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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcaaatgttcataaggtggtgtagggaagatcatctttgttcaactctattattaaactattcaagaacttgattccttttcaccttgtgtctgtttcagGAATATTATGATACTGGCTGAAAGTCAGACTGTTTATGCCATTGACCTTCTTGGTTTTGGTGCATCTGATAAGCCATCAGGCTTTGCATATACAATGGAA

Basic information

species Vitis vinifera
transcript Vv18s0089g01420.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0089g01420.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA20G35660.1 (Glycine max), 3'ss of exon 1
--tcaaatgttcataaggtggtgtagggaagatcatctttgttcaactctattattaaactattcaagaacttgattccttttcaccttgtgtctgtttcagGAATATTATGATACTGGCTGAAAGTCAGACTGTTTATGCCATTGACCTTCTTGGTTTTGGTGCATCTGATAAGCCATCAGGCTTTGCATATACAATGGAA
  ||||| ||        |  | |    |   | |   |    |||     | ||  || |   | || |  | | |  ||||     | | |||  ||||||||||| |  | ||||||  | | | | ||||||||||| ||||| |||||||||||||| || || ||||||||  ||||||||  |||||| ||||||
cctcaaaagtcaccttttttttcttctcat--ttactctctaacaatgtagtcatcgaattgaaccagtaggtaagtattttttgttgtttttcttcttcagGAATATCAGCACACTGGCCCAGAATTATACTGTTTATGCTATTGATCTTCTTGGTTTTGGGGCTTCAGATAAGCCTCCAGGCTTTCAATATACCATGGAA
















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|110376208|gb|EC941257.1|EC941257
EST:     CCTGTTCTTCTTGTTCACGGCTTCGGCGCCTCCATTGCTCACTGGCGCAG                         GAATATTATGATACTGGCTGAAAGTCAGACTGTTTATGCCATTGACCTTCT
genomic: CCTGTTCTTCTTGTTCACGGCTTCGGCGCCTCCATTGCTCACTGGCGCAGgtttcttttg ... tctgtttcagGAATATTATGATACTGGCTGAAAGTCAGACTGTTTATGCCATTGACCTTCT
EST: gi|294964820|gb|GW838623.1|GW838623
EST:     CCTGTTCTTCTTGTTCACGGCTTCGGCGCCTCCATTGCTCACTGGCGCAG                         GAATATTATGATACTGGCTGAAAGTCAGACTGTTTATGCCATTGACCTTCT
genomic: CCTGTTCTTCTTGTTCACGGCTTCGGCGCCTCCATTGCTCACTGGCGCAGgtttcttttg ... tctgtttcagGAATATTATGATACTGGCTGAAAGTCAGACTGTTTATGCCATTGACCTTCT
EST: gi|110708386|gb|EE085867.1|EE085867
EST:     CCTGTTCTTCTTGTTCACGGCTTCGGCGCCTCCATTGCTCACTGGCGCAG                         GAATATTATGATACTGGCTGAAAGTCAGACTGTTTATGCCATTGACCTTCT
genomic: CCTGTTCTTCTTGTTCACGGCTTCGGCGCCTCCATTGCTCACTGGCGCAGgtttcttttg ... tctgtttcagGAATATTATGATACTGGCTGAAAGTCAGACTGTTTATGCCATTGACCTTCT
EST: gi|351012301|gb|FQ429986.1|FQ429986
EST:     CCTGTTCTTCTTGTTCACGGCTTCGGCGCCTCCATTGCTCACTGGCGCAG                         GAATATTATGATACTGGCTGAAAGTCAGACTGTTTATGCCATTGACCTTCT
genomic: CCTGTTCTTCTTGTTCACGGCTTCGGCGCCTCCATTGCTCACTGGCGCAGgtttcttttg ... tctgtttcagGAATATTATGATACTGGCTGAAAGTCAGACTGTTTATGCCATTGACCTTCT
EST: gi|26264357|gb|CA815420.1|CA815420
EST:     CCTGTTCTTCTTGTTCACGGCTTCGGCGCCTCCATTGCTCACTGGCGCAG                         GAATATTATGATACTGGCTGAAAGTCAGACTGTTTATGCCATTGACCTTCT
genomic: CCTGTTCTTCTTGTTCACGGCTTCGGCGCCTCCATTGCTCACTGGCGCAGgtttcttttg ... tctgtttcagGAATATTATGATACTGGCTGAAAGTCAGACTGTTTATGCCATTGACCTTCT
EST: gi|77584623|gb|DV221395.1|DV221395
EST:     CCTGTTCTTCTTGTTCACGGCTTCGGCGCCTCCATTGCTCACTGGCGCAG                         GAATATTATGATACTGGCTGAAAGTCAGACTGTTTATGCCATTGACCTTCT
genomic: CCTGTTCTTCTTGTTCACGGCTTCGGCGCCTCCATTGCTCACTGGCGCAGgtttcttttg ... tctgtttcagGAATATTATGATACTGGCTGAAAGTCAGACTGTTTATGCCATTGACCTTCT
EST: gi|110711535|gb|EE088128.1|EE088128
EST:     CCTGTTCTTCTTGTTCACGGCTTCGGCGCCTCCATTGCTCACTGGCGCAG                         GAATATTATGATACTGGCTGAAAGTCAGACTGTTTATGCCATTGACCTTCT
genomic: CCTGTTCTTCTTGTTCACGGCTTCGGCGCCTCCATTGCTCACTGGCGCAGgtttcttttg ... tctgtttcagGAATATTATGATACTGGCTGAAAGTCAGACTGTTTATGCCATTGACCTTCT
EST: gi|110712201|gb|EE089554.1|EE089554
EST:     CCTGTTCTTCTTGTTCACGGCTTCGGCGCCTCCATTGCTCACTGGCGCAA                         GAATATTATGATACTGGCTGAAAGTCAGACTGTTTATGCCATTGACCTTCT
genomic: CCTGTTCTTCTTGTTCACGGCTTCGGCGCCTCCATTGCTCACTGGCGCAGgtttcttttg ... tctgtttcagGAATATTATGATACTGGCTGAAAGTCAGACTGTTTATGCCATTGACCTTCT
EST: gi|352790430|gb|FQ478070.1|FQ478070
EST:     CCTGTTCTTCTTGTTCACGGCTTCGGCGCCTCCATTGCTCACTGGCGCAG                         GAATATTATGATACTGGCTGAAAGTCAGACTGTTTATGCCATTGACCTTCT
genomic: CCTGTTCTTCTTGTTCACGGCTTCGGCGCCTCCATTGCTCACTGGCGCAGgtttcttttg ... tctgtttcagGAATATTATGATACTGGCTGAAAGTCAGACTGTTTATGCCATTGACCTTCT
EST: gi|352798352|gb|FQ480377.1|FQ480377
EST:     CCTGTTCTTCTTGTTCACGGCTTCGGCGCCTCCATTGCTCACTGGCGCAG                         GAATATTATGATACTGGCTGAAAGTCAGACTGTTTATGCCATTGACCTTCT
genomic: CCTGTTCTTCTTGTTCACGGCTTCGGCGCCTCCATTGCTCACTGGCGCAGgtttcttttg ... tctgtttcagGAATATTATGATACTGGCTGAAAGTCAGACTGTTTATGCCATTGACCTTCT
EST: gi|351038339|gb|FQ461031.1|FQ461031
EST:     CCTGTTCTTCTTGTTCACGGCTTCGGCGCCTCCATTGCTCACTGGCGCAG                         GAATATTATGATACTGGCTGAAAGTCAGACTGTTTATGCCATTGACCTTCT
genomic: CCTGTTCTTCTTGTTCACGGCTTCGGCGCCTCCATTGCTCACTGGCGCAGgtttcttttg ... tctgtttcagGAATATTATGATACTGGCTGAAAGTCAGACTGTTTATGCCATTGACCTTCT
EST: gi|351048153|gb|FQ442123.1|FQ442123
EST:     CCTGTTCTTCTTGTTCACGGCTTCGGCGCCTCCATTGCTCACTGGCGCAG                         GAATATTATGATACTGGCTGAAAGTCAGACTGTTTATGCCATTGACCTTCT
genomic: CCTGTTCTTCTTGTTCACGGCTTCGGCGCCTCCATTGCTCACTGGCGCAGgtttcttttg ... tctgtttcagGAATATTATGATACTGGCTGAAAGTCAGACTGTTTATGCCATTGACCTTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctattattaaactattcaagaacttgattccttttcaccttgtgtctgtttcagGAATATTATGATACTGGCTGAAAGTCAGACTGTTTATGCCATTGACCTTCTTGGTTTTGGTGCATCTGATAAGCCATCAGGCTTTGCATATACAATGGAA
                      acttgat  putative branch site (score: 5)
                                             tctgtttc  putative PPT
     tattaaactattcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcaaatgttcataaggtggtgtagggaagatcatctttgttcaactctattattaaactattcaagaacttgattccttttcaccttgtgtctgtttcagGAATATTATGATACTGGCTGAAAGTCAGACTGTTTATGCCATTGACCTTCTTGGTTTTGGTGCATCTGATAAGCCATCAGGCTTTGCATATACAATGGAA

- - - - - - - ggtggtg
- - - - - - - - - - - agggaaga
- - - - - - - - - - - - - - - - - - - - -caactct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caagaac