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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagcataaatgctattgtttttgttcttacaactcaatgtaacatttagaactggttttccaaattttgtttcctaatcactttggttttttgccttcagCAAAAATGGCTAGACTAAAACAAGCCAAAGAAGAGGCTGAAAAGGAGATTGCTGCTTACCGAGCCCAGGTTGAACTTGAGTTCCAGAAGAAATTGGCTGA

Basic information

species Vitis vinifera
transcript Vv08s0040g01910.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0040g01910.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA03G33790.1 (Glycine max), 3'ss of exon 2
aagcataaatgctattgtttttgttcttacaactcaatgtaacatttag-aactggttttccaaattttgtttcctaatcactttggttttttgccttcagCAAAAATGGCTAGACTAAAACAAGCCAAAGAAGAGGCTGAAAAGGAGATTGCTGCTTACCGAGCCCAGGTTGAACTTGAGTTCCAGAAGAAATTGGCTGA
   | |  ||  || | || |  | ||   |  |  |    | ||  |  | ||   ||   ||| |        | |  | | ||| | |     || || |||| |||||||||| || |||||||||||||||||||||||||| ||||| |  ||  | || ||| | ||    ||||| || |||||| || |  |
ctacctttattgtactattgtactcctattaggtagaatctatatcgaatatctttattggtaaactaaccagtatcagtattctggatctac-tgttaagAAAAATTGGCTAGACTGAAGCAAGCCAAAGAAGAGGCTGAAAAGGAAATTGCCGAGTATAGGGCTCAGTTGGAGTACGAGTTTCAAAAGAAAGTGTCACA

upper sequence: Vv08s0040g01910.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA13G20310.3 (Glycine max), 3'ss of exon 2
aagcataaatgctattgtttttgttcttacaactcaatgtaacatt-tagaactggttttccaaattttgtttcctaatcactttggttttttgccttcagCAAAAATGGCTAGACTAAAACAAGCCAAAGAAGAGGCTGAAAAGGAGATTGCTGCTTACCGAGCCCAGGTTGAACTTGAGTTCCAGAAGAAATTGGCTGA
     |    |     |  | | || ||   |||   | |   ||| ||    | | |||    |  ||  |   |  |  || ||  | | | |  | || |||| |||||||  | ||||| ||||| |||||||||||||||||||||||||  |||||||| ||  | ||   |||||| || |||||| || | ||
ttttgtttgggggggggggtgtattattgatactttctattttattataactatcgctttttgtacattaatcaatgtttcctctgcatctatactat-agAAAAATTGGCTAGGTTGAAACAGGCCAAGGAAGAGGCTGAAAAGGAGATTGCTGAATACCGAGCTCAACTAGAGGCTGAGTTTCAAAAGAAAGTGTCAGA

upper sequence: Vv08s0040g01910.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA10G06010.2 (Glycine max), 3'ss of exon 2
--aagcataaatgctattgtttttgttcttacaactcaatgtaacatttagaactggttttccaaattttgtttcctaatcactttggttttttgccttcagCAAAAATGGCTAGACTAAAACAAGCCAAAGAAGAGGCTGAAAAGGAGATTGCTGCTTACCGAGCCCAGGTTGAACTTGAGTTCCAGAAGAAATTGGCTGA
   |   | | |  | || || |||||  |   |   | |    ||  || | ||  |||    | |  |   | ||   | |||      | |    | || |||| |||||||  | || |||||||| ||||||||||||||||||||||||   |||||||| ||  | ||   |||||| || |||||| || | ||
tttattttgatttttgttattattgttacttgcatatattaccgcaactaaatcttttttgtacactgatcaatgctgtcctcttca--cgtctattgtaagAAAAATTGGCTAGGTTGAAGCAAGCCAAGGAAGAGGCTGAAAAGGAGATTGCTCAATACCGAGCTCAACTAGAGGCTGAGTTTCAAAAGAAAGTGTCAGA

upper sequence: Vv08s0040g01910.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT4G23710.1 (Arabidopsis thaliana), 3'ss of exon 2
-aagcataaatgctattgtttttgttcttacaactcaatgtaacatttagaactggttttccaaattttgtttcctaatcactttggttttttgccttcagCAAAAATGGCTAGACTAAAACAAGCCAAAGAAGAGGCTGAAAAGGAGATTGCTGCTTACCGAGCCCAGGTTGAACTTGAGTTCCAGAAGAAATTGGCTGA
      |   | ||  |  |     | | |||  |       | ||  ||     |  || ||| || || ||   ||||  | ||  ||||    ||||||||||||| ||||||| || |||||||| ||||| |||||||  ||| ||||||   ||  | ||      || |  | |||||||| |||| | |  | 
tgtaactttgtactcatcatggaaatttaacagttgggcactaaatg-agttgcagaattacaacttgtgattgagaatctgtatgtgttttgattttcagCAAAAATGACTAGACTGAAGCAAGCCAAGGAAGAAGCTGAAACAGAGGTTGCTGAGCACAAAACCAGTACAGAGCAGGGGTTCCAGAGGAAACTCGAAGC

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|110404650|gb|EC970042.1|EC970042
EST:     CACATTGTCAATGCTGCCAGAAGTG                         CTAAAATGGCTAGACTAAAACAAGCCAAAGAAGAGGCTGAAAAGGAGATTG
genomic: CACATTGTCAATGCTGCCAGAAGTGgtaggcttgc ... ttgccttcagCAAAAATGGCTAGACTAAAACAAGCCAAAGAAGAGGCTGAAAAGGAGATTG
EST: gi|30131526|gb|CB916865.1|CB916865
EST:     GCTAGCTGCAGAACAAGAAGCTCAACACATTGTCAATGCTGCCAGAAGTG                         CAAAAATGGCTAGACTAAAACAAGCCAAAGAAGAGGCTGAAAAGGAGATTG
genomic: GCTAGCTGCAGAACAAGAAGCTCAACACATTGTCAATGCTGCCAGAAGTGgtaggcttgc ... ttgccttcagCAAAAATGGCTAGACTAAAACAAGCCAAAGAAGAGGCTGAAAAGGAGATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagaactggttttccaaattttgtttcctaatcactttggttttttgccttcagCAAAAATGGCTAGACTAAAACAAGCCAAAGAAGAGGCTGAAAAGGAGATTGCTGCTTACCGAGCCCAGGTTGAACTTGAGTTCCAGAAGAAATTGGCTGA
                          tcctaat  putative branch site (score: 2)
                                         ttttttgccttc  putative PPT
                aaattttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagcataaatgctattgtttttgttcttacaactcaatgtaacatttagaactggttttccaaattttgtttcctaatcactttggttttttgccttcagCAAAAATGGCTAGACTAAAACAAGCCAAAGAAGAGGCTGAAAAGGAGATTGCTGCTTACCGAGCCCAGGTTGAACTTGAGTTCCAGAAGAAATTGGCTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
aagcataa
- - - - - - - - - - - - - - -caactca