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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaaaagaatcttccaaaaaaattaaggacttcggatcattcttttttttctttgataggcaaaggacttattgttttatttttgaattattgggaaacagGATTATGTGCCAACTGTTTTCGACAATTTCAGTGCAAATGTGGTTGTCAATGGGGCCACTGTTAACCTTGGGTTGTGGGATACTGCTG

Basic information

species Vitis vinifera
transcript Vv04s0023g03860.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g03860.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA02G05160.1 (Glycine max), 3'ss of exon 1
gaaaagaatcttccaaaaaaattaaggacttcggatcattcttttttttctttgataggcaaaggacttattgttttatttttgaa--ttattgggaaacagGATTATGTGCCAACTGTTTTCGACAATTTCAGTGCAAATGTGGTTGTCAATGGGGCCACTGTTAACCTTGGGTTGTGGGATACTGCTG
  |  |  | |      | |  | |     ||  || | | | ||| ||  |  | |   |      ||||| ||  || | |  |  || || ||||| |||||||||||||||||||||||||||||||||| |||||||||||||| ||||| ||||||||||| || || || ||||| ||||| |
--attgtgtttcatgctatatatgatattatcttataaatatgtttattgataaagaaaaatgatcattatttttgcatctcttcactttgtttggaaatagGATTATGTGCCAACTGTTTTCGACAATTTCAGCGCAAATGTGGTTGTGAATGGAGCCACTGTTAATCTAGGATTATGGGACACTGCCG

upper sequence: Vv04s0023g03860.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA11G08380.1 (Glycine max), 3'ss of exon 2
gaaaagaatcttccaaaaaaattaaggacttcggatcattcttttttttctttga---taggcaaaggactt---attgttttatttttgaattattgggaaacagGATTATGTGCCAACTGTTTTCGACAATTTCAGTGCAAATGTGGTTGTCAATGGGGCCACTGTTAACCTTGGGTTGTGGGATACTGCTG
     |  || |       | |||   | || || | |   ||||||||  |  |   ||||  ||  | ||   |  ||| ||||| |    ||||   ||||||||||||||||| |||||||| |||||||||||||||||||||||||||||||||  || ||| || || || ||||||||||||||||
-----gtctcattttgttta-ttataaagtttggttaacgttttttttttataaacattaggttaacaatttgataacgttgtatttgttgtgtatttaaaaacagGATTATGTGCCGACTGTTTTTGACAATTTCAGTGCAAATGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTG

upper sequence: Vv04s0023g03860.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA16G23340.1 (Glycine max), 3'ss of exon 1
gaaaagaatcttccaaaaaaattaaggacttcggatcattcttttttttcttt-gataggcaaaggacttattgttttatttttgaa--ttattgggaaacagGATTATGTGCCAACTGTTTTCGACAATTTCAGTGCAAATGTGGTTGTCAATGGGGCCACTGTTAACCTTGGGTTGTGGGATACTGCTG
   ||   | || |||    ||  | ||  ||   | ||   | |  || ||  || ||  | |  | || || ||| || | |  |  || || ||||| |||||||||||||||||||||||||||||||||| |||||||||||||| ||||| ||||||||||| || || || ||||| ||||| |
---aattgtgtttcaatgctatatatgatatcctcttataaatatgcttattgagaaagaaagataattttttttttcatctcttcactttgtttggaaatagGATTATGTGCCAACTGTTTTCGACAATTTCAGCGCAAATGTGGTTGTGAATGGAGCCACTGTTAATCTAGGATTATGGGACACTGCCG

upper sequence: Vv04s0023g03860.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA01G36880.4 (Glycine max), 3'ss of exon 1
gaaaagaatcttccaaaaaaattaaggacttcggatcattcttttttttctttgataggcaaaggacttattgttttattt--ttgaatt-----attgggaaacagGATTATGTGCCAACTGTTTTCGACAATTTCAGTGCAAATGTGGTTGTCAATGGGGCCACTGTTAACCTTGGGTTGTGGGATACTGCTG
    |  || |   |  ||  ||      ||    |  ||  |||| || | | ||  |||   |  | | | ||| |||   ||| |||     |||   ||||||||||||||||| |||||||| ||||||||||| |||||||||||||||||||||  || ||| || || || ||||||||||||||||
---tattatttattatgaagtttgg----ttaacgttttttgttttgttttgtaatgagcatttggttaactatttgattacgttgtatttgtatatttaaaaacagGATTATGTGCCGACTGTTTTTGACAATTTCAGCGCAAATGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTG

upper sequence: Vv04s0023g03860.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA01G36880.2 (Glycine max), 3'ss of exon 2
gaaaagaatcttccaaaaaaattaaggacttcggatcattcttttttttctttgataggcaaaggacttattgttttatt--tttgaat-----tattgggaaacagGATTATGTGCCAACTGTTTTCGACAATTTCAGTGCAAATGTGGTTGTCAATGGGGCCACTGTTAACCTTGGGTTGTGGGATACTGCTG------------
    |  || |   |  ||  ||      ||    |  ||  |||| || | | ||  |||   |  | | | ||| |||   ||| ||     ||||   ||||||||||||||||| |||||||| ||||||||||| |||||||||||||||||||||  || ||| || || || ||||||||||||||||            
---tattatttattatgaagtttgg----ttaacgttttttgttttgttttgtaatgagcatttggttaactatttgattacgttgtatttgtatatttaaaaacagGATTATGTGCCGACTGTTTTTGACAATTTCAGCGCAAATGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTGGTAATGCTGCGT

upper sequence: Vv04s0023g03860.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT4G35950.1 (Arabidopsis thaliana), 3'ss of exon 1
------gaaaagaatcttccaaaaaaattaaggacttcggatcattc--ttttttttctttgataggcaaa---ggacttat-tgtttta-------tttttgaattattgg-gaaacagGATTATGTGCCAACTGTTTTCGACAATTTCAGTGCAAATGTGGTTGTCAATGGGGCCACTGTTAACCTTGGGTTGTGGGATACTGCTG
         ||  ||  |||       ||  |   |  |  |||||   || |  || |   |||    ||   |||   ||   |  ||       | | |  |||      | ||||||||||||| || ||||||||||| || || ||||||||||||||||| ||||| ||||| || || ||||| |||||||||||||| |
gtattcatcaatcattctccctcctttttttgatatctgattcatttgattctgattgtgccatatatgaattgggatccatacatactaaaaatgttgtatacatttccattggaacagGATTATGTTCCGACTGTTTTCGATAACTTTAGTGCAAATGTGGTTGTTAATGGAGCCACGGTGAATCTTGGATTGTGGGATACTGCAG

upper sequence: Vv04s0023g03860.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT2G17800.2 (Arabidopsis thaliana), 3'ss of exon 2
------------------------------------------------------------------------------------gaaaagaatcttccaaaaaaattaaggacttcggatcattcttttttttctttgatagg---caaaggacttattgttttatt------tttgaattattgggaaacagGATTATGTGCCAACTGTTTTCGACAATTTCAGTGCAAATGTGGTTGTCAATGGGGCCACTGTTAACCTTGGGTTGTGGGATACTGCTG
                                                                                      |   || |||     || |       |     || ||| ||||||    ||   |||       |  |||  | | | |||      | | ||||  || | ||||||||||||| || ||||||||||| || || || |||||||||||||| ||||| |||||||| || |||||| | |||||||| || |
gtataatgttccttccttagattgaatcatattctgtgttctgtgaattacaagcttcaaaattgtcttctctattgattgatgagaccaaagcttgtggcaatacatgaatcgatccataatttttttttggtgttatgaggatttgtggagctttgtatctcattgaatcttgtaaattcatgtggaacagGATTATGTACCGACTGTTTTCGATAACTTTAGCGCAAATGTGGTTGTTAATGGAGCCACTGTGAATCTTGGGCTATGGGATACCGCAG

upper sequence: Vv04s0023g03860.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT3G51300.1 (Arabidopsis thaliana), 3'ss of exon 1
gaaaagaatcttccaaaaaaattaaggacttcggatcattcttttttttctttgataggcaaaggacttattgttttatttttgaattattgggaaacagGATTATGTGCCAACTGTTTTCGACAATTTCAGTGCAAATGTGGTTGTCAATGGGGCCACTGTTAACCTTGGGTTGTGGGATACTGCTG
          ||       |||||     |   | |  || |||  || |    | |  |||   |  |  |||||  | |||   || | |  | ||||||||||||||| || |||||||| ||||||||||| ||||| || || |||||   |||||| || ||||| |||||||| ||||| |
---------gttatgtcccaattattctttcatgtttcttgtttcattaccacaacaa-caacatatctcatgtttcttgtttcttttgtggatatacagGATTATGTGCCTACCGTTTTCGATAATTTCAGTGCCAATGTTGTGGTTAATGGAAGCACTGTGAATCTTGGATTGTGGGACACTGCAG

upper sequence: Vv04s0023g03860.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ09765 (Selaginella moellendorffii), 3'ss of exon 1
gaaaagaatcttccaaaaaaattaaggacttcggatcattcttttttttctttgataggcaaaggacttattgttttatttttgaattattgggaaacagGATTATGTGCCAACTGTTTTCGACAATTTCAGTGCAAATGTGGTTGTCAATGGGGCCACTGTTAACCTTGGGTTGTGGGATACTGCTG
                          || ||||  |  ||||||  ||| | |             || | | | ||    | | ||  ||    |||||||||| || || |||||||| || || ||||| || |||||||||||| ||||   |||||| ||||||||| | ||||| |||||||
----------------------gtgagatttcgttttgttctttcctttttct-------------ctaactctcttgggctgggatcgttcatcaacagGATTACGTTCCCACTGTTTTTGATAACTTCAGCGCCAATGTGGTTGTCGATGGCAACACTGTCAACCTTGGGCTCTGGGACACTGCTG

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|110376013|gb|EC941052.1|EC941052
EST:     TTGGCAAAACTTGTCTCCTTATCTCCTATACCAGCAACACTTTCCCCATG                         GATTATGTGCCAACTGTTTTCGACAATTTCAGTGCAAATGTGGTTGTCAAT
genomic: TTGGCAAAACTTGTCTCCTTATCTCCTATACCAGCAACACTTTCCCCACGgtgagtcctc ... tgggaaacagGATTATGTGCCAACTGTTTTCGACAATTTCAGTGCAAATGTGGTTGTCAAT
EST: gi|110713128|gb|EE088780.1|EE088780
EST:     TTGGCAAAACTTGTCTCCTTATCTCCTATACCAGCAACACTTTCCCCACG                         GATTATGTGCCAACTGTTTTCGACAATTTCAGTGCAAATGTGGTTGTCAAT
genomic: TTGGCAAAACTTGTCTCCTTATCTCCTATACCAGCAACACTTTCCCCACGgtgagtcctc ... tgggaaacagGATTATGTGCCAACTGTTTTCGACAATTTCAGTGCAAATGTGGTTGTCAAT
EST: gi|110390015|gb|EC954898.1|EC954898
EST:     ATACCAGCAACACTTTCCCCATG                         GATTATGTGCCAACTGTTTTCGACAATTTCAGTGCAAATGTGGTTGTCAAT
genomic: ATACCAGCAACACTTTCCCCACGgtgagtcctc ... tgggaaacagGATTATGTGCCAACTGTTTTCGACAATTTCAGTGCAAATGTGGTTGTCAAT
EST: gi|87586594|gb|DY474807.1|DY474807
EST:     TTGGCAAAACTTGTCTCCTTATCTCCTATACCAGCAACACTTTCCCCATG                         GATTATGTGCCAACTGTTTTCGACAATTTCAGTGCAAATGTGGTTGTCAAT
genomic: TTGGCAAAACTTGTCTCCTTATCTCCTATACCAGCAACACTTTCCCCACGgtgagtcctc ... tgggaaacagGATTATGTGCCAACTGTTTTCGACAATTTCAGTGCAAATGTGGTTGTCAAT
EST: gi|110404309|gb|EC969170.1|EC969170
EST:     GCAACACTTTCCCCATG                         GATTATGTGCCAACTGTTTTCGACAATTTCAGTGCAAATGTGGTTGTCAAT
genomic: GCAACACTTTCCCCACGgtgagtcctc ... tgggaaacagGATTATGTGCCAACTGTTTTCGACAATTTCAGTGCAAATGTGGTTGTCAAT
EST: gi|33410493|gb|CF216120.1|CF216120
EST:     TTGGCAAAACTTGTCTCCTTATCTCCTATACCAGCAACACTTTCCCCATG                         GATTATGTGCCAACTGTTTTCGACAATTTCAGTGCAAATGTGGTTGTCGAT
genomic: TTGGCAAAACTTGTCTCCTTATCTCCTATACCAGCAACACTTTCCCCACGgtgagtcctc ... tgggaaacagGATTATGTGCCAACTGTTTTCGACAATTTCAGTGCAAATGTGGTTGTCAAT
EST: gi|110366542|gb|EC930452.1|EC930452
EST:     CCTATACCAGCAACACTTTCCCCCATG                         GATTATGTGCCAACTGTTTTCGACAATTTCAGTGCAAATGTGGTTGTCAA
genomic: CCTATACCAGCAACACTTT-CCCCACGgtgagtcctc ... tgggaaacagGATTATGTGCCAACTGTTTTCGACAATTTCAGTGCAAATGTGGTTGTCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttctttgataggcaaaggacttattgttttatttttgaattattgggaaacagGATTATGTGCCAACTGTTTTCGACAATTTCAGTGCAAATGTGGTTGTCAATGGGGCCACTGTTAACCTTGGGTTGTGGGATACTGCTG
    ctttgat  putative branch site (score: 5)
                    acttattgttttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaaaagaatcttccaaaaaaattaaggacttcggatcattcttttttttctttgataggcaaaggacttattgttttatttttgaattattgggaaacagGATTATGTGCCAACTGTTTTCGACAATTTCAGTGCAAATGTGGTTGTCAATGGGGCCACTGTTAACCTTGGGTTGTGGGATACTGCTG

-aaaagaa
- - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - aggcaaa