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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcaaccatagtaggacgtagtaaatatgaaatttctcttcaaaagcttcagacagcatgactgtttttgacttttcagttcatttttcactcttcaacagGTTTGGCTGCTCCAGCAATTGCTGCAGGATTTAGTGCATTAGCTCCTACTCTAGGCACAATAATTCCGGTGATTGGAGCAAGTGGGTTTGCAGCAGCTGC

Basic information

species Vitis vinifera
transcript Vv04s0023g02940.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g02940.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os10g36830.1 (Oryza sativa), 3'ss of exon 4
gcaaccatagtaggacgtagtaaatatgaaatttctcttcaaaagcttcaga-cagcatgactgtttttgacttttcagttcatttttcactcttcaacagGTTTGGCTGCTCCAGCAATTGCTGCAGGATTTAGTGCATTAGCTCCTACTCTAGGCACAATAATTCCGGTGATTGGAGCAAGTGGGTTTGCAGCAGCTGC
       || || ||| |   | | ||     |   |||   ||   ||||| ||  || | | | | | |||    | ||   | |  ||| |    ||||||| |||||||||||||||||||||||||| | |||  | | ||| ||  |   |||| | || ||  | || ||||| ||||||||||| ||    ||
------gta-tatgacctgaaagaaatttggatgaacttatgaaatgtcagatcaagataagt-tctgtaactgaataatttcgtctgaacttt----cagGTTTAGCTGCTCCAGCAATTGCTGCAGGATTCACTGCTCTGGTTCCAACATTGCACACACTTATCCCTTTAATAGGAGCTAGTGGGTTTGCTGCTATAGC

upper sequence: Vv04s0023g02940.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os03g02170.1 (Oryza sativa), 3'ss of exon 4
------gcaaccatagtaggacgtagtaaatatgaaatttctcttcaaaagcttcagacagcatgactgtttttgacttttcagttcatttttcactcttcaacagGTTTGGCTGCTCCAGCAATTGCTGCAGGATTTAGTGCATTAGCTCCTACTCTAGGCACAATAATTCCGGTGATTGGAGCAAGTGGGTTTGCAGCAGCTGC
        || | |   |     |  |  |     ||  |||   | |  | ||| | |      | |  | |  ||  || |  |  | || ||   |   |||||||| ||||||||||||||||||||||| ||| ||||  | ||||| || || |||||| |  | || || || ||||| || || ||||| ||    ||
gtatgaaaaaacttcagaaattctgctggacgctgaacatctgaacta--gtttctgtcgctcatattactctaaacggttgatattctcttccaactt--gacagGTTTAGCTGCTCCAGCAATTGCTGCAGGGTTTGGTGCTCTTGCTCCAACCCTGGGCACACTTGTCCCTGTTATAGGAGCTAGCGGATTTGCTGCTATGGC

upper sequence: Vv04s0023g02940.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G092776_T04 (Zea mays), 3'ss of exon 6
gcaaccatagtaggacgtagtaaatatgaaatttctcttcaaaagcttcagacagcatgactgtttttgacttttcagttcatttttcactcttcaacagGTTTGGCTGCTCCAGCAATTGCTGCAGGATTTAGTGCATTAGCTCCTACTCTAGGCACAATAATTCCGGTGATTGGAGCAAGTGGGTTTGCAGCAGCTGC-----------------------------------------------------
                                                             || ||   |   |  | ||| | ||  || |    |||||||| ||||| ||||| ||||||||||||||| ||||  ||||||| || || |||||| |  | ||  | || || || ||||| ||||| ||    ||                                                     
------------------------------------------------------------gtgattcatatgctctaattc-tcttcgaccc---gacaggtttagctgcaccagccattgctgcaggatttggtgctctagctccaacactgggcacacttgtccctttcatagGGGCTAGTGGATTTGCTGCTATGGCTGCTGCGGCAGGATCTGTTGCTGGCTCTGTGGCAGTTGCTGCCTCATTTGGAG

upper sequence: Vv04s0023g02940.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G092776_T07 (Zea mays), 3'ss of exon 5
--------gcaa-ccatagta-ggacgtagt-aaatatgaaatttctcttcaaaagcttcagacagcatgactgtttttgacttttcagttc--atttttcactcttcaacagGTTTGGCTGCTCCAGCAATTGCTGCAGGATTTAGTGCATTAGCTCCTACTCTAGGCACAATAATTCCGGTGATTGGAGCAAGTGGGTTTGCAGCAGCTGC
        ||   ||| |  | | |  || | ||||    ||  |||   ||  |  ||  |||| ||  ||      ||| |  |  | ||  ||| |   |    | |||||||| ||||| ||||| ||||||||||||||| ||||  ||||||| || || |||||| |  | ||  | || || || ||||| ||||| ||    ||
gtaggactgcgttccagatcatgtatctaatgaaatgctgaacatcttggcatca--tttggaca-cactacaccaggtgattcatatgctctaattctcttcgacccgacagGTTTAGCTGCACCAGCCATTGCTGCAGGATTTGGTGCTCTAGCTCCAACACTGGGCACACTTGTCCCTTTCATAGGGGCTAGTGGATTTGCTGCTATGGC

upper sequence: Vv04s0023g02940.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA16G24310.1 (Glycine max), 3'ss of exon 4
---------gcaaccatagtaggacgtagtaaatatgaaatttctcttcaaaagcttcagacagcatgactgtttttgacttt--tcagttcatttttcactcttcaacagGTTTGGCTGCTCCAGCAATTGCTGCAGGATTTAGTGCATTAGCTCCTACTCTAGGCACAATAATTCCGGTGATTGGAGCAAGTGGGTTTGCAGCAGCTGC
         | |  | | || |    |  ||| | |    |    | | | ||  | ||||       ||| ||  ||  | |  |   ||   |||| ||  ||||||||| || ||||| ||||| |||||||||||  || |||| |||||||| ||| | || ||  | || || || ||||| |||||||||||||| ||||||||
gtatggattggagaccttgttgtcttttctaactgtattgtggaacat-ataatttccagatgaataaacttttactggatatgattgtttttattttaaccattcaacagGGTTAGCTGCACCAGCCATTGCTGCAGGTCTTGGTGCTTTAGCTCCAACTTTGGGTACTCTGATCCCTGTAATTGGTGCAAGTGGGTTTGCTGCAGCTGC

upper sequence: Vv04s0023g02940.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA02G05680.1 (Glycine max), 3'ss of exon 4
---------gcaaccatagtaggacgtagtaaatatgaaatttctcttcaaaagcttcagacagcatgactgtttttgactt---ttcagttcatttttcactcttcaacagGTTTGGCTGCTCCAGCAATTGCTGCAGGATTTAGTGCATTAGCTCCTACTCTAGGCACAATAATTCCGGTGATTGGAGCAAGTGGGTTTGCAGCAGCTGC
         | |  | | || |    |  ||| | |    |      | | ||  ||||||       | | ||  ||| |    ||   ||   |||| ||  ||||||||| || ||||| ||||| |||||||||||  || ||||||||||||| ||| | || ||  | || || || ||||| |||||||| ||||| || |||||
gtatggattggagaccttgttgtcttttctaactgtattgtggaatat-ataattttcagatgaataaatttttactgaatagaattgttttttattttaacctttcaacagGGTTAGCTGCACCAGCCATTGCTGCAGGTCTTGGTGCATTAGCTCCAACTTTGGGTACTCTGATCCCTGTAATTGGTGCAAGTGGATTTGCTGCGGCTGC

upper sequence: Vv04s0023g02940.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT2G18100.1 (Arabidopsis thaliana), 3'ss of exon 4
gcaaccatagtaggacgtagtaaatatga-aatttctcttcaaaagcttcagacagcatgac--tgtttttg---------acttttcagttcatttt--tcac------tcttcaacagGTTTGGCTGCTCCAGCAATTGCTGCAGGATTTAGTGCATTAGCTCCTACTCTAGGCACAATAATTCCGGTGATTGGAGCAAGTGGGTTTGCAGCAGCTGC
         ||| || ||  |  |  ||  ||| ||||||| || | ||   | |  | ||   ||| ||||         | || | | |   ||||  | ||      | |  |||||| ||||||||||||||||| |||||||| ||  ||||||| ||||| ||||||||||||||| ||||||| |||||||| ||||||||||| ||||||||
---------gtatgatgtcttctaactgttaatatctcttccaacgtttagaaaattaagagtatgtgtttggaaaatgctaattcttaatctgttttgattacatattatgtgaaacagGATTGGCTGCTCCAGCAATAGCTGCAGGGTTCGGTGCATTGGCTCCAACTCTAGGCACAATAGTTCCGGTAATTGGAGCCAGTGGGTTTGCTGCAGCTGC

upper sequence: Vv04s0023g02940.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT4G36210.2 (Arabidopsis thaliana), 3'ss of exon 3
gcaaccatagtaggacgtagtaaatatgaaatttctcttcaaaagcttcagacagcatga-ctgtttttgacttttcagttcatttttcactcttcaacagGTTTGGCTGCTCCAGCAATTGCTGCAGGATTTAGTGCATTAGCTCCTACTCTAGGCACAATAATTCCGGTGATTGGAGCAAGTGGGTTTGCAGCAGCTGC
         ||| | |  | | ||   |   ||    ||| |||       | |   ||| ||| ||     | ||   || |  |     | ||||||||| |||||||||||||| || |||||||||||| ||||||| || || || || |||||||| |||||||||||||||||  | || ||||| || || ||
---------gtacggcaaattcaaagcg---ttaacattctaaattagagcatattttgaactggttacctatcttacatttacatggttatattcaacagGATTGGCTGCTCCAGCTATAGCTGCAGGATTTGGTGCATTGGCACCAACACTGGGCACAATTATTCCGGTGATTGGAGCTGGGGGTTTTGCTGCTGCGGC

upper sequence: Vv04s0023g02940.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ30548 (Selaginella moellendorffii), 3'ss of exon 4
gcaaccatagtaggacgtagtaaatatgaaatttctcttcaaaagcttcagacagcatgactgtttttgacttttcagttcatttttcactcttcaacagGTTTGGCTGCTCCAGCAATTGCTGCAGGATTTAGTGCATTAGCTCCTACTCTAGGCACAATAATTCCGGTGATTGGAGCAAGTGGGTTTGCAGCAGCTGC
                                               | |  |   | |  ||| ||   | |  |||    |||  |  |     |||||| | || ||||| |||||||| || || ||    || ||||||||  |    || ||  |  ||||  | |||||||||||||| ||||||||||||||
----------------------------------------------gttattctttaagcttgtctt---cctcacagag-gtttaccgtttcaatacagGTCTAGCGGCTCCGGCAATTGCAGCTGGTTTAGCCGCTTTAGCTCCGGCAGCTGGAACGGTTGTTCCTATCATTGGAGCAAGTGGTTTTGCAGCAGCTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcagacagcatgactgtttttgacttttcagttcatttttcactcttcaacagGTTTGGCTGCTCCAGCAATTGCTGCAGGATTTAGTGCATTAGCTCCTACTCTAGGCACAATAATTCCGGTGATTGGAGCAAGTGGGTTTGCAGCAGCTGC
                   ttttgac  putative branch site (score: 3)
                                 ttcatttttcactctt  putative PPT
                                 ttcattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaaccatagtaggacgtagtaaatatgaaatttctcttcaaaagcttcagacagcatgactgtttttgacttttcagttcatttttcactcttcaacagGTTTGGCTGCTCCAGCAATTGCTGCAGGATTTAGTGCATTAGCTCCTACTCTAGGCACAATAATTCCGGTGATTGGAGCAAGTGGGTTTGCAGCAGCTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
gcaacca
- - - - - - - - - - -aaatatga
- - - - - - - - - - - - - - - - - - - -caaaagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - gcatgac