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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGATGGAAGCAACAGTTGTTGACGGTAATGGAACAGAGACAGGTCATATAATTGTGACGACTATTGGTGGTAGAAATGGCCAACCAAAGCAGgtatatatgcttgagcacattccttaggttttggatctcatagcatgtcaggagatgccatttttgcctttttaggtgattaacattttcttgggttcta...

Basic information

species Vitis vinifera
transcript Vv14s0060g00600.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0060g00600.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA10G28530.2 (Glycine max), 5'ss of exon 3
GAGATGGAAGCAACAGTTGTTGACGGTAATGGAACAGAGACAGGTCATATAATTGTGACGACTATTGGTGGTAGAAATGGCCAACCAAAGCAGgtatatatgcttgagcacattccttaggttttggatctcatagcatgtcaggagatgccatttttgcctttttaggtgattaacattttcttgggttcta-------
|| |||||||| ||||||||||| || |||||||| |||||||| ||||| |||||||| || ||||| ||||||||||| || || |||||||||||  | |     | | ||  ||   || |  |||  ||| ||         ||||| |||     |  |||  |   |  || | |||    ||||        
GAAATGGAAGCCACAGTTGTTGATGGCAATGGAACGGAGACAGGACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAGgtataccttccc---ccccttttttcctttatcaatcatata-cacactcatttatgccgtttgaaa-tgattaact--cttgcactgtctcactttctgtgcttac

upper sequence: Vv14s0060g00600.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA20G22600.3 (Glycine max), 5'ss of exon 3
GAGATGGAAGCAACAGTTGTTGACGGTAATGGAACAGAGACAGGTCATATAATTGTGACGACTATTGGTGGTAGAAATGGCCAACCAAAGCAGgtatatatgcttgagcacattccttaggttttggatctcatagcatgtcaggagatgccatttttgcctttttaggtgattaacattttcttgggttcta-------------
|| |||||||| ||||||||||| || || ||||| |||||||| ||||| |||||||| || ||||| ||||||||||| || || |||||||||||  | |       | ||  ||    | |  |||| |||  |             ||||| |||  ||| |  ||||||||  || |   |  ||               
GAAATGGAAGCCACAGTTGTTGATGGCAACGGAACGGAGACAGGACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAGgtataccttccc---tcctttttttctaatatcaatcttata-tacact---------catttatgcagtttgaaatgattaactcttgcactgtctcatttactgtgcttac

upper sequence: Vv14s0060g00600.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA19G41420.1 (Glycine max), 5'ss of exon 3
GAGATGGAAGCAACAGTTGTTGACGGTAATGGAACAGAGACAGGTCATATAATTGTGACGACTATTGGTGGTAGAAATGGCCAACCAAAGCAGgtatatatgcttgagcacattccttaggttttggatctcatagcatgtcaggagatgccatttttgcctttttaggtgattaacattttcttgggttcta-----
|| |||||||| || ||||| || ||||| ||||||||||| || ||||| ||||| || || ||||| ||||||||||| ||||| |||||||||||  | |     |   ||  |    |     ||    ||   || | ||| |||   ||        |||   |  |  ||  | || |    |||      
GAAATGGAAGCCACCGTTGTCGATGGTAACGGAACAGAGACCGGACATATTATTGTTACTACCATTGGGGGTAGAAATGGTCAACCGAAGCAGgtataccttcc----cttctttttccactaacatatactgtactgtgactgga-atgtagttcgaaataatttgactactgtactgtctcattttctctctgctg

upper sequence: Vv14s0060g00600.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA03G38850.2 (Glycine max), 5'ss of exon 3
GAGATGGAAGCAACAGTTGTTGACGGTAATGGAACAGAGACAGGTCATATAATTGTGACGACTATTGGTGGTAGAAATGGCCAACCAAAGCAGgtatatatgcttgagcacattccttaggttttggatctcatagcatgtcaggagatgccatttttgcctttttaggtgattaacattttcttgggttcta-
|| |||||||| || ||||| || ||||| ||||| ||||| || ||||| ||||| || || ||||| ||||||||||| ||||| |||||||| |   | ||        || |        || |       |        | ||||   |||       |||   | ||| ||  | || |  | |||  
GAAATGGAAGCCACCGTTGTCGATGGTAACGGAACGGAGACCGGACATATCATTGTTACTACCATTGGGGGTAGAAATGGTCAACCGAAGCAGgtgttccttctcccttctttttcccctaacatgtactgtgctgtggaaactgggatgtagtttgaaataatttgact-attgactgtctcctttgctctgc

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|32270380|gb|CD719539.1|CD719539
EST:     GTCATATAATTGTGACGACTATTGGTGGTAGAAATGGCCAACCAAAGCAG                         ACAATAAGTTACATGGCTGAGCGCGTTGTTGGGCATGGATCATTTGGAGTT
genomic: GTCATATAATTGTGACGACTATTGGTGGTAGAAATGGCCAACCAAAGCAGgtatatatgc ... ataattccagACAATAAGTTACATGGCTGAGCGCGTTGTTGGGCATGGATCATTTGGAGTT
EST: gi|32270854|gb|CD720013.1|CD720013
EST:     GTCATATAATTGTGACGACTATTGGTGGTAGAAATGGCCAACCAAAGCAG                         ACAATAAGTTACATGGCTGAGCGCGTTGTTGGGCATGGATCATTTGGAGTT
genomic: GTCATATAATTGTGACGACTATTGGTGGTAGAAATGGCCAACCAAAGCAGgtatatatgc ... ataattccagACAATAAGTTACATGGCTGAGCGCGTTGTTGGGCATGGATCATTTGGAGTT
EST: gi|46917569|gb|CN546898.1|CN546898
EST:     GTCATATAATTGTGACGACTATTGGTGGTAGAAATGGCCAACCAAAGCAG                         ACAATAAGTTACATGGCTGAGCGCGTTGTTGGGCATGGATCATTTGGAGTT
genomic: GTCATATAATTGTGACGACTATTGGTGGTAGAAATGGCCAACCAAAGCAGgtatatatgc ... ataattccagACAATAAGTTACATGGCTGAGCGCGTTGTTGGGCATGGATCATTTGGAGTT
EST: gi|30326170|gb|CD009432.1|CD009432
EST:     GTCATATAATTGTGACGACTATTGGTGGTAGAAATGGCCAACCAAAGCAG                         ACAATAAGTTACATGGCTGAGCGCGTTGTTGGGCATGGATCATTTGGAGTT
genomic: GTCATATAATTGTGACGACTATTGGTGGTAGAAATGGCCAACCAAAGCAGgtatatatgc ... ataattccagACAATAAGTTACATGGCTGAGCGCGTTGTTGGGCATGGATCATTTGGAGTT
EST: gi|71858122|gb|DT007177.1|DT007177
EST:     GTCATATAATTGTGACGACTATTGGTGGTAGAAATGGCCAACCAAAGCAG                         ACAATAAGTTACATGGCTGAGCGCGTTGTTGGGCATGGATCATTTGGAGTT
genomic: GTCATATAATTGTGACGACTATTGGTGGTAGAAATGGCCAACCAAAGCAGgtatatatgc ... ataattccagACAATAAGTTACATGGCTGAGCGCGTTGTTGGGCATGGATCATTTGGAGTT
EST: gi|161718942|gb|FC067353.1|FC067353
EST:     GTCATATAATTGTGACAACTATTGGTGGTAGAAATGGCCAACCAAAGCAG                         ACAATAAGTTACATGGCTGAGCGCGTTGTTGGGCATGGATCATTTGGAGTT
genomic: GTCATATAATTGTGACGACTATTGGTGGTAGAAATGGCCAACCAAAGCAGgtatatatgc ... ataattccagACAATAAGTTACATGGCTGAGCGCGTTGTTGGGCATGGATCATTTGGAGTT
EST: gi|110712249|gb|EE089658.1|EE089658
EST:     GTCATATAATTGTGACGACTATTGGTGGTAGAAATGGCCAACCAAAGCAG                         ACAATAAGTTACATGGCTGAGCGCGTTGTTGGGCATGGATCATTTGGAGTT
genomic: GTCATATAATTGTGACGACTATTGGTGGTAGAAATGGCCAACCAAAGCAGgtatatatgc ... ataattccagACAATAAGTTACATGGCTGAGCGCGTTGTTGGGCATGGATCATTTGGAGTT
EST: gi|30256245|gb|CB972088.1|CB972088
EST:     GTCATATAATTGTGACAACTATTGGTGGTAGAAATGGCTAACCAAAGCAG                         ACAATAAGTTACATGGCTGAGCGCGTTGTTGGGCATGGATCATTTGGAGTT
genomic: GTCATATAATTGTGACGACTATTGGTGGTAGAAATGGCCAACCAAAGCAGgtatatatgc ... ataattccagACAATAAGTTACATGGCTGAGCGCGTTGTTGGGCATGGATCATTTGGAGTT
EST: gi|110689423|gb|EE065633.1|EE065633
EST:     GTCATATAATTGTGACGACTATTGGTGGTAGAAATGGCCAACCAAAGCAG                         ACAATAAGTTACATGGCTGAGCGCGTTGTTGGGCATGGATCATTTGGAGTT
genomic: GTCATATAATTGTGACGACTATTGGTGGTAGAAATGGCCAACCAAAGCAGgtatatatgc ... ataattccagACAATAAGTTACATGGCTGAGCGCGTTGTTGGGCATGGATCATTTGGAGTT
EST: gi|30327244|gb|CD010506.1|CD010506
EST:     GTCATATAATTGTGACAACTATTGGTGGTAGAAATGGCCAACCAAAGCAG                         ACAATAAGTTACATGGCTGAGCGCGTTGTTGGGCATGGATCATTTGGAGTT
genomic: GTCATATAATTGTGACGACTATTGGTGGTAGAAATGGCCAACCAAAGCAGgtatatatgc ... ataattccagACAATAAGTTACATGGCTGAGCGCGTTGTTGGGCATGGATCATTTGGAGTT
EST: gi|161713248|gb|FC063076.1|FC063076
EST:     GTCATATAATTGTGACGACTATTGGTGGTAGAAATGGCCAACCAAAGCAG                         ACAATAAGTTACATGGCTGAGCGCGTTGTTGGGCATGGATCATTTGGAGTT
genomic: GTCATATAATTGTGACGACTATTGGTGGTAGAAATGGCCAACCAAAGCAGgtatatatgc ... ataattccagACAATAAGTTACATGGCTGAGCGCGTTGTTGGGCATGGATCATTTGGAGTT
EST: gi|161718839|gb|FC065074.1|FC065074
EST:     GTCATATAATTGTGACGACTATTGGTGGTAGAAATGGCCAACCAAAGCAG                         ACAATAAGTTACATGGCTGAGCGCGTTGTTGGGCATGGATCATTTGGAGTT
genomic: GTCATATAATTGTGACGACTATTGGTGGTAGAAATGGCCAACCAAAGCAGgtatatatgc ... ataattccagACAATAAGTTACATGGCTGAGCGCGTTGTTGGGCATGGATCATTTGGAGTT
EST: gi|33405711|gb|CF211338.1|CF211338
EST:     GTCATATAATTGTGACGACTATTGGTGGTAGAAATGGCCAACCAAAGCAG                         ACAATAAGTTACATGGCTGAGCGCGTTGTTGGGCATGGATCATTTGGAGTT
genomic: GTCATATAATTGTGACGACTATTGGTGGTAGAAATGGCCAACCAAAGCAGgtatatatgc ... ataattccagACAATAAGTTACATGGCTGAGCGCGTTGTTGGGCATGGATCATTTGGAGTT
EST: gi|71858672|gb|DT007727.1|DT007727
EST:     GTCATATAATTGTGACGACTATTGGTGGTAGAAATGGCCAACCAAAGCAG                         ACAATAAGTTACATGGCTGAGCGCGTTGTTGGGCATGGATCATTTGGAGTT
genomic: GTCATATAATTGTGACGACTATTGGTGGTAGAAATGGCCAACCAAAGCAGgtatatatgc ... ataattccagACAATAAGTTACATGGCTGAGCGCGTTGTTGGGCATGGATCATTTGGAGTT
EST: gi|32247650|gb|CD713469.1|CD713469
EST:     ATAATTGTGACGACTATTGGTGGGACAAATGGCCAACCAAAGCAG                         ACAATAAGTTACATGGCTGAGCGCGTTGTTGGGCATGGATCATTTGGAGTT
genomic: ATAATTGTGACGACTATTGGTGGTAGAAATGGCCAACCAAAGCAGgtatatatgc ... ataattccagACAATAAGTTACATGGCTGAGCGCGTTGTTGGGCATGGATCATTTGGAGTT
EST: gi|30327832|gb|CD011094.1|CD011094
EST:     GTCATATAATTGTGACGACTATTGGTGGTAGAAATGGCCAACCAAAGCAG                         ACAATAAGTTACATGGCTGAGCGCGTTGTTGGGCATGGATCATTTGGAGTT
genomic: GTCATATAATTGTGACGACTATTGGTGGTAGAAATGGCCAACCAAAGCAGgtatatatgc ... ataattccagACAATAAGTTACATGGCTGAGCGCGTTGTTGGGCATGGATCATTTGGAGTT
EST: gi|30327902|gb|CD011164.1|CD011164
EST:     GTCATATAATTGTGACGACTATTGGTGGTAGAAATGGCCAACCAAAGCAG                         ACAATAAGTTACATGGCTGAGCGCGTTGTTGGGCATGGATCATTTGGAGTT
genomic: GTCATATAATTGTGACGACTATTGGTGGTAGAAATGGCCAACCAAAGCAGgtatatatgc ... ataattccagACAATAAGTTACATGGCTGAGCGCGTTGTTGGGCATGGATCATTTGGAGTT
EST: gi|30325367|gb|CD008629.1|CD008629
EST:     GTCATATAATTGTGACGACTATTGGTGGTAGAAATGGCCAACCAAAGCAG                         ACAATAAGTTACATGGCTGAGCGCGTTGTTGGGCATGGATCATTTGGAGTT
genomic: GTCATATAATTGTGACGACTATTGGTGGTAGAAATGGCCAACCAAAGCAGgtatatatgc ... ataattccagACAATAAGTTACATGGCTGAGCGCGTTGTTGGGCATGGATCATTTGGAGTT
EST: gi|30325513|gb|CD008775.1|CD008775
EST:     GTCATATAATTGTGACGACTATTGGTGGTAGAAATGGCCAACCAAAGCAG                         ACAATAAGTTACATGGCTGAGCGCGTTGTTGGGCATGGATCATTTGGAGTT
genomic: GTCATATAATTGTGACGACTATTGGTGGTAGAAATGGCCAACCAAAGCAGgtatatatgc ... ataattccagACAATAAGTTACATGGCTGAGCGCGTTGTTGGGCATGGATCATTTGGAGTT
EST: gi|110687881|gb|EE065793.1|EE065793
EST:     GTCATATAATTGTGACGACTATTGGTGGTAGAAATGGCCAACCAAAGCAG                         ACAATAAGTTACATGGCTGAGCGCGTTGTTGGGCATGGATCATTTGGAGTT
genomic: GTCATATAATTGTGACGACTATTGGTGGTAGAAATGGCCAACCAAAGCAGgtatatatgc ... ataattccagACAATAAGTTACATGGCTGAGCGCGTTGTTGGGCATGGATCATTTGGAGTT
EST: gi|34547149|gb|CF515381.1|CF515381
EST:     GTCATATAATTGTGACGACTATTGGTGGTAGAAATGGCCAGCCAAAGCAG                         ACAATAAGTTACATGGCTGAGCGCGTTGTTGGGCATGGATCATTTGGAGTT
genomic: GTCATATAATTGTGACGACTATTGGTGGTAGAAATGGCCAACCAAAGCAGgtatatatgc ... ataattccagACAATAAGTTACATGGCTGAGCGCGTTGTTGGGCATGGATCATTTGGAGTT
EST: gi|30325747|gb|CD009009.1|CD009009
EST:     GTCATATAATTGTGACAACTATTGGTGGTAGAAATGGCCAACCAAAGCAG                         ACAATAAGTTACATGGCTGAGCGCGTTGTTGGGCATGGATCATTTGGAGTT
genomic: GTCATATAATTGTGACGACTATTGGTGGTAGAAATGGCCAACCAAAGCAGgtatatatgc ... ataattccagACAATAAGTTACATGGCTGAGCGCGTTGTTGGGCATGGATCATTTGGAGTT
EST: gi|30325454|gb|CD008716.1|CD008716
EST:     GTCATATAATTGTGACAACTATTGGTGGTAGAAATGGCCAACCAAAGCAG                         ACAATAAGTTACATGGCTGAGCGCGTTGTTGGGCATGGATCATTTGGAGTT
genomic: GTCATATAATTGTGACGACTATTGGTGGTAGAAATGGCCAACCAAAGCAGgtatatatgc ... ataattccagACAATAAGTTACATGGCTGAGCGCGTTGTTGGGCATGGATCATTTGGAGTT
EST: gi|71859213|gb|DT008268.1|DT008268
EST:     GTCATATAATTGTGACAACTATTGGTGGTAGAAATGGCCAACCAAAGCAG                         ACAATAAGTTACATGGCTGAGCGCGTTGTTGGGCATGGATCATTTGGAGTT
genomic: GTCATATAATTGTGACGACTATTGGTGGTAGAAATGGCCAACCAAAGCAGgtatatatgc ... ataattccagACAATAAGTTACATGGCTGAGCGCGTTGTTGGGCATGGATCATTTGGAGTT
EST: gi|30323811|gb|CD007073.1|CD007073
EST:     GTCATATAATTGTGACAACTATTGGTGGTAGAAATGGCCAACCAAAGCAG                         ACAATAAGTTACATGGCTGAGCGCGTTGTTGGGCATGGATCATTTGGAGTT
genomic: GTCATATAATTGTGACGACTATTGGTGGTAGAAATGGCCAACCAAAGCAGgtatatatgc ... ataattccagACAATAAGTTACATGGCTGAGCGCGTTGTTGGGCATGGATCATTTGGAGTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGATGGAAGCAACAGTTGTTGACGGTAATGGAACAGAGACAGGTCATATAATTGTGACGACTATTGGTGGTAGAAATGGCCAACCAAAGCAGgtatatatgcttgagcacattccttaggttttggatctcatagcatgtcaggagatgccatttttgcctttttaggtgattaacattttcttgggttcta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caggaga