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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gacttatcttacccaatttttctagatgcattattaatcctttgtcattactggtttctttcttcaatgaattttatcttaccaatgaagaaatttccagGGTCTCAGTTTCTCTCCAGAAATGCAGCATAAAGCGACAAAAACCTTTTCTGGAGGATGGCGAATGCGAATTGCTCTTGCTCGTGCACTGTTTATAGAGC

Basic information

species Vitis vinifera
transcript Vv02s0025g02160.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g02160.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os02g58020.2 (Oryza sativa), 3'ss of exon 5
---gacttatcttacccaatttttctagatgcattattaatcctttgtcattactggtttctttcttcaatgaattttatcttaccaatgaagaaatttccagGGTCTCAGTTTCTCTCCAGAAATGCAGCATAAAGCGACAAAAACCTTTTCTGGAGGATGGCGAATGCGAATTGCTCTTGCTCGTGCACTGTTTATAGAGC
    || | || || |  || |  ||   |     | ||     |   | |  | |  | |   ||| | |  || ||  || |    || |    |||||||||||| |||||| |||| |||||||| | ||||   ||||||   |||||||| |||||||| ||| |||||||||| || ||||| || || || ||||
ttgaacatttcataactcatatc-ctgattattccagtagaatatgcccttgccagagtacgcactttattatatgtt--ctgattggtggaactctttccagGGTCTTAGTTTCACTCCTGAAATGCAACGTAAACGCACAAAACAGTTTTCTGGTGGATGGCGCATGAGAATTGCTCTAGCACGTGCTCTCTTCATTGAGC

upper sequence: Vv02s0025g02160.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA20G16170.1 (Glycine max), 3'ss of exon 4
gacttatcttacccaatttttctagatgcattattaatcctttgtcat--tactggtttctttcttcaatgaattttatcttaccaatgaagaa-atttccagGGTCTCAGTTTCTCTCCAGAAATGCAGCATAAAGCGACAAAAACCTTTTCTGGAGGATGGCGAATGCGAATTGCTCTTGCTCGTGCACTGTTTATAGAGC
|  |  | ||||    ||  |  | ||   || | | |  ||| | ||   || |      |  ||| |  |   | |||||||  || |||   |||| |||||| | |||||| |||| || |||||| | || || |||||||| ||||||||||||||||| |||||||| ||||||||||||||| ||||||||||||
ggttacttttact---ttcattaaaatttgttgtaagtattttcttatgacacagaaacactctttccaaaatcatgatcttactgatcaagggcattttcagGGTTTGAGTTTCACTCCTGAGATGCAGAAAAAGGCAACAAAAACATTTTCTGGAGGATGGCGGATGCGAATAGCTCTTGCTCGTGCATTGTTTATAGAGC

upper sequence: Vv02s0025g02160.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA13G10530.1 (Glycine max), 3'ss of exon 4
gacttatcttacccaatttttctagatgcattattaatcctttgtcattactggtttctttcttcaatgaattttatcttaccaatgaagaa-atttccagGGTCTCAGTTTCTCTCCAGAAATGCAGCATAAAGCGACAAAAACCTTTTCTGGAGGATGGCGAATGCGAATTGCTCTTGCTCGTGCACTGTTTATAGAGC
   || | ||||      ||   | ||| | || | ||  | |  ||  || |      |  ||| |  |   |||||||||  || |||   |||| |||||| | |||||| |||| || |||||| | || || |||||||| ||||||||||||||||| |||||||| ||||||||||||||| ||||||||||||
tggttcttttacttc-cattaaaatatgtagtaattattttcttacaaaacagaaacactctttccaaaatcattatcttactgatcaagggcattttcagGGTTTGAGTTTCACTCCTGAGATGCAGAAGAAGGCAACAAAAACATTTTCTGGAGGATGGCGGATGCGAATAGCTCTTGCTCGTGCATTGTTTATAGAGC

upper sequence: Vv02s0025g02160.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT1G64550.1 (Arabidopsis thaliana), 3'ss of exon 5
gacttatcttacccaatttttctagatgcattattaatcctttgtcattactggtttctttcttcaatgaattt-tatcttaccaatgaagaa-atttccagGGTCTCAGTTTCTCTCCAGAAATGCAGCATAAAGCGACAAAAACCTTTTCTGGAGGATGGCGAATGCGAATTGCTCTTGCTCGTGCACTGTTTATAGAGC
   ||   | |       | |  | ||   |   |  || ||||| |        ||||   | |    || ||  |      |  ||   || |||| |||||||| |||||| |||||||||||||||  ||||| ||||| || ||||| ||||||||| ||||||||||||| |||||||||||||| ||||||||||
--tttgggtgatatctcctgttgaaatcgttgcatgttcttttgttaccttcaacttctgagtactgctaacttgcaaacgttcgctgtgcaatattttcagGGTCTAAGTTTCACTCCAGAAATGCAGCTGAAAGCTACAAATACTTTTTCAGGAGGATGGAGAATGCGAATTGCACTTGCTCGTGCACTATTTATAGAGC

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|71881643|gb|DT030698.1|DT030698
EST:     AGTTCATTGATGCATACTCCGCTGAGTCGCGTGCAGGTTCCATTCTTGCG                         GGTCTCAGTTTCTCTCCAGAAATGCAGCATAAAGCGACAAAAACCTTTTCT
genomic: AGTTCATTGATGCATACTCCGCTGAGTCGCGTGCAGGTTCCATTCTTGCGgtcagttcac ... aaatttccagGGTCTCAGTTTCTCTCCAGAAATGCAGCATAAAGCGACAAAAACCTTTTCT
EST: gi|352768712|gb|FQ467924.1|FQ467924
EST:     AGTTCATTGATGCATACTCCGCTGAGTCGCGTGCAGGTTCCATTCTTGCG                         GGTCTCAGTTTCTCTCCCGAAATGCAGCATAAAGCGAC
genomic: AGTTCATTGATGCATACTCCGCTGAGTCGCGTGCAGGTTCCATTCTTGCGgtcagttcac ... aaatttccagGGTCTCAGTTTCTCTCCAGAAATGCAGCATAAAGCGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattactggtttctttcttcaatgaattttatcttaccaatgaagaaatttccagGGTCTCAGTTTCTCTCCAGAAATGCAGCATAAAGCGACAAAAACCTTTTCTGGAGGATGGCGAATGCGAATTGCTCTTGCTCGTGCACTGTTTATAGAGC
                              atcttac  putative branch site (score: 3)
                                                tttcc  putative PPT
                    aatgaattttatctta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gacttatcttacccaatttttctagatgcattattaatcctttgtcattactggtttctttcttcaatgaattttatcttaccaatgaagaaatttccagGGTCTCAGTTTCTCTCCAGAAATGCAGCATAAAGCGACAAAAACCTTTTCTGGAGGATGGCGAATGCGAATTGCTCTTGCTCGTGCACTGTTTATAGAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - -cttaccc
- - - - - - - - - - - - gatgcat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccaatga