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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttccctttataattttggaatgacgtaatctataagttttttgttttagaatagatcctatattctttgtataataatgacttcttatgtgtgacacagAGAGATCAGAGCAACTAGACTGGGATGCACGCTTGAATATTATCATGGGAGCTGCAAAAGGACTAGCCTACCTGCATCATGATTGTTCCCCTCGGATTAT

Basic information

species Vitis vinifera
transcript Vv02s0087g00170.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0087g00170.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA01G35390.1 (Glycine max), 3'ss of exon 10
-----tttccctttataattttggaatgacgtaatctataagttttttgttttagaatagatcctatattctttgtataataatgacttcttatgtgtgacacagAGAGATCAGAGCAACTAGACTGGGATGCACGCTTGAATATTATCATGGGAGCTGCAAAAGGACTAGCCTACCTGCATCATGATTGTTCCCCTCGGATTAT
       |   |||    |||   | | || |  || ||  || |  ||| || |  || |||  |  ||    | ||||| |||  || | |||  |   ||||| ||| | |||||||||||||||||| ||||||||||||| |||||||||||||||||||| || |||||| |||| ||||||||||||||  |||| ||
cagaagatgtattttccttttaaaatttacatcttcaat--gtatcgtgtctttgcttaaatc--aatttggggggataatgatg-tttgtgatgcattgaacagAAAGAGCTGAGCAACTAGACTGGGATTCACGCTTGAATATAATCATGGGAGCTGCAAAAGGGCTTGCCTACTTGCACCATGATTGTTCCCCCAGGATCAT

upper sequence: Vv02s0087g00170.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA09G34940.2 (Glycine max), 3'ss of exon 11
-----tttccctttataattttggaatgacgtaatctataagttttttgttttagaatagatcctatattctttgtataataatgacttcttatgtgtgacacagAGAGATCAGAGCAACTAGACTGGGATGCACGCTTGAATATTATCATGGGAGCTGCAAAAGGACTAGCCTACCTGCATCATGATTGTTCCCCTCGGATTAT
       |   |||    |||   | | || |  ||  |  || |  | | || |  || |||  |  ||    | ||||| |||  || | |||  |   ||||| ||| | || ||||||||||||||| | ||||||||||| |||||||||||||||||||| || |||||| |||| ||||||||||||||  |||| ||
cagaagatgtgttttccttttgaaatttacatcttcagt--gtatcgtatctttgcttaaatc--aatttggggggataatgatg-tttgtgatgcattgaacagAAAGAGCTGATCAACTAGACTGGGATTCGCGCTTGAATATAATCATGGGAGCTGCAAAAGGGCTTGCCTACTTGCACCATGATTGTTCCCCCAGGATCAT

upper sequence: Vv02s0087g00170.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT1G31420.2 (Arabidopsis thaliana), 3'ss of exon 11
tttccctttataattttggaatgacgtaatctata-agttttttgttttagaatagatcctatattctttgtataataatgacttcttatgtgtgacacagAGAGATCAGAGCAACTAGACTGGGATGCACGCTTGAATATTATCATGGGAGCTGCAAAAGGACTAGCCTACCTGCATCATGATTGTTCCCCTCGGATTAT
               |  ||   |  |  ||| ||  | | | |    ||  ||  ||     ||||  ||   | |  |   |||||   | |   | ||||||    |||||| | ||||||||| ||||| | ||||| ||||| |||||||| |||||  || | ||  |||||||||||||||| |||||||||||
--------------gtatgatcaatctgctctttatggctctcttccatattatgaatg----attcactgagaagt--ttggttcttgaat-tagtagAGAGAGGC--GAGCAATTGGACTGGGATTCACGCGTAAATATCATCATAGGAGCTGCGAAAGGGTTATCATATTTGCATCATGATTGTTCTCCTCGGATTAT

upper sequence: Vv02s0087g00170.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT1G31420.1 (Arabidopsis thaliana), 3'ss of exon 11
tttccctttataattttggaatgacgtaatctata-agttttttgttttagaatagatcctatattctttgtataataatgacttcttatgtgtgacacagAGAGATCAGAGCAACTAGACTGGGATGCACGCTTGAATATTATCATGGGAGCTGCAAAAGGACTAGCCTACCTGCATCATGATTGTTCCCCTCGGATTAT
               |  ||   |  |  ||| ||  | | | |    ||  ||  ||     ||||  ||   | |  |   |||||   | |   | ||||||    |||||| | ||||||||| ||||| | ||||| ||||| |||||||| |||||  || | ||  |||||||||||||||| ||||||||   
--------------gtatgatcaatctgctctttatggctctcttccatattatgaatg----attcactgagaagt--ttggttcttgaat-tagTAGAGAGAGGC--GAGCAATTGGACTGGGATTCACGCGTAAATATCATCATAGGAGCTGCGAAAGGGTTATCATATTTGCATCATGATTGTTCTCCTCGGAT---

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|110696915|gb|EE073446.1|EE073446
EST:     GTTAATTTATGATTACTTACCTGGCGGTAGCCTGGATGAAGCTCTTCATG                         AGAGATCAGAGCAACTAGACTGGGATGCACGCTTGAATATTATCATGGGAG
genomic: GTTAATTTATGATTACTTACCTGGCGGTAGCCTGGATGAGGCTCTTCATGgtgagatccc ... tgtgacacagAGAGATCAGAGCAACTAGACTGGGATGCACGCTTGAATATTATCATGGGAG
EST: gi|110703464|gb|EE080335.1|EE080335
EST:     GTTAATTTATGATTACTTACCTGGCGGTAGCCTGGATGAGGCTCTTCATG                         AGAGATCAGAGCAACTAGACTGGGATGCACGCTTGAATATTATCATGGGAG
genomic: GTTAATTTATGATTACTTACCTGGCGGTAGCCTGGATGAGGCTCTTCATGgtgagatccc ... tgtgacacagAGAGATCAGAGCAACTAGACTGGGATGCACGCTTGAATATTATCATGGGAG
EST: gi|30303383|gb|CB980177.1|CB980177
EST:     GTTAATTTATGATTACTTACCTGGCGGTAGCCTGGATGAGGCTCTTCATG                         AGAGATCAGAGCAACTAGACTGGGATGCACGCTTGAATATTATCATGGGAG
genomic: GTTAATTTATGATTACTTACCTGGCGGTAGCCTGGATGAGGCTCTTCATGgtgagatccc ... tgtgacacagAGAGATCAGAGCAACTAGACTGGGATGCACGCTTGAATATTATCATGGGAG
EST: gi|30303577|gb|CB980371.1|CB980371
EST:     GTTAATTTATGATTACTTACCTGGCGGTAGCCTGGATGAGGCTCTTCATG                         AGAGATCAGAGCAACTAGACTGGGATGCACGCTTGAATATTATCATGGGAG
genomic: GTTAATTTATGATTACTTACCTGGCGGTAGCCTGGATGAGGCTCTTCATGgtgagatccc ... tgtgacacagAGAGATCAGAGCAACTAGACTGGGATGCACGCTTGAATATTATCATGGGAG
EST: gi|110687636|gb|EE065268.1|EE065268
EST:     GTTAATTTATGATTACTTACCTGGCGGTAGCCTGGATGAGGCTCTTCATG                         AGAGATCAGAGCAACTAGACTGGGATGCACGCTTGAATATTATCATGGGAG
genomic: GTTAATTTATGATTACTTACCTGGCGGTAGCCTGGATGAGGCTCTTCATGgtgagatccc ... tgtgacacagAGAGATCAGAGCAACTAGACTGGGATGCACGCTTGAATATTATCATGGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttagaatagatcctatattctttgtataataatgacttcttatgtgtgacacagAGAGATCAGAGCAACTAGACTGGGATGCACGCTTGAATATTATCATGGGAGCTGCAAAAGGACTAGCCTACCTGCATCATGATTGTTCCCCTCGGATTAT
              tatattctttgtataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttccctttataattttggaatgacgtaatctataagttttttgttttagaatagatcctatattctttgtataataatgacttcttatgtgtgacacagAGAGATCAGAGCAACTAGACTGGGATGCACGCTTGAATATTATCATGGGAGCTGCAAAAGGACTAGCCTACCTGCATCATGATTGTTCCCCTCGGATTAT

- -cccttta
- - - - - - - - -ggaatga
- - - - - - - - - - - - - - - - - - - - - - - - -gaataga