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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cattactcttccttgtattcattggtggcaatttctgtagatttgaaattctttcttgatgctaaatttttcaagcaggccattgttttttagtatgcagGTCATGCTTCTTGGTTTTGTGCTCCTTGGACGTTCTCTTGAAGAGAAGGCGAGGATCAGGGCATCTAGCGATATGAATAAACTTTTA

Basic information

species Vitis vinifera
transcript Vv04s0008g01960.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g01960.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os03g08070.3 (Oryza sativa), 3'ss of exon 4
--cattactcttccttgtattcattggtggcaatttctg-----tagatttgaaattctttcttgatgctaaatttttcaagcaggccattgttttttagtatgcagGTCATGCTTCTTGGTTTTGTGCTCCTTGGACGTTCTCTTGAAGAGAAGGCGAGGATCAGGGCATCTAGCGATATGAATAAACTTTTA
   ||||||       | |||  |||     | ||  ||     |  |||   | ||   | |   |   | | |  |   | ||    || | || ||| ||||||||||||||||| || |||||||| |||||||| ||||||||||| |  || ||| | | ||| ||||||||||||||| | ||  | 
ctaattacttcctaccgcattacttgaactgatttggtgattgatgaattaacagttgaatatgttttgcataataatgttgaagaaacttttcttgtagCATGCAGGTCATGCTTCTCGGATTTGTGCTTCTTGGACGATCTCTTGAAGAAAGTGCCAGGCTTAAGGCTTCTAGCGATATGAATGAGCTCGTT

upper sequence: Vv04s0008g01960.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os03g08070.1 (Oryza sativa), 3'ss of exon 3
--cattact--cttccttgtattcatt-ggtggcaatttctgtagatttgaaattctttcttgatgctaaatttttcaagcaggccattgttttttagtatgcagGTCATGCTTCTTGGTTTTGTGCTCCTTGGACGTTCTCTTGAAGAGAAGGCGAGGATCAGGGCATCTAGCGATATGAATAAACTTTTA
     |||    || |||| | | ||| ||||     |    ||    |  |||   || |  ||  |||  | || ||| |     || | || ||| ||||||||||||||||| || |||||||| |||||||| ||||||||||| |  || ||| | | ||| ||||||||||||||| | ||  | 
cttcctaccgcattacttgaactgatttggtgattgatgaattaacagttgaatatgttttgcataataa--tgttgaagaaac---ttttcttgtagcatgcagGTCATGCTTCTCGGATTTGTGCTTCTTGGACGATCTCTTGAAGAAAGTGCCAGGCTTAAGGCTTCTAGCGATATGAATGAGCTCGTT

upper sequence: Vv04s0008g01960.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA04G05900.1 (Glycine max), 3'ss of exon 2
cattactcttccttgtattcattggtggcaatttc--tgtagatttgaaattctttcttgatgctaaatttttcaagcaggccattg--ttttttagtatgcagGTCATGCTTCTTGGTTTTGTGCTCCTTGGACGTTCTCTTGAAGAGAAGGCGAGGATCAGGGCATCTAGCGATATGAATAAACTTTTA
   |  ||||| |   |     |  |     | |   ||   |||   |  |  || ||||   |||  |  ||| |   |  ||||  | |||||| ||||||||||||||||||||||||||||| || ||||||||||| ||||| ||||| |||||   ||||||||||||||||||| ||||  | 
---ttgtcttcgtaaaagatgctatttcttgtcttattgacaattcttacattcttgttgagtataagctcctcatgtgagt-attgaatcttttagcatgcagGTCATGCTTCTTGGTTTTGTGCTTCTGGGACGTTCTCTGGAAGAAAAGGCAAGGATTCAGGCATCTAGCGATATGAATGAACTGCTT

upper sequence: Vv04s0008g01960.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA04G05900.2 (Glycine max), 3'ss of exon 3
cattactcttccttgtattcattggtggcaatttctgtagatttgaaattctttcttgatgctaaatttttcaagcaggccattg--ttttttagtatgcagGTCATGCTTCTTGGTTTTGTGCTCCTTGGACGTTCTCTTGAAGAGAAGGCGAGGATCAGGGCATCTAGCGATATGAATAAACTTTTA
                                                           |  |||  |  ||| |   |  ||||  | |||||| ||||||||||||||||||||||||||||| || ||||||||||| ||||| ||||| |||||   ||||||||||||||||||| ||||  | 
----------------------------------------------------------gta-taagctcctcatgtgagt-attgaatcttttagCATGCAGGTCATGCTTCTTGGTTTTGTGCTTCTGGGACGTTCTCTGGAAGAAAAGGCAAGGATTCAGGCATCTAGCGATATGAATGAACTGCTT

upper sequence: Vv04s0008g01960.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA06G05890.1 (Glycine max), 3'ss of exon 4
cattactcttccttgtattcattggtggcaatttctgtagatttgaaattctttcttgatgctaaatttttcaagcaggccattg--ttttttagtatgcagGTCATGCTTCTTGGTTTTGTGCTCCTTGGACGTTCTCTTGAAGAGAAGGCGAGGATCAGGGCATCTAGCGATATGAATAAACTTTTA
 |   ||   | |||||     || |    |||    ||  ||   |  |  || ||||   |||  |  ||| |   |  ||||  | |||||| ||||||||||||||||||||||| ||||| || ||||||||||| || || ||||| |||||   ||||||||||||||||||| ||||  | 
-acctcttgcctttgtaaaagatgctatttattgtcttaacttcttacattcttgttgagtataagctcctcatgtgagt-attgaatcttttagcatgcagGTCATGCTTCTTGGTTTCGTGCTTCTGGGACGTTCTCTGGAGGAAAAGGCAAGGATTCAGGCATCTAGCGATATGAATGAACTGCTT

upper sequence: Vv04s0008g01960.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G21930.1 (Arabidopsis thaliana), 3'ss of exon 4
-------------------cattactcttccttgtattcattggtggcaatttctgtagatttgaaattctttcttgatgctaaatttttcaagca-ggccattgttttttagtatgcagGTCATGCTTCTTGGTTTTGTGCTCCTTGGACGTTCTCTTGAAGAGAAGGCGAGGATCAGGGCATCTAGCGATATGAATAAACTTTTA
                   |   |             |  ||  |   | || |  || ||   |||| |  | |  ||  ||||||| | |   |  ||  ||||  |||||||||||||||||||| ||||| |||||||||||||| |||||| | ||||| |  || | | |    ||||||| |||||||||| |||| || 
gtgagtttctctagcagatccacaagaggatgaaagctttttattattacttccactacatgcaaaatacagtttcaatagtaaatttctgattgatagctcttgtcatttagtatgcagGTCATGCTGCTTGGCTTTGTGCTCCTTGGTCGTTCTTTGGAAGAAAGAGCAAAGCTTCAAGCATCTACCGATATGAATGAACTATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaattctttcttgatgctaaatttttcaagcaggccattgttttttagtatgcagGTCATGCTTCTTGGTTTTGTGCTCCTTGGACGTTCTCTTGAAGAGAAGGCGAGGATCAGGGCATCTAGCGATATGAATAAACTTTTA
              tgctaaa  putative branch site (score: 2)
                                     ttgtttttt  putative PPT
                                    attgttttttagtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cattactcttccttgtattcattggtggcaatttctgtagatttgaaattctttcttgatgctaaatttttcaagcaggccattgttttttagtatgcagGTCATGCTTCTTGGTTTTGTGCTCCTTGGACGTTCTCTTGAAGAGAAGGCGAGGATCAGGGCATCTAGCGATATGAATAAACTTTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - -ctcttcc
- - - - - - - - - - - tggtggc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caggcca