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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgatattcaagcgcatggtgcttgcttaaaactcaattctggtggtgtagattgttttctgattattaggttatattcaattgtttttttccctaatcagGTACGACTGTGGCATGTTCATGATCAAATATGCTGATTTCTATAGCAGAGGCATAGAGCTCTGTTTCAACCAG

Basic information

species Vitis vinifera
transcript Vv05s0020g01220.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g01220.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA17G03010.1 (Glycine max), 3'ss of exon 7
-tgatattcaagcgcatggtgcttgcttaaaac---tcaattctggtggt-gtagattgttttctgattattaggttatattcaattgtttttttccctaatcagGTACGACTGTGGCATGTTCATGATCAAATATGCTGATTTCTATAGCAGAGGCATAGAGCTCTGTTTCAACCAG
 |   ||   |        | |||  ||   ||   | ||   |  | |  | || ||||   |  ||||||    || || |||||   | |||       |||||| || |||||  |||| ||||||||||||||||| ||||||||||||  | | | | | ||||||||||||
ataccatctcaattttcattcctttttttgtacctctgaacagtatttgcagcagtttgtgggcgaattatttt-ctaaatgcaatttgatattt----ggacagGTATGATTGTGGGGTGTTTATGATCAAATATGCTGACTTCTATAGCAGAAACTTGGGGTTGTGTTTCAACCAG

upper sequence: Vv05s0020g01220.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: PP1S210_63V6.1 (Physcomitrella patens), 3'ss of exon 9
------------------------------------tgatattcaagcgcatggtgcttgcttaaaactcaattctg---gtggtgtagat-tgttttctg-attattaggttatattcaattgtttttttccctaatc----agGTACGACTGTGGCATGTTCATGATCAAATATGCTGATTTCTATAGCAGAGGCATAGAGCTCTGTTTCAACCAG
                                    |  |||| |  |  |      |  | |  ||     ||  |    | || |  || |||  |||   | |||| | |   | |   ||  ||| |   |  ||    |||| ||||||||||||||||||| | ||||||||||||||  | ||| | ||      | |  | ||||  || 
gtacatgtgtatttccccatattaagagtagcaagtttttatttagaccaaaaaccttatcattgaatagtgtttcgtacatcgtctttatatgtcctctttgtcattaaggttgttgcggctgggtttgtttgttgtcttgcagGTGCGACTGTGGCATGTTCATGTTGAAATATGCTGATTTTCACAGCCGTGGGGCCTCGTTAAGCTTCACTCAA
















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|110381017|gb|EC946325.1|EC946325
EST:     AGTTCTTGGGAGCAAGAATACGTAGAAGACCTTCCTGAACAGAAGAATGG                         GTACGACTGTGGCATGTTCATGATCAAATATGCTGATTTCTATAGCAGAGG
genomic: AGTTCTTGGGAGCAAGAATACGTAGAAGACCTTCCTGAACAGAAGAATGGgtgtgtatat ... ccctaatcagGTACGACTGTGGCATGTTCATGATCAAATATGCTGATTTCTATAGCAGAGG
EST: gi|351032678|gb|FQ462392.1|FQ462392
EST:     AGTTCTTGGGAGCAAGAATACGTAGAAGACCTTCCTGAACAGAAGAATGG                         GTACGACTGTGGCATGTTCATGATCAAATATGCTGATTTCTATAGCAGAGG
genomic: AGTTCTTGGGAGCAAGAATACGTAGAAGACCTTCCTGAACAGAAGAATGGgtgtgtatat ... ccctaatcagGTACGACTGTGGCATGTTCATGATCAAATATGCTGATTTCTATAGCAGAGG
EST: gi|352768767|gb|FQ467979.1|FQ467979
EST:     AGTTCTTGGGAGCAAGAATACGTAGAAGACCTTCCTGAACAGAAGAATGG                         GTACGACTGTGGCATGTTCATGATCAAATATGCTGATTTCTATAGCAGAGG
genomic: AGTTCTTGGGAGCAAGAATACGTAGAAGACCTTCCTGAACAGAAGAATGGgtgtgtatat ... ccctaatcagGTACGACTGTGGCATGTTCATGATCAAATATGCTGATTTCTATAGCAGAGG
EST: gi|352777420|gb|FQ474054.1|FQ474054
EST:     AGTTCTTGGGAGCAAGAATACGTAGAAGACCTTCCTGAACAGAAGAATGG                         GTACGACTGTGGCATGTTCATGATCAAATATGCTGATTTCTATAGCAGAGG
genomic: AGTTCTTGGGAGCAAGAATACGTAGAAGACCTTCCTGAACAGAAGAATGGgtgtgtatat ... ccctaatcagGTACGACTGTGGCATGTTCATGATCAAATATGCTGATTTCTATAGCAGAGG
EST: gi|352777702|gb|FQ466755.1|FQ466755
EST:     AGTTCTTGGGAGCAAGAATACGTAGAAGACCTTCCTGAACAGAAGAATGG                         GTACGACTGTGGCATGTTCATGATCAAATATGCTGATTTCTATAGCAGAGG
genomic: AGTTCTTGGGAGCAAGAATACGTAGAAGACCTTCCTGAACAGAAGAATGGgtgtgtatat ... ccctaatcagGTACGACTGTGGCATGTTCATGATCAAATATGCTGATTTCTATAGCAGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtagattgttttctgattattaggttatattcaattgtttttttccctaatcagGTACGACTGTGGCATGTTCATGATCAAATATGCTGATTTCTATAGCAGAGGCATAGAGCTCTGTTTCAACCAG
           ttctgat  putative branch site (score: 3)
                                   ttgtttttttccct  putative PPT
                attattaggttatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgatattcaagcgcatggtgcttgcttaaaactcaattctggtggtgtagattgttttctgattattaggttatattcaattgtttttttccctaatcagGTACGACTGTGGCATGTTCATGATCAAATATGCTGATTTCTATAGCAGAGGCATAGAGCTCTGTTTCAACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - -caagcgc
- - - - - - - - - -gcttgct
- - - - - - - - - - - - - -aaaactc
- - - - - - - - - - - - - - - - - - - - ggtggtg