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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGTGCTGCCTCCATTTGTGCCATTTGCCCAGGCGTTTGCAGCTGTAATCACAGCTGCTCTTACTGGTTCCCTCTATTATGTGGCTGCCTCTCCAAAAGgttgattatatcaaacctcttttaaacaatgtacctaatcatttcatttcctacactttgatttacaagtttctttttccacatcag

Basic information

species Vitis vinifera
transcript Vv02s0012g01220.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0012g01220.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: LOC_Os03g01014.1 (Oryza sativa), 5'ss of exon 6
GGAGTGCTGCCTCCATTTGTGCCATTTGCCCAGGCGTTTGCAGCTGTAATCACAGCTGCTCTTACTGGTTCCCTCTATTATGTGGCTGCCTCTCCAAAAGgttgattatatcaaacctcttttaaacaatgtacctaatcatttcatttcctacactttgatttacaagtttctttttccacatcag---------------------
||  || ||||||||||||| |||||||| ||  |||||||||| |  ||||| || ||||| || || || ||||||||||||||| |  | || ||||||   |   ||       |||||       | |   | |    |   ||| |  |      | |  |  | | | | | ||  |                        
GGCATGGTGCCTCCATTTGTTCCATTTGCTCAAACGTTTGCAGCAGCCATCACTGCGGCTCTCACAGGATCACTCTATTATGTGGCTACTGCCCCGAAAGgtgactctaatttgcatgcttttctgtttggaaggaagtggcattgattcttgaaaccaagtgtg-acatatatatatacatgttgtgatatatttgtatgattgcag

upper sequence: Vv02s0012g01220.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA11G04660.2 (Glycine max), 5'ss of exon 6
GGAGTGCTGCCTCCATTTGTGCCATTTGCCCAGGCGTTTGCAGCTGTAATCACAGCTGCTCTTACTGGTTCCCTCTATTATGTGGCTGCCTCTCCAAAAGgttgattatatcaaacctcttttaaacaatg--tacctaatcatttcatttcctacactttg--atttacaagtttctttttccacatcag-------------
|| ||||||||||||||||| |||||||| ||||| |||||||||||| | || ||||  ||||||||||| ||||||||  ||||||||||||| ||||||   ||   | |   | |||||  |   |   ||| |  |  |     |   || |   ||  || | | | |   | | ||    |                
GGTGTGCTGCCTCCATTTGTTCCATTTGCTCAGGCATTTGCAGCTGTACTTACTGCTGTCCTTACTGGTTCTCTCTATTACATGGCTGCCTCTCCTAAAGgtgactttgtttattgcccttttgtattttccctacttcgttctcagtctgattaaatgatggcatctcccaatggttctatcttttttttttctctctttcag

upper sequence: Vv02s0012g01220.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA01G40650.4 (Glycine max), 5'ss of exon 6
GGAGTGCTGCCTCCATTTGTGCCATTTGCCCAGGCGTTTGCAGCTGTAATCACAGCTGCTCTTACTGGTTCCCTCTATTATGTGGCTGCCTCTCCAAAAGgttgattatatcaaacctcttttaaacaatgtacctaatc--------atttcatttcctacactttgatttacaagtt---tctttttccacatcag----
|| ||||||||||||||||| |||||||| || || ||||| |||||  | |||||||  ||||||||||| ||||||||  ||||||||||||| |||||| || | | | ||    |  ||  | | | | |||| |          | | |||  | |     |    ||   |||   ||||||||    ||      
GGTGTGCTGCCTCCATTTGTTCCATTTGCTCAAGCATTTGCGGCTGTTCTTACAGCTGTCCTTACTGGTTCTCTCTATTACATGGCTGCCTCTCCTAAAGgt-gactttgttaatttccccttttatattttccctactttgttctcagtctgattaacgatggcctctcctaatggttctgtctttttctctctctttcag

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|352769120|gb|FQ471068.1|FQ471068
EST:     CACAGCTGCTCTTACTGGTTCCCTCTATTATGTGGCTGCCTCTCCAAAAG                         ATCCTACTTATGTGGTTGCACCAGTTTTGCAATCTCGCTCCGGTCGTGCGG
genomic: CACAGCTGCTCTTACTGGTTCCCTCTATTATGTGGCTGCCTCTCCAAAAGgttgattata ... tccacatcagATCCTACTTATGTGGTTGCACCAGTTTTGCAATCTCGCTCCGGTCGTGCGG
EST: gi|351012152|gb|FQ426874.1|FQ426874
EST:     CACAGCTGCTCTTACTGGTTCCCTCTATTATGTGGCTGCCTCTCCAAA-G                         ATCCTACTTATGTGGTTGCACCAGTTTTGCAATCTCGCTCCGGCCGTGCGG
genomic: CACAGCTGCTCTTACTGGTTCCCTCTATTATGTGGCTGCCTCTCCAAAAGgttgattata ... tccacatcagATCCTACTTATGTGGTTGCACCAGTTTTGCAATCTCGCTCCGGTCGTGCGG
EST: gi|352776642|gb|FQ465440.1|FQ465440
EST:     CACAGCTGCTCTTACTGGTTCCCTCTATTATGTGGCTGCCTCTCCAAAAG                         ATCCTACTTATGTGGTTGCACCAGTTTTGCAATCTCGCTCCGGTCGTGCGG
genomic: CACAGCTGCTCTTACTGGTTCCCTCTATTATGTGGCTGCCTCTCCAAAAGgttgattata ... tccacatcagATCCTACTTATGTGGTTGCACCAGTTTTGCAATCTCGCTCCGGTCGTGCGG
EST: gi|349828788|gb|FQ419121.1|FQ419121
EST:     CACAGCTGCTCTTACTGGTTCCCTCTATTATGTGGCTGCCTCTCCAAAAG                         ATCCTACTTATGTGGTTGCACCAGTTTTGCAATCTCGCTCCGGCCGTGCGG
genomic: CACAGCTGCTCTTACTGGTTCCCTCTATTATGTGGCTGCCTCTCCAAAAGgttgattata ... tccacatcagATCCTACTTATGTGGTTGCACCAGTTTTGCAATCTCGCTCCGGTCGTGCGG
EST: gi|352781173|gb|FQ466486.1|FQ466486
EST:     CACAGCTGCTCTTACTGGTTCCCTCTATTATGTGGCTGCCTCTCCAAAAG                         ATCCTACTTATGTGGTTGCACCAGTTTTGCAATCTCGCTCCGGTCGTGCGG
genomic: CACAGCTGCTCTTACTGGTTCCCTCTATTATGTGGCTGCCTCTCCAAAAGgttgattata ... tccacatcagATCCTACTTATGTGGTTGCACCAGTTTTGCAATCTCGCTCCGGTCGTGCGG
EST: gi|156737157|gb|EV241278.1|EV241278
EST:     CACAGCTGCTCTTACTGGTTCCCTCTATTATGTGGCTGCCTCTCCAAAAG                         ATCCTACTTATGTGGTTGCACCAGTTTTGCAATCTCGCTCCGGTCGTGCGG
genomic: CACAGCTGCTCTTACTGGTTCCCTCTATTATGTGGCTGCCTCTCCAAAAGgttgattata ... tccacatcagATCCTACTTATGTGGTTGCACCAGTTTTGCAATCTCGCTCCGGTCGTGCGG
EST: gi|110363320|gb|EC926898.1|EC926898
EST:     CACAGCTGCTCTTACTGGTTCCCTCTATTATGTGGCTGCCTCTCCAAAAG                         ATCCTACTTATGTGGTTGCACCAGTTTTGCAATCTCGCTCCGGTCGTGCGG
genomic: CACAGCTGCTCTTACTGGTTCCCTCTATTATGTGGCTGCCTCTCCAAAAGgttgattata ... tccacatcagATCCTACTTATGTGGTTGCACCAGTTTTGCAATCTCGCTCCGGTCGTGCGG
EST: gi|351012567|gb|FQ430131.1|FQ430131
EST:     CACAGCTGCTCTTACTGGTTCCCTCTATTATGTGGCTGCCTCTCCAAAAG                         ATCCTACTTATGTGGTTGCACCATTTTTGCAATCTCGCTCCGGCCGTGCGG
genomic: CACAGCTGCTCTTACTGGTTCCCTCTATTATGTGGCTGCCTCTCCAAAAGgttgattata ... tccacatcagATCCTACTTATGTGGTTGCACCAGTTTTGCAATCTCGCTCCGGTCGTGCGG
EST: gi|349828983|gb|FQ419515.1|FQ419515
EST:     CACAGCTGCTCTTACTGGTTCCCTCTATTATGTGGCTGCCTCTCCAAAAG                         ATCCTACTTATGTGGTTGCACCAGTTTTGCAATCTCGCTCCGGTCGTGCGG
genomic: CACAGCTGCTCTTACTGGTTCCCTCTATTATGTGGCTGCCTCTCCAAAAGgttgattata ... tccacatcagATCCTACTTATGTGGTTGCACCAGTTTTGCAATCTCGCTCCGGTCGTGCGG
EST: gi|351024867|gb|FQ430692.1|FQ430692
EST:     CACAGCTGCTCTTACTGGTTCCCTCTATTATGTGGCTGCCTCTCCAAAAG                         ATCCTACTTATGTGGTTGCACCAGTT
genomic: CACAGCTGCTCTTACTGGTTCCCTCTATTATGTGGCTGCCTCTCCAAAAGgttgattata ... tccacatcagATCCTACTTATGTGGTTGCACCAGTT
EST: gi|110380859|gb|EC946157.1|EC946157
EST:     CACAGCTGCTCTTACTGGTTCCCTCTATTATGTGGCTGCCTCTCCAAAAG                         ATCCTACTTATGTGGTTGCACCAGTTTTGCAATCTCGCTCCGGTCGTGCGG
genomic: CACAGCTGCTCTTACTGGTTCCCTCTATTATGTGGCTGCCTCTCCAAAAGgttgattata ... tccacatcagATCCTACTTATGTGGTTGCACCAGTTTTGCAATCTCGCTCCGGTCGTGCGG
EST: gi|352769544|gb|FQ468472.1|FQ468472
EST:     CACAGCTGCTCTTACTGGTTCCCTCTATTATGTGGCTGCCTCTCCAAAAG                         ATCCTACTTATGTGGTTGCACCAGTTTTGCAATCTCGCTCCGGTCGTGCGG
genomic: CACAGCTGCTCTTACTGGTTCCCTCTATTATGTGGCTGCCTCTCCAAAAGgttgattata ... tccacatcagATCCTACTTATGTGGTTGCACCAGTTTTGCAATCTCGCTCCGGTCGTGCGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGTGCTGCCTCCATTTGTGCCATTTGCCCAGGCGTTTGCAGCTGTAATCACAGCTGCTCTTACTGGTTCCCTCTATTATGTGGCTGCCTCTCCAAAAGgttgattatatcaaacctcttttaaacaatgtacctaatcatttcatttcctacactttgatttacaagtttctttttccacatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT