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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttttacatctcttttacacctaccattttcttgaattagcatgcacatgtattaatgtggtgtaatctgtttattgacttcaatgtacttctttcccagTGCCTCTTCTTCTTGTGGGATATGGATTTGGAGCTTCATTTGTTGCCCTTTTTGCTCAGTTGGGTGGTGGAATATATACAAAAGCAGCAGATGTTGGAGC

Basic information

species Vitis vinifera
transcript Vv09s0054g00700.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0054g00700.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os02g33490.1 (Oryza sativa), 3'ss of exon 6
tttttacatctcttttacacctaccattttcttgaattagca---tgcacatgtattaatgtggtgtaatctgtttattgacttca-atgtacttctttcccagTGCCTCTTCTTCTTGTGGGATATGGATTTGGAGCTTCATTTGTTGCCCTTTTTGCTCAGTTGGGTGGTGGAATATATACAAAAGCAGCAGATGTTGGAGC
  ||| |   |   | ||||     ||  |  |   || |||    |  | | |||| |  |||  || |   ||| |  | |||| || || ||| |    |||||||||||| |||||||||||||| ||||| || || ||||| |||||||||||||||||||||||||||||||| || ||||| || ||||| |||||
--tttcctggttgataacactggttatggttatatgtttgcaattagttcttttattcaaatggaatatttcttttgtcaatttcacatttatttcctgt--agTGCCTCTTCTCCTTGTGGGATATGGTTTTGGTGCGTCTTTTGTCGCCCTTTTTGCTCAGTTGGGTGGTGGAATATACACCAAAGCTGCTGATGTCGGAGC

upper sequence: Vv09s0054g00700.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G075900_T01 (Zea mays), 3'ss of exon 6
---------------------------------------------------tttttacatctcttttacacctacc-----attttcttgaat-----tagcatgcacatgtattaatgtggtgtaatctgtttattgacttcaatgtacttctttccc--agTGCCTCTTCTTCTTGTGGGATATGGATTTGGAGCTTCATTTGTTGCCCTTTTTGCTCAGTTGGGTGGTGGAATATATACAAAAGCAGCAGATGTTGGAGC
                                                    || | || |  || |  || ||        ||||    |||     || |||     | | | || |     | ||     |  ||| |   ||||  || ||      |||||||||||| |||||||||||||| ||||| || || |||||||||||||||||||||||||||||||||||||| || ||||| || |||||||||||
gtaagtttcttgtacacaatacacctgaaaacacactagattacaatccaacttgtccaccaattatctacttattttattgtttttgcaaattgcaataccattttgttatgtgaaaggaacattattctgctgctgattcatatgttttttttgtgtgtagTGCCTCTTCTCCTTGTGGGATATGGTTTTGGTGCCTCTTTTGTTGCCCTTTTTGCTCAGTTGGGTGGTGGAATATACACGAAAGCTGCTGATGTTGGAGC

upper sequence: Vv09s0054g00700.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA07G00350.1 (Glycine max), 3'ss of exon 6
tttttacatctcttttacacctaccattttcttgaattagcatgcacatgtattaatgtggtgtaatctgtttattgactt--caatgtacttctttccc---agTGCCTCTTCTTCTTGTGGGATATGGATTTGGAGCTTCATTTGTTGCCCTTTTTGCTCAGTTGGGTGGTGGAATATATACAAAAGCAGCAGATGTTGGAGC
 | | ||||   ||  |    |  |  ||   | |  ||   |     |   |   | |    |||| |||  ||||| ||   ||  | ||| ||| ||   ||||||||||||||| || |||||||||||||| || || |||||||| || |||||||||||||||||||||||||| ||||| ||||| |||||||||||
-tatgacatgatttaaatttttgtccgttctgtcacctattctctctctccctctctctc---taatttgtc-attgattttttaaaattcttgttttccttcagTGCCTCTTCTTCTAGTTGGATATGGATTTGGTGCCTCCTTTGTTGCACTATTTGCTCAGTTGGGTGGTGGAATATACACAAAGGCAGCTGATGTTGGAGC

upper sequence: Vv09s0054g00700.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA08G24120.2 (Glycine max), 3'ss of exon 6
-----tttttacatctcttttacacctaccattttcttgaattagcatgcacatgtattaatgtggtgtaatctgtttattgacttcaatgtacttctttcccagTGCCTCTTCTTCTTGTGGGATATGGATTTGGAGCTTCATTTGTTGCCCTTTTTGCTCAGTTGGGTGGTGGAATATATACAAAAGCAGCAGATGTTGGAGC
        | ||||   ||| |    |     ||   | |  ||   |     | | | ||  ||| |  |||  ||| |   | |   |||  | |||   |||||||||||||||| || |||||||||||||| || || |||||||| || ||||| |||||||||||||||||||| ||||| || || |||||||||||
tttgaccgtgacatgattttaatttttgttcattctctcacctattctctctctctctcaaattggcg--atcgatttttgagcattcttgttttcctt---cagTGCCTCTTCTTCTAGTTGGATATGGATTTGGTGCCTCCTTTGTTGCACTATTTGCCCAGTTGGGTGGTGGAATATACACAAAGGCCGCTGATGTTGGAGC

upper sequence: Vv09s0054g00700.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT1G16780.1 (Arabidopsis thaliana), 3'ss of exon 7
-tttttacatctcttttacacctaccattttcttgaattagcatgcacatgtattaatgtggtgtaatctgtttattgacttcaatgt---acttctttcccagTGCCTCTTCTTCTTGTGGGATATGGATTTGGAGCTTCATTTGTTGCCCTTTTTGCTCAGTTGGGTGGTGGAATATATACAAAAGCAGCAGATGTTGGAGC
 | ||  ||  | ||| ||   | | |    |  ||| | ||||   |||||| || |||    |  |  | ||| ||| || | | |   | || | |  |||||||||||||||||||||||||||| ||||| || |||||||||||| | ||||||||||||||||||||||||||||| || | ||| ||||| || ||
ttgttctcaaatgtttaacgtttgcaaa---cccgaaattgcatttgcatgtactagtgttacttt-ttagcttaatgatttgactttcccatttttcttacagTGCCTCTTCTTCTTGTGGGATATGGTTTTGGTGCATCATTTGTTGCCTTATTTGCTCAGTTGGGTGGTGGAATATATACTAAGGGAGCTGATGTCGGGGC

upper sequence: Vv09s0054g00700.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT1G78920.1 (Arabidopsis thaliana), 3'ss of exon 6
----tttttacatctcttttacacctaccattttcttgaattagcatgcacatgtattaatgtggtgtaatctgtttattgacttcaatgtacttctttcccagTGCCTCTTCTTCTTGTGGGATATGGATTTGGAGCTTCATTTGTTGCCCTTTTTGCTCAGTTGGGTGGTGGAATATATACAAAAGCAGCAGATGTTGGAGC
    | || |  | |     | |  |  ||||| | ||    |   || |  |  |||||  | ||   || | || ||||| ||   |||  |||| |  |||| |||||||||||||| |||||||| ||||| ||||| ||||||||| | ||||||||||||||||||||||||||||| || | ||| |||||||| ||
attctcttgatttattgaccagaatttgcatttgcatgggcgatagtggagct--attaaacttgtaagatttattgattgaattttctgt--ttctcttacagTACCTCTTCTTCTTGTCGGATATGGTTTTGGTGCTTCGTTTGTTGCCTTATTTGCTCAGTTGGGTGGTGGAATATATACTAAGGGAGCTGATGTTGGGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatgtattaatgtggtgtaatctgtttattgacttcaatgtacttctttcccagTGCCTCTTCTTCTTGTGGGATATGGATTTGGAGCTTCATTTGTTGCCCTTTTTGCTCAGTTGGGTGGTGGAATATATACAAAAGCAGCAGATGTTGGAGC
                           tattgac  putative branch site (score: 2)
                                       tgtacttctttccc  putative PPT
     tattaatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttttacatctcttttacacctaccattttcttgaattagcatgcacatgtattaatgtggtgtaatctgtttattgacttcaatgtacttctttcccagTGCCTCTTCTTCTTGTGGGATATGGATTTGGAGCTTCATTTGTTGCCCTTTTTGCTCAGTTGGGTGGTGGAATATATACAAAAGCAGCAGATGTTGGAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - catctct
- - - - - - - - - -cctacca
- - - - - - - - - - - - - - - - - - - - catgcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caatgta