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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attggaaggctcttactcctatgttttagtattgaatctgttctctttgcattgccatgatgctcatacctggggctaagcaaattggaggtttttgcagCAAAGCTTTTTAGAAGAGTTGGAAAAGACTGTTGCGCTGTTGGCATTTGAAGATTTCTCTAACTGCCCTGTTGGTGAACTCCTGGACATATCACAACGCC

Basic information

species Vitis vinifera
transcript Vv10s0116g00670.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0116g00670.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA15G07570.3 (Glycine max), 3'ss of exon 5
--attggaaggctcttactcctatgttttagtattgaatctgttctctttgcattgccatgatgctcatacctggggctaagcaaattggaggtt--tttgcagCAAAGCTTTTTAGAAGAGTTGGAAAAGACTGTTGCGCTGTTGGCATTTGAAGATTTCTCTAACTGCCCTGTTGGTGAACTCCTGGACATATCACAACGCC
  ||||   |    | |     ||     |      | |   || |  |||       ||  |   || || ||| |||||   | |||   |||   || |||||||||||||| ||||||||||| | ||||||||| ||  | || ||||||||| | |||||||| |||||||| || || || ||||||||||| ||| 
taattgcttgtagttaagaaaaatacaaaatgggaaagtaaattgttattgtggaaa-attttatgca-acttggtgctaac--acttgcctgttggatttcagCAAAGCTTTTTGGAAGAGTTGGAGAGGACTGTTGCACTTCTTGCCTTTGAAGATGTTTCTAACTGTCCTGTTGGAGAGCTGCTTGACATATCACAGCGCT

upper sequence: Vv10s0116g00670.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA13G31720.1 (Glycine max), 3'ss of exon 4
attggaaggctcttactcctatgttttagtattgaatctgttctctttgcattgccatgatgctcatacctggggctaagcaaattggaggtt--tttgcagCAAAGCTTTTTAGAAGAGTTGGAAAAGACTGTTGCGCTGTTGGCATTTGAAGATTTCTCTAACTGCCCTGTTGGTGAACTCCTGGACATATCACAACGCC
 |  |||   ||  |          | | |  | | | ||     |||| ||     || | |  | || |||||||||   | |||   |||   || |||||||| ||||| ||||||||||| | ||||||||| ||  | || ||||||||| | |||||||| |||||||| || || || ||||||||||| ||  
ttaagaaaaatccaatatgggaaagtaaattgttattgtggaaaatttgtatgtaactgtttcagagacttggggctaat--acttgcctgttggatttcagCAAAGTTTTTTGGAAGAGTTGGAGAGGACTGTTGCACTTCTTGCCTTTGAAGATGTTTCTAACTGTCCTGTTGGAGAGCTGCTTGACATATCACAGCGTT
















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|27579957|gb|CB002652.1|CB002652
EST:     AGGCTCTGGAGTTTGCTCAGGAGGAGCTCGCACCAAGGGGAGAAGAAAAT                         CAAAGCTTTTTAGAAGAGTTGGAAAAGACTGTTGCGCTGTTGGCATTTGAA
genomic: AGGCTCTGGAGTTTGCTCAGGAGGAGCTCGCACCAAGGGGAGAAGAAAATgtaattctca ... gtttttgcagCAAAGCTTTTTAGAAGAGTTGGAAAAGACTGTTGCGCTGTTGGCATTTGAA
EST: gi|34546271|gb|CF514503.1|CF514503
EST:     AGGCTCTGGAGTTTGCTCAGGAGGAGCTCGCACCAAGGGGAGAAGAAAAT                         CAAAGCTTTTTAGAAGAGTTGGAAAAGACTGTTGCGCTGTTGGCATTTGAA
genomic: AGGCTCTGGAGTTTGCTCAGGAGGAGCTCGCACCAAGGGGAGAAGAAAATgtaattctca ... gtttttgcagCAAAGCTTTTTAGAAGAGTTGGAAAAGACTGTTGCGCTGTTGGCATTTGAA
EST: gi|110702440|gb|EE081156.1|EE081156
EST:     AGGCTCTGGAGTTTGCTCAGGAGGAGCTCGCACCAAGGGGAGAAGAAAAT                         CAAAGCTTTTTAGAAGAGTTGGAAAAGACTGTTGCGCTGTTGGCATTTGAA
genomic: AGGCTCTGGAGTTTGCTCAGGAGGAGCTCGCACCAAGGGGAGAAGAAAATgtaattctca ... gtttttgcagCAAAGCTTTTTAGAAGAGTTGGAAAAGACTGTTGCGCTGTTGGCATTTGAA
EST: gi|34544716|gb|CF512948.1|CF512948
EST:     AGGCTCTGGAGTTTGCTCAGGAGGAGCTCGCACCAAGGGGAGAAGAAAAT                         CAAAGCTTTTTAGAAGAGTTGGAAAAGACTGTTGCGCTGTTGGCATTTGAA
genomic: AGGCTCTGGAGTTTGCTCAGGAGGAGCTCGCACCAAGGGGAGAAGAAAATgtaattctca ... gtttttgcagCAAAGCTTTTTAGAAGAGTTGGAAAAGACTGTTGCGCTGTTGGCATTTGAA
EST: gi|110415950|gb|EC981891.1|EC981891
EST:     AGGCTCTGGAGTTTGCTCAGGAGGAGCTCGCACCAAGGGGAGAAGAAAAT                         CAAAGCTTTTTAGAAGAGTTGGAAAAGACTGTTGCGCTGTTGGCATTTGAA
genomic: AGGCTCTGGAGTTTGCTCAGGAGGAGCTCGCACCAAGGGGAGAAGAAAATgtaattctca ... gtttttgcagCAAAGCTTTTTAGAAGAGTTGGAAAAGACTGTTGCGCTGTTGGCATTTGAA
EST: gi|32246915|gb|CD712734.1|CD712734
EST:     AGGCTCTGGAGTTTGCTCAGGAGGAGCTCGCACCAAGGGGAGAAGAAAAT                         CAAAGCTTTTTAGAAGAGTTGGAAAAGACTGTTGCGCTGTTGGCATTTGAA
genomic: AGGCTCTGGAGTTTGCTCAGGAGGAGCTCGCACCAAGGGGAGAAGAAAATgtaattctca ... gtttttgcagCAAAGCTTTTTAGAAGAGTTGGAAAAGACTGTTGCGCTGTTGGCATTTGAA
EST: gi|83275082|gb|DV939178.1|DV939178
EST:     AGGCTCTGGAGTTTGCTCAGGAGGAGCTCGCACCAAGGGGAGAAGAAAAT                         CAAAGCTTTTTAGAAGAGTTGGAAAAGACTGTTGCGCTGTTGGCATTTGAA
genomic: AGGCTCTGGAGTTTGCTCAGGAGGAGCTCGCACCAAGGGGAGAAGAAAATgtaattctca ... gtttttgcagCAAAGCTTTTTAGAAGAGTTGGAAAAGACTGTTGCGCTGTTGGCATTTGAA
EST: gi|30323272|gb|CD006534.1|CD006534
EST:     AGGCTCTGGAGTTTGCTCAGGAGGAGCTCGCACCAAGGGGAGAAGAAAAT                         CAAAGCTTTTTAGAAGAGTTGGAAAAGACTGTTGCGCTGTTGGCATTTGAA
genomic: AGGCTCTGGAGTTTGCTCAGGAGGAGCTCGCACCAAGGGGAGAAGAAAATgtaattctca ... gtttttgcagCAAAGCTTTTTAGAAGAGTTGGAAAAGACTGTTGCGCTGTTGGCATTTGAA
EST: gi|45770907|gb|CN006759.1|CN006759
EST:     AGGCTCTGGAGTTTGCTCAGGAGGAGCTCGCACCAAGGGGAGAAGAAAAT                         CAAAGCTTTTTAGAAGAGTTGGAAAAGACTGTTGCGCTGTTGGCATTTGAA
genomic: AGGCTCTGGAGTTTGCTCAGGAGGAGCTCGCACCAAGGGGAGAAGAAAATgtaattctca ... gtttttgcagCAAAGCTTTTTAGAAGAGTTGGAAAAGACTGTTGCGCTGTTGGCATTTGAA
EST: gi|27578911|gb|CB001606.1|CB001606
EST:     AGGCTCTGGAGTTTGCTCAGGAGGAGCTCGCACCAAGGGGAGAAGAAAAT                         CAAAGCTTTTTAGAAGAGTTGGAAAAGACTGTTGCGCTGTTGGCATTTGAA
genomic: AGGCTCTGGAGTTTGCTCAGGAGGAGCTCGCACCAAGGGGAGAAGAAAATgtaattctca ... gtttttgcagCAAAGCTTTTTAGAAGAGTTGGAAAAGACTGTTGCGCTGTTGGCATTTGAA
EST: gi|110408401|gb|EC974037.1|EC974037
EST:     AGGCTCTGGAGTTTGCTCAGGAGGAGCTCGCACCAAGGGGAGAAGAAAAT                         CAAAGCTTTTTAGAAGAGTTGGAAAAGACTGTTGCGCTGTTGGCATTTGAA
genomic: AGGCTCTGGAGTTTGCTCAGGAGGAGCTCGCACCAAGGGGAGAAGAAAATgtaattctca ... gtttttgcagCAAAGCTTTTTAGAAGAGTTGGAAAAGACTGTTGCGCTGTTGGCATTTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgcattgccatgatgctcatacctggggctaagcaaattggaggtttttgcagCAAAGCTTTTTAGAAGAGTTGGAAAAGACTGTTGCGCTGTTGGCATTTGAAGATTTCTCTAACTGCCCTGTTGGTGAACTCCTGGACATATCACAACGCC
                                              tttttgc  CT-rich tract
                                    aaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attggaaggctcttactcctatgttttagtattgaatctgttctctttgcattgccatgatgctcatacctggggctaagcaaattggaggtttttgcagCAAAGCTTTTTAGAAGAGTTGGAAAAGACTGTTGCGCTGTTGGCATTTGAAGATTTCTCTAACTGCCCTGTTGGTGAACTCCTGGACATATCACAACGCC

- -ggaaggc
- - - - - - - - -cctatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - ccatgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catacct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagcaaa