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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtagccttccctaagatctgttttaacagctgttggtgccaagttataaactgtttttattgtgtttttaagGTTTCCCTTGTTAGCAAGGACTCATCTATGTTGGATGGACTTGACAATGCCAGTATTGAGATGGAAGAAGCTAAG

Basic information

species Vitis vinifera
transcript Vv14s0066g02540.t01
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: GLYMA18G49000.1 (Glycine max), 3'ss of exon 19
----gtttgtag-ccttccctaag--atctgttttaacagctgttggtgccaagt-tata-aactgtttttattgtgtttttaagGTTTCCCTTGTTAGCAAGGACTCATCTATGTTGGATGGACTTGACAATGCCAGTATTGAGATGGAAGAAGCTAAG
    |||| ||    ||  ||||   |  | ||| | ||| | || |||     | |||   |||      |||||  | ||| |||||| |||||||| || ||||| || ||||||||||| |||||||||||||||||||| ||||||||||| |||
gttggtttttaaattttttctaaagaaagtatttaatcagttttttgtgttggatatatttgactaaaagaattgtaatgtta-gGTTTCACTTGTTAGTAAAGACTCCTCCATGTTGGATGGTCTTGACAATGCCAGTATTGAAATGGAAGAAGCCAAG

upper sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: GLYMA09G37610.1 (Glycine max), 3'ss of exon 17
------gtttgtagccttccctaagatc-tgttttaacagctgttggtgccaag--ttataaactgtttttattgtgtttttaagGTTTCCCTTGTTAGCAAGGACTCATCTATGTTGGATGGACTTGACAATGCCAGTATTGAGATGGAAGAAGCTAAG
       |||  |  ||| |  |||    | ||| | | | | || |||       |  |  |||  | | ||| |  | ||| |||||| |||||||| || ||||| || ||||||||||| |||||||||||||||||||| ||||||||||| |||
gttggtttttaaaatctttctaaagggagtatttaatctgttttttgtgttggatatctttgactaatataattttaatgtta-gGTTTCACTTGTTAGTAAAGACTCCTCCATGTTGGATGGGCTTGACAATGCCAGTATTGAAATGGAAGAAGCCAAG

upper sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: GLYMA13G05060.1 (Glycine max), 3'ss of exon 21
gtttgtagccttccct----aagatctgttttaacagctgttggtgccaa-gttataaactgtttttattgtgttttt--aagGTTTCCCTTGTTAGCAAGGACTCATCTATGTTGGATGGACTTGACAATGCCAGTATTGAGATGGAAGAAGCTAAG
|||||| | ||| ||     || |  | |||   | | | ||    | ||  |  |  |||| |||  || | |||||  |||||||||||||||||||||||||  || ||||||||||| ||||| ||||| |||  ||| ||| ||||||| |||
gtttgtggtctttcccctgaaaaaaatatttggtctgtttttttatcgaatatgtttgactgatttggttatcttttttgaagGTTTCCCTTGTTAGCAAGGACTACTCCATGTTGGATGGGCTTGAAAATGCAAGTTCTGAAATGAAAGAAGCCAAG

upper sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: GLYMA19G02260.1 (Glycine max), 3'ss of exon 17
gtttgtagccttccct----aagatctgttttaacagctgttggtgccaagttataaactgtttttattg--tgtttttaagGTTTCCCTTGTTAGCAAGGACTCATCTATGTTGGATGGACTTGACAATGCCAGTATTGAGATGGAAGAAGCTAAG
|||||| | ||| ||     || |  | ||  | | | | ||  |      |  |  |||| |||  ||   | |||| |||||||||||||||||||||||||  || ||||||||||| ||||| ||||| |||  ||| ||| ||||||| |||
gtttgtggtctttcccccgaaaaaaatattcgatctgtttttt-tattggatgcttgactgatttggttaacttttttgaagGTTTCCCTTGTTAGCAAGGACTACTCCATGTTGGATGGGCTTGAAAATGCAAGTTCTGAAATGAAAGAAGCCAAG

upper sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: AT3G01310.2 (Arabidopsis thaliana), 3'ss of exon 20
gtttgtagccttccct-aagatctgttttaacagctgttggtgcca---agttataaactgtttttattgtgttttta-agGTTTCCCTTGTTAGCAAGGACTCATCTATGTTGGATGGACTTGACAATGCCAGTATTGAGATGGAAGAAGCTAAG
||||||    ||| || | ||    | ||    | || |   | ||    || |  || |  |||| || | ||| |  |||||||  | |||||||||||||| || ||||||||||| ||||| |||||||| ||||| |||||||  || |||
gtttgtccttttctctcatgagaactcttggtggttggtaaggtcatatggtcactaatttcttttcttttttttctctagGTTTCTTTGGTTAGCAAGGACTCTTCCATGTTGGATGGTCTTGATAATGCCAGCATTGAAATGGAAGCGGCCAAG

upper sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: AT5G15070.2 (Arabidopsis thaliana), 3'ss of exon 20
gtttgtagccttccctaagat--ctgttttaacagctgttggtgcca-agttataaactgtttttattgtgtttttaagGTTTCCCTTGTTAGCAAGGACTCATCTATGTTGGATGGACTTGACAATGCCAGTATTGAGATGGAAGAAGCTAAG
|||||     |||  | |  |  ||  | ||    |||    || || | | || || ||| || ||  | || |  ||||||| || || || |||||||| || ||||||||||| ||||| |||||||| | ||| ||||||| |||||||
gtttgccattttcttttacctagctagtatagtgcctggcaatgtcataatcattaaatgtctt-atctttttctctagGTTTCTCTGGTAAGTAAGGACTCTTCCATGTTGGATGGCCTTGATAATGCCAGCAGTGAAATGGAAGCAGCTAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgttttaacagctgttggtgccaagttataaactgtttttattgtgtttttaagGTTTCCCTTGTTAGCAAGGACTCATCTATGTTGGATGGACTTGACAATGCCAGTATTGAGATGGAAGAAGCTAAG
   ttttaac  putative branch site (score: 2)
                                             tgttttt  putative PPT
                          ttataaactgttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtagccttccctaagatctgttttaacagctgttggtgccaagttataaactgtttttattgtgtttttaagGTTTCCCTTGTTAGCAAGGACTCATCTATGTTGGATGGACTTGACAATGCCAGTATTGAGATGGAAGAAGCTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC