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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aactcttctcatgatgatgggagaaaatattggataaacttaattttctgtttctttttgttggctggctgtcttcttaaattattgcttgtttatgcagTTCTCTGGCATAAATGGGGTTCTGTACTACACTCCTCAAATTCTTGAGCAGGCAGGTGTTGGAGTTATTCTTTCAAACATAGGCATTAGTTCAGCCTCTA

Basic information

species Vitis vinifera
transcript Vv03s0038g03940.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0038g03940.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA06G00220.1 (Glycine max), 3'ss of exon 4
aactcttctcatgatgatgggagaaaatattggataaacttaattttctgtttctttttgttggctggctgtctt---cttaaattattgcttgttta-tgcagTTCTCTGGCATAAATGGGGTTCTGTACTACACTCCTCAAATTCTTGAGCAGGCAGGTGTTGGAGTTATTCTTTCAAACATAGGCATTAGTTCAGCCTCTA
    | |    | ||  |   |     |||   |   | | |    |   | |  |  || ||    | | |  |   ||||  | | | ||  || | ||||||||||||| ||||||||||| || ||||| || |||||||||||||||||||||||||||||   | |||||||||   ||||| || ||||  | ||| 
----cattaactaatctttaaaatctttatgtcaaccaataaggcctggctatgctactggtgaaaagttatgctggacttatttaaatcctctttaagtgcagTTCTCTGGTATAAATGGGGTCCTCTACTATACACCTCAAATTCTTGAGCAGGCAGGTGTTGGTTATCTTCTTTCAAGTCTAGGCCTTGGTTCTACTTCTT

upper sequence: Vv03s0038g03940.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA13G05980.1 (Glycine max), 3'ss of exon 4
aactcttctcatgatgatgggagaaaatattggataaactta-attttctgtttctttt--tgttggctggctgtctt---cttaaattattgcttgttta-tgcagTTCTCTGGCATAAATGGGGTTCTGTACTACACTCCTCAAATTCTTGAGCAGGCAGGTGTTGGAGTTATTCTTTCAAACATAGGCATTAGTTCAGCCTCTA
       |   |  | ||     | ||  ||   | ||| || |    |||  |||  |  || ||    | | |  |   || |  ||  | ||  || | ||||||||||||| ||||||||||| || ||||| || |||||||||||||||||||||||||||||   | ||||||||| | ||||| || ||||  | ||| 
-------catttacttatctttaacaactttatgtcaacctataaggcctggctctgctactggtgaaaagttatgctggactcattttcatcctctttgagtgcagTTCTCTGGTATAAATGGGGTCCTCTACTATACGCCTCAAATTCTTGAGCAGGCAGGTGTTGGTTATCTTCTTTCAAGCCTAGGCCTTGGTTCTACTTCTT

upper sequence: Vv03s0038g03940.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA06G00220.2 (Glycine max), 3'ss of exon 4
aactcttctcatgatgatgggagaaaatattggataaact--taattttctgtt-tctttttgttggctggctgtctt---cttaaattattgcttgttta-tgcagTTCTCTGGCATAAATGGGGTTCTGTACTACACTCCTCAAATTCTTGAGCAGGCAGGTGTTGGAGTTATTCTTTCAAACATAGGCATTAGTTCAGCCTCTA
   | |||      | ||     |||   ||   | |||   |||      | | |  |  || ||    | | |  |   ||||  | | | ||  || | ||||||||||||| ||||||||||| || ||||| || |||||||||||||||||||||||||||||   | |||||||||   ||||| || ||||  |     
--ttattcattaactaatctttaaaatctttatgtcaaccaataaggcctggctatgctactggtgaaaagttatgctggacttatttaaatcctctttaagTGCAGTTCTCTGGTATAAATGGGGTCCTCTACTATACACCTCAAATTCTTGAGCAGGCAGGTGTTGGTTATCTTCTTTCAAGTCTAGGCCTTGGTTCTAC-----

upper sequence: Vv03s0038g03940.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA02G48150.1 (Glycine max), 3'ss of exon 3
----aactcttctcatgatgatgggagaaaatattggataaacttaattttctgtttctttttgttggctggctgtcttcttaaattattgcttgtttatgcagTTCTCTGGCATAAATGGGGTTCTGTACTACACTCCTCAAATTCTTGAGCAGGCAGGTGTTGGAGTTATTCTTTCAAACATAGGCATTAGTTCAGCCTCTA
    |    ||| |   |  ||    ||| ||  |  |  || |  |  |  |       | |||   |||  |||| ||| ||||  |   |      | ||||||||||| ||||||||||| || ||||| || |||||||||||||||||||||||||||||   | ||||||||||| | ||| |  ||||  | ||| 
ggtgattgattcactaaacaatcattgaacatcattaaccaattgtacctagtaaaaagctatgt---ctgattgtcatct-aaatcctctttaaacattacagTTCTCTGGTATAAATGGGGTGCTCTACTATACACCTCAAATTCTTGAGCAGGCAGGTGTTGGGTATCTTCTTTCAAACCTGGGCCTCGGTTCTACTTCTG

upper sequence: Vv03s0038g03940.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA14G00330.1 (Glycine max), 3'ss of exon 4
-------------------------------------------------------------------------------------aactcttctcatgatgatgggagaaaatattggataaac-----ttaattttctgtttctttttg------ttggctggctgtcttcttaaattattgcttgtttat-gcagTTCTCTGGCATAAATGGGGTTCTGTACTACACTCCTCAAATTCTTGAGCAGGCAGGTGTTGGAGTTATTCTTTCAAACATAGGCATTAGTTCAGCCTCTA
                                                                                     || |||   |    | |   |   |  ||||   ||| |     ||||     |||  ||  |         || ||| ||||| |||  || |  |  ||    || |||||||||||| ||||||| ||| || ||||| || |||||||||||||||||||||||||||||   | ||||||||||| | ||| |  ||||  | ||| 
gtaatgacattttttaaaacttctgttaatctaacttcggtgaaattgtcagaaaactatttagacatattaggatatattttttaaatctcaactcattcagtaggtgatttattcactaaccaatcattaacccattgtacctagtaaaaagctatgtctgactgtcatct--aactcctctttaaacatcgcagTTCTCTGGTATAAATGTGGTGCTCTACTATACACCTCAAATTCTTGAGCAGGCAGGTGTTGGTTATCTTCTTTCAAACCTGGGCCTCGGTTCTACTTCTG

upper sequence: Vv03s0038g03940.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT4G35300.2 (Arabidopsis thaliana), 3'ss of exon 5
aactcttctcatgatgatgggagaaaatattggataaacttaattttctgtttctttttgttggctggctgtcttcttaaattattgcttgtttatgcagTTCTCTGGCATAAATGGGGTTCTGTACTACACTCCTCAAATTCTTGAGCAGGCAGGTGTTGGAGTTATTCTTTCAAACATAGGCATTAGTTCAGCCTCTA
     |    ||    |    | ||| || || || |    |    |       ||| || |   |   ||| ||| |   |  |  ||||   ||||||||||| ||||| || || ||||| |||||||| || ||||| ||||||||||| ||||| ||  |  | || || ||||| || ||||||||  ||||  
-gtagtctagatagccacatca-aaattagtgaatcacagaagaaataatgcggtttatgctaattctatgttttcctgcttcct--cttggaaatgcagTTCTCAGGCATCAACGGAGTTCTTTACTACACACCGCAAATCCTTGAGCAGGCGGGTGTCGGGATCCTACTATCGAACATGGGGATTAGTTCTTCCTCAG

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|30304821|gb|CB981615.1|CB981615
EST:     GAGTCAAGCATGCACTAGTTGTTGGGGTGGGGATTCAGATACTTCAGCAG                         TTCTCTGGCATAAATGGGGTTCTGTACTACACTCCTCAAATTCTTGAGCAG
genomic: GAGTCAAGCATGCACTAGTTGTTGGGGTGGGGATTCAGATACTTCAGCAGgtaaaaaata ... gtttatgcagTTCTCTGGCATAAATGGGGTTCTGTACTACACTCCTCAAATTCTTGAGCAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctgtttctttttgttggctggctgtcttcttaaattattgcttgtttatgcagTTCTCTGGCATAAATGGGGTTCTGTACTACACTCCTCAAATTCTTGAGCAGGCAGGTGTTGGAGTTATTCTTTCAAACATAGGCATTAGTTCAGCCTCTA
                                          cttgttt  CT-rich tract
                          tcttcttaaattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aactcttctcatgatgatgggagaaaatattggataaacttaattttctgtttctttttgttggctggctgtcttcttaaattattgcttgtttatgcagTTCTCTGGCATAAATGGGGTTCTGTACTACACTCCTCAAATTCTTGAGCAGGCAGGTGTTGGAGTTATTCTTTCAAACATAGGCATTAGTTCAGCCTCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - -ctcatga
- - - - - - - - - -ggagaaa
- - - - - - - - - - - - - - - -ggataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggctggc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtcttc