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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttatgttttgaaagatgtcagaaattaggaataattaatatgagagtttgctaaatattgttaagattgtcaaccaacttgtcagtatttgaaatacagGTGGTAGCAGGTGGAGGTGCTGTTGAGGCTGCTTTATCTGTGTATTTGGAGTACCTTGCAACAACTTTAGGATCCCGAGAGCAGTTGGCAATTGCAGAAT

Basic information

species Vitis vinifera
transcript Vv15s0021g02230.t01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0021g02230.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA05G29870.1 (Glycine max), 3'ss of exon 13
----------------------tttatgttttgaaagatgtcagaaa-----ttaggaataattaatatga--gagtttgctaaatattgttaagattgtcaaccaacttgtcagtatttgaaatacagGTGGTAGCAGGTGGAGGTGCTGTTGAGGCTGCTTTATCTGTGTATTTGGAGTACCTTGCAACAACTTTAGGATCCCGAGAGCAGTTGGCAATTGCAGAAT
                       |  |  ||||   ||  ||| ||      ||  || ||| |  |   |  ||  |   |  || |||       |||      | || | | ||| | |||| ||||||||||| ||||||||||||||||| || || ||||| || ||||||||||||||||| |||||||||||||| |||||||||||||| || |||||||
gtatcctgcatacgtagctttcatcctactttggttgaaatcaaaatgttgctttagattaagtttttcaaatgatgtctttttattttgccttccctgt-gcttgattttttaatatataaaattcagGTGGTAGCTGGTGGAGGTGCTGTTGAAGCAGCATTATCAGTTTATTTGGAGTACCTTGCTACAACTTTAGGATCTCGAGAGCAGTTGGCTATAGCAGAAT

upper sequence: Vv15s0021g02230.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA08G12970.1 (Glycine max), 3'ss of exon 13
----------------------tttatgttttgaaagatgtcagaaattag-----gaataa----ttaatatgagagtttgctaaatattgttaagattgtcaaccaacttgtcagtatttgaaatacagGTGGTAGCAGGTGGAGGTGCTGTTGAGGCTGCTTTATCTGTGTATTTGGAGTACCTTGCAACAACTTTAGGATCCCGAGAGCAGTTGGCAATTGCAGAAT
                       |  |  ||||   ||  ||| || || |     || |||    || | ||||    ||  ||  | |  ||    ||||     |  || |   ||| | |||| ||||||||||| |||||||||||||||||||| || ||||| || ||||| ||||||||||| |||||||||||||| || ||||||||||| || |||||||
gtatcctgcatacatagctttcatcctactttggttgaaatcaaaattttgctttagattaagtttttcaaatgaagtctttttatttttccttcc--ttgtgctttattttttatatatataaaattcagGTGGTAGCTGGTGGAGGTGCTGTTGAGGCAGCATTATCAGTTTATTTAGAGTACCTTGCTACAACTTTAGGATCTCGGGAGCAGTTGGCTATAGCAGAAT

upper sequence: Vv15s0021g02230.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: AT3G20050.1 (Arabidopsis thaliana), 3'ss of exon 13
tttatgttttgaaagatgtcagaaattaggaataattaatatgagagtttgctaaatattgttaagattgtcaaccaacttgtcagtat--ttgaaatacagGTGGTAGCAGGTGGAGGTGCTGTTGAGGCTGCTTTATCTGTGTATTTGGAGTACCTTGCAACAACTTTAGGATCCCGAGAGCAGTTGGCAATTGCAGAAT
                 || | |       | |   |  ||       |   |  || | |  ||||      |  |  ||    || |  |||  | ||||||||| || ||||||||||| |||||  | || || ||||||||| ||||| ||||||| ||||| || || || || || || ||||| || || ||||
-----------------gtaacattcctttactttctgttagacatactccttgcatttagcaaagaacaaacattacatttcttgtttccttgtcaaacagGTGGTTGCGGGTGGAGGTGCAGTTGAATCAGCATTGTCTGTGTATCTGGAGCACCTTGCTACAACCTTGGGCTCTCGCGAACAATTGGCCATCGCTGAAT

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|110699451|gb|EE076471.1|EE076471
EST:     CTTTGCATGATGCTCTATCAATTGTCAAGAGGACCCTTGAATCCAACACG                         GTGGTAGCAGGTGGAGGTGCTGTTGAGGCTGCTTTATCTGTGTATTTGGAG
genomic: CTTTGCATGATGCTCTATCAATTGTCAAGAGGACCCTTGAATCCAACACGgtaaaccttg ... tgaaatacagGTGGTAGCAGGTGGAGGTGCTGTTGAGGCTGCTTTATCTGTGTATTTGGAG
EST: gi|110702474|gb|EE081230.1|EE081230
EST:     CTTTGCATGATGCTCTATCAATTGTCAAGAGGACCCTTGAATCCAACACG                         GTGGTAGCAGGTGGAGGTGCTGTTGAGGCTGCTTTATCTGTGTATTTGGAG
genomic: CTTTGCATGATGCTCTATCAATTGTCAAGAGGACCCTTGAATCCAACACGgtaaaccttg ... tgaaatacagGTGGTAGCAGGTGGAGGTGCTGTTGAGGCTGCTTTATCTGTGTATTTGGAG
EST: gi|26264285|gb|CA815348.1|CA815348
EST:     CTTTGCATGATGCTCTATCAATTGTCAAGAGGACCCTTGAATCCAACACG                         GTGGTAGCAGGTGGAGGTGCTGTTGAGGCTGCTTTATCTGTGTATTTGGAG
genomic: CTTTGCATGATGCTCTATCAATTGTCAAGAGGACCCTTGAATCCAACACGgtaaaccttg ... tgaaatacagGTGGTAGCAGGTGGAGGTGCTGTTGAGGCTGCTTTATCTGTGTATTTGGAG
EST: gi|351037610|gb|FQ462593.1|FQ462593
EST:     CTTTGCATGATGCTCTATCAATTGTCAAGAGGACCCTTGAATCCAACACG                         GTGGTAGCAGGTGGAGGTGCTGTTGAGGCTGCTTTATCTGTGTATTTGGAG
genomic: CTTTGCATGATGCTCTATCAATTGTCAAGAGGACCCTTGAATCCAACACGgtaaaccttg ... tgaaatacagGTGGTAGCAGGTGGAGGTGCTGTTGAGGCTGCTTTATCTGTGTATTTGGAG
EST: gi|110701345|gb|EE078813.1|EE078813
EST:     CTTTGCATGATGCTCTATCAATTGTCAAGAGGACCCTTGAATCCAACACG                         GTGGTAGCAGGTGGAGGTGCTGTTGAGGCTGCTTTATCTGTGTATTTGGAG
genomic: CTTTGCATGATGCTCTATCAATTGTCAAGAGGACCCTTGAATCCAACACGgtaaaccttg ... tgaaatacagGTGGTAGCAGGTGGAGGTGCTGTTGAGGCTGCTTTATCTGTGTATTTGGAG
EST: gi|351017726|gb|FQ436079.1|FQ436079
EST:     CTTTGCATGATGCTCTATCAATTGTCAAGAGGACCCTTGAATCCAACACG                         GTGGTAGCAGGTGGAGGTGCTGTTGAGGCTGCTTTATCTGTGTATTTGGAG
genomic: CTTTGCATGATGCTCTATCAATTGTCAAGAGGACCCTTGAATCCAACACGgtaaaccttg ... tgaaatacagGTGGTAGCAGGTGGAGGTGCTGTTGAGGCTGCTTTATCTGTGTATTTGGAG
EST: gi|37187670|gb|CF607023.1|CF607023
EST:     CTTTGCATGATGCTCTATCAATTGTCAAGAGGACCCTTGAATCCAACACG                         GTGGTAGCAGGTGGAGGTGCTGT
genomic: CTTTGCATGATGCTCTATCAATTGTCAAGAGGACCCTTGAATCCAACACGgtaaaccttg ... tgaaatacagGTGGTAGCAGGTGGAGGTGCTGT
EST: gi|34545258|gb|CF513490.1|CF513490
EST:     CTTTGCATGATGCTCTATCAATTGTCAAGAGGACCCTTGAATCCAACACG                         GTGGTAGCAGGTGGAGGTGCTGTTGAGGCTGCTTTATCTGTGTATTTGGAG
genomic: CTTTGCATGATGCTCTATCAATTGTCAAGAGGACCCTTGAATCCAACACGgtaaaccttg ... tgaaatacagGTGGTAGCAGGTGGAGGTGCTGTTGAGGCTGCTTTATCTGTGTATTTGGAG
EST: gi|33403784|gb|CF209411.1|CF209411
EST:     CTTTGCATGATGCTCTATCAATTGTCAAGAGGACCCTTGAATCCAACACG                         GTGGTAGCAGGTGGAGGTGCTGTTGAGGCTGCTTTATCTGTGTATTTGGAG
genomic: CTTTGCATGATGCTCTATCAATTGTCAAGAGGACCCTTGAATCCAACACGgtaaaccttg ... tgaaatacagGTGGTAGCAGGTGGAGGTGCTGTTGAGGCTGCTTTATCTGTGTATTTGGAG
EST: gi|32272417|gb|CD721576.1|CD721576
EST:     CTTTGCATGATGCTCTATCAATTGTCAAGAGGACCCTTGAATCCAACACG                         GTGGTAGCAGGTGGAGGTGCTGTTGAGGCTGCTTTATCTGTGTATTTGGAG
genomic: CTTTGCATGATGCTCTATCAATTGTCAAGAGGACCCTTGAATCCAACACGgtaaaccttg ... tgaaatacagGTGGTAGCAGGTGGAGGTGCTGTTGAGGCTGCTTTATCTGTGTATTTGGAG
EST: gi|110688105|gb|EE066273.1|EE066273
EST:     CTTTGCATGATGCTCTATCAATTGTCAAGAGGACCCTTGAATCCAACACG                         GTGGTAGCAGGTGGAGGTGCTGTTGAGGCTGCTTTATCTGTGTATTTGGAG
genomic: CTTTGCATGATGCTCTATCAATTGTCAAGAGGACCCTTGAATCCAACACGgtaaaccttg ... tgaaatacagGTGGTAGCAGGTGGAGGTGCTGTTGAGGCTGCTTTATCTGTGTATTTGGAG
EST: gi|351048864|gb|FQ431529.1|FQ431529
EST:     CTTTGCATGATGCTCTATCAATTGTCAAGAGGACCCTTGAATCCAACACG                         GTGGTAGCAGGTGGAGGTGCTGTTGAGGCTGCTTTATCTGTGTATTTGGAG
genomic: CTTTGCATGATGCTCTATCAATTGTCAAGAGGACCCTTGAATCCAACACGgtaaaccttg ... tgaaatacagGTGGTAGCAGGTGGAGGTGCTGTTGAGGCTGCTTTATCTGTGTATTTGGAG
EST: gi|30138039|gb|CB923377.1|CB923377
EST:     GTCAAGAGGACCCTTGAATCCAACACG                         GTGGTAGCAGGTGGAGGTGCTGTTGAGGCTGCTTTATCTGTGTATTTGGAG
genomic: GTCAAGAGGACCCTTGAATCCAACACGgtaaaccttg ... tgaaatacagGTGGTAGCAGGTGGAGGTGCTGTTGAGGCTGCTTTATCTGTGTATTTGGAG
EST: gi|110371042|gb|EC934755.1|EC934755
EST:     CTTTGCATGATGCTCTATCAATGGTCAAGAGGACCCTTGAATCCAACACG                         GTGGTAGCAGGTGGAGGTGCTGTTGAGGCTGCTTTATCTGTGTATTTGGAG
genomic: CTTTGCATGATGCTCTATCAATTGTCAAGAGGACCCTTGAATCCAACACGgtaaaccttg ... tgaaatacagGTGGTAGCAGGTGGAGGTGCTGTTGAGGCTGCTTTATCTGTGTATTTGGAG
EST: gi|161712591|gb|FC062193.1|FC062193
EST:     CTTTGCATGATGCTCTATCAATTGTCAAGAGGACCCTTGAATCCAACACG                         GTGGTAGCAGGTGGAGGTGCTGTTGAGGCTGCTTTATCTGTGTATTTGGAG
genomic: CTTTGCATGATGCTCTATCAATTGTCAAGAGGACCCTTGAATCCAACACGgtaaaccttg ... tgaaatacagGTGGTAGCAGGTGGAGGTGCTGTTGAGGCTGCTTTATCTGTGTATTTGGAG
EST: gi|26266195|gb|CA817258.1|CA817258
EST:     CTTGAATCCAACACG                         GTGGTAGCAGGTGGAGGTGCTGTTGAGGCTGCTTTATCTGTGTATTTGGAG
genomic: CTTGAATCCAACACGgtaaaccttg ... tgaaatacagGTGGTAGCAGGTGGAGGTGCTGTTGAGGCTGCTTTATCTGTGTATTTGGAG
EST: gi|110362101|gb|EC925611.1|EC925611
EST:     CTTTGCATGATGCTCTATCAATTGTCAAGAGGACCCTTGAATCCAACACG                         GTGGTAGCAGGTGGAGGTGCTGTTGAGGCTGCTTTATCTGTGTATTTGGAG
genomic: CTTTGCATGATGCTCTATCAATTGTCAAGAGGACCCTTGAATCCAACACGgtaaaccttg ... tgaaatacagGTGGTAGCAGGTGGAGGTGCTGTTGAGGCTGCTTTATCTGTGTATTTGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtttgctaaatattgttaagattgtcaaccaacttgtcagtatttgaaatacagGTGGTAGCAGGTGGAGGTGCTGTTGAGGCTGCTTTATCTGTGTATTTGGAGTACCTTGCAACAACTTTAGGATCCCGAGAGCAGTTGGCAATTGCAGAAT
    tgctaaa  putative branch site (score: 2)
       taaatattgttaagat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttatgttttgaaagatgtcagaaattaggaataattaatatgagagtttgctaaatattgttaagattgtcaaccaacttgtcagtatttgaaatacagGTGGTAGCAGGTGGAGGTGCTGTTGAGGCTGCTTTATCTGTGTATTTGGAGTACCTTGCAACAACTTTAGGATCCCGAGAGCAGTTGGCAATTGCAGAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - -tgaaaga
- - - - - - - - - - agaaatt
- - - - - - - - - - - - - - ggaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcaacca