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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctgttttatcatttaactatggttgcagttcattataatggttttagagttttggttttgattgtttctctttctctaacttgtcaatgacgttcatagGTTGTGGAGCTTGATTTTCTCTATCCAAGTGAGGGCATCCACAGAAGGTGGGACAGTGGTTATCGAATAACATCAACGGCTGCAACTTGGGATCAATCTG

Basic information

species Vitis vinifera
transcript Vv06s0004g01090.t01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g01090.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA08G47680.3 (Glycine max), 3'ss of exon 12
--------tctgttttatcatttaactatggttgcagttcattataatggttttagagttttggttttgattgtttctctttctctaacttgtcaatgacgttcatagGTTGTGGAGCTTGATTTTCTCTATCCAAGTGAGGGCATCCACAGAAGGTGGGACAGTGGTTATCGAATAACATCAACGGCTGCAACTTGGGATCAATCTG
        | ||| || |   || |    |   | | |||| | || ||  | |     |     |     |   |||| || || | ||| | ||||       |||||||| || ||||||||||||||||| |||||||| ||||||||| | ||||| | ||||||| | || ||| |||||||||| || |||||||||||||
aagatctatatgtcttttgggttgaaacagtccgtacttcaat-tattgactctgccactagacctaatccttgctctcattatccatcttttaaatg-------tagGTTGTTGAACTTGATTTTCTCTATCCTAGTGAGGGAATCCACAGACGATGGGATAATGGTTATAGGATTACAGCAACGGCTGCTACATGGGATCAATCTG

upper sequence: Vv06s0004g01090.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA18G53810.1 (Glycine max), 3'ss of exon 14
------tctgttttatcatttaactatggttgcagttca-ttataatggttttagagttttggttttgattgtttctctttctctaacttgtcaatgacgttcatagGTTGTGGAGCTTGATTTTCTCTATCCAAGTGAGGGCATCCACAGAAGGTGGGACAGTGGTTATCGAATAACATCAACGGCTGCAACTTGGGATCAATCTG-
       || || |    || || || |  || | |||| ||||   |  | |     | |   |     |   |||| || || | ||| | ||||       |||||||| || ||||||||||||||||| |||||||| ||||||||  | ||||| | ||||||| | || ||| |||| ||||| || ||||||||||||| 
gcaaaaactcttgttgagttgaaata-gtctgtacttcaattattgagtctctgccactatacctaatccttgctctcattatccatcttttaaatg-------taggTTGTTGAACTTGATTTTCTCTATCCTAGTGAGGGAATCCACAGGCGATGGGATAATGGTTATAGGATTACAGCAACTGCTGCTACATGGGATCAATCTGC

upper sequence: Vv06s0004g01090.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA10G44050.1 (Glycine max), 3'ss of exon 14
---------------------------------------------------------------tctgttttatcatttaactatggttgcagttcattataatggttttagagttttggttttgattgtttct-------ctttctcta---acttgtcaatgacgttc-----atagGTTGTGGAGCTTGATTTTCTCTATCCAAGTGAGGGCATCCACAGAAGGTGGGACAGTGGTTATCGAATAACATCAACGGCTGCAACTTGGGATCAATCTG
                                                               | ||| | ||    |  || || |     |    || ||||||    |  ||     |  |  |||| |        ||  ||  |    ||  ||| | || ||       ||||| || || |||||||||||||||||||||||||||||||| | | | ||||| |  |||||| | || ||| |||| || || || | |||||||||||
gtttgctgttaaaattgtatttcattatgacatttggtataacagttcttctgcatttctatttgtgtgtgatttcctgtctctgttcagtatgtcatacaatggtggccggtttggacataagcctgttaccagacagactggcttcatgctctcatcattaaccttttaactgtagGTGGTTGAACTTGATTTTCTCTATCCAAGTGAGGGCATCCATAAACGTTGGGATAAAGGTTATAGGATTACAGCAACCGCAGCTACATTGGATCAATCTG

upper sequence: Vv06s0004g01090.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA20G38770.1 (Glycine max), 3'ss of exon 14
------------------------------------------------------------tctgttttatcatttaactatggttgcagttcattataatggttttagagttttggttttgattgtttctctttctctaacttgtcaatgacgttc-----atagGTTGTGGAGCTTGATTTTCTCTATCCAAGTGAGGGCATCCACAGAAGGTGGGACAGTGGTTATCGAATAACATCAACGGCTGCAACTTGGGATCAATCTG
                                                              |||   ||   ||  || || |     |    |  ||||||   | |  |  |  | | | | |   || |||     ||  ||| | || ||       ||||| || || |||||||||||||||||||||||||||||||| | | | ||||| |  |||||| | || ||| |||| || || || | |||||||||||
gtttgctgttaaaattgtattccattatgaaatttggtataacagttctgcaatgcttttagtgtgcgatttcttgtctctgttcagtatgtcatgcaatggtggaaaa--taagcctgttactatacttccttcatgctctcatcatttaccttttaactgtagGTGGTTGAACTTGATTTTCTCTATCCAAGTGAGGGCATCCATAAACGTTGGGATAAAGGTTATAGGATTACAGCAACCGCAGCTACATTGGATCAATCTG

upper sequence: Vv06s0004g01090.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: AT3G13670.1 (Arabidopsis thaliana), 3'ss of exon 14
-tctgttttatcatttaactatggttgcagttcattataat-ggttttagagttttggttttgattgt---ttctctttctctaacttgtcaatgacgttcatagGTTGTGGAGCTTGATTTTCTCTATCCAAGTGAGGGCATCCACAGAAGGTGGGACAGTGGTTATCGAATAACATCAACGGCTGCAACTTGGGATCAATCTG
 |  |  ||  |   ||   |||  |    | | ||    |  ||||| ||  | | |  ||||||     ||||| |  | |  ||| |  ||  | |  | |||||||||| ||||||||||| ||||||||||| |||||||||||  | |||||  |||| |   |||| |||||||| || || ||    |||||| |||
gttagacttcaccgatatagatgaatttcttccgtttccttcagttttggatctgtcgcgttgatttctaattctcctgttttcgcttat--atctcctctacagGTTGTGGAACTTGATTTTCTGTATCCAAGTGAAGGCATCCACAGGCGTTGGGATGGTGGATTCAGAATCACATCAACAGCAGCCACAACCGATCAAGCTG

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|352786685|gb|FQ479892.1|FQ479892
EST:     GAAGCCGATGGGGGGTAGTCATGTCTCGCAATGCTGGCTTTAGTGATCAG                         GTTGTGGAGCTTGATTTTCTCTATCCAAGTGAGGGCATCCACAGAAGGTGG
genomic: GAAGCCGATGGGGGGTAGTCATGTCTCGCAATGCTGGCTTTAGTGATCAGgttgggcttt ... acgttcatagGTTGTGGAGCTTGATTTTCTCTATCCAAGTGAGGGCATCCACAGAAGGTGG
EST: gi|351049335|gb|FQ429078.1|FQ429078
EST:     GAAGCCGATGGGGGGTAGTCATGTCTCGCAATGCTGGCTTTAGTGATCAG                         GTTGTGGAGCTTGATTTTCTCTATCCAAGTGAGGGCATCCACAGAAGGTGG
genomic: GAAGCCGATGGGGGGTAGTCATGTCTCGCAATGCTGGCTTTAGTGATCAGgttgggcttt ... acgttcatagGTTGTGGAGCTTGATTTTCTCTATCCAAGTGAGGGCATCCACAGAAGGTGG
EST: gi|351057055|gb|FQ448572.1|FQ448572
EST:     GAAGCCGATGGGGGGTAGTCATGTCTCGCAATGCTGGCTTTAGTGATCAG                         GTTGTGGAGCTTGATTTTCTCTATCCAAGTGAGGGCATCCACAGAAGGTGG
genomic: GAAGCCGATGGGGGGTAGTCATGTCTCGCAATGCTGGCTTTAGTGATCAGgttgggcttt ... acgttcatagGTTGTGGAGCTTGATTTTCTCTATCCAAGTGAGGGCATCCACAGAAGGTGG
EST: gi|110398634|gb|EC965103.1|EC965103
EST:     GAAGCCGATGGGGGGTAGTCATGTCTCGCAATGCTGGCTTTAGTGATCAG                         GTTGTGGAGCTTGATTTTCTCTATCCAAGTGAGGGCATCCACAGAAGGTGG
genomic: GAAGCCGATGGGGGGTAGTCATGTCTCGCAATGCTGGCTTTAGTGATCAGgttgggcttt ... acgttcatagGTTGTGGAGCTTGATTTTCTCTATCCAAGTGAGGGCATCCACAGAAGGTGG
EST: gi|110363867|gb|EC927492.1|EC927492
EST:     GAAGCCGATGGGGGGTAGTCATGTCTCGCAATGCTGGCTTTAGTGATCAG                         GTTGTGGAGCTTGATTTTCTCTATCCAAGTGAGGGCATCCACAGAAGGTGG
genomic: GAAGCCGATGGGGGGTAGTCATGTCTCGCAATGCTGGCTTTAGTGATCAGgttgggcttt ... acgttcatagGTTGTGGAGCTTGATTTTCTCTATCCAAGTGAGGGCATCCACAGAAGGTGG
EST: gi|110698357|gb|EE075776.1|EE075776
EST:     GAAGCCGATGGGGGGTAGTCATGTCTCGCAATGCTGGCTTTAGTGATCAG                         GTTGTGGAGCTTGATTTTCTCTATCCAAGTGAGGGCATCCACAGAAGGTGG
genomic: GAAGCCGATGGGGGGTAGTCATGTCTCGCAATGCTGGCTTTAGTGATCAGgttgggcttt ... acgttcatagGTTGTGGAGCTTGATTTTCTCTATCCAAGTGAGGGCATCCACAGAAGGTGG
EST: gi|351049006|gb|FQ431550.1|FQ431550
EST:     GAAGCCGATGGGGGGTAGTCATGTCTCGCAATGCTGGCTTTAGTGATCAG                         GTTGTGGAGCTTGATTTTCTCTATCCAAGTGAGGGCATCCACAGAAGGTGG
genomic: GAAGCCGATGGGGGGTAGTCATGTCTCGCAATGCTGGCTTTAGTGATCAGgttgggcttt ... acgttcatagGTTGTGGAGCTTGATTTTCTCTATCCAAGTGAGGGCATCCACAGAAGGTGG
EST: gi|110424497|gb|EC990860.1|EC990860
EST:     GAAGCCGATGGGGGGTAGTCATGTCTCGCAATGCTGGCTTTAGTGATCAG                         GTTGTGGAGCTTGATTTTCTCTATCCAAGTGAGGGCATCCACAGAAGGTGG
genomic: GAAGCCGATGGGGGGTAGTCATGTCTCGCAATGCTGGCTTTAGTGATCAGgttgggcttt ... acgttcatagGTTGTGGAGCTTGATTTTCTCTATCCAAGTGAGGGCATCCACAGAAGGTGG
EST: gi|110382715|gb|EC947034.1|EC947034
EST:     GAAGCCGATGGGGGGTAGTCATGTCTCGCAATGCTGGCTTTAGTGATCAG                         GTTGTGGAGCTTGATTTTCTCTATCCAAGTGAGGGCATCCACAGAAGGTGG
genomic: GAAGCCGATGGGGGGTAGTCATGTCTCGCAATGCTGGCTTTAGTGATCAGgttgggcttt ... acgttcatagGTTGTGGAGCTTGATTTTCTCTATCCAAGTGAGGGCATCCACAGAAGGTGG
EST: gi|110388914|gb|EC953715.1|EC953715
EST:     GAAGCCGATGGGGGGTAGTCATGTCTCGCAATGCTGGCTTTAGTGATCAG                         GTTGTGGAGCTTGATTTTCTCTATCCAAGTGAGGGCATCCACAGAAGGTGG
genomic: GAAGCCGATGGGGGGTAGTCATGTCTCGCAATGCTGGCTTTAGTGATCAGgttgggcttt ... acgttcatagGTTGTGGAGCTTGATTTTCTCTATCCAAGTGAGGGCATCCACAGAAGGTGG
EST: gi|110698358|gb|EE075777.1|EE075777
EST:     GAAGCCGATGGGGGGTAGTCATGTCTCGCAATGCTGGCTTTAGTGATCAG                         GTTGTGGAGCTTGATTTTCTCTATCCAAGTGAGGGCATCCACAGAAGGTGG
genomic: GAAGCCGATGGGGGGTAGTCATGTCTCGCAATGCTGGCTTTAGTGATCAGgttgggcttt ... acgttcatagGTTGTGGAGCTTGATTTTCTCTATCCAAGTGAGGGCATCCACAGAAGGTGG
EST: gi|110715907|gb|EE094492.1|EE094492
EST:     GAAGCCGATGGGGGGTAGTCATGTCTCGCAATGCTGGCTTTAGTGATCAG                         GTTGTGGAGCTTGATTTTCTCTATCCAAGTGAGGGCATCCACAGAAGGTGG
genomic: GAAGCCGATGGGGGGTAGTCATGTCTCGCAATGCTGGCTTTAGTGATCAGgttgggcttt ... acgttcatagGTTGTGGAGCTTGATTTTCTCTATCCAAGTGAGGGCATCCACAGAAGGTGG
EST: gi|110698359|gb|EE075778.1|EE075778
EST:     GAAGCCGATGGGGGGTAGTCATGTCTCGCAATGCTGGCTTTAGTGATCAG                         GTTGTGGAGCTTGATTTTCTCTATCCAAGTGAGGGCATCCACAGAAGGTGG
genomic: GAAGCCGATGGGGGGTAGTCATGTCTCGCAATGCTGGCTTTAGTGATCAGgttgggcttt ... acgttcatagGTTGTGGAGCTTGATTTTCTCTATCCAAGTGAGGGCATCCACAGAAGGTGG
EST: gi|110373006|gb|EC937209.1|EC937209
EST:     GAAGCCGATGGGGGGTAGTCATGTCTCGCAATGCTGGCTTTAGTGATCAG                         GTTGTGGAGCTTGATTTTCTCTATCCAAGTGAGGGCATCCACAGAAGGTGG
genomic: GAAGCCGATGGGGGGTAGTCATGTCTCGCAATGCTGGCTTTAGTGATCAGgttgggcttt ... acgttcatagGTTGTGGAGCTTGATTTTCTCTATCCAAGTGAGGGCATCCACAGAAGGTGG
EST: gi|37188771|gb|CF608120.1|CF608120
EST:     GAAGCCGATGGGGGGTAGTCATGTCTCGCAATGCTGGCTTTAGTGATCAG                         GTTGTGGAGCTTGATTTTCTCTATCCAAGTGAGGGCATCCACAGAAGGTGG
genomic: GAAGCCGATGGGGGGTAGTCATGTCTCGCAATGCTGGCTTTAGTGATCAGgttgggcttt ... acgttcatagGTTGTGGAGCTTGATTTTCTCTATCCAAGTGAGGGCATCCACAGAAGGTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagagttttggttttgattgtttctctttctctaacttgtcaatgacgttcatagGTTGTGGAGCTTGATTTTCTCTATCCAAGTGAGGGCATCCACAGAAGGTGGGACAGTGGTTATCGAATAACATCAACGGCTGCAACTTGGGATCAATCTG
                             ctctaac  putative branch site (score: 2)
           ttttgatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctgttttatcatttaactatggttgcagttcattataatggttttagagttttggttttgattgtttctctttctctaacttgtcaatgacgttcatagGTTGTGGAGCTTGATTTTCTCTATCCAAGTGAGGGCATCCACAGAAGGTGGGACAGTGGTTATCGAATAACATCAACGGCTGCAACTTGGGATCAATCTG

- - - - - - - - - - tggttgc