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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaatatcccctgaagatgtaaaaaacattcaagttggtgcattcagttatgtgatggtactattatgccctgacctttctgttcatactgtgcttgtagGTGCCATTGGTGCTGAGTGGTTGAAAGCATTCAAAGGCTATATTGAGAATCCAGAGTCAATGCTGCTCTAGATACATGGGTATTTTTTTTTCAGAAAGTT

Basic information

species Vitis vinifera
transcript Vv11s0016g01870.t01
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g01870.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: LOC_Os02g01500.1 (Oryza sativa), 3'ss of exon 18
aaaatatcccctgaagatgtaaaaaacattcaagttggtgcattcagttatgtgatggtactattatgccctgacctttctgttcatactgtgcttgtagGTGCCATTGGTGCTGAGTGGTTGAAAGCATTCAAAGGCTATATTGAGAATCCAGAGTCAATGCTGCTCTAGATACATGGGT------ATTTTTTTTTCAGAAAGTT
    ||| | || |||   ||    | || || | | || |        ||  | | | |     ||  | |      | ||| | | || |      |||||| || || || || |   ||||||||||||| |||||||| ||||||||| | |||||| | || |  |   |  | |      |  | || |||        
---gtatactcttaagccttatctga-atacatgatagttctacggaccataggctagaaa----ataactttgttcatgtgtgctttctct------agGTGCTATCGGCGCAGAATTTCTGAAAGCATTCAAGGGCTATATCGAGAATCCAAACTCAATGTTACTGTGAAGTTAAAGATCAGCAAAACTATTCTTCTC------

upper sequence: Vv11s0016g01870.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: AT1G54220.2 (Arabidopsis thaliana), 3'ss of exon 18
aaaatatcccctgaagatgtaaaaaacattcaagttggtgcattcagttatgtgatggtactattatgccctgacctttctgttcatactgtgcttgtagGTGCCATTGGTGCTGAGTGGTTGAAAGCATTCAAAGGCTATATTGAGAATCCAGAGTCAATGCTGCTCTAGATACATGGGTATTTTTTTTTCAGAAAGTT-
               |   |  |   ||||||   |  |  ||||| | ||        | | |      || |  ||  | ||| |||||       |||||||||||| ||||| |||||||||||||| || || || || ||||| ||  | || ||| | ||||| | | |     |           ||||    
---------------gtaatccagttcattcatcatcattgattcattcattcatcatcattgtagaaatctaatattcttcttcttactgc------agGTGCCATTGGAGCTGAATGGTTGAAAGCATTTAAGGGATACATCGAGAACCCTAAATCTATGTTACTCTAAA-AGAGAACCAACCACGCAATGGAAAAAAA
















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|110364343|gb|EC923926.1|EC923926
EST:     TGCTTCGTTCATGCCTGTCACCTTGAGCTGTGATCACCGTGTAATTGATG                         GTGCCATTGGTGCTGAGTGGTTGAAAGCATTCAAAGGCTATATTGAGAATC
genomic: TGCTTCGTTCATGCCTGTCACCTTGAGCTGTGATCACCGTGTAATTGATGgtaggtagtt ... gtgcttgtagGTGCCATTGGTGCTGAGTGGTTGAAAGCATTCAAAGGCTATATTGAGAATC
EST: gi|110361992|gb|EC925498.1|EC925498
EST:     TGCTTCGTTCATGCCTGTCACCTTGAGCTGTGATCACCGTGTAATTGATG                         GTGCCATTGGTGCTGAGTGGTTGAAAGCATTCAAAGGCTATATTGAGAATC
genomic: TGCTTCGTTCATGCCTGTCACCTTGAGCTGTGATCACCGTGTAATTGATGgtaggtagtt ... gtgcttgtagGTGCCATTGGTGCTGAGTGGTTGAAAGCATTCAAAGGCTATATTGAGAATC
EST: gi|30131574|gb|CB916913.1|CB916913
EST:     TGCTTCGTTCATGCCTGTCACCTTGAGCTGTGATCACCGTGTAATTGATG                         GTGCCATTGGTGCTGAGTGGTTGAAAGCATTCAAAGGCTATATTGAGAATC
genomic: TGCTTCGTTCATGCCTGTCACCTTGAGCTGTGATCACCGTGTAATTGATGgtaggtagtt ... gtgcttgtagGTGCCATTGGTGCTGAGTGGTTGAAAGCATTCAAAGGCTATATTGAGAATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttatgtgatggtactattatgccctgacctttctgttcatactgtgcttgtagGTGCCATTGGTGCTGAGTGGTTGAAAGCATTCAAAGGCTATATTGAGAATCCAGAGTCAATGCTGCTCTAGATACATGGGTATTTTTTTTTCAGAAAGTT
                       ccctgac  putative branch site (score: 3)
             tactattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaatatcccctgaagatgtaaaaaacattcaagttggtgcattcagttatgtgatggtactattatgccctgacctttctgttcatactgtgcttgtagGTGCCATTGGTGCTGAGTGGTTGAAAGCATTCAAAGGCTATATTGAGAATCCAGAGTCAATGCTGCTCTAGATACATGGGTATTTTTTTTTCAGAAAGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
aaaatat
- - - -cccctga
- - - - - - - - - -taaaaaa
- - - - - - - - - - - - - cattcaa
- - - - - - - - - - - - - - - - - - - -gcattca
- - - - - - - - - - - - - - - - - - - - - - - - - -gtgatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tatgccc