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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaaagtttatgcatctagccatctagagatatttctaattcgtctttttgttttttcttgttctttccctcatgcttcaatcaaattgttgtatttcagGTTTCTGTTCTTGCTGATGAAATCTTAAAGAATGTGGAGTATGATGCTTTGAGAATTGTTTTCAACAAGTTCCGTTCAATTATCTCATTTGTACCAACAA

Basic information

species Vitis vinifera
transcript Vv17s0000g07300.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g07300.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA06G22050.3 (Glycine max), 3'ss of exon 6
ttaaagtttatgcatctagccatctagagatat-ttctaattcgtctttttgttttttcttgttctttccctcatgcttcaatcaaattgttgtat--ttcagGTTTCTGTTCTTGCTGATGAAATCTTAAAGAATGTGGAGTATGATGCTTTGAGAATTGTTTTCAACAAGTTCCGTTCAATTATCTCATTTGTACCAACAA
   ||  | |   |  |    |  || | ||   || | ||   |       | ||    ||   | || |   |||   |  | | |||||| ||  ||||||| |||||  | || ||||| ||  ||||||||||||||||||| || || || |||||||||||||| || | |||  || |   |||| | |||||| 
---aaaataagctagttgaatacataaatatggattttgatgatttacagaatcttgcactgaaatgtctccactgccctatgctatttgttggatctttcagGTGTCTGTCTTGGCAGATGACATTCTAAAGAATGTGGAGTATGACGCATTAAGGATTGTTTTCAACAAATTTCATTCTGTTGTACAATTTTTGCCAACAG

upper sequence: Vv17s0000g07300.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA04G32460.1 (Glycine max), 3'ss of exon 5
ttaaagtttat---gcatctagccatctagagatatttctaattcgtctttttgttttttcttgttctttccctcatgcttcaatcaaattgttgtat--ttcagGTTTCTGTTCTTGCTGATGAAATCTTAAAGAATGTGGAGTATGATGCTTTGAGAATTGTTTTCAACAAGTTCCGTTCAATTATCTCATTTGTACCAACAA
  ||| | | |    ||| ||  ||| |  | ||||   | |||          | ||    ||   | || |   || |  |  | | |||||| ||  ||||||| |||||  | || ||||| ||  ||||||||||||||||||| || || || |||||||||||||| || | |||  || |   |||| | |||||| 
-aaaattgtctccaacatatatacattttaa-atatgcttgatttacaca---atcttgcactgaaatgtctccactgttctatgctatttgttggatctttcagGTGTCTGTCTTGGCAGATGACATTCTAAAGAATGTGGAGTATGACGCATTAAGGATTGTTTTCAACAAATTTCATTCTGTTGTACAATTTTTGCCAACAG
















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|27579395|gb|CB002090.1|CB002090
EST:     TTGAGCTATGCATAACTGAATTGCAGAAAAATCCTCTGAATTATACACAG                         GTTTCTGTTCTTGCTGATGAAATCTTAAAGAATGTGGAGTATGATGCTTTG
genomic: TTGAGCTATGCATAACTGAATTGCAGAAAAATCCTCTGAATTATACACAGgtcaatttct ... tgtatttcagGTTTCTGTTCTTGCTGATGAAATCTTAAAGAATGTGGAGTATGATGCTTTG
EST: gi|161719749|gb|FC066095.1|FC066095
EST:     TTGAGCTATGCATAACTGAATTGCAGAAAAATCCTCTGAATTATACACAG                         GTTTCTGTTCTTGCTGATGAAATCTT
genomic: TTGAGCTATGCATAACTGAATTGCAGAAAAATCCTCTGAATTATACACAGgtcaatttct ... tgtatttcagGTTTCTGTTCTTGCTGATGAAATCTT
EST: gi|30134656|gb|CB919994.1|CB919994
EST:     TTGAGCTATGCATAACTGAATTGCAGAAAAATCCTCTGAATTATACACAG                         GTTTCTGTTCTTGCTGATGAAATCTTAAAGAATGTGGAGTATGATGCTTTG
genomic: TTGAGCTATGCATAACTGAATTGCAGAAAAATCCTCTGAATTATACACAGgtcaatttct ... tgtatttcagGTTTCTGTTCTTGCTGATGAAATCTTAAAGAATGTGGAGTATGATGCTTTG
EST: gi|110378840|gb|EC943994.1|EC943994
EST:     TTGAGCTATGCATAACTGAATTGCAGAAAAATCCTCTGAATTATACACAG                         GTTTCTGTTCTTGCTGATGAAATCTTAAAGAATGTGGAGTATGATGCTTTG
genomic: TTGAGCTATGCATAACTGAATTGCAGAAAAATCCTCTGAATTATACACAGgtcaatttct ... tgtatttcagGTTTCTGTTCTTGCTGATGAAATCTTAAAGAATGTGGAGTATGATGCTTTG
EST: gi|110711663|gb|EE088400.1|EE088400
EST:     TTGAGCTATGCATAACTGAATTGCAGAAAAATCCTCTGAATTATACACAG                         GTTTCTGTTCTTGCTGATGAAATCTTAAAGAATGTGGAGTATGATGCTTTG
genomic: TTGAGCTATGCATAACTGAATTGCAGAAAAATCCTCTGAATTATACACAGgtcaatttct ... tgtatttcagGTTTCTGTTCTTGCTGATGAAATCTTAAAGAATGTGGAGTATGATGCTTTG
EST: gi|161719379|gb|FC068295.1|FC068295
EST:     TTGAGCTATGCATAACTGAATTGCAGAAAAATCCTCTGAATTATACACAG                         GTTTCTGTTCTTGCTGATGAAATCTTAA-GAATGTGGAGTATGATGCTTTG
genomic: TTGAGCTATGCATAACTGAATTGCAGAAAAATCCTCTGAATTATACACAGgtcaatttct ... tgtatttcagGTTTCTGTTCTTGCTGATGAAATCTTAAAGAATGTGGAGTATGATGCTTTG
EST: gi|27580503|gb|CB003198.1|CB003198
EST:     TTGAGCTATGCATAACTGAATTGCAGAAAAATCCTCTGAATTATACACAG                         GTTTCTGTTCTTGCTGATGAAATCTTAAAGAATGTGGAGTATGATGCTTTG
genomic: TTGAGCTATGCATAACTGAATTGCAGAAAAATCCTCTGAATTATACACAGgtcaatttct ... tgtatttcagGTTTCTGTTCTTGCTGATGAAATCTTAAAGAATGTGGAGTATGATGCTTTG
EST: gi|27579723|gb|CB002418.1|CB002418
EST:     TTGAGCTATGCATAACTGAATTGCAGAAAAATCCTCTGAATTATACACAG                         GTTTCTGTTCTTGCTGATGAAATCTTAAAGAATGTGGAGTATGATGCTTTG
genomic: TTGAGCTATGCATAACTGAATTGCAGAAAAATCCTCTGAATTATACACAGgtcaatttct ... tgtatttcagGTTTCTGTTCTTGCTGATGAAATCTTAAAGAATGTGGAGTATGATGCTTTG
EST: gi|34320546|gb|CF373300.1|CF373300
EST:     TTGAGCTATGCATAACTGAATTGCAGAAAAATCCTCTGAATTATACACAG                         GTTTCTGTTCTTGCTGATGAAATCTTAAAGAATGTGGAGTATGATGCTTTG
genomic: TTGAGCTATGCATAACTGAATTGCAGAAAAATCCTCTGAATTATACACAGgtcaatttct ... tgtatttcagGTTTCTGTTCTTGCTGATGAAATCTTAAAGAATGTGGAGTATGATGCTTTG
EST: gi|27579412|gb|CB002107.1|CB002107
EST:     TTGAGCTATGCATAACTGAATTGCAGAAAAATCCTCTGAATTATACACAG                         GTTTCTGTTCTTGCTGATGAAATCTTAAAGAATGTGGAGTATGATGCTTTG
genomic: TTGAGCTATGCATAACTGAATTGCAGAAAAATCCTCTGAATTATACACAGgtcaatttct ... tgtatttcagGTTTCTGTTCTTGCTGATGAAATCTTAAAGAATGTGGAGTATGATGCTTTG
EST: gi|110393077|gb|EC957966.1|EC957966
EST:     TTGAGCTATGCATAACTGAATTGCAGAAAAATCCTCTGAATTATACACAG                         GTTTCTGTTCTTGCTGATGAAATCTTAAAGAATGTGGAGTATGATGCTTTG
genomic: TTGAGCTATGCATAACTGAATTGCAGAAAAATCCTCTGAATTATACACAGgtcaatttct ... tgtatttcagGTTTCTGTTCTTGCTGATGAAATCTTAAAGAATGTGGAGTATGATGCTTTG
EST: gi|33402169|gb|CF207796.1|CF207796
EST:     TTGAGCTATGCATAACTGAATTGCAGAAAAATCCTCTGAATTATACACAG                         GTTTCTGTTCTTGCTGATGAAATCTTAAAGAATGTGGAGTATGATGCTTTG
genomic: TTGAGCTATGCATAACTGAATTGCAGAAAAATCCTCTGAATTATACACAGgtcaatttct ... tgtatttcagGTTTCTGTTCTTGCTGATGAAATCTTAAAGAATGTGGAGTATGATGCTTTG
EST: gi|161714443|gb|FC063863.1|FC063863
EST:     TTGAGCTATGCATAACTGAATTGCAGAAAAATCCTCTGAATTATACACAG                         GTTTCTGTTCTTGCTGATGAAATCTTAAAGAATGTGGAGTATGATGCTTTG
genomic: TTGAGCTATGCATAACTGAATTGCAGAAAAATCCTCTGAATTATACACAGgtcaatttct ... tgtatttcagGTTTCTGTTCTTGCTGATGAAATCTTAAAGAATGTGGAGTATGATGCTTTG
EST: gi|27581659|gb|CB004354.1|CB004354
EST:     TTGAGCTATGCATAACTGAATTGCAGAAAAATCCTCTGAATTATACACAG                         GTTTCTGTTCTTGCTGATGAAATCTTAAAGAATGTGGAGTATGATGCTTTG
genomic: TTGAGCTATGCATAACTGAATTGCAGAAAAATCCTCTGAATTATACACAGgtcaatttct ... tgtatttcagGTTTCTGTTCTTGCTGATGAAATCTTAAAGAATGTGGAGTATGATGCTTTG
EST: gi|71868993|gb|DT018048.1|DT018048
EST:     TTGAGCTATGCATAACTGAATTGCAGAAAAATCCTCTGAATTATACACAG                         GTTTCTGTTCTTGCTGATGAAATCTTAAAGAATGTGGAGTATGATGCTTTG
genomic: TTGAGCTATGCATAACTGAATTGCAGAAAAATCCTCTGAATTATACACAGgtcaatttct ... tgtatttcagGTTTCTGTTCTTGCTGATGAAATCTTAAAGAATGTGGAGTATGATGCTTTG
EST: gi|110407251|gb|EC972848.1|EC972848
EST:     TTGAGCTATGCATAACTGAATTGCAGAAAAATCCTCTGAATTATACACAG                         GTTTCTGTTCTTGCTGATGAAATCTTAAAGAATGTGGAGTATGATGCTTTG
genomic: TTGAGCTATGCATAACTGAATTGCAGAAAAATCCTCTGAATTATACACAGgtcaatttct ... tgtatttcagGTTTCTGTTCTTGCTGATGAAATCTTAAAGAATGTGGAGTATGATGCTTTG
EST: gi|30321885|gb|CD005147.1|CD005147
EST:     TTGAGCTATGCATAACTGAATTGCAGAAAAATCCTCTGAATTATACACAG                         GTTTCTGTTCTTGCTGATGAAATCTTAAAGAATGTGGAGTATGATGCTTTG
genomic: TTGAGCTATGCATAACTGAATTGCAGAAAAATCCTCTGAATTATACACAGgtcaatttct ... tgtatttcagGTTTCTGTTCTTGCTGATGAAATCTTAAAGAATGTGGAGTATGATGCTTTG
EST: gi|110425845|gb|EC992238.1|EC992238
EST:     TTGAGCTATGCATAACTGAATTGCAGAAAAATCCTCTGAATTATACACAG                         GTTTCTGTTCTTGCTGATGAAATCTTAAAGAATGTGGAGTATGATGCTTTG
genomic: TTGAGCTATGCATAACTGAATTGCAGAAAAATCCTCTGAATTATACACAGgtcaatttct ... tgtatttcagGTTTCTGTTCTTGCTGATGAAATCTTAAAGAATGTGGAGTATGATGCTTTG
EST: gi|30321961|gb|CD005223.1|CD005223
EST:     TTGAGCTATGCATAACTGAATTGCAGAAAAATCCTCTGAATTATACACAG                         GTTTCTGTTCTTGCTGATGAAATCTTAAAGAATGTGGAGTATGATGCTTTG
genomic: TTGAGCTATGCATAACTGAATTGCAGAAAAATCCTCTGAATTATACACAGgtcaatttct ... tgtatttcagGTTTCTGTTCTTGCTGATGAAATCTTAAAGAATGTGGAGTATGATGCTTTG
EST: gi|26264079|gb|CA815142.1|CA815142
EST:     TTGAGCTATGCATAACTGAATTGCAGAAAAATCCTCTGAATTATACACAG                         GTTTCTGTTCTTGCTGATGAAATCTTAAAGAATGTGGAGTATGATGCTTTG
genomic: TTGAGCTATGCATAACTGAATTGCAGAAAAATCCTCTGAATTATACACAGgtcaatttct ... tgtatttcagGTTTCTGTTCTTGCTGATGAAATCTTAAAGAATGTGGAGTATGATGCTTTG
EST: gi|30321594|gb|CD004856.1|CD004856
EST:     TTGAGCTATGCATAACTGAATTGCAGAAAAATCCTCTGAATTATACACAG                         GTTTCTGTTCTTGCTGA
genomic: TTGAGCTATGCATAACTGAATTGCAGAAAAATCCTCTGAATTATACACAGgtcaatttct ... tgtatttcagGTTTCTGTTCTTGCTGA
EST: gi|37189009|gb|CF608358.1|CF608358
EST:     AGAAAAATCCTCTGAATTATACACAG                         GTTTCTGTTCTTGCTGATGAAATCTTAAAGAATGTGGAGTATGATGCTTTG
genomic: AGAAAAATCCTCTGAATTATACACAGgtcaatttct ... tgtatttcagGTTTCTGTTCTTGCTGATGAAATCTTAAAGAATGTGGAGTATGATGCTTTG
EST: gi|110701285|gb|EE078691.1|EE078691
EST:     TTGAGCTATGCATAACTGAATTGCAGAAAAATCCTCTGAATTATACACAG                         GTTTCTGTTCTTGCTGATGAAATCTTAAAGAATGTGGAGTATGATGCTTTG
genomic: TTGAGCTATGCATAACTGAATTGCAGAAAAATCCTCTGAATTATACACAGgtcaatttct ... tgtatttcagGTTTCTGTTCTTGCTGATGAAATCTTAAAGAATGTGGAGTATGATGCTTTG
EST: gi|110730013|gb|EE106609.1|EE106609
EST:     TTGAGCTATGCATAACTGAATTGCAGAAAAATCCTCTGAATTATACACAG                         GTTTCTGTTCTTGCTGATGAAATCTTAAAGAATGTGGAGTATGATGCTTTG
genomic: TTGAGCTATGCATAACTGAATTGCAGAAAAATCCTCTGAATTATACACAGgtcaatttct ... tgtatttcagGTTTCTGTTCTTGCTGATGAAATCTTAAAGAATGTGGAGTATGATGCTTTG
EST: gi|110686575|gb|EE064367.1|EE064367
EST:     TTGAGCTATGCATAACTGAATTGCAGAAAAATCCTCTGAATTATACACAG                         GTTTCTGTTCTTGCTGATGAAATCTTAAAGAATGTGGAGTATGATGCTTTG
genomic: TTGAGCTATGCATAACTGAATTGCAGAAAAATCCTCTGAATTATACACAGgtcaatttct ... tgtatttcagGTTTCTGTTCTTGCTGATGAAATCTTAAAGAATGTGGAGTATGATGCTTTG
EST: gi|110366906|gb|EC930825.1|EC930825
EST:     TTGAGCTATGCATAACTGAATTGCAGAAAAATCCTCTGAATTATACACAG                         GTTTCTGTTCTTGCTGATGAAATCTTAAAGAATGTGGAGTATGATGCTTTG
genomic: TTGAGCTATGCATAACTGAATTGCAGAAAAATCCTCTGAATTATACACAGgtcaatttct ... tgtatttcagGTTTCTGTTCTTGCTGATGAAATCTTAAAGAATGTGGAGTATGATGCTTTG
EST: gi|32250032|gb|CD715851.1|CD715851
EST:     TTGAGCTATGCATAACTGAATTGCAGAAAAATCCTCTGAATTATACACAG                         GTTTCTGTTCTTGCTGATGAAATCTTAAAGAATGTGGAGTATGATGCTTTG
genomic: TTGAGCTATGCATAACTGAATTGCAGAAAAATCCTCTGAATTATACACAGgtcaatttct ... tgtatttcagGTTTCTGTTCTTGCTGATGAAATCTTAAAGAATGTGGAGTATGATGCTTTG
EST: gi|30129869|gb|CB915208.1|CB915208
EST:     TTGAGCTATGCATAACTGAATTGCAGAAAAATCCTCTGAATTATACACAG                         GCTTCTGTTCTTGCTGATGACATCTTANAGAATGTGGAGTATGATGCTTTG
genomic: TTGAGCTATGCATAACTGAATTGCAGAAAAATCCTCTGAATTATACACAGgtcaatttct ... tgtatttcagGTTTCTGTTCTTGCTGATGAAATCTTAAAGAATGTGGAGTATGATGCTTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttgttttttcttgttctttccctcatgcttcaatcaaattgttgtatttcagGTTTCTGTTCTTGCTGATGAAATCTTAAAGAATGTGGAGTATGATGCTTTGAGAATTGTTTTCAACAAGTTCCGTTCAATTATCTCATTTGTACCAACAA
                                      aaattgttgtattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttaaagtttatgcatctagccatctagagatatttctaattcgtctttttgttttttcttgttctttccctcatgcttcaatcaaattgttgtatttcagGTTTCTGTTCTTGCTGATGAAATCTTAAAGAATGTGGAGTATGATGCTTTGAGAATTGTTTTCAACAAGTTCCGTTCAATTATCTCATTTGTACCAACAA

- - - - - -gcatcta
- - - - - - - - - gccatct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatcaaa