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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACTTTGTGGAGGCTGGGGCAATTGCTGTGAGGCGTGTTCGGAAAGATGACATGCGCCATGTTGCCAAGGCAACTGGTGCAACTATGgtatgtttcttaactctgcttcccaattgatatcaccgggtgaggttgttttaatatgctcttggaatttacaaataagaatgctttaatgtttttgttc...

Basic information

species Vitis vinifera
transcript Vv15s0021g02230.t01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0021g02230.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: LOC_Os04g46620.1 (Oryza sativa), 5'ss of exon 11
TACTTTGTGGAGGCTGGGGCAATTGCTGTGAGGCGTGTTCGGAAAGATGACATGCGCCATGTTGCCAAGGCAACTGGTGCAACTATGgtatgtttcttaactctgcttcccaattgatatcac--cgggtgaggttgtttta-atatg-ctcttggaatttacaaataagaatgctttaatgtttttgttc------------------------------------------------------------------------------------------------
||||| || |||||||| ||||||||||| |||||||| || || || ||  ||||||||||||||||||| ||||||||||||||||||||  ||     |    |  | | |||  | |||   ||   |  |  || |  | ||| ||  | ||||| | |||| |  | ||        ||  | |                                                                                                 
TACTTCGTTGAGGCTGGAGCAATTGCTGTAAGGCGTGTGCGTAAGGAGGATTTGCGCCATGTTGCCAAGGCTACTGGTGCAACTATGgtatgcctcaccttttgtttatcgagttgtaaccacattggaatacataattgtgcagatgactaatagaattaataaatgatgaagcgacttcccttgcgatacccctgtaattttagtcttaagtttgttgcttctagtcctaatattaatgctacaccaactgtttggtgctgtcctaatttggtagtaaattgcag

upper sequence: Vv15s0021g02230.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GRMZM2G110626_T01 (Zea mays), 5'ss of exon 11
TACTTTGTGGAGGCTGGGGCAATTGCTGTGAGGCGTGTTCGGAAAGATGACATGCGCCATGTTGCCAAGGCAACTGGTGCAACTATGgtatgtttcttaactctgcttcccaattgatatcaccgggtgaggttgttttaatatgctcttggaatt-tacaaataagaatgct-ttaatgtttttgttc
|||||||| |||||||| || ||||| || |||||||| || || || ||  |||||||||||||||| || ||||||||||||||||||   |  ||   | | |||   |||| | || |       |    |          || || | ||| ||     |||| |    || |  ||   ||  
TACTTTGTTGAGGCTGGAGCTATTGCAGTAAGGCGTGTGCGCAAGGAAGATTTGCGCCATGTTGCCAAAGCCACTGGTGCAACTATGgta-actgattgcttttacttattaattaaaattaaaatacaaaaccgaacaccaggcctgttagcattgtaaggtcaagagtatagtttagattaaagta-

upper sequence: Vv15s0021g02230.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GRMZM2G039263_T02 (Zea mays), 5'ss of exon 9
TACTTTGTGGAGGCTGGGGCAATTGCTGTGAGGCGTGTTCGGAAAGATGACATGCGCCATGTTGCCAAGGCAACTGGTGCAACTATGgtatgttt------cttaactctgcttcccaattgatatc-----accgggtgaggttgttttaatat--gctcttggaatttacaaataagaatgctttaatgtttttgttc---------------------------------------------------------------------
|||||||| |||||||| || ||||| || |||||||| || || || ||  |||| ||||||||||| || |||||||||||||||||||| ||      |  || | ||| |     |   | |         ||| | || ||    |   |    |||||   ||    || |  ||| |   |   | |||  |                                                                      
TACTTTGTTGAGGCTGGTGCGATTGCAGTAAGGCGTGTGCGCAAGGAAGATTTGCGACATGTTGCCAAAGCCACTGGTGCAACTATGgtatgcttacatgacaaaattgtgcgtttgcgtgtgtgtgtggggggtgggggggggtgacagagcttcaattcttgaggttcttgaaaagtaatacagaagactgtttaatgaagtgttaattatgatgatgtttactgcattattagtattatacgtggcttagcaattaaacctttcag

upper sequence: Vv15s0021g02230.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA08G12970.1 (Glycine max), 5'ss of exon 11
TACTTTGTGGAGGCTGGGGCAATTGCTGTGAGGCGTGTTCGGAAAGATGACATGCGCCATGTTGCCAAGGCAACTGGTGCAACTATGgtatgtttcttaactctgcttcccaattgatatcaccgggtgaggttgttt-taatatgctcttggaatttacaaataagaatgctttaatgtttttgttc
|||||||| |||||||||||||||||||| || ||||| |||||||| ||||||||||||||||||||||| |||||||||||  ||||| | || |    | |  ||   |||| | ||  |   || ||   |||   | ||         | ||  || |   ||||| |     | |   | | 
TACTTTGTTGAGGCTGGGGCAATTGCTGTAAGACGTGTGCGGAAAGAGGACATGCGCCATGTTGCCAAGGCTACTGGTGCAACATTGgtaggattttgtttttttgtttttaatttaaattgcaatgttagcaagttgacagtaaaactgaatatttgtcacaacggaatgttgattagatagggct-

upper sequence: Vv15s0021g02230.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA05G29870.1 (Glycine max), 5'ss of exon 11
TACTTTGTGGAGGCTGGGGCAATTGCTGTGAGGCGTGTTCGGAAAGATGACATGCGCCATGTTGCCAAGGCAACTGGTGCAACTATGgtatgtttcttaactctgcttcccaattgatatcaccgggtgaggttgttt-taatatgctcttggaatttacaaataagaatgctttaatgtttttgttc
|||||||| |||||||||||||||||||| || ||||| |||||||| ||||||||||||||||||||||| |||||||||||  ||||| | || ||   | |  |    |||| | ||  |    | ||   |||   | ||         | ||  || |   || || |     | |   | ||
TACTTTGTTGAGGCTGGGGCAATTGCTGTAAGACGTGTGCGGAAAGAGGACATGCGCCATGTTGCCAAGGCTACTGGTGCAACATTGgtaggcttttttttttt-ttaataaatttaaattgcaattttagcaagttgacagtaaagctgaatatttgtcacaatggagtgttgattagatagggctc

upper sequence: Vv15s0021g02230.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: AT3G20050.1 (Arabidopsis thaliana), 5'ss of exon 11
TACTTTGTGGAGGCTGGGGCAATTGCTGTGAGGCGTGTTCGGAAAGATGACATGCGCCATGTTGCCAAGGCAACTGGTGCAACTATGgtatgtttcttaactctgcttcccaattgatatcaccgggtgaggttgttttaatatgctcttggaatttacaaataagaatgctttaatgtttttgttc
|||||||| ||||| || || |||||||| |||||||| || ||||| |||||||| |||||||||||||| || || || ||| |||||  || ||   ||  ||||     |  ||| |        | |||||   | ||   | |   || | | | ||    || |||||   |||| |   
TACTTTGTAGAGGCAGGAGCTATTGCTGTTAGGCGTGTGCGCAAAGAAGACATGCGTCATGTTGCCAAGGCGACAGGAGCGACTCTGgtac-ttcctgcgctaggctttt---tcaataccc-------atgttgtcaaactaaaatttc--aactaatatattt--atccttta---ttttag---

upper sequence: Vv15s0021g02230.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: EFJ12438 (Selaginella moellendorffii), 5'ss of exon 11
TACTTTGTGGAGGCTGGGGCAATTGCTGTGAGGCGTGTTCGGAAAGATGACATGCGCCATGTTGCCAAGGCAACTGGTGCAACTATGgtatgtttcttaactctgcttcccaattgatatcaccgggtgaggttgttttaatatgctcttggaatttacaaataagaatgctttaatgtttttgttc
|| ||||| || || || ||||| |||||  | ||||||||||| || ||| |||| ||||| ||||||||||||||||| || |||||  | ||    | | |  || | |   ||  | ||    ||| |    | |   || || |  |                                   
TATTTTGTAGAAGCAGGAGCAATAGCTGTACGCCGTGTTCGGAAGGAGGACCTGCGGCATGTGGCCAAGGCAACTGGTGCTACAATGgtgggatt---gagtataatttcaag--gaatttac----tgaagcgaatctc-cattctatcag-----------------------------------

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:     CCAAGGCATCTGCTGCAACTATG                         GTTTCAACGTTTGCTGACATGGAAGGGGATGAGACATTTGATTCATCATTT
genomic: CCAAGGCAACTGGTGCAACTATGgtatgtttct ... tgttctgcagGTTTCAACGTTTGCTGACATGGAAGGGGATGAGACATTTGATTCATCATTT
EST: gi|110719721|gb|EE095097.1|EE095097
EST:     TTCGGAAAGACGACATGCGCCATGTTGCCAAGGCAACTGGTGCAACTATG                         GTTTCAACGTTTGCTGACATGGAAGGG
genomic: TTCGGAAAGATGACATGCGCCATGTTGCCAAGGCAACTGGTGCAACTATGgtatgtttct ... tgttctgcagGTTTCAACGTTTGCTGACATGGAAGGG
EST: gi|26264285|gb|CA815348.1|CA815348
EST:     TTCGGAAAGACGACATGCGCCATGTTGCCAAGGCAACTGGTGCAACTATG                         GTTTCAACGTTTGCTGACATGGAAGGGGATGAGACATTTGATTCATCATTT
genomic: TTCGGAAAGATGACATGCGCCATGTTGCCAAGGCAACTGGTGCAACTATGgtatgtttct ... tgttctgcagGTTTCAACGTTTGCTGACATGGAAGGGGATGAGACATTTGATTCATCATTT
EST: gi|351037610|gb|FQ462593.1|FQ462593
EST:     TTCGGAAAGACGACATGCGCCATGTTGCCAAGGCAACTGGTGCAACTATG                         GTTTCAACGTTTGCTGACATGGAAGGGGATGAGACATTTGATTCATCATTT
genomic: TTCGGAAAGATGACATGCGCCATGTTGCCAAGGCAACTGGTGCAACTATGgtatgtttct ... tgttctgcagGTTTCAACGTTTGCTGACATGGAAGGGGATGAGACATTTGATTCATCATTT
EST: gi|110701345|gb|EE078813.1|EE078813
EST:     TTCGGAAAGACGACATGCGCCATGTTGCCAAGGCAACTGGTGCAACTATG                         GTTTCAACGTTTGCTGACATGGAAGGGGATGAGACATTTGATTCATCATTT
genomic: TTCGGAAAGATGACATGCGCCATGTTGCCAAGGCAACTGGTGCAACTATGgtatgtttct ... tgttctgcagGTTTCAACGTTTGCTGACATGGAAGGGGATGAGACATTTGATTCATCATTT
EST: gi|351017726|gb|FQ436079.1|FQ436079
EST:     TTCGGAAAGACGACATGCGCCATGTTGCCAAGGCAACTGGTGCAACTATG                         GTTTCAACGTTTGCTGACATGGAAGGGGATGAGACATTTGATTCATCATTT
genomic: TTCGGAAAGATGACATGCGCCATGTTGCCAAGGCAACTGGTGCAACTATGgtatgtttct ... tgttctgcagGTTTCAACGTTTGCTGACATGGAAGGGGATGAGACATTTGATTCATCATTT
EST: gi|37187670|gb|CF607023.1|CF607023
EST:     TTCGGAAAGACGACATGCGCCATGTTGCCAAGGCAACTGGTGCAACTATG                         GTTTCAACGTTTGCTGACATGGAAGGGGATGAGACATTTGATTCATCATTT
genomic: TTCGGAAAGATGACATGCGCCATGTTGCCAAGGCAACTGGTGCAACTATGgtatgtttct ... tgttctgcagGTTTCAACGTTTGCTGACATGGAAGGGGATGAGACATTTGATTCATCATTT
EST: gi|33403784|gb|CF209411.1|CF209411
EST:     TTCGGAAAGACGACATGCGCCATGTTGCCAAGGCAACTGGTGCAACTATG                         GTTTCAACGTTTGCTGACATGGAAGGGGATGAGACATTTGATTCATCATTT
genomic: TTCGGAAAGATGACATGCGCCATGTTGCCAAGGCAACTGGTGCAACTATGgtatgtttct ... tgttctgcagGTTTCAACGTTTGCTGACATGGAAGGGGATGAGACATTTGATTCATCATTT
EST: gi|71882935|gb|DT031990.1|DT031990
EST:     TTCGGAAAGACGACATGCGCCATGTTGCCAAGGCAACTGGTGCAACTATG                         GTTTCAACGTTTGCTGACATGGAAGGGGATGAGACATTTGATTCATCATTT
genomic: TTCGGAAAGATGACATGCGCCATGTTGCCAAGGCAACTGGTGCAACTATGgtatgtttct ... tgttctgcagGTTTCAACGTTTGCTGACATGGAAGGGGATGAGACATTTGATTCATCATTT
EST: gi|30322269|gb|CD005531.1|CD005531
EST:     TTCGGAAAGACGACATGCGCCATGTTGCCAAGGCAACTGGTGCAACTATG                         GTTTCAACGTTTGCTGACATGGAAGGGGATGAGACATTTGATTCATCATTT
genomic: TTCGGAAAGATGACATGCGCCATGTTGCCAAGGCAACTGGTGCAACTATGgtatgtttct ... tgttctgcagGTTTCAACGTTTGCTGACATGGAAGGGGATGAGACATTTGATTCATCATTT
EST: gi|32272417|gb|CD721576.1|CD721576
EST:     GCGCCATGTTGCCAAGGCAACTGGTGCAACTATG                         GTTTCAACGTTTGCTGACATGGAAGGGGATGAGACATTTGATTCATCATTT
genomic: GCGCCATGTTGCCAAGGCAACTGGTGCAACTATGgtatgtttct ... tgttctgcagGTTTCAACGTTTGCTGACATGGAAGGGGATGAGACATTTGATTCATCATTT
EST: gi|110688105|gb|EE066273.1|EE066273
EST:     TTCGGAAAGACGACATGCGCCATGTTGCCAAGGCAACTGGTGCAACTATG                         GTTTCAACGTTTGCTGACATGGAAGGGGACGAGACATTTGATTCATCATTT
genomic: TTCGGAAAGATGACATGCGCCATGTTGCCAAGGCAACTGGTGCAACTATGgtatgtttct ... tgttctgcagGTTTCAACGTTTGCTGACATGGAAGGGGATGAGACATTTGATTCATCATTT
EST: gi|351048864|gb|FQ431529.1|FQ431529
EST:     TTCGGAAAGACGACATGCGCCATGTTGCCAAGGCAACTGGTGCAACTATG                         GTTTCAACGTTTGCTGACATGGAAGGGGATGAGACATTTGATTCATCATTT
genomic: TTCGGAAAGATGACATGCGCCATGTTGCCAAGGCAACTGGTGCAACTATGgtatgtttct ... tgttctgcagGTTTCAACGTTTGCTGACATGGAAGGGGATGAGACATTTGATTCATCATTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TACTTTGTGGAGGCTGGGGCAATTGCTGTGAGGCGTGTTCGGAAAGATGACATGCGCCATGTTGCCAAGGCAACTGGTGCAACTATGgtatgtttcttaactctgcttcccaattgatatcaccgggtgaggttgttttaatatgctcttggaatttacaaataagaatgctttaatgtttttgttc

- - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gggtgag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ataagaa