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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggttatctagctttaatgtttgcattactaaaccaaacctttaagttttttatacagggtgaagaacagcctgaaaaagctgagggattgagaatattacagaatttaaatcatgaactctgaatctcttcttatctgttactcacagAGAGCTTGGTATTGGAATAGTAGCATATAGCCCTCTTGGTCGTGGATTCTTTGGTGGGAAGGCAGTTGTGGAGAGCTTGCCCACTCAGAGTATCCTG

Basic information

species Vitis vinifera
transcript Vv05s0020g04130.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g04130.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM5G813143_T02 (Zea mays), 3'ss of exon 4
gttggttatctagctttaatgtttgcattactaaaccaaacctttaagttttttatacagggtgaagaacagcctgaaaaagctgagggattgagaatattacagaatttaaatcatgaactc-tgaatctcttcttatctgttactcacagAGAGCTTGGTATTGGAATAGTAGCATATAGCCCTCTTGGTCGTGGATTCTTTGGTGGGAAGGCAGTTGTGGAGAGCTTGCCCACTCAGAGTATCCTG
                                                    ||  |     | |  |||         |   |       |  |  |  |  |  ||  | |||||| | |  |   | | |  | |    || |   ||| ||||||||||||||||||||  |||||||||| ||||| ||||| ||||||| ||| | ||||| ||| ||  |  | ||  |  | ||| |  ||
----------------------------------------------------ttgcaagttctaattaacttatgcttcatttttcttatctttggttcgttgaacatcgatatcatgcatttatctgtttgtcataaatgcttgcattcagGGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTG

upper sequence: Vv05s0020g04130.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA10G38900.1 (Glycine max), 3'ss of exon 4
-------gttggttat-ctagctttaatgtttgcattactaa-------accaaacctttaagttt---tttatacagggtgaagaacagcctgaaaaagctgagggattgagaatattacagaa--tttaaatcatga-----actctgaatctcttcttat-------ctgttactcacagAGAGCTTGGTATTGGAATAGTAGCATATAGCCCTCTTGGTCGTGGATTCTTTGGTGGGAAGGCAGTTGTGGAGAGCTTGCCCACTCAGAGTATCCTG
         | |  ||  || || || ||  |  |||   ||       |    || |||    ||   |||  |   | |  |  |   |      | |||      || |      |||| ||  | | ||  |  |      || |  || |||   |||        |  || |   ||| | ||||| ||||||||||| |||||||| |||||||||||||| || ||||  || |||||||| || ||||  ||||| | ||||||  | |||
gtgtttaaatagaaatattaactctagtgcatatattgtcaataacacaattgtacatttgcacttgagttttaatttgatatattaactctcagttatgcttctaacttaaattatctacaaaacatctgaaagaaaattgttgctgtatatgtctaactatgaagcattttgtaattgtagACAACTTGGGATTGGAATAGTGGCATATAGTCCTCTTGGTCGTGGCTTTTTTGCAGGAAAGGCAGTGGTAGAGACTTTGCCTAGTCAGAGCTTGCTG

upper sequence: Vv05s0020g04130.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA10G38890.2 (Glycine max), 3'ss of exon 4
---------gttggttatctagctttaatgtttgcattacta--------aaccaaacc----tttaagttttttatacagggtgaagaacagcc----tgaaaaagct----gagggattgagaatat-tacagaatttaaatcatgaactctgaatctcttcttat----ctgttactcacagAGAGCTTGGTATTGGAATAGTAGCATATAGCCCTCTTGGTCGTGGATTCTTTGGTGGGAAGGCAGTTGTGGAGAGCTTGCCCACTCAGAGTATCCTG
         || |  || ||| || || ||||   |||   |        |   | ||     ||| |  || || |  | | ||      | |     |  | | ||      |  ||||||  || |  | |  || | ||| |  || | | |||    |   ||    |   | ||  ||| || ||||| ||||||||||| ||||||||||||||||||| ||| || || |  ||||||||||  || ||||  ||||| | ||||||    |||
gtaatttaagtagaataactacctctactgttgatattgtcacttgttacagttatactggagtttgatattcttgtctaagatgttttctaactcttttagacatgcatttaaatagattgattatctgcaaaatatctgaatga--aattattaattgtctagcatagaacatgtgcttgcagGGAACTTGGGATTGGAATAGTGGCATATAGCCCTCTTGGTCATGGCTTTTTCGCAGGGAAGGCAGCGGTAGAGACTTTGCCTAGTCAGAGCGCACTG

upper sequence: Vv05s0020g04130.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S158_112V6.2 (Physcomitrella patens), 3'ss of exon 5
gttggttatctagctttaatgtttgcattactaaaccaaacctttaagttttttatacagggtgaagaacagcctgaaaaagctgagggattgagaatattacagaatttaaatca-tgaactctgaatctcttcttatctgttactcacagAGAGCTTGGTATTGGAATAGTAGCATATAGCCCTCTTGGTCGTGGATTCTTTGGTGGGAAGGCAGTTGTGGAGAG-CTTGCCCACTCAGAGTATCCTG--
                                              |||  |  ||  |  |  ||| ||  | | |||            |    | | |  | |  || | | | || |   | || | |  ||| |          ||| |||||||| |||||||||||  | |||||||||||||| || ||||||||   |||||| || || || ||||  || |   |   ||| ||||     
------------------------------------------accgagtaata-atgaaatgacaaggactacatcaaatcttcacactgctagttaaagtctacagattcactgagtggataataaaaccccacttct---------gcagGGAGCTTGGAATTGGAATAGTGCCCTATAGCCCTCTTGGGCGAGGATTCTTCTCTGGGAAAGCCGTCGTTGAGAAACTGGAAGAGCAAGACTATCGATTC

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|33409014|gb|CF214641.1|CF214641
EST:     TATTCTTTCTGGGCCCGTGAAATTGAAGAAGATATAATTCCACTCTGCCG                         AGAGCTTGGTATTGGAATAGTAGCATATAGCCCTCTTGGTCGTGGATTCTT
genomic: TATTCTTTCTGGGCCCGTGAAATTGAAGAAGATATAATTCCACTCTGCCGgttggttatc ... ttactcacagAGAGCTTGGTATTGGAATAGTAGCATATAGCCCTCTTGGTCGTGGATTCTT
EST: gi|33408926|gb|CF214553.1|CF214553
EST:     TATTCTTTCTGGGCCCGTGAAATTGAAGAAGATATAATTCCACTCTGCCG                         AGAGCTTGGTATTGGAATAGTAGCATATAGCCCTCTTGGTCGTGGATTCTT
genomic: TATTCTTTCTGGGCCCGTGAAATTGAAGAAGATATAATTCCACTCTGCCGgttggttatc ... ttactcacagAGAGCTTGGTATTGGAATAGTAGCATATAGCCCTCTTGGTCGTGGATTCTT
EST: gi|32458980|gb|CD800154.1|CD800154
EST:     TATTCTTTCTGGGCCCGTGAAATTGAAGAAGATATAATTCCACTCTGCCG                         AGAGCTTGGTATTGGAATAGTAGCATATAGCCCTCTTGGTCGTGGATTCTT
genomic: TATTCTTTCTGGGCCCGTGAAATTGAAGAAGATATAATTCCACTCTGCCGgttggttatc ... ttactcacagAGAGCTTGGTATTGGAATAGTAGCATATAGCCCTCTTGGTCGTGGATTCTT
EST: gi|30254582|gb|CB971327.1|CB971327
EST:     TATTCTTTCTGGGCCCGTGAAATTGAAGAAGATATAATTCCACTCTGCCG                         AGAGCTTGGTATTGGAATAGTAGCATATAGCCCTCTTGGTCGTGGATTCTT
genomic: TATTCTTTCTGGGCCCGTGAAATTGAAGAAGATATAATTCCACTCTGCCGgttggttatc ... ttactcacagAGAGCTTGGTATTGGAATAGTAGCATATAGCCCTCTTGGTCGTGGATTCTT
EST: gi|110712082|gb|EE089299.1|EE089299
EST:     ATTCTTTCTGGGNNCCGTGAA-TTGGAGAAGATATAATTCCACTCTGCCG                         AGAGCTTGGTATTGGAATAGTAGCATATAGCCCTCTTGGTCGTGGATTCTT
genomic: ATTCTTTCTGGGC-CCGTGAAATTGAAGAAGATATAATTCCACTCTGCCGgttggttatc ... ttactcacagAGAGCTTGGTATTGGAATAGTAGCATATAGCCCTCTTGGTCGTGGATTCTT
EST: gi|33407206|gb|CF212833.1|CF212833
EST:     TATTCTTTCTGGGCCCGTGAAATTGAAGAAGATATAATTCCACTCTGCCG                         AGAGCTTGGTATTGGAATAGTAGCATATAGCCCTCTTGGTCGTGGATTCTT
genomic: TATTCTTTCTGGGCCCGTGAAATTGAAGAAGATATAATTCCACTCTGCCGgttggttatc ... ttactcacagAGAGCTTGGTATTGGAATAGTAGCATATAGCCCTCTTGGTCGTGGATTCTT
EST: gi|33406944|gb|CF212571.1|CF212571
EST:     TATTCTTTCTGGGCCCGTGAAATTGAAGAAGATATAATTCCACTCTGCCG                         AGAGCTTGGTATTGGAATAGTAGCATATAGCCCTCTTGGTCGTGGATTCTT
genomic: TATTCTTTCTGGGCCCGTGAAATTGAAGAAGATATAATTCCACTCTGCCGgttggttatc ... ttactcacagAGAGCTTGGTATTGGAATAGTAGCATATAGCCCTCTTGGTCGTGGATTCTT
EST: gi|110373812|gb|EC938182.1|EC938182
EST:     TATTCTTTCTGGGCCCGTGAAATTGAAGAAGATATAATTCCACTCTGCCG                         AGAGCTTGGTATTGGAATAGTAGCATATAGCCCTCTTGGTCGTGGATTCTT
genomic: TATTCTTTCTGGGCCCGTGAAATTGAAGAAGATATAATTCCACTCTGCCGgttggttatc ... ttactcacagAGAGCTTGGTATTGGAATAGTAGCATATAGCCCTCTTGGTCGTGGATTCTT
EST: gi|30254500|gb|CB971245.1|CB971245
EST:     TATTCTTTCTGGGCCCGTGAAATTGAAGAAGATATAATTCCACTCTGCCG                         AGAGCTTGGTATTGGAATAGTAGCATATAGCCCTCTTGGTCGTGGATTCTT
genomic: TATTCTTTCTGGGCCCGTGAAATTGAAGAAGATATAATTCCACTCTGCCGgttggttatc ... ttactcacagAGAGCTTGGTATTGGAATAGTAGCATATAGCCCTCTTGGTCGTGGATTCTT
EST: gi|110374215|gb|EC938843.1|EC938843
EST:     TATTCTTTCTGGGCCCGTGAAATTGAAGAAGATATAATTCCACTCTGCCG                         AGAGCTTGGTATTGGAATAGTAGCATATAGCCCTCTTGGTCGTGGATTCTT
genomic: TATTCTTTCTGGGCCCGTGAAATTGAAGAAGATATAATTCCACTCTGCCGgttggttatc ... ttactcacagAGAGCTTGGTATTGGAATAGTAGCATATAGCCCTCTTGGTCGTGGATTCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atattacagaatttaaatcatgaactctgaatctcttcttatctgttactcacagAGAGCTTGGTATTGGAATAGTAGCATATAGCCCTCTTGGTCGTGGATTCTTTGGTGGGAAGGCAGTTGTGGAGAGCTTGCCCACTCAGAGTATCCTG
                               tctcttcttatctgtt  CT-rich tract
         aatttaaatcatgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggttatctagctttaatgtttgcattactaaaccaaacctttaagttttttatacagggtgaagaacagcctgaaaaagctgagggattgagaatattacagaatttaaatcatgaactctgaatctcttcttatctgttactcacagAGAGCTTGGTATTGGAATAGTAGCATATAGCCCTCTTGGTCGTGGATTCTTTGGTGGGAAGGCAGTTGTGGAGAGCTTGCCCACTCAGAGTATCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT