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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcaattcgtctttttttcatatatatatatatgatgctggcacatacacatatgtgagctcctagtcggtagctaatttctctgaaaattttccattcagGATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCCCATAATGCAATTCGAAATGATCCAAGGATCAACTGGATCTGCAAGCCTGTGCACA

Basic information

species Vitis vinifera
transcript Vv15s0021g02480.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0021g02480.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os03g40180.1 (Oryza sativa), 3'ss of exon 3
tcaattcgtctt-tttttcatatatatatatatgatgctggcacatacacatatgtgagctcctagtcggtagctaatttctctgaaaattttccattcagGATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCCCATAATGCAATTCGAAATGATCCAAGGATCAACTGGATCTGCAAGCCTGTGCACA
    | | | |   ||| |  | || | |  | |||| |     | |   || | |  ||      |   |  ||   || |||       ||  || ||||| || || ||||| |||| |||||| ||||| || |||| ||| || | ||| || || ||||| ||||||||||||||| ||||||||||||||||||
---gtacatttcactttactgagatctttcaaagatgattatcaaca---atgtatctgccttccattaatgacttggttttctttgg---tttaatgcagGACTCCACCTACAAGTACTTTGAGATCATCCTTGTGGATGTTGCTCACAGTGCTATCCGCAATGACCCAAGGATCAACTGGCTCTGCAAGCCTGTGCACA

upper sequence: Vv15s0021g02480.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os05g19370.1 (Oryza sativa), 3'ss of exon 3
tcaattcgtctttttttcatatatatatatatgatgctggcacatacacatatgtgagctcctagtcggtagctaatttctctgaaaattttccattcagGATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCCCATAATGCAATTCGAAATGATCCAAGGATCAACTGGATCTGCAAGCCTGTGCACA
    |   | ||  |||||     || |    || | ||||| | | |   || | |||| ||  ||  ||  |  ||| | |  |     |  ||  |||| || || ||||| |||| |||||| ||||| || |||| ||| || |  || || || ||||| ||||||||||||||| ||||||||||||||||||
---gtatat-ttgatttcactgggatcttgcggaagatggcaaaaaaa---atttcagctgcttttcattaattcctttgttttcattggcttaatgtagGACTCCACCTACAAGTACTTTGAGATCATCCTTGTGGATGTTGCTCACAGCGCTATCCGCAATGACCCAAGGATCAACTGGCTCTGCAAGCCTGTGCACA

upper sequence: Vv15s0021g02480.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G034794_T03 (Zea mays), 3'ss of exon 1
-tcaattcgtctttttttcatatatatatatatgatgctggcacatacacatatgtgagctcctagtcggtagctaatttctctgaaaattttccattcagGATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCCCATAATGCAATTCGAAATGATCCAAGGATCAACTGGATCTGCAAGCCTGTGCACA
 |    |    |   ||     ||   | |||| |||   | |  | ||    ||| ||  |  |  |   | ||   |  | | |    |   ||  ||||||   || ||||| |||| |||||| || || |||||||  ||||| | | | || || ||||||||||||||||||||| | ||||| ||||||||||
gtatgcttaattgagttgagcttaacaagatatcatg--agaattttcatccttgtcagtactgatgccacatctggctcttgtta---ctggacaa-cagGATAGCACCTACAAGTACTTTGAGATCATTCTTGTTGATGTGGCCCACACTACCATCCGCAATGATCCAAGGATCAACTGGCTATGCAATCCTGTGCACA

upper sequence: Vv15s0021g02480.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT4G17390.1 (Arabidopsis thaliana), 3'ss of exon 3
-------tcaattcgtctttttttcatatatatatatatgatgctg-gcacatacacatatgtgagctcctagtcggtagctaatttctctgaaaattttccattcagGATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCCCATAATGCAATTCGAAATGATCCAAGGATCAACTGGATCTGCAAGCCTGTGCACA
       |||    || |||  ||  ||  |   |||   || |||   |  |    |||     |   | |||  |||     ||  |       |||||   |||||| ||||| ||||| ||||| ||||| ||||| || ||  |||| || |||||  | |||||||||||||||||||||||||||||||| ||||||||||
gtatgcatcacactgtttttagttactagttgc-tatgccatcctgtaaatgtgttaatagtatggaatcaagtgagtaatggtttggttctctggttttc---tcagGACTCTACCTACAAGTACTACGAGATTATCCTTGTAGACCCTGCACACAATGCCGTCCGAAATGATCCAAGGATCAACTGGATCTGCAACCCTGTGCACA

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|30305539|gb|CB982333.1|CB982333
EST:     GCCGGAAATTAGGTGGTCTGAAAGTTCTCAACTCGTACTGGATAAATGAG                         GATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCCCATAAT
genomic: GTCGGAAATTAGGTGGTCTGAAAGTTCTCAACTCGTACTGGATAAACGAGgttggttgtg ... ttccattcagGATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCCCATAAT
EST: gi|349828916|gb|FQ419249.1|FQ419249
EST:     GCCGGAAATTAGGTGGTCTGAAAGTTCTCAACTCGTACTGGATAAATGAG                         GATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCCCATAAT
genomic: GTCGGAAATTAGGTGGTCTGAAAGTTCTCAACTCGTACTGGATAAACGAGgttggttgtg ... ttccattcagGATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCCCATAAT
EST: gi|110428939|gb|EC995423.1|EC995423
EST:     CTGAAAGTTCTCAACTCGTACTGGATAAATGAG                         GATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCCCATAAT
genomic: CTGAAAGTTCTCAACTCGTACTGGATAAACGAGgttggttgtg ... ttccattcagGATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCCCATAAT
EST: gi|110687547|gb|EE065083.1|EE065083
EST:     GCCGGAAATTAGGTGGTCTGAAAGTTCTCAACTCGTACTGGATAAATGAG                         GATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCTCATAAT
genomic: GTCGGAAATTAGGTGGTCTGAAAGTTCTCAACTCGTACTGGATAAACGAGgttggttgtg ... ttccattcagGATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCCCATAAT
EST: gi|29783719|gb|CB350095.2|CB350095
EST:     GCCGGAAATTAGGTGGTCTGAAAGTTCTCAACTCGTACTGGATAAATGAG                         GATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCTCATAAT
genomic: GTCGGAAATTAGGTGGTCTGAAAGTTCTCAACTCGTACTGGATAAACGAGgttggttgtg ... ttccattcagGATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCCCATAAT
EST: gi|110716420|gb|EE091396.1|EE091396
EST:     GCCGGAAATTAGGTGGTCTGAAAGTTCTCAACTCGTACTGGATAAATGAG                         GATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCCCATAAT
genomic: GTCGGAAATTAGGTGGTCTGAAAGTTCTCAACTCGTACTGGATAAACGAGgttggttgtg ... ttccattcagGATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCCCATAAT
EST: gi|37188816|gb|CF608165.1|CF608165
EST:     GCCGGAAATTAGGTGGTCTGAAAGTTCTCAACTCGTACTGGATAAATGAG                         GATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCCCATAAT
genomic: GTCGGAAATTAGGTGGTCTGAAAGTTCTCAACTCGTACTGGATAAACGAGgttggttgtg ... ttccattcagGATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCCCATAAT
EST: gi|110690582|gb|EE067807.1|EE067807
EST:     GCCGGAAATTAGGTGGTCTGAAAGTTCTCAACTCGTACTGGATAAATGAG                         GATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCTCATAAT
genomic: GTCGGAAATTAGGTGGTCTGAAAGTTCTCAACTCGTACTGGATAAACGAGgttggttgtg ... ttccattcagGATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCCCATAAT
EST: gi|30297287|gb|CB974081.1|CB974081
EST:     GCCGGAAATTAGGTGGTCTGAAAGTTCTCAACTCGTACTGGATAAATGAG                         GATTCTACATACAAATACTATGAGATAATCCTAGTCGATGCTGCTCATAAT
genomic: GTCGGAAATTAGGTGGTCTGAAAGTTCTCAACTCGTACTGGATAAACGAGgttggttgtg ... ttccattcagGATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCCCATAAT
EST: gi|110360131|gb|EC922799.1|EC922799
EST:     GCCGGAAATTAGGTGGTCTGAAAGTTCTCAACTCGTACTGGATAAATGAG                         GATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCCCATAAT
genomic: GTCGGAAATTAGGTGGTCTGAAAGTTCTCAACTCGTACTGGATAAACGAGgttggttgtg ... ttccattcagGATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCCCATAAT
EST: gi|351038884|gb|FQ457559.1|FQ457559
EST:     GCCGGAAATTAGGTGGTCTGAAAGTTCTCAACTCGTACTGGATAAATGAG                         GATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCCCATAAT
genomic: GTCGGAAATTAGGTGGTCTGAAAGTTCTCAACTCGTACTGGATAAACGAGgttggttgtg ... ttccattcagGATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCCCATAAT
EST: gi|110731428|gb|EE105841.1|EE105841
EST:     GTCGGAAATTAGGTGGTCTGAAAGTTCTCAACTCGTACTGGATAAACGAG                         GATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCCCATAAT
genomic: GTCGGAAATTAGGTGGTCTGAAAGTTCTCAACTCGTACTGGATAAACGAGgttggttgtg ... ttccattcagGATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCCCATAAT
EST: gi|110703945|gb|EE081326.1|EE081326
EST:     GCCGGAAATTAGGTGGTCTGAAAGTTCTCAACTCGTACTGGATAAATGAG                         GATTCTACATACAAATACTATGAGATAATTCTAGTTGATGCTGCCCATAAT
genomic: GTCGGAAATTAGGTGGTCTGAAAGTTCTCAACTCGTACTGGATAAACGAGgttggttgtg ... ttccattcagGATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCCCATAAT
EST: gi|110384901|gb|EC949369.1|EC949369
EST:     GCCGGAAATTAGGTGGTCTGAAAGTTCTCAACTCGTACTGGATAAATGAG                         GATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCTCATAAT
genomic: GTCGGAAATTAGGTGGTCTGAAAGTTCTCAACTCGTACTGGATAAACGAGgttggttgtg ... ttccattcagGATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCCCATAAT
EST: gi|26265189|gb|CA816252.1|CA816252
EST:     GCCGGAAATTAGGTGGTCTGAAAGTTCTCAACTCGTACTGGATAAATGAG                         GATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCTCATAAT
genomic: GTCGGAAATTAGGTGGTCTGAAAGTTCTCAACTCGTACTGGATAAACGAGgttggttgtg ... ttccattcagGATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCCCATAAT
EST: gi|110374851|gb|EC939789.1|EC939789
EST:     GCCGGAAATTAGGTGGTCTGAAAGTTCTCAACTCGTACTGGATAAATGAG                         GATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCCCATAAT
genomic: GTCGGAAATTAGGTGGTCTGAAAGTTCTCAACTCGTACTGGATAAACGAGgttggttgtg ... ttccattcagGATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCCCATAAT
EST: gi|110722129|gb|EE098087.1|EE098087
EST:     GTCGGAAATTAGGTGGTCTGAAAGTTCTCAACTCGTACTGGATAAACGAG                         GATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCCCATAAT
genomic: GTCGGAAATTAGGTGGTCTGAAAGTTCTCAACTCGTACTGGATAAACGAGgttggttgtg ... ttccattcagGATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCCCATAAT
EST: gi|110689554|gb|EE065890.1|EE065890
EST:     GCCGGAAATTAGGTGGTCTGAAAGTTCTCAACTCGTACTGGATAAATGAG                         GATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCTCATAAT
genomic: GTCGGAAATTAGGTGGTCTGAAAGTTCTCAACTCGTACTGGATAAACGAGgttggttgtg ... ttccattcagGATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCCCATAAT
EST: gi|110724837|gb|EE101012.1|EE101012
EST:     GTCGGAAATTAGGTGGTCTGAAAGTTCTCAACTCGTACTGGATAAACGAG                         GATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCCCATAAT
genomic: GTCGGAAATTAGGTGGTCTGAAAGTTCTCAACTCGTACTGGATAAACGAGgttggttgtg ... ttccattcagGATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCCCATAAT
EST: gi|110732519|gb|EE107877.1|EE107877
EST:     GTCGGAAATTAGGTGGTCTGAAAGTTCTCAACTCGTACTGGATAAACGAG                         GATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCCCATAAT
genomic: GTCGGAAATTAGGTGGTCTGAAAGTTCTCAACTCGTACTGGATAAACGAGgttggttgtg ... ttccattcagGATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCCCATAAT
EST: gi|37188968|gb|CF608317.1|CF608317
EST:     GCCGGAAATTAGGTGGTCTGAAAGTTCTCAACTCGTACTGGATAAATGAG                         GATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCCCATAAT
genomic: GTCGGAAATTAGGTGGTCTGAAAGTTCTCAACTCGTACTGGATAAACGAGgttggttgtg ... ttccattcagGATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCCCATAAT
EST: gi|110687793|gb|EE065609.1|EE065609
EST:     GCCGGAAATTAGGTGGTCTGAAAGTTCTCAACTCGTACTGGATAAATGAG                         GATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCCCATAAT
genomic: GTCGGAAATTAGGTGGTCTGAAAGTTCTCAACTCGTACTGGATAAACGAGgttggttgtg ... ttccattcagGATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCCCATAAT
EST: gi|110706844|gb|EE082724.1|EE082724
EST:     GCCGGAAATTAGGTGGTCTGAAAGTTCTCAACTCGTACTGGATAAATGAG                         GATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCCCATAAT
genomic: GTCGGAAATTAGGTGGTCTGAAAGTTCTCAACTCGTACTGGATAAACGAGgttggttgtg ... ttccattcagGATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCCCATAAT
EST: gi|110710410|gb|EE086731.1|EE086731
EST:     GCCGGAAATTAGGTGGTCTGAAAGTTCTCAACTCGTACTGGATAAATGAG                         GATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCCCATAAT
genomic: GTCGGAAATTAGGTGGTCTGAAAGTTCTCAACTCGTACTGGATAAACGAGgttggttgtg ... ttccattcagGATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCCCATAAT
EST: gi|30305479|gb|CB982273.1|CB982273
EST:     GCCGGAAATTAGGTGGTCTGAAAGTTCTCAACTCGTACTGGATAAATGAG                         GATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCCCATAAT
genomic: GTCGGAAATTAGGTGGTCTGAAAGTTCTCAACTCGTACTGGATAAACGAGgttggttgtg ... ttccattcagGATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCCCATAAT
EST: gi|110688678|gb|EE067502.1|EE067502
EST:     GCCGGAAATTAGGTGGTCTGAAAGTTCTCAACTCGTACTGGATAAATGAG                         GATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCTCATAAT
genomic: GTCGGAAATTAGGTGGTCTGAAAGTTCTCAACTCGTACTGGATAAACGAGgttggttgtg ... ttccattcagGATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCCCATAAT
EST: gi|71875160|gb|DT024215.1|DT024215
EST:     GCCGGAAATTAGGTGGTCTGAAAGTTCTCAACTCGTACTGGATAAATGAG                         GATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCTCATAAT
genomic: GTCGGAAATTAGGTGGTCTGAAAGTTCTCAACTCGTACTGGATAAACGAGgttggttgtg ... ttccattcagGATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCCCATAAT
EST: gi|22008858|gb|BQ793892.1|BQ793892
EST:     GCCGGAAATTAGGTGGTCTGAAAGTTCTCAACTCGTACTGGATAAATGAG                         GATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCCCATAAT
genomic: GTCGGAAATTAGGTGGTCTGAAAGTTCTCAACTCGTACTGGATAAACGAGgttggttgtg ... ttccattcagGATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCCCATAAT
EST: gi|352785725|gb|FQ475728.1|FQ475728
EST:     GCCGGAAATTAGGTGGTCTGAAAGTTCTCAACTCGTACTGGATAAATGAG                         GATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCCCATAAT
genomic: GTCGGAAATTAGGTGGTCTGAAAGTTCTCAACTCGTACTGGATAAACGAGgttggttgtg ... ttccattcagGATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCCCATAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acacatatgtgagctcctagtcggtagctaatttctctgaaaattttccattcagGATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCCCATAATGCAATTCGAAATGATCCAAGGATCAACTGGATCTGCAAGCCTGTGCACA
                         agctaat  putative branch site (score: 3)
                                           ttttccattc  putative PPT
                                     tgaaaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcaattcgtctttttttcatatatatatatatgatgctggcacatacacatatgtgagctcctagtcggtagctaatttctctgaaaattttccattcagGATTCTACATACAAATACTATGAGATAATCCTAGTTGATGCTGCCCATAATGCAATTCGAAATGATCCAAGGATCAACTGGATCTGCAAGCCTGTGCACA

- - - - - - - - - - - - - - - - - -gctggca
- - - - - - - - - - - - - - - - - - - - - catacac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaatt