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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgttttgtatccaagctcctccgtttggttgccgagaaaggagaaagaaggaagggaagggagaaagagaagaaaactttttaatcttagtttgtgctttgtggttcagGCATGTTTGGATTCTGGATTCTTCTATGTGATCAATCACGGAATCAGCCAGGAATTTATGGACGAGGTTTTCGCCCAAAGCAAAAGGTTTTTCACTTTGC

Basic information

species Vitis vinifera
transcript Vv11s0016g03200.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g03200.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os01g09300.2 (Oryza sativa), 3'ss of exon 1
gtgcgttttgtatccaagctcctccgtttggttgccgagaaaggagaaagaaggaagggaagggagaaagagaagaaaactttttaatcttagtttgtgctttgtggttcagGCATGTTTGGATTCTGGATTCTTCTATGTGATCAATCACGGAATCAGCCAGGAATTTATGGACGAGGTTTTCGCCCAAAGCAAAAGGTTTTTCACTTTGC
            | ||  || |   ||     |||   |   |    | | |       ||  |      |  | |    ||  ||| |  |  ||      |       |||||||| ||||||| || |||||||||||| |  |||| ||||| |||||||| || ||||| || ||||| ||||| ||||| |  || ||     | |
---------actttcagacttcattgtcactgtgctctgctggttctatgtatttt---aatagtttttaaccatattttttcctaaacaaatgtttcatccttcttcatagGCATGTCTGGATTCAGGCTTCTTCTATGTGGTGGATCATGGAATAAGCCAGGAGTTAATGGATGATGTTTTTGCCCAGAGCAAGAAATTCTTTGACCTTC

upper sequence: Vv11s0016g03200.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA01G01170.2 (Glycine max), 3'ss of exon 1
gtgcgttttgtatccaagctcctccgtttggttgccgagaaaggagaaagaaggaagggaagggagaaagagaagaaaactttttaatcttagtttgtgctttgtggttcagGCATGTTTGGATTCTGGATTCTTCTATGTGATCAATCACGGAATCAGCCAGGAATTTATGGACGAGGTTTTCGCCCAAAGCAAAAGGTTTTTCACTTTGC
    |||||   | |   ||| |     || ||    | ||   |    |     ||   | |          |    |  ||    |  | |||| |    | || || |||||||||||||||| || || ||||| ||  ||||||| ||||| ||||||||||| |||||||||||||| || || ||||| | ||| ||| || | |
----gtttttgcttc---ctcttttacatgatttgtcacaattcactttgtttttagaccatgatctttttttatgtcatcttaatgttgttgtttttttgctttgttttagGCATGTTTGGATTCCGGTTTTTTCTACGTTGTCAATCATGGAATAAGCCAGGAATTCATGGACGAGGTTTTTGCGCAGAGCAAGAAGTTCTTCTCTCTTC

upper sequence: Vv11s0016g03200.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA16G08470.1 (Glycine max), 3'ss of exon 1
gtgcgttttgtatccaagctcctccgtttggttgccgagaaaggagaaagaaggaagggaagggagaaagagaagaaaactttttaatcttagtttgtgctttgtggttcagGCATGTTTGGATTCTGGATTCTTCTATGTGATCAATCACGGAATCAGCCAGGAATTTATGGACGAGGTTTTCGCCCAAAGCAAAAGGTTTTTCACTTTGC
     |||||  |||    | | |  |||| ||   ||   | ||      |  | |  |                     | ||||| ||   || || |||    || |||||||||||||||| || || ||||| ||  ||||||| ||||| ||||||||||| ||||| |||||||| || || ||||| |  || ||| || | |
---gtttttgcttcctcaattcac--tttgttttttgaaccatgattttttatcatgtca---------------------tattaatgtt---ttttgtttttgtttttagGCATGTTTGGATTCCGGTTTTTTCTACGTTGTCAATCATGGAATAAGCCAGGAATTCATGGAAGAGGTTTTTGCACAGAGCAAGAAATTCTTCTCTCTTC

upper sequence: Vv11s0016g03200.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT1G35190.1 (Arabidopsis thaliana), 3'ss of exon 1
gtgcgttttgtatccaagctcctccgtttgg----ttgccga--------gaaaggagaaagaaggaagggaagg-----gagaaagagaagaaaacttttt------aatcttagtttgtgct-ttgtgg-ttcagGCATGTTTGGATTCTGGATTCTTCTATGTGATCAATCACGGAATCAGCCAGGAATTTATGGACGAGGTTTTCGCCCAAAGCAAAAGGTTTTTCACTTTGC
||  || |   |||  || |  ||  ||| |    |||  |         || |    ||    | | |  | |      ||  |  | ||||    |||||      |||  |  | || |   || ||| |||||||||||||||||| |||||| ||||||||||||||||| || || ||| | || || |||||||| |||||||  || ||||| | | ||||  || | |
gtttgtctcccatctcagtttttcgattttgcatgttgttgttttcttttgacaaatcaattttgcatgttatgaatcttgatcattaaaagattttttttttgattcaatgatgatatgggtaattatggcttcagGCATGTTTGGATTGTGGATTTTTCTATGTGATCAATCATGGGATAAGCGAAGAGTTCATGGACGATGTTTTCGAGCAGAGCAAGAAGCTTTTTGCTCTTC

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|71860593|gb|DT009648.1|DT009648
EST:     TTGATCTCTCCAGTCCAGACATTCACAAATCCGTTTCTTTACTCAAGCAG                         GCATGTTTGGATTCTGGATTCTTCTATGTGATCAATCACGGAATCAGCCAG
genomic: TTGATCTCTCCAGTCCAGACATTCACAAATCCGTTTCTTTACTCAAGCAGgtgcgttttg ... tgtggttcagGCATGTTTGGATTCTGGATTCTTCTATGTGATCAATCACGGAATCAGCCAG
EST: gi|71862772|gb|DT011827.1|DT011827
EST:     TTGATCTCTCCAGTCCAGACATTCACAAATCCGTTTCTTTACTCAAGCAG                         GCATGTTTGGATTCTGGATTCTTCTATGTGATCAATCACGGAATCAGCCAG
genomic: TTGATCTCTCCAGTCCAGACATTCACAAATCCGTTTCTTTACTCAAGCAGgtgcgttttg ... tgtggttcagGCATGTTTGGATTCTGGATTCTTCTATGTGATCAATCACGGAATCAGCCAG
EST: gi|71861743|gb|DT010798.1|DT010798
EST:     TTGATCTCTCCAGTCCAGACATTCACAAATCCGTTTCTTTACTCAAGCAG                         GCATGTTTGGATTCTGGATTCTTCTATGTGATCAATCACGGAATCAGCCAG
genomic: TTGATCTCTCCAGTCCAGACATTCACAAATCCGTTTCTTTACTCAAGCAGgtgcgttttg ... tgtggttcagGCATGTTTGGATTCTGGATTCTTCTATGTGATCAATCACGGAATCAGCCAG
EST: gi|71862499|gb|DT011554.1|DT011554
EST:     TTGATCTCTCCAGTCCAGACATTCACAAATCCGTTTCTTTACTCAAGCAG                         GCATGTTTGGATTCTGGATTCTTCTATGTGATCAATCACGGAATCAGCCAG
genomic: TTGATCTCTCCAGTCCAGACATTCACAAATCCGTTTCTTTACTCAAGCAGgtgcgttttg ... tgtggttcagGCATGTTTGGATTCTGGATTCTTCTATGTGATCAATCACGGAATCAGCCAG
EST: gi|71861630|gb|DT010685.1|DT010685
EST:     TTGATCTCTCCAGTCCAGACATTCACAAATCCGTTTCTTTACTCAAGCAG                         GCATGTTTGGATTCTGGATTCTTCTATGTGATCAATCACGGAATCAGCCAG
genomic: TTGATCTCTCCAGTCCAGACATTCACAAATCCGTTTCTTTACTCAAGCAGgtgcgttttg ... tgtggttcagGCATGTTTGGATTCTGGATTCTTCTATGTGATCAATCACGGAATCAGCCAG
EST: gi|71864491|gb|DT013546.1|DT013546
EST:     TTGATCTCTCCAGTCCAGACATTCACAAATCCGTTTCTTTACTCAAGCAG                         GCATGTTTGGATTCTGGATTCTTCTATGTGATCAATCACGGAATCAGCCAG
genomic: TTGATCTCTCCAGTCCAGACATTCACAAATCCGTTTCTTTACTCAAGCAGgtgcgttttg ... tgtggttcagGCATGTTTGGATTCTGGATTCTTCTATGTGATCAATCACGGAATCAGCCAG
EST: gi|71864483|gb|DT013538.1|DT013538
EST:     TTGATCTCTCCAGTCCAGACATTCACAAATCCGTTTCTTTACTCAAGCAG                         GCATGTTTGGATTCTGGATTCTTCTATGTGATCAATCACGGAATCAGCCAG
genomic: TTGATCTCTCCAGTCCAGACATTCACAAATCCGTTTCTTTACTCAAGCAGgtgcgttttg ... tgtggttcagGCATGTTTGGATTCTGGATTCTTCTATGTGATCAATCACGGAATCAGCCAG
EST: gi|71863373|gb|DT012428.1|DT012428
EST:     TTGATCTCTCCAGTCCAGACATTCACAAATCCGTTTCTTTACTCAAGCAG                         GCATGTTTGGATTCTGGATTCTTCTATGTGATCAATCACGGAATCAGCCAG
genomic: TTGATCTCTCCAGTCCAGACATTCACAAATCCGTTTCTTTACTCAAGCAGgtgcgttttg ... tgtggttcagGCATGTTTGGATTCTGGATTCTTCTATGTGATCAATCACGGAATCAGCCAG
EST: gi|294965788|gb|GW839243.1|GW839243
EST:     TTGATCTCTCCAGTCCAGACATTCACCAATCCGTTTCTTTACTCAAGCAG                         GCATGTTTGGATTCTGGATTCTTCTATGTGATCAATCACGGAATCAGCCAG
genomic: TTGATCTCTCCAGTCCAGACATTCACAAATCCGTTTCTTTACTCAAGCAGgtgcgttttg ... tgtggttcagGCATGTTTGGATTCTGGATTCTTCTATGTGATCAATCACGGAATCAGCCAG
EST: gi|71865183|gb|DT014238.1|DT014238
EST:     TTGATCTCTCCTGTCCAGACATTCACAAATCCGTTTCTTTACTCAAGCAG                         GCATGTTTGGATTCTGGATTCTTCTATGTGATCAATCACGGAATCAGCCAG
genomic: TTGATCTCTCCAGTCCAGACATTCACAAATCCGTTTCTTTACTCAAGCAGgtgcgttttg ... tgtggttcagGCATGTTTGGATTCTGGATTCTTCTATGTGATCAATCACGGAATCAGCCAG
EST: gi|71864565|gb|DT013620.1|DT013620
EST:     TTGATCTCTCCAGTCCAGACATTCACAAATCCGTTTCTTTACTCAAGCAG                         GCATGTTTGGATTCTGGATTCTTCTATGTGATCAATCACGGAATCAGCCAG
genomic: TTGATCTCTCCAGTCCAGACATTCACAAATCCGTTTCTTTACTCAAGCAGgtgcgttttg ... tgtggttcagGCATGTTTGGATTCTGGATTCTTCTATGTGATCAATCACGGAATCAGCCAG
EST: gi|110690968|gb|EE068534.1|EE068534
EST:     TTGATCTCTCCTGTCCAGACATTCACAAATCCGTTTCTTTACTCAAGCAG                         GCATGTTTGGATTCTGGATTCTTCTATGTGATCAATCACGGAATCAGCCAG
genomic: TTGATCTCTCCAGTCCAGACATTCACAAATCCGTTTCTTTACTCAAGCAGgtgcgttttg ... tgtggttcagGCATGTTTGGATTCTGGATTCTTCTATGTGATCAATCACGGAATCAGCCAG
EST: gi|110404543|gb|EC969762.1|EC969762
EST:     TTGATCTCTCCTGTCCAGACATTCACAAATCCGTTTCTTTACTCAAGCAG                         GCATGTTTGGATTCTGGATTCTTCTATGTGATCAATCACGGAATCAGCCAG
genomic: TTGATCTCTCCAGTCCAGACATTCACAAATCCGTTTCTTTACTCAAGCAGgtgcgttttg ... tgtggttcagGCATGTTTGGATTCTGGATTCTTCTATGTGATCAATCACGGAATCAGCCAG
EST: gi|71863525|gb|DT012580.1|DT012580
EST:     TTGATCTCTCCTGTCCAGACATTCACAAATCCGTTTCTTTACTCAAGCAG                         GCATGTTTGGATTCTGGATTCTTCTATGTGATCAATCACGGAATCAGCCAG
genomic: TTGATCTCTCCAGTCCAGACATTCACAAATCCGTTTCTTTACTCAAGCAGgtgcgttttg ... tgtggttcagGCATGTTTGGATTCTGGATTCTTCTATGTGATCAATCACGGAATCAGCCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggaagggagaaagagaagaaaactttttaatcttagtttgtgctttgtggttcagGCATGTTTGGATTCTGGATTCTTCTATGTGATCAATCACGGAATCAGCCAGGAATTTATGGACGAGGTTTTCGCCCAAAGCAAAAGGTTTTTCACTTTGC
                        ttttaat  putative branch site (score: 3)
                  aaaactttttaatctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgttttgtatccaagctcctccgtttggttgccgagaaaggagaaagaaggaagggaagggagaaagagaagaaaactttttaatcttagtttgtgctttgtggttcagGCATGTTTGGATTCTGGATTCTTCTATGTGATCAATCACGGAATCAGCCAGGAATTTATGGACGAGGTTTTCGCCCAAAGCAAAAGGTTTTTCACTTTGC

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