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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actctggattgcttacaagtaagatggatctttgttaaattcaagttacctcatgcaaatactctacatgatgttctaacttttcatcctcttgttgcagTCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCTCGGATGTTTAGTGAGAATAAGCGTGAGTACAACAGAAGAGTGAGGGAAA

Basic information

species Vitis vinifera
transcript Vv17s0000g05820.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g05820.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA06G20310.1 (Glycine max), 3'ss of exon 4
actctggattgcttacaagtaagatggatctttgttaaat-tcaagttacctcat-gcaaatactctaca-tgatgttctaacttttcatcctctt--gttgcagTCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCTCGGATGTTTAGTGAGAATAAGCGTGAGTACAACAGAAGAGTGAGGGAAA
| ||| | | || ||| || | | || | || | || | | | | | || | | || |||||| | || || | ||||||||| |||| |||||||||||||| |||||||||||||| || ||||| ||||| |||||||||||||| |||||||||||||| |||||||||||||||
----tttatttcctg-aaataaataaaatatatagcaagtatcctgctatgcagtagtcatcattttataattattttctaaaaggtaattttcctcctttgcagTCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCTGAAGCAGCTCGAATGTTTAGTGAGAACAAGCGTGAGTACAATCGAAGAGTGAGGGAAA

upper sequence: Vv17s0000g05820.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA05G01270.1 (Glycine max), 3'ss of exon 5
actctggattgcttacaagtaagatggatctttgttaaattcaagttacctcat-gcaaatactctaca-tgatgttctaac---ttttcatcctcttgttgcagTCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCTCGGATGTTTAGTGAGAATAAGCGTGAGTACAACAGAAGAGTGAGGGAAA
| | || | | | || || | || || ||||| | | | | | | | || | | || |||| | | | || ||| ||||||| |||| |||||||||||||| |||||||||||||| |||||||| ||||| |||||||||||||| |||||||||||||| |||||||||| ||||
---atcattggcacatatatcagttg--ttttacttgtattcatggtgtatagtagtcagcatgttataattattttctgaaaggtaattattactctgtggcagTCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCAGAAGCAGCTCGAATGTTTAGTGAGAACAAGCGTGAGTACAATCGAAGAGTGAGAGAAA

upper sequence: Vv17s0000g05820.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA04G34170.2 (Glycine max), 3'ss of exon 5
actctggattgcttacaagtaagatggatctttgttaaat-tcaagttacctcatg--caa-atactctacatgatgttctaacttttcatcctctt--gttgcagTCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCTCGGATGTTTAGTGAGAATAAGCGTGAGTACAACAGAAGAGTGAGGGAAA
| | | | || ||| | | | | | | || | || | | || || ||||| || || |||||| | || || | ||||||||| |||| |||||||||||||| |||||||||||||| || ||||| ||||| |||||||| ||||| |||||||| ||||| |||||||||||||||
-----gaaataaaaaaaaataaaaaaagtatatagcatttatcctgctatgtagtaatcatcatgctcta-attattttctaaaaggtaattttcctcctttgcagTCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCTGAAGCAGCTCGAATGTTTAGCGAGAACAAGCGTGAATACAATCGAAGAGTGAGGGAAA

upper sequence: Vv17s0000g05820.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA17G10640.2 (Glycine max), 3'ss of exon 5
actctggattgcttacaagtaagatggatctttgttaaattcaagttacctcat-gcaaatactctaca-tgatgttctaac---ttttcatcctcttgttgcagTCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCTCGGATGTTTAGTGAGAATAAGCGTGAGTACAACAGAAGAGTGAGGGAAA
| | ||| | || | | |||||| || | | |||| | | | | | || | | || |||| | | || || ||||||| |||| |||||||||||||| |||||||||||||| |||||||| ||||| |||||||||||||| ||||| |||||||| ||||||| || ||||
-ttatatattatcttca--tgattctactctttggta--tccctgttatatagtagtcagcatgttataattattttctgaaagatacatattactctgcggcagTCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCAGAAGCAGCTCGAATGTTTAGTGAGAACAAGCGGGAGTACAATCGAAGAGTTAGAGAAA

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|351044280|gb|FQ447634.1|FQ447634
EST:     ATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAG                         TCACTGCTCTGTGATCTCAACCCCAATTCTCCTGCATATTCAGAAGCTGCT
genomic: ATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAGgtattgtcaa ... cttgttgcagTCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCT
EST: gi|349823648|gb|FQ415058.1|FQ415058
EST:     ATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAG                         TCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCT
genomic: ATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAGgtattgtcaa ... cttgttgcagTCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCT
EST: gi|351029672|gb|FQ427512.1|FQ427512
EST:     ATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAG                         TCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCT
genomic: ATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAGgtattgtcaa ... cttgttgcagTCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCT
EST: gi|110726002|gb|EE103053.1|EE103053
EST:     ATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAG                         TCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCT
genomic: ATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAGgtattgtcaa ... cttgttgcagTCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCT
EST: gi|110426330|gb|EC992735.1|EC992735
EST:     ATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAG                         TCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCT
genomic: ATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAGgtattgtcaa ... cttgttgcagTCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCT
EST: gi|349812793|gb|FQ410435.1|FQ410435
EST:     ATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAG                         TCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCT
genomic: ATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAGgtattgtcaa ... cttgttgcagTCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCT
EST: gi|351040450|gb|FQ434583.1|FQ434583
EST:     ATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAG                         TCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCT
genomic: ATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAGgtattgtcaa ... cttgttgcagTCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCT
EST: gi|351033819|gb|FQ447857.1|FQ447857
EST:     ATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAG                         TCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCT
genomic: ATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAGgtattgtcaa ... cttgttgcagTCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCT
EST: gi|351024032|gb|FQ423455.1|FQ423455
EST:     ATCAGTGGAGTCCTATATATGGTGTAGCAGCTATACTTACGTCTATTCAG                         TCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCT
genomic: ATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAGgtattgtcaa ... cttgttgcagTCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCT
EST: gi|349830568|gb|FQ416866.1|FQ416866
EST:     ATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAG                         TCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCT
genomic: ATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAGgtattgtcaa ... cttgttgcagTCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCT
EST: gi|351031294|gb|FQ445319.1|FQ445319
EST:     ATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAG                         TCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCT
genomic: ATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAGgtattgtcaa ... cttgttgcagTCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCT
EST: gi|351014290|gb|FQ437292.1|FQ437292
EST:     ATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAG                         TCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCT
genomic: ATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAGgtattgtcaa ... cttgttgcagTCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCT
EST: gi|110731799|gb|EE106527.1|EE106527
EST:     ATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAG                         TCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCT
genomic: ATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAGgtattgtcaa ... cttgttgcagTCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCT
EST: gi|349826891|gb|FQ418982.1|FQ418982
EST:     ATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAG                         TCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCT
genomic: ATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAGgtattgtcaa ... cttgttgcagTCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCT
EST: gi|351035318|gb|FQ459585.1|FQ459585
EST:     ATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAG                         TCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCT
genomic: ATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAGgtattgtcaa ... cttgttgcagTCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCT
EST: gi|110700261|gb|EE078097.1|EE078097
EST:     ATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAG                         TCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCT
genomic: ATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAGgtattgtcaa ... cttgttgcagTCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCT
EST: gi|110421523|gb|EC987821.1|EC987821
EST:     ATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAG                         TCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCT
genomic: ATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAGgtattgtcaa ... cttgttgcagTCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCT
EST: gi|349824373|gb|FQ417760.1|FQ417760
EST:     ATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAG                         TCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCT
genomic: ATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAGgtattgtcaa ... cttgttgcagTCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCT
EST: gi|351014644|gb|FQ437646.1|FQ437646
EST:     ATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAG                         TCACTGCTCTGTGATCCCAACCCCAACTCTCCTGCAAATTCAGAAGCTGCT
genomic: ATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAGgtattgtcaa ... cttgttgcagTCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCT
EST: gi|351044244|gb|FQ447598.1|FQ447598
EST:     ATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAG                         TCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCT
genomic: ATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAGgtattgtcaa ... cttgttgcagTCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCT
EST: gi|110361377|gb|EC924844.1|EC924844
EST:     ATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAG                         TCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCT
genomic: ATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAGgtattgtcaa ... cttgttgcagTCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCT
EST: gi|351013685|gb|FQ433837.1|FQ433837
EST:     ATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAG                         TCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCT
genomic: ATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAGgtattgtcaa ... cttgttgcagTCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCT
EST: gi|349823308|gb|FQ402507.1|FQ402507
EST:     ATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAG                         TCACTGCTCTGTGACCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCT
genomic: ATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAGgtattgtcaa ... cttgttgcagTCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCT
EST: gi|110389048|gb|EC953859.1|EC953859
EST:     ATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAG                         TCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCT
genomic: ATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAGgtattgtcaa ... cttgttgcagTCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCT
EST: gi|351016912|gb|FQ424339.1|FQ424339
EST:     ATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAG                         TCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCT
genomic: ATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAGgtattgtcaa ... cttgttgcagTCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCT
EST: gi|349829768|gb|FQ421286.1|FQ421286
EST:     ATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAG                         TCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCT
genomic: ATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAGgtattgtcaa ... cttgttgcagTCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCT
EST: gi|351029101|gb|FQ435301.1|FQ435301
EST:     ATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAG                         TCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCT
genomic: ATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAGgtattgtcaa ... cttgttgcagTCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCT
EST: gi|30302161|gb|CB978955.1|CB978955
EST:     ATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAG                         TCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAGATTCAGAAGCTGCT
genomic: ATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAGgtattgtcaa ... cttgttgcagTCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCT
EST: gi|351024814|gb|FQ430639.1|FQ430639
EST:     ATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAG                         TCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCT
genomic: ATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAGgtattgtcaa ... cttgttgcagTCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCT
EST: gi|351053304|gb|FQ459172.1|FQ459172
EST:     ATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAG                         TCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCT
genomic: ATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAGgtattgtcaa ... cttgttgcagTCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCT
EST: gi|110714545|gb|EE091578.1|EE091578
EST:     ATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAG                         TCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCT
genomic: ATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAGgtattgtcaa ... cttgttgcagTCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttacctcatgcaaatactctacatgatgttctaacttttcatcctcttgttgcagTCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCTCGGATGTTTAGTGAGAATAAGCGTGAGTACAACAGAAGAGTGAGGGAAA
                            ttctaac  putative branch site (score: 1)
 cttttcatcctcttgt  CT-rich tract
 taactttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actctggattgcttacaagtaagatggatctttgttaaattcaagttacctcatgcaaatactctacatgatgttctaacttttcatcctcttgttgcagTCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCTCGGATGTTTAGTGAGAATAAGCGTGAGTACAACAGAAGAGTGAGGGAAA

-ctctgga
- - - - -tgcttac
- - - - - - - - aagtaaga
- - - - - - - - - - - - - - - - - - aaattcaa
- - - - - - - - - - - - - - - - - - - - - - - - -ctcatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctctaca