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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tccattttttttttttccattttgcttccaccaaattcctgattatgacagttgcaaacttgcatgattttctatgactaattttttgttacttgcccagGTACTCCCCTATGATCAACTGATGCAGGAATTAGATGTTACAAATGTACGTGAACTTGAAGATTTTCTTATCAATGAGTGCATGTATGCG

Basic information

species Vitis vinifera
transcript Vv15s0021g01580.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0021g01580.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os07g30840.4 (Oryza sativa), 3'ss of exon 3
--------tccattttttttttttccattttgcttcca--ccaaattcctgattatgacagttgcaaacttgcatgattttctatgactaattttttgttacttgcccagGTACTCCCCTATGATCAACTGATGCAGGAATTAGATGTTACAAATGTACGTGAACTTGAAGATTTTCTTATCAATGAGTGCATGTATGCG
        |  | | || | |||| | ||     ||    | |  ||  || ||  |||| |   |||  ||| || |||| ||| |  |  ||| | ||       ||||| || || ||||||||||| ||||| ||||| |||||| | |||||| | ||||| |||||||| || |||||||||||||||||  ||
caagttcatgtagtattatcttttaccttaaaactctgttctatgtttttgctttagacaatactaaatgtgcttggtttt-tattatca--tttctatt-------cagGTGCTACCATATGATCAACTCATGCAAGAATTGGATGTTTCCAATGTAAGAGAACTCGAAGATTTCCTCATCAATGAGTGCATGTACTCG

upper sequence: Vv15s0021g01580.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G171745_T05 (Zea mays), 3'ss of exon 2
--tccattttttttttttccattttgcttccaccaaattcctgattatgacagttgcaaacttgcatgattttctatgactaattttttgttacttgcccagGTACTCCCCTATGATCAACTGATGCAGGAATTAGATGTTACAAATGTACGTGAACTTGAAGATTTTCTTATCAATGAGTGCATGTATGCG
   | || ||        |  || | |        || |     | || |||  || | |  |  | | |  ||  |   | | | |   ||  ||   ||| |||| || |||||||| || ||||| || ||||| ||| |||||||| | ||||| |||||||| || |||||||||||||||||| ||
cgactatcttcccggcgccgtttatccccgttatgaactaggattcataaca-ctgtagaactctaaggtactcacttgtttactata-attctttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTAGACGTTTCAAATGTAAGAGAACTCGAAGATTTCCTAATCAATGAGTGCATGTATTCG

upper sequence: Vv15s0021g01580.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G152100_T02 (Zea mays), 3'ss of exon 1
tccattttttttttttccattttgcttccaccaaattcctgattatgacagt--tgcaaacttgcatgattttctatgactaattttttgttacttgcccagGTACTCCCCTATGATCAACTGATGCAGGAATTAGATGTTACAAATGTACGTGAACTTGAAGATTTTCTTATCAATGAGTGCATGTATGCG
   |   || || |  | |  |   || |     |||||  | |||     |  || | | ||  |   |  ||  |   | ||| |   ||  ||   ||| |||| || |||||||| || ||||| || || |||||| | || ||| | ||||| ||||||||||| |||||||||||||||||||| 
-gaagcgttcttgtagcaaaatcttttactttctattccatactatatttttcctgtagaattctaatgtactcctttttttattata-attttttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATGCA

upper sequence: Vv15s0021g01580.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G027551_T01 (Zea mays), 3'ss of exon 1
tccattttttttttttccattttgcttccaccaaattcctgattatgacagt-tgcaaacttgcatgattttctatgactaattttttgttacttgcccagGTACTCCCCTATGATCAACTGATGCAGGAATTAGATGTTACAAATGTACGTGAACTTGAAGATTTTCTTATCAATGAGTGCATGTATGCG
   |   || || |  | |  |   || |     |||||  | |||       | || | ||  |   |  ||  |   | | | |   ||  ||   ||| |||| || |||||||| || ||||| || || |||||| | || ||| | ||||| ||||||||||| |||||||||||||||||||| 
ataagcgttcttgtagcaaaatcttttactttctattccatactatattttcctacagaattctaatgtactcctttttttactata-attttttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATGCA

upper sequence: Vv15s0021g01580.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G085670_T03 (Zea mays), 3'ss of exon 3
tccattttttttttttccattttgcttccaccaaattcctgattatgacagt--tgcaaacttgcatgattttctatgactaattttttgttacttgcccagGTACTCCCCTATGATCAACTGATGCAGGAATTAGATGTTACAAATGTACGTGAACTTGAAGATTTTCTTATCAATGAGTGCATGTATGCG
   |   || || |  | |  |   || |     |||||  | |||     |  || | | ||  |   |  ||  |   | | | |   ||  ||   ||| |||| || |||||||| || ||||| || || |||||| | || ||| | ||||| ||||||||||| |||||||||||||||||| | 
-gaagcgttcttgtagcaaaatcttttactttctattccatactatatttttcctgtagaattctaatgtactcctttttttactata-attttttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATTCA

upper sequence: Vv15s0021g01580.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G152100_T01 (Zea mays), 3'ss of exon 3
tccattttttttttttccattttgcttccaccaaattcctgattatgacagttgcaaacttgcatgattttctatgactaattttttgt-tacttgcccagGTACTCCCCTATGATCAACTGATGCAGG-AATTAGATGTTACAAATGTACGTGAACTTGAAGATTTTCTTATCAATGAGTGCATGTATGCG
            |     |||||     ||   | | | ||  |   | ||||| |   || ||   |     |   | ||  || ||  |  |     |||   |   |   |   |||||   ||    |  ||||| |   ||                                              
--gtaagagaactcgaagattttctaatcaatgagtgcatgtatgcaagagttggatgtttccaacgtaagagaactcgaagattatgcatgttcatgtagGGTATTGTCAGAGGCAAACTGGATCAACTGAGAAGATGCTTTGAA----------------------------------------------

upper sequence: Vv15s0021g01580.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G115277_T02 (Zea mays), 3'ss of exon 3
tccattttttttttttccattttgcttccaccaaattcctgattatgacagt--tgcaaacttgcatgattttctatgactaattttttgttacttgcccagGTACTCCCCTATGATCAACTGATGCAGGAATTAGATGTTACAAATGTACGTGAACTTGAAGATTTTCTTATCAATGAGTGCATGTATGCG
   |   || || |  | |  |   || |     |||||  |  ||     |  || | | ||  |   |  ||  |   | | | | | ||  ||   ||| |||| || |||||||| || ||||| || || |||||| | || ||| | ||||| ||||||||||| |||||||||||||||||| | 
-gaagcgttcttgtagcaaaatcttttactttctattccataccatatttttcctgtagaattctaatgtactcctttttttactatatttt-tttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATTCA

upper sequence: Vv15s0021g01580.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G152805_T01 (Zea mays), 3'ss of exon 3
tccattttttttttttccattttgcttccaccaaattcctgattatgacagt--tgcaaacttgcatgattttctatgactaattttttgttacttgcccagGTACTCCCCTATGATCAACTGATGCAGGAATTAGATGTTACAAATGTACGTGAACTTGAAGATTTTCTTATCAATGAGTGCATGTATGCG
   |   || || |  | |  |   || |     |||||  |  ||     |  || | | ||  |   |  ||  |   | | | |   ||  ||   ||| |||| || |||||||| || ||||| || || |||||| | || ||| | ||||| ||||||||||| |||||||||||||||||| | 
-gaagcgttcttgtagcaaaatcttttactttctattccataccatatttttcctgtagaattctaatgtactcctttttttactata-attttttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATTCA

upper sequence: Vv15s0021g01580.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA13G25690.1 (Glycine max), 3'ss of exon 3
----tccattttttttttttccattttgcttccaccaaattcctgat--tatgacagttgcaaacttgcatgattttctatgactaattttttgttacttgcccagGTACTCCCCTATGATCAACTGATGCAGGAATTAGATGTTACAAATGTACGTGAACTTGAAGATTTTCTTATCAATGAGTGCATGTATGCG
      |   ||| | |  ||  |||||||      |   |||| ||  | ||||| | |||| |        ||||  |  |  |||| ||| | |  |   |||||||| |||||||| |||||||||||||| |||||||| |||||||| ||||| |||||||||||||| || ||||| ||||||||||||
atataactggtttctctgctcttttttgctgttttgagtgtccttatcttttgacattggcaatca-----atttttacaaaatcaattgtttttcaaat-ttcagGTACTACCCTATGACCAACTGATGCAGGAGTTAGATGTGACAAATGTTCGTGAGCTTGAAGATTTTCTAATTAATGAATGCATGTATGCG

upper sequence: Vv15s0021g01580.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA15G35760.1 (Glycine max), 3'ss of exon 3
----------tccattttttttttttccattttgcttccaccaaattcctgat--tatgacagttgcaaacttgcatgattttctatgactaattttttgttacttgcccagGTACTCCCCTATGATCAACTGATGCAGGAATTAGATGTTACAAATGTACGTGAACTTGAAGATTTTCTTATCAATGAGTGCATGTATGCG
            |   ||| ||| |||  |||||||      |   |||| ||  | ||||| | |||| |    ||  ||||  |  |  |||| ||| |        |||||||| |||||||| |||||||||||||| |||||||| |||||||| ||||| |||||||||||||| || ||||| ||||||||||||
tgtagaatataactggtttgtttgttcttttttgctgttttgagtgtccttatcttttgacattggcaatc----atttttttacaaaatcaattattttt--------cagGTACTACCCTATGACCAACTGATGCAGGAGTTAGATGTGACAAATGTTCGTGAGCTTGAAGATTTTCTAATTAATGAATGCATGTATGCG

upper sequence: Vv15s0021g01580.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA18G48710.1 (Glycine max), 3'ss of exon 3
-tccattttttttttttcc--attttgcttccaccaaattcctgattatgacagttgcaaacttgca-tgattttctatgactaattttttgttacttgcccagGTACTCCCCTATGATCAACTGATGCAGGAATTAGATGTTACAAATGTACGTGAACTTGAAGATTTTCTTATCAATGAGTGCATGTATGCG
   || |    ||| ||||   | ||||       |   |     |  | | | ||  | | ||| | | | ||| ||  | |   ||||  ||  ||    ||||||| |||||| | |||||||||||||| |||||  | |||||||| |||||||||||||||||||| || | ||| ||||||||  | 
acacactaaagtttcttcctggtattgccgtt-tgaggctgagtgtctttatattttgacatttgtaatcaatttttaaaagtgcgttttattt--ttctttaGGTACTACCCTATAACCAACTGATGCAGGAGTTAGACATGACAAATGTTCGTGAACTTGAAGATTTTCTAATTAGTGAATGCATGTACTC-

upper sequence: Vv15s0021g01580.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT1G02090.1 (Arabidopsis thaliana), 3'ss of exon 3
-tccattttttttttttccat--tttgcttccaccaaattcctgattatgacagttgcaaacttgcatgattttcta--tgactaatttttt---gttacttgcc-cagGTACTCCCCTATGATCAACTGATGCAGGAATTAGATGTTACAAATGTACGTGAACTTGAAGATTTTCTTATCAATGAGTGCATGTATGCG
 |  |||| | ||   | |||  |||||| |  | |  | |    ||     |  |     |     || ||  |||  ||| |   | | |     | ||||    ||||| | |||||||||  ||| |||   || ||||||||| | ||||| || ||||| || || |||||||||||||| ||||||||||||
gtatatttgtcttaggttcatgatttgctcctgctatctactctgttccattatctttttcccctgctgtttgcctaactgaatgtctctctcactctgcttgttatagGTATTGCCCTATGATACACTAATGGTCGAGTTAGATGTTTCCAATGTTCGCGAACTCGAGGACTTTCTTATCAATGAATGCATGTATGCG

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|351022721|gb|FQ428630.1|FQ428630
EST:     CCCTAAAGTTAAAGCAGCTTACTGTACTTACACTGGCTGAGACAAACAAG                         GTACTCCCCTATGATCAACTGATGCAGGAATTAGATGTTACAAATGTACGT
genomic: CCCTAAAGTTAAAGCAGCTTACTGTACTTACACTGGCTGAGACAAACAAGgtaatctatt ... acttgcccagGTACTCCCCTATGATCAACTGATGCAGGAATTAGATGTTACAAATGTACGT
EST: gi|351024207|gb|FQ423630.1|FQ423630
EST:     CCCTAAAGTTAAAGCAGCTTACTGTACTTACACTGGCTGAGACAAACAAG                         GTACTCCCCTATGATCAACTGATGCAGGAATTAGATGTTACAAATGTACGT
genomic: CCCTAAAGTTAAAGCAGCTTACTGTACTTACACTGGCTGAGACAAACAAGgtaatctatt ... acttgcccagGTACTCCCCTATGATCAACTGATGCAGGAATTAGATGTTACAAATGTACGT
EST: gi|351030256|gb|FQ432194.1|FQ432194
EST:     CCCTAAAGTTAAAGCAGCTTACTGTACTTACACTGGCTGAGACAAACAAG                         GTACTCCCCTATGATCAACTGATGCAGGAATTAGATGTTACAAATGTACGT
genomic: CCCTAAAGTTAAAGCAGCTTACTGTACTTACACTGGCTGAGACAAACAAGgtaatctatt ... acttgcccagGTACTCCCCTATGATCAACTGATGCAGGAATTAGATGTTACAAATGTACGT
EST: gi|161721497|gb|FC069725.1|FC069725
EST:     CCCTAAAGTTAAAGCAGCTTACTGTACTTACACTGGCTGAGACAAACAAG                         GTACTCCCCTATGATCAACTGATGCAGGAATTAGATGTTACAAATGTACGT
genomic: CCCTAAAGTTAAAGCAGCTTACTGTACTTACACTGGCTGAGACAAACAAGgtaatctatt ... acttgcccagGTACTCCCCTATGATCAACTGATGCAGGAATTAGATGTTACAAATGTACGT
EST: gi|351028781|gb|FQ433211.1|FQ433211
EST:     CCCTAAAGTTAAAGCAGCTTACTGTACTTACACTGGCTGAGACAAACAAG                         GTACTCCCCTATGATCAACTGATGCAGGAATTAGATGTTACAAATGTACGT
genomic: CCCTAAAGTTAAAGCAGCTTACTGTACTTACACTGGCTGAGACAAACAAGgtaatctatt ... acttgcccagGTACTCCCCTATGATCAACTGATGCAGGAATTAGATGTTACAAATGTACGT
EST: gi|352798513|gb|FQ480538.1|FQ480538
EST:     CCCTAAAGTTAAAGCAGCTTACTGTACTTACACTGGCTGAGACAAACAAG                         GTACTCCCCTATGATCAACTGATGCAGGAATTAGATGTTACAAATGTACGT
genomic: CCCTAAAGTTAAAGCAGCTTACTGTACTTACACTGGCTGAGACAAACAAGgtaatctatt ... acttgcccagGTACTCCCCTATGATCAACTGATGCAGGAATTAGATGTTACAAATGTACGT
EST: gi|351039449|gb|FQ461316.1|FQ461316
EST:     CCCTAAAGTTAAAGCAGCTTACTGTACTTACACTGGCTGAGACAAACAAG                         GTACTCCCCTATGATCAACTGATGCAGGAATTAGATGTTACAAATGTACGT
genomic: CCCTAAAGTTAAAGCAGCTTACTGTACTTACACTGGCTGAGACAAACAAGgtaatctatt ... acttgcccagGTACTCCCCTATGATCAACTGATGCAGGAATTAGATGTTACAAATGTACGT
EST: gi|351029115|gb|FQ435315.1|FQ435315
EST:     CCCTAAAGTTAAAGCAGCTTACTGTACTTACACTGGCTGAGACAAACAAG                         GTACTCCCCTATGATCAACTGATGCAGGAATTAGATGTTACAAATGTACGT
genomic: CCCTAAAGTTAAAGCAGCTTACTGTACTTACACTGGCTGAGACAAACAAGgtaatctatt ... acttgcccagGTACTCCCCTATGATCAACTGATGCAGGAATTAGATGTTACAAATGTACGT
EST: gi|352791342|gb|FQ479729.1|FQ479729
EST:     CCCTAAAGTTAAAGCAGCTTACTGTACTTACACTGGCTGAGACAAACAAG                         GTACTCCCCTATGATCAACTGATGCAGGAATTAGATGTTACAAATGTACGT
genomic: CCCTAAAGTTAAAGCAGCTTACTGTACTTACACTGGCTGAGACAAACAAGgtaatctatt ... acttgcccagGTACTCCCCTATGATCAACTGATGCAGGAATTAGATGTTACAAATGTACGT
EST: gi|351025041|gb|FQ433458.1|FQ433458
EST:     CCCTAAAGTTAAAGCAGCTTACTGTACTTACACTGGCTGAGACAAACAAG                         GTACTCCCCTATGATCAACTGATGCAGGAATTAGATGTTACAAATGTACGT
genomic: CCCTAAAGTTAAAGCAGCTTACTGTACTTACACTGGCTGAGACAAACAAGgtaatctatt ... acttgcccagGTACTCCCCTATGATCAACTGATGCAGGAATTAGATGTTACAAATGTACGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgacagttgcaaacttgcatgattttctatgactaattttttgttacttgcccagGTACTCCCCTATGATCAACTGATGCAGGAATTAGATGTTACAAATGTACGTGAACTTGAAGATTTTCTTATCAATGAGTGCATGTATGCG
                              gactaat  putative branch site (score: 2)
                                              cttgccc  putative PPT
                     attttctatgactaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tccattttttttttttccattttgcttccaccaaattcctgattatgacagttgcaaacttgcatgattttctatgactaattttttgttacttgcccagGTACTCCCCTATGATCAACTGATGCAGGAATTAGATGTTACAAATGTACGTGAACTTGAAGATTTTCTTATCAATGAGTGCATGTATGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
-ccatttt
- - - - - - - - - - - - - -ccaccaa
- - - - - - - - - - - - - - - - - -ttcctga
- - - - - - - - - - - - - - - - - - - - - - - - - - tgcaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatgat