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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attcttctagtcatttggtgaaaaatatgggattgcaattgttttaaaacttttaaataaagatgccttaaccattttattttcctggttttttctacagGTTCATATGTGACTCATGAAACAAACCATTTTGTTTACTTCTATTTGGACCAAAAGGCAGTCTTGCTGTTCAAATCTGGTTGAGAGTGGTGATGATGTTG

Basic information

species Vitis vinifera
transcript Vv05s0077g02110.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0077g02110.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA15G16050.1 (Glycine max), 3'ss of exon 2
--attcttctag--tcatttggtgaaaaatatgggattgcaattgttttaaaacttttaa--ataaagatgccttaaccattttattttcctggttttttctacagGTTCATATGTGACTCATGAAACAAACCATTTTGTTTACTTCTATTTGGACCAAAAGGCAGTCTTGCTGTTCAAATCTGGTTGAGAGTGGTGATGATGTTG
   || |||| |  |    |  | | |    || | |     ||      | || ||| |  || ||  ||| || |    ||| | |||||      || | |||| |||||||||||||||||||||||||| |||||||| ||||||||||| || || ||||| || || || |||||||| |      | |||  |   ||
tgcttgttcttgactagcctacttatattcttgcggtaatgtttagaacgacacattttattattaaagtgcatttatggatttgtcttcct------ttttgcagGCTCATATGTGACTCATGAAACAAACCACTTTGTTTATTTCTATTTGGATCAGAAAGCAGTTTTACTCTTTAAATCTGGCTAGAGAAGTTGACAACCATG

upper sequence: Vv05s0077g02110.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA15G16060.2 (Glycine max), 3'ss of exon 2
----------------attcttctagtcatttgg-----tgaaaaatatgg-gattgcaattgtt-ttaaaactt---ttaaataaagatgcc-ttaac---cattt-tattttcctggttttttctacagGTTCATATGTGACTCATGAAACAAACCATTTTGTTTACTTCTATTTGGACCAAAAGGCAGTCTTGCTGTTCAAATCTGGTTGAGAGTGGTGATGATGTTG
                 || |||  | ||||  |     | ||  | |||  |||  || || || ||    |||   |||  || || |  | || |    ||||  | |  | ||  |  ||| | ||||||||||||||||||||||||||||||| |||||||| ||||| ||||| || || || || || || |                               
agacgatttattctttttttttcctgacattcagacaattaaaccaaatgaagataacatttcttgttcttgcttagcttacttatagttatcattgaagTGCATTCATGTACTTCTCTTGCTTTTTGCAGGTTCATATGTGACTCATGAAACAAACCACTTTGTTTATTTCTACTTGGATCAGAAAGCGGTTTTACTCT-------------------------------

upper sequence: Vv05s0077g02110.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA15G16060.1 (Glycine max), 3'ss of exon 2
attcttctagtcatttggtgaaa--aatatgggattgca-attgttttaaaacttttaaataaagatgccttaac--cattt-tattttcctggttttttctacagGTTCATATGTGACTCATGAAACAAACCATTTTGTTTACTTCTATTTGGACCAAAAGGCAGTCTTGCTGTTCAAATCTGGTTGAGAGTGGTGATGATGTTG-
      |     |||     |||  || ||   ||| |   || ||    | |||    |||   ||   | ||   ||||  | |  | ||  |  ||| | ||||||||||||||||||||||||||||||| |||||||| ||||| ||||| || || || || || || || |||||||| | ||  |  |  || |     
------cagacaattaaaccaaatgaagataacatttcttgttcttgcttagcttacttatagttatcattgaagtgcattcatgtacttctcttgctttttgcagGTTCATATGTGACTCATGAAACAAACCACTTTGTTTATTTCTACTTGGATCAGAAAGCGGTTTTACTCTTTAAATCTGGCT-AGCCTTATTGTGGTAGCAA

upper sequence: Vv05s0077g02110.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA09G04830.1 (Glycine max), 3'ss of exon 2
---attcttctagtcatttggtgaaaaatatgggattgcaattgttttaaaacttttaaataaagatgccttaaccattttattttcctggttttttctacagGTTCATATGTGACTCATGAAACAAACCATTTTGTTTACTTCTATTTGGACCAAAAGGCAGTCTTGCTGTTCAAATCTGGTTGAGAGTGGTGATGATGTTG
   |   | || ||   ||| | |   ||||  |  |  |||       |  | ||||| ||  || |     |  | |  ||||  |   |  ||| | |||| |||||||||||||||||||||||||| |||||||| ||||||||||| || || || || || || || |||||||| |      | |||  |   ||
acaaaattgcttgtt-cttgcttagttatattcgtgtcaaataagaacgactcatttaattattgaagtgc--attaatggatttctcgcttcctttttgcagGCTCATATGTGACTCATGAAACAAACCACTTTGTTTATTTCTATTTGGATCAGAAAGCTGTTTTACTCTTTAAATCTGGCTAGAGAAGTTGACAACAATG

upper sequence: Vv05s0077g02110.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT4G15930.1 (Arabidopsis thaliana), 3'ss of exon 2
attcttctagt-catttggtgaaaaatatgggattgca--attgtttt---aaaacttttaaat--aaagatgccttaaccattttattttcctggttttttctacagGTTCATATGTGACTCATGAAACAAACCATTTTGTTTACTTCTATTTGGACCAAAAGGCAGTCTTGCTGTTCAAATCTGGTTGAGAGTGGTGATGATGTTG-
       |  | ||| |    ||  |||  || ||  |  |||  | |    || |||| | ||   ||  |   | |||||| ||| | |       |||  | ||||||| ||||| || ||||| ||||||||||| |||||||||||  | ||||| || || ||  |||| ||||| || |||| ||| |  |||  |    | 
-cagaagtgatacatctctgaaaccatactggcttctattattcatctgcagaatctttcacattcgaaacttattcaaccatattactct-------tttcttgcagGTTCTTATGTAACGCATGAGACAAACCATTTCGTTTACTTCTACCTCGACCAGAAAGCTGTGCTGCTCTTCAAGTCGGGTTAAGAATT-TGAAAACCAAGA

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|110415832|gb|EC981770.1|EC981770
EST:     CGATAAGAAGCATGGACCTACCTGGCATTGCATTGTCGGTCGCAATTTCG                         GTTCATATGTGACTCATGAAACAAACCATTTTGTTTACTTCTATTTGGACC
genomic: CGATAAGAAGCATGGACCTACCTGGCATTGCATTGTCGGTCGCAATTTCGgtaattcccg ... ttttctacagGTTCATATGTGACTCATGAAACAAACCATTTTGTTTACTTCTATTTGGACC
EST: gi|349822936|gb|FQ399915.1|FQ399915
EST:     CGATAAGAAGCATGGACCTACCTGGCATTGCATTGTCGGTCGCAATTTCG                         GTTCATATGTGACTCATGAAACAAACCATTTTGTTTACTTCTATTTGGACC
genomic: CGATAAGAAGCATGGACCTACCTGGCATTGCATTGTCGGTCGCAATTTCGgtaattcccg ... ttttctacagGTTCATATGTGACTCATGAAACAAACCATTTTGTTTACTTCTATTTGGACC
EST: gi|110705677|gb|EE082803.1|EE082803
EST:     CGATAAGAAGCATGGACCTACCTGGCATTGCATTGTCGGTCGCAATTTCG                         GTTCATATGTGACTCATGAAACAAACCATTTTGTTTACTTCTATTTGGACC
genomic: CGATAAGAAGCATGGACCTACCTGGCATTGCATTGTCGGTCGCAATTTCGgtaattcccg ... ttttctacagGTTCATATGTGACTCATGAAACAAACCATTTTGTTTACTTCTATTTGGACC
EST: gi|110365922|gb|EC929475.1|EC929475
EST:     CGATAAGAAGCATGGACCTACCTGGCATTGCATTGTCGGTCGCAATTTCG                         GTTCATATGTGACTCATGAAACAAACCATTTTGTTTACTTCTATTTGGACC
genomic: CGATAAGAAGCATGGACCTACCTGGCATTGCATTGTCGGTCGCAATTTCGgtaattcccg ... ttttctacagGTTCATATGTGACTCATGAAACAAACCATTTTGTTTACTTCTATTTGGACC
EST: gi|30136271|gb|CB921609.1|CB921609
EST:     CGATAAGAAGCATGGACCTACCTGGCATTGCATTGTCGGTCGCAATTTCG                         GTTCATATGTGACTCATGAAACAAACCATTTTGTTTACTTCTATTTGGACC
genomic: CGATAAGAAGCATGGACCTACCTGGCATTGCATTGTCGGTCGCAATTTCGgtaattcccg ... ttttctacagGTTCATATGTGACTCATGAAACAAACCATTTTGTTTACTTCTATTTGGACC
EST: gi|110428464|gb|EC994938.1|EC994938
EST:     CGATAAGAAGCATGGACCTACCTGGCATTGCATTGTCGGTCGCAATTTCG                         GTTCATATGTGACTCATGAAACAAACCATTTTGTTTACTTCTATTTGGACC
genomic: CGATAAGAAGCATGGACCTACCTGGCATTGCATTGTCGGTCGCAATTTCGgtaattcccg ... ttttctacagGTTCATATGTGACTCATGAAACAAACCATTTTGTTTACTTCTATTTGGACC
EST: gi|34544540|gb|CF512772.1|CF512772
EST:     CGACAAGAAGCATGGACCTACCTGGCATTGCATTGTCGGTCGCAATTTCG                         GTTCATATGTGACTCATGAAACAAACCATTTTGTTTACTTCTATTTGGACC
genomic: CGATAAGAAGCATGGACCTACCTGGCATTGCATTGTCGGTCGCAATTTCGgtaattcccg ... ttttctacagGTTCATATGTGACTCATGAAACAAACCATTTTGTTTACTTCTATTTGGACC
EST: gi|34543853|gb|CF512085.1|CF512085
EST:     CGACAAGAAGCATGGACCTACCTGGCATTGCATTGTCGGTCGCAATTTCG                         GTTCATATGTGACTCATGAAACAAACCATTTTGTTTACTTCTATTTGGACC
genomic: CGATAAGAAGCATGGACCTACCTGGCATTGCATTGTCGGTCGCAATTTCGgtaattcccg ... ttttctacagGTTCATATGTGACTCATGAAACAAACCATTTTGTTTACTTCTATTTGGACC
EST: gi|30127749|gb|CB913088.1|CB913088
EST:     CGATAAGAAGCATGGACCTACCTGGCATTGCATTGTCGGTCGCAATTTCG                         GTTCATATGTGACTCATGAAACAAACCATTTTGTTTACTTCTATTTGGACC
genomic: CGATAAGAAGCATGGACCTACCTGGCATTGCATTGTCGGTCGCAATTTCGgtaattcccg ... ttttctacagGTTCATATGTGACTCATGAAACAAACCATTTTGTTTACTTCTATTTGGACC
EST: gi|32456411|gb|CD797585.1|CD797585
EST:     ATAAGAAGCATGGACCTACCTGGCACATTGCATTGTCGGTCGCAATTTCG                         GTTCATATGTGACTCATGAAACAAACCATTTTGTTTACTTCTATTTGGACC
genomic: ATAAGAAGCATGGACCTACCTGG--CATTGCATTGTCGGTCGCAATTTCGgtaattcccg ... ttttctacagGTTCATATGTGACTCATGAAACAAACCATTTTGTTTACTTCTATTTGGACC
EST: gi|110702866|gb|EE079212.1|EE079212
EST:     CGATAAGAAGCATGGACCTACCTGGCATTGCATTGTCGGTCGCAATTTCG                         GTTCATATGTGACTCATGAAACAAACCATTTTGTTTACTTCTATTTGGACC
genomic: CGATAAGAAGCATGGACCTACCTGGCATTGCATTGTCGGTCGCAATTTCGgtaattcccg ... ttttctacagGTTCATATGTGACTCATGAAACAAACCATTTTGTTTACTTCTATTTGGACC
EST: gi|34362768|gb|CF404353.1|CF404353
EST:     CGATAAGAAGCATGGACCTACCTGGCATTGCATTGTCGGTCGCAATTTCG                         GTTCATATGTGACTCATGAAACAAACCATTTTGTTTACTTCTATTTGGACC
genomic: CGATAAGAAGCATGGACCTACCTGGCATTGCATTGTCGGTCGCAATTTCGgtaattcccg ... ttttctacagGTTCATATGTGACTCATGAAACAAACCATTTTGTTTACTTCTATTTGGACC
EST: gi|110376712|gb|EC941782.1|EC941782
EST:     CGATAAGAAGCATGGACCTACCTGGCATTGCATTGTCGGTCGCAATTTCG                         GTTCATATGTGACTCATGAAACAAACCATTTTGTTTACTTCTATTTGGACC
genomic: CGATAAGAAGCATGGACCTACCTGGCATTGCATTGTCGGTCGCAATTTCGgtaattcccg ... ttttctacagGTTCATATGTGACTCATGAAACAAACCATTTTGTTTACTTCTATTTGGACC
EST: gi|30131911|gb|CB917250.1|CB917250
EST:     CGATAAGAAGCATGGACCTACCTGGCATTGCATTGTCGGTCGCAATTTCG                         GTTCATATGTGACTCATGAAACAAACCATTTTGTTTACTTCTATTTGGACC
genomic: CGATAAGAAGCATGGACCTACCTGGCATTGCATTGTCGGTCGCAATTTCGgtaattcccg ... ttttctacagGTTCATATGTGACTCATGAAACAAACCATTTTGTTTACTTCTATTTGGACC
EST: gi|34416663|gb|CF415417.1|CF415417
EST:     CGATAAGAAGCATGGACCTACCTGGCATTGCATTGTCGGTCGCAATTTCG                         GTTCATATGTGACTCATGAAACAAACCATTTTGTTTACTTCTATTTGGACC
genomic: CGATAAGAAGCATGGACCTACCTGGCATTGCATTGTCGGTCGCAATTTCGgtaattcccg ... ttttctacagGTTCATATGTGACTCATGAAACAAACCATTTTGTTTACTTCTATTTGGACC
EST: gi|110384168|gb|EC948587.1|EC948587
EST:     CGATAAGAAGCATGGACCTACCTGGCATTGCATTGTCGGTCGCAATTTCG                         GTTCATATGTGACTCATGAAACAAACCATTTTGTTTACTTCTATTTGGACC
genomic: CGATAAGAAGCATGGACCTACCTGGCATTGCATTGTCGGTCGCAATTTCGgtaattcccg ... ttttctacagGTTCATATGTGACTCATGAAACAAACCATTTTGTTTACTTCTATTTGGACC
EST: gi|110691067|gb|EE068745.1|EE068745
EST:     CGATAAGAAGCATGGACCTACCTGGCATTGCATTGTCGGTCGCAATTTCG                         GTTCATATGTGACTCATGAAACAAACCATTTTGTTTACTTCTATTTGGACC
genomic: CGATAAGAAGCATGGACCTACCTGGCATTGCATTGTCGGTCGCAATTTCGgtaattcccg ... ttttctacagGTTCATATGTGACTCATGAAACAAACCATTTTGTTTACTTCTATTTGGACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaacttttaaataaagatgccttaaccattttattttcctggttttttctacagGTTCATATGTGACTCATGAAACAAACCATTTTGTTTACTTCTATTTGGACCAAAAGGCAGTCTTGCTGTTCAAATCTGGTTGAGAGTGGTGATGATGTTG
                    ccttaac  putative branch site (score: 3)
                             ttttattttcctggtt  putative PPT
                      ttaaccattttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attcttctagtcatttggtgaaaaatatgggattgcaattgttttaaaacttttaaataaagatgccttaaccattttattttcctggttttttctacagGTTCATATGTGACTCATGAAACAAACCATTTTGTTTACTTCTATTTGGACCAAAAGGCAGTCTTGCTGTTCAAATCTGGTTGAGAGTGGTGATGATGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- -cttctag
- - - - - - - - - - aaaaata
- - - - - - - - - - - - - - - - - - - - - - -aaaactt
- - - - - - - - - - - - - - - - - - - - - - - - - - - aaataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatgcct