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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtttgaattatgacatttgtatgatgattcctaaattaaaggacctgattttcttcaacactattcaacttctaacaccatatggttattgctttatagGTGCTTCGTGAATTTAATCATGTTAATCCACAAGATGATGAGGAAGGGAAAGTGTTTCTCAATGCAAGA

Basic information

species Vitis vinifera
transcript Vv08s0007g01460.t01
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g01460.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA03G16440.1 (Glycine max), 3'ss of exon 15
agtttgaattatgacat-ttgtatgatgatt----cctaaattaaaggacctgattttcttcaacactattcaactt-ctaacaccatatggttattgctttatagGTGCTTCGTGAATTTAATCATGTTAATCCACAAGATGATGAGGAAGGGAAAGTGTTTCTCAATGCAAGA
      |  ||||  || ||  ||||| |||      |  |||   |  |   || |    | |    ||| ||||  ||||||  || ||||  ||| |  |||||||||||| ||||||||||||||||||||||||||||| || ||||| ||||| |||    |  || | 
-----tatctatggtatatttcatgataattggattttttattgttgctctgaatgtctaactattacattgaactagctaacattatgtggtagttgata-atagGTGCTTCGAGAATTTAATCATGTTAATCCACAAGATGACGAAGAAGGAAAAGTTTTTGCTGACACACGC

upper sequence: Vv08s0007g01460.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA01G26350.1 (Glycine max), 3'ss of exon 15
agtttgaattatgacat-ttgtatgatgatt----cctaaattaaaggacctgattttcttcaacactattcaactt-ctaacaccatatggttattgctttatagGTGCTTCGTGAATTTAATCATGTTAATCCACAAGATGATGAGGAAGGGAAAGTGTTTCTCAATGCAAGA
      |  ||||  || ||  ||||| |||      |  |||   |  |   || |    | |    ||| ||||| ||||||  || ||||  ||| |  |||||||||||| ||||||||||||||||||||||||||||| || ||||| ||| | |||    |  |  | 
-----tatctatggtatatttcatgataattggattttttattgtggctctgaatgtctaactattacattgaacttgctaacattatgtggtagttgata-atagGTGCTTCGAGAATTTAATCATGTTAATCCACAAGATGACGAAGAAGGAAAATTTTTTGCTGACACTCGT

upper sequence: Vv08s0007g01460.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: AT3G54010.1 (Arabidopsis thaliana), 3'ss of exon 15
agtttgaattatgacatttgtatgatgattcctaaattaaaggacctgattttcttcaacactattcaacttctaacaccatatggttattgctttatagGTGCTTCGTGAATTTAATCATGTTAATCCACAAGATGATGAGGAAGGGAAAGTGTTTCTCAATGCAAGA
        | ||   | |  | |||| |      ||||  || |   |  ||| ||  |   | |   |    |||  ||| |               ||||||| || ||||||||||||||||| ||||||||||| || ||||| ||| | |||    |  |||| 
-------gtaatagaagtcatgtgataacc----aattccagtattagcatttgtttcattgtgtctgagcggtaaatccaaaac------------cagGTGCTCCGGGAATTTAATCATGTTAACCCACAAGATGAAGATGAAGGAAAAATATTTGGTGACACAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgattttcttcaacactattcaacttctaacaccatatggttattgctttatagGTGCTTCGTGAATTTAATCATGTTAATCCACAAGATGATGAGGAAGGGAAAGTGTTTCTCAATGCAAGA
                         ttctaac  putative branch site (score: 1)
                                            ttgcttt  putative PPT
                                                tttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtttgaattatgacatttgtatgatgattcctaaattaaaggacctgattttcttcaacactattcaacttctaacaccatatggttattgctttatagGTGCTTCGTGAATTTAATCATGTTAATCCACAAGATGATGAGGAAGGGAAAGTGTTTCTCAATGCAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - -tgattcc
- - - - - - - - - - - - - - - - -aaattaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caacttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacacca