GLYMA04G37810.1 (Glycine max), 5'ss of exon 12
TGCTCTTATTGCTCATTTCCAAAACTCGAGCTTGATGAATGAGGATAAACGTTGCCGCCCTATTCTATTTCATACTGATGGTCCAAATGCAGGTGATCAGgtaggacatctgacataaagtatgttctctattttgttgttgg-atctcggatgtaaacctgtttaagaatattc-tttattctaattggtaatgactatta-
||||||||||||||||||||| || || ||| |||||||||| |||||||| ||||| |||||||| || ||||| ||||| |||||||| ||||||| ||||   || ||           |||   |||||||  | |||  | ||   |||||     |    |  ||||    || ||||  |  ||  | | | ||  
TGCTCTTATTGCTCATTTCCAGAATTCAAGCCTGATGAATGAAGATAAACGGTGCCGTCCTATTCTCTTCCATACAGATGGCCCAAATGCTGGTGATCCGgtaaatcagcttgttctttagttgtaa-ctattttccttttgctaactacaatgtattatggaactactatatcagcttgttct--tcagttgtaattgtttt

upper sequence: Vv17s0000g00240.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: GLYMA06G17250.1 (Glycine max), 5'ss of exon 12
TGCTCTTATTGCTCATTTCCAAAACTCGAGCTTGATGAATGAGGATAAACGTTGCCGCCCTATTCTATTTCATACTGATGGTCCAAATGCAGGTGATCAGgtaggacatctgacataaagtatgttctctattttgttgttgg-atctcggatgtaaacctgtttaagaatattctttattctaattggtaatgactatta
|||||||||||||||||| || || || ||| | |||||||| ||||||||||||||||| ||||| || ||||| ||||| |||||||| ||||||| ||||   || ||           |||   |||||||| | |||  | ||   |||||     |    |  ||||    |  |    ||  |  ||   | ||
TGCTCTTATTGCTCATTTTCAGAATTCAAGCCTAATGAATGAAGATAAACGTTGCCGCCCCATTCTCTTCCATACAGATGGCCCAAATGCTGGTGATCCGgtaaatcagcttgttctttagttgtaa-ctattttgcttttgctaactacaatgtattatggaactactatatctgcttgttattttccttttgctaacta

upper sequence: Vv17s0000g00240.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: AT5G61960.2 (Arabidopsis thaliana), 5'ss of exon 13
TGCTCTTATTGCTCATTTCCAAAACTCGAGCTTGATGAATGAGGATAAACGTTGCCGCCCTATTCTATTTCATACTGATGGTCCAAATGCAGGTGATCAGgtaggacatctgacataaagtatgttc--tctattttgttgttggatctcggatgtaaacct----gtttaagaata--ttctttat-tctaattggtaatgactatta----------------------------------------
 ||||||||||| |||||||| ||||| ||||| ||||| || || ||||||||||| |||||||| || || ||||||||||||||||| ||||||||||||     |    | | |   |  | |    | ||| |||         |  ||| |   |      || |||  |   ||| |||| ||  |    || ||| ||  |                                        
AGCTCTTATTGCCCATTTCCAGAACTCAAGCTTAATGAACGAAGACAAACGTTGCCGACCTATTCTCTTCCACACTGATGGTCCAAATGCTGGTGATCAGgtaaagattaaagcttcatacaattccgtcttgtttggttcccattatccatatgcacttccttcacttcaagtgtgatttcattatatcataagattagtgagtaaaagaagattcatatgatttcctttgttgttatatcaccacag

upper sequence: Vv17s0000g00240.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: AT5G07290.1 (Arabidopsis thaliana), 5'ss of exon 13
TGCTCTTATTGCTCATTTCCAAAACTCGAGCTTGATGAATGAGGATAAACGTTGCCGCCCTATTCTATTTCATACTGATGGTCCAAATGCAGGTGATCAGgtaggacatctgacataaagtatgttctctattttgttgttggatctcggatgtaaacctgtttaagaatattctttattctaattggta-atgactatta-----
 ||||||||||| |||||||| ||||| || |||||||| || || ||||||||| | |||||||| || || |||| |||||||||||| |||||||||||| |  |   ||||     |   ||    || |  || ||  | ||   |  |    |||||  |    ||  | |  |||  | | ||  |    | ||     
AGCTCTTATTGCCCATTTCCAGAACTCAAGTTTGATGAACGAAGACAAACGTTGCAGGCCTATTCTCTTCCACACTGCTGGTCCAAATGCTGGTGATCAGgtaaggaa---gacaagggctcaattg---atatccttattcaaactataacctctttctgttgcaagtaatcatatcatctggtagttatgtattcactatagcg

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|33404602|gb|CF210229.1|CF210229
EST:     GTTGCCGCCCTATTCTATTTCATACTGATGGTCCAAATGCAGGTGATCAG                         GAGCCATTCCCCATGGGTAGCAATATACGATCAAGACCAGGCAAAGCTCGA
genomic: GTTGCCGCCCTATTCTATTTCATACTGATGGTCCAAATGCAGGTGATCAGgtaggacatc ... gtgtggctagGAGCCATTCCCCATGGGTAGCAATATACGATCAAGACCAGGCAAAGCTCGA
EST: gi|110376881|gb|EC941957.1|EC941957
EST:     GTTGCCGCCCTATTCTATTTCATACTGATGGTCCAAATGCAGGTGATCAG                         GAGCCATTCCCCATGGGTAGCAATATACGATCAAGACCAGGCAAAGCTCGA
genomic: GTTGCCGCCCTATTCTATTTCATACTGATGGTCCAAATGCAGGTGATCAGgtaggacatc ... gtgtggctagGAGCCATTCCCCATGGGTAGCAATATACGATCAAGACCAGGCAAAGCTCGA
EST: gi|161716528|gb|FC065225.1|FC065225
EST:     GTTGCCGCCCTATTCTATTTCATACTGATGGTCCAAATGCAGGTGATCAG                         GAGCCATTCCCCATGGGTAGCAATATACGATCAAGACCAGGCAAAGCTCGA
genomic: GTTGCCGCCCTATTCTATTTCATACTGATGGTCCAAATGCAGGTGATCAGgtaggacatc ... gtgtggctagGAGCCATTCCCCATGGGTAGCAATATACGATCAAGACCAGGCAAAGCTCGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTCTTATTGCTCATTTCCAAAACTCGAGCTTGATGAATGAGGATAAACGTTGCCGCCCTATTCTATTTCATACTGATGGTCCAAATGCAGGTGATCAGgtaggacatctgacataaagtatgttctctattttgttgttggatctcggatgtaaacctgtttaagaatattctttattctaattggtaatgactatta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gacataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagaata