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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagctgctaattaggctgccccttgttataaatataatgcattgctttgcgcttttttttttttttttttccttttaatttgatttttcctgtgtggtagGGGATGCATTCGTTGGAGGTTTTTTGTCTCAGTTGGTTCAAGAGAAGCCTATTGAAGAATGTGTGAGAGCTGGTTGCTATGCTTCACATGTTATAATCCA

Basic information

species Vitis vinifera
transcript Vv13s0019g04480.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g04480.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA19G36630.1 (Glycine max), 3'ss of exon 11
-aagctgctaattaggctgccccttgtt-ataaatataatgcattgctttgcgcttttttttttttttttttccttttaatttgatttttcctgtgtggtagGGGATGCATTCGTTGGAGGTTTTTTGTCTCAGTTGGTTCAAGAGAAGCCTATTGAAGAATGTGTGAGAGCTGGTTGCTATGCTTCACATGTTATAATCCA
   |   | |   ||| |  |     |  |      || ||    ||     |||  |  |||| |||  |   |  |   ||  | |||  ||| || |||| |||||||| |||||||| ||| | ||||| |||||||| |||||||| ||||||||||||||||||||||| || |||||  || ||||||| |||||
tggggcac-agccaggatttcataaatagacggtggtagtgacaagcaagatgctgctgattttgtttcatgtttcatcccttattgttttgtgtttg-tagGAGATGCATTTGTTGGAGGATTTCTTTCTCAATTGGTTCAGGAGAAGCCCATTGAAGAATGTGTGAGAGCTGGCTGTTATGCAGCAAATGTTATCATCCA

upper sequence: Vv13s0019g04480.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA03G33910.2 (Glycine max), 3'ss of exon 10
aagctgctaattaggctgccccttgtta-taaatataatgcattgctttgcgcttttttttttttttttttccttttaatttgatttttcctgtgtg-gtagGGGATGCATTCGTTGGAGGTTTTTTGTCTCAGTTGGTTCAAGAGAAGCCTATTGAAGAATGTGTGAGAGCTGGTTGCTATGCTTCACATGTTATAATCCA
   |||      || | |    | || | || | ||   | | ||    ||    |     |||| |||     || | |     || |  | |||  ||||| |||||||| || ||||| ||| | ||||| |||||||| |||||||| |||||||| || ||||||||||| || |||||  || | ||||| |||||
-tactgaggcacagccaggatttcgtaaatagacattg-gtagtgacaagcaagatgccaattttgtttcatgattcattccttattgttttatgtttgtagGAGATGCATTTGTCGGAGGATTTCTTTCTCAATTGGTTCAGGAGAAGCCCATTGAAGAGTGCGTGAGAGCTGGCTGTTATGCAGCAAACGTTATCATCCA

upper sequence: Vv13s0019g04480.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA10G06580.1 (Glycine max), 3'ss of exon 11
--------------------------------------------------------------------aagctgctaattaggctgccccttgttataaatataatgcattgctttgcgcttttttttttttttttttccttttaatttgatttttcctgtgtggtagGGGATGCATTCGTTGGAGGTTTTTTGTCTCAGTTGGTTCAAGAGAAGCCTATTGAAGAATGTGTGAGAGCTGGTTGCTATGCTTCACATGTTATAATCCA
                                                                    | | |  | |  ||   |   |   || |   | |  |  ||   | ||     ||      ||  | ||   | || ||  ||| ||    | | | ||| ||||| || || ||||| ||| | || || |||||| |  ||||||| ||||||||||||||||||||||| || |||||  |  ||||||| |||||
gtataaacctattgtttttaatatttaaatatgtacagttaagtttatggccaatttattacattttgatgatagtgacaagctcgattccaattttgtctcttttaaatgtgtgtggaaacttaaaaaattaatgtta--tatacttatattcttttgtttttgcagGAGATGCTTTTGTGGGAGGATTTCTTTCGCAATTGGTTAAGCAGAAGCCCATTGAAGAATGTGTGAGAGCTGGGTGTTATGCAGCCAATGTTATCATCCA

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|110405809|gb|EC971362.1|EC971362
EST:     CCCTGTGATCTTGCTGCCCAAGGAGAAGCTGGTTGATACCAATGGAGCAG                         GGGATGCATTCGTTGGAGGTTTTTTGTCTCAGTTGGTTCAAGAGAAGCCTA
genomic: CCCTGTGATCTTGCTGCCCAAGGAGAAGCTGGTTGATACCAATGGAGCAGgtatgaactc ... tgtgtggtagGGGATGCATTCGTTGGAGGTTTTTTGTCTCAGTTGGTTCAAGAGAAGCCTA
EST: gi|266635514|gb|GT568891.1|GT568891
EST:     CCCTGTGATCTTGCTGCCCAAGGAGAAGCTGGTTGATACCAATGGAGCAG                         GGGATGCATTCGTTGGAGGTTTTTTGTCTCAGTTGGTTCAAGAGAAGCCTA
genomic: CCCTGTGATCTTGCTGCCCAAGGAGAAGCTGGTTGATACCAATGGAGCAGgtatgaactc ... tgtgtggtagGGGATGCATTCGTTGGAGGTTTTTTGTCTCAGTTGGTTCAAGAGAAGCCTA
EST: gi|110418987|gb|EC985176.1|EC985176
EST:     CCCTGTGATCTTGCTGCCCAAGGAGAAGCTGGTTGATACCAATGGAGCAG                         GGGATGCATTCGTTGGAGGTTTTTTGTCTCAGTTGGTTCAAGAGAAGCCTA
genomic: CCCTGTGATCTTGCTGCCCAAGGAGAAGCTGGTTGATACCAATGGAGCAGgtatgaactc ... tgtgtggtagGGGATGCATTCGTTGGAGGTTTTTTGTCTCAGTTGGTTCAAGAGAAGCCTA
EST: gi|352786944|gb|FQ475977.1|FQ475977
EST:     CCCTGTGATCTTGCTGCCCAAGGAGAAGCTGGTTGATACCAATGGAGCAG                         GGGATGCATTCGTTGGAGGTTTTTTGTCTCAGTTGGTTCAAGAGAAGCCTA
genomic: CCCTGTGATCTTGCTGCCCAAGGAGAAGCTGGTTGATACCAATGGAGCAGgtatgaactc ... tgtgtggtagGGGATGCATTCGTTGGAGGTTTTTTGTCTCAGTTGGTTCAAGAGAAGCCTA
EST: gi|32457185|gb|CD798359.1|CD798359
EST:     CCCTGTGATCTTGCTGCCCAAGGAGAAGCTGGTTGATACCAATGGAGCAG                         GGGATGCATTCGTTGGAGGTTTTTTGTCTCAGTTGGTTCAAGAGAAGCCTA
genomic: CCCTGTGATCTTGCTGCCCAAGGAGAAGCTGGTTGATACCAATGGAGCAGgtatgaactc ... tgtgtggtagGGGATGCATTCGTTGGAGGTTTTTTGTCTCAGTTGGTTCAAGAGAAGCCTA
EST: gi|18459290|gb|BM437568.1|BM437568
EST:     CCCTGTGATCTTGCTGCCCAAGGAGAATCTGGTTGATACCAATGGAGCAA                         GGGATGCATTCGTTGGAGGTTTTTTGTCTCAGTTGGTTCAAGAGAAGCCTA
genomic: CCCTGTGATCTTGCTGCCCAAGGAGAAGCTGGTTGATACCAATGGAGCAGgtatgaactc ... tgtgtggtagGGGATGCATTCGTTGGAGGTTTTTTGTCTCAGTTGGTTCAAGAGAAGCCTA
EST: gi|110399344|gb|EC965847.1|EC965847
EST:     CCCTGTGATCTTGCTGCCCAAGGAGAAGCTGGTTGATACCAATGGAGCAG                         GCGATGCATTCGTTGGAGGTTTTTTGTCTCAGTTGGTTCAAGAGAAGCCAA
genomic: CCCTGTGATCTTGCTGCCCAAGGAGAAGCTGGTTGATACCAATGGAGCAGgtatgaactc ... tgtgtggtagGGGATGCATTCGTTGGAGGTTTTTTGTCTCAGTTGGTTCAAGAGAAGCCTA
EST: gi|30302319|gb|CB979113.1|CB979113
EST:     CCCTGTGATCTTGCTGCCCAAGGAGAAGCTGGTTGATACCAATGGAGCAG                         GGGATGCATTCGTTGGAGGTTTTTTGTCTCAGTTGGTTCAAGAGAAGCCTA
genomic: CCCTGTGATCTTGCTGCCCAAGGAGAAGCTGGTTGATACCAATGGAGCAGgtatgaactc ... tgtgtggtagGGGATGCATTCGTTGGAGGTTTTTTGTCTCAGTTGGTTCAAGAGAAGCCTA
EST: gi|352790621|gb|FQ475379.1|FQ475379
EST:     CCCTGTGATCTTGCTGCCCAAGGAGAAGCTGGTTGATACCAATGGAGCAG                         GGGATGCATTCGTTGGAGGTTTTTTGTCTCAGTTGGTTCAAGAGAAGCCTA
genomic: CCCTGTGATCTTGCTGCCCAAGGAGAAGCTGGTTGATACCAATGGAGCAGgtatgaactc ... tgtgtggtagGGGATGCATTCGTTGGAGGTTTTTTGTCTCAGTTGGTTCAAGAGAAGCCTA
EST: gi|83275808|gb|DV939816.1|DV939816
EST:     CCCTGTGATCTCGCTGCCCAAGGAGAAGCTGGTTGATACCAATGGAGCAG                         GGGATGCATTCGTTGGAGGTTTTTTGTCTCAGTTGGTTCAAGAGAAGCCTA
genomic: CCCTGTGATCTTGCTGCCCAAGGAGAAGCTGGTTGATACCAATGGAGCAGgtatgaactc ... tgtgtggtagGGGATGCATTCGTTGGAGGTTTTTTGTCTCAGTTGGTTCAAGAGAAGCCTA
EST: gi|110698283|gb|EE075646.1|EE075646
EST:     CCCTGTGATCTTGCTGCCCAAGGAGAAGCTGGTTGATACCNATGGAGCAG                         GCGATGCATTCCGTTGGAGGGTTTTTGTCTCAGNTGGNTCAAGA
genomic: CCCTGTGATCTTGCTGCCCAAGGAGAAGCTGGTTGATACCAATGGAGCAGgtatgaactc ... tgtgtggtagGGGATGCATTC-GTTGGAGGTTTTTTGTCTCAGTTGGTTCAAGA
EST: gi|22013186|gb|BQ798220.1|BQ798220
EST:     CCCTGTGATCTTGCTGCCCAAGGAGAAGCTGGTTGATACCAATGGAGCAG                         GGGATGCATTCGTTGGAGGTTTTTTGTCTCAGTTGGTTCAAGAGAAGCCTA
genomic: CCCTGTGATCTTGCTGCCCAAGGAGAAGCTGGTTGATACCAATGGAGCAGgtatgaactc ... tgtgtggtagGGGATGCATTCGTTGGAGGTTTTTTGTCTCAGTTGGTTCAAGAGAAGCCTA
EST: gi|32245795|gb|CD711614.1|CD711614
EST:     CCCTGTGATCTTGCTGCCCAAGGAGAAGCTGGTTGATACCAATGGAGCAG                         GGGATGCATTTGTTGGAGGTTTTTTGTCTCAGTTGGTTCAAGAGAAGCCAA
genomic: CCCTGTGATCTTGCTGCCCAAGGAGAAGCTGGTTGATACCAATGGAGCAGgtatgaactc ... tgtgtggtagGGGATGCATTCGTTGGAGGTTTTTTGTCTCAGTTGGTTCAAGAGAAGCCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgcgcttttttttttttttttttccttttaatttgatttttcctgtgtggtagGGGATGCATTCGTTGGAGGTTTTTTGTCTCAGTTGGTTCAAGAGAAGCCTATTGAAGAATGTGTGAGAGCTGGTTGCTATGCTTCACATGTTATAATCCA
       tttttttttttttttt  CT-rich tract
       tttttttttttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagctgctaattaggctgccccttgttataaatataatgcattgctttgcgcttttttttttttttttttccttttaatttgatttttcctgtgtggtagGGGATGCATTCGTTGGAGGTTTTTTGTCTCAGTTGGTTCAAGAGAAGCCTATTGAAGAATGTGTGAGAGCTGGTTGCTATGCTTCACATGTTATAATCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- -ctgctaa
- - - - - - - -ctgcccc
- - - - - - - - - - - - - - -aaatata