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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actgatttattatgatattttcctgattaatttccaatactgaagtttatctttgctgttgatcctatataatttaaaatagcgtgtccttgttttgcagATACCCGGGCTGGTAAATGTTGATTTTGCAGATGTAAAGGCAGTCATGAAGGACTCTGGAACTGCAATGCTTGGAGTGGGGGTTTCTTCCAGCAAAAACC

Basic information

species Vitis vinifera
transcript Vv19s0090g01320.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0090g01320.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os04g56970.2 (Oryza sativa), 3'ss of exon 4
actgatttattatgatattttcctgattaatttccaatactgaagtttatctttgctgttgatcctatataatt-taaaatag-cgtgtccttgttttgcagATACCCGGGCTGGTAAATGTTGATTTTGCAGATGTAAAGGCAGTCATGAAGGACTCTGGAACTGCAATGCTTGGAGTGGGGGTTTCTTCCAGCAAAAACC
                                   | || |     |||||| ||||| ||   || | | ||   | ||||  | | |      |||||||||||| || || || |||||||||||||| ||||| || || || |||||  |||||||||||||||||||||| || || ||||||||||||||||| |
--------------------------------gtaagtattctt-cttatctatgctgctgtaact-tgtgatcacacaatactcatctgaaaactttgcagATACCTGGACTTGTCAATGTTGATTTTGCTGATGTGAAAGCTGTTATGAAAAACTCTGGAACTGCAATGCTTGGTGTTGGTGTTTCTTCCAGCAAAAATC

upper sequence: Vv19s0090g01320.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G119773_T01 (Zea mays), 3'ss of exon 4
actgatttattatgatattttcctgattaatttccaatactgaagtttatctttgctgttgatcctatataatttaaaatagcgtgtccttgttttgcagATACCCGGGCTGGTAAATGTTGATTTTGCAGATGTAAAGGCAGTCATGAAGGACTCTGGAACTGCAATGCTTGGAGTGGGGGTTTCTTCCAGCAAAAACC
                   |   || ||  |  ||  | |||   | || |||  |||   ||  | ||| || ||   ||   ||        ||||||||||| || || || |||||||||||||| |||||||| || ||||||||  ||||||||||||| ||||| || || || ||||||||||||||||| |
------------------gtgggtggtttctcccctttcctgc--tctaacttatctgcaaattgt-tatcatgtacctta---tgagtgaacattgcagATACCGGGACTTGTCAATGTTGATTTTGCTGATGTAAAAGCTGTCATGAAAAACTCTGGAACTGCCATGCTCGGTGTTGGTGTTTCTTCCAGCAAAAATC

upper sequence: Vv19s0090g01320.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA18G10030.1 (Glycine max), 3'ss of exon 5
-------actgatttattatgatattttcctgattaatttccaatactgaagtttatctttgctgttgatcctatataatttaaaatagcgtgtccttgttttgcagATACCCGGGCTGGTAAATGTTGATTTTGCAGATGTAAAGGCAGTCATGAAGGACTCTGGAACTGCAATGCTTGGAGTGGGGGTTTCTTCCAGCAAAAACC
         || |     || ||| ||     |||||| |  | |||  |  || || |  |||  | |    || | ||| |   |  |||||| ||   || |||||||| ||||| |||||||| |||||||| |||||||| || || ||||| ||||||||||||||||||||||| ||||| ||||| ||||| |||||||
tttcagtgttgctcctccatcataattggacaattaatgtaaagtac--attttgatgtcagcttatcagg--atgttattcagtgttacgtgtcttt---ttacagATACCTGGGCTTGTAAATGTGGATTTTGCTGATGTAAAAGCTGTGATGAAAGACTCTGGAACTGCAATGCTTGGTGTGGGTGTTTCCTCCAGTAAAAACC

upper sequence: Vv19s0090g01320.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA08G43500.1 (Glycine max), 3'ss of exon 5
actgatttattatgatattttcctgattaatttccaat-actgaagtttat-ctttgctgttgatcctatataatttaaaatagcgtgtccttgttttgcagATACCCGGGCTGGTAAATGTTGATTTTGCAGATGTAAAGGCAGTCATGAAGGACTCTGGAACTGCAATGCTTGGAGTGGGGGTTTCTTCCAGCAAAAACC
  |  || | | |      | |   || | |   |||| | ||||   ||   |||| |||      |  |  || | |  |   ||  | |  |||| |||||||||||||| |||||||| |||||||| |||||||| || || ||||| |||||||||||||| |||||||| ||||| ||||| ||||| |||||||
--tatttgagtgttgctcctccaccataattggacaattaatgaaaagtacattttgatgtcagcttttgaggatattatttgctgttgcatctttttacagATACCCGGGCTTGTAAATGTGGATTTTGCTGATGTAAAAGCTGTGATGAAAGACTCTGGAACTGCTATGCTTGGTGTGGGTGTTTCCTCCAGTAAAAACC

upper sequence: Vv19s0090g01320.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA02G46530.1 (Glycine max), 3'ss of exon 4
--actgatttattatgatattttcctgattaatttccaatactgaagtttatctttgctgttgatc-ctatataatttaaaatagcgtgtccttgttttgcagATACCCGGGCTGGTAAATGTTGATTTTGCAGATGTAAAGGCAGTCATGAAGGACTCTGGAACTGCAATGCTTGGAGTGGGGGTTTCTTCCAGCAAAAACC
  |||  || || ||      ||   | ||    | ||   |    || | ||  |||| ||  |  ||  | | | |||| |   ||| | |    |||||| |||| || || || ||||| ||||||||||||||||| || || ||||| |||||||| ||||||||||||||||| || ||||| ||| | |||||||
tcacttcttcataattgggcattttggctttgcattcatgtcaagggtatgtccatgctttttttttctcgacattataaactgttgtgccttc---ttgcagGTACCTGGACTTGTCAATGTGGATTTTGCAGATGTAAAAGCTGTGATGAAAGACTCTGGGACTGCAATGCTTGGAGTAGGTGTTTCCTCCGGTAAAAACC

upper sequence: Vv19s0090g01320.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA14G02110.1 (Glycine max), 3'ss of exon 4
---actgatttattatgatattttcctgattaatttccaatactgaagtttatctttgctgttgatcctatataatttaaaatagcgtgtccttgttttgcagATACCCGGGCTGGTAAATGTTGATTTTGCAGATGTAAAGGCAGTCATGAAGGACTCTGGAACTGCAATGCTTGGAGTGGGGGTTTCTTCCAGCAAAAACC
    ||  || || ||      ||   | ||    |  |   |    || | ||  ||   ||  | ||  | |   |||| | | ||| | |    |||||| |||| || || || ||||| |||||||| |||||||| || || ||||| |||||||| |||||||||||||| || || ||||| ||| | |||||||
acttctccttcataattgggcattgtggctttgcatttatgtcaagggtatgtccatggatttttttctcaacacagtaaactggtgtgccttc---ttgcagGTACCTGGACTTGTCAATGTAGATTTTGCTGATGTAAAAGCTGTGATGAAAGACTCTGGGACTGCAATGCTTGGTGTAGGTGTTTCATCCGGTAAAAACC

upper sequence: Vv19s0090g01320.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G55280.1 (Arabidopsis thaliana), 3'ss of exon 4
actgatttattatgatattttcctgattaatttccaatactgaagttta-tctttgctg-ttgatcctatataattt----aaaatagcgtgtcct----tgttttgcagATACCCGGGCTGGTAAATGTTGATTTTGCAGATGTAAAGGCAGTCATGAAGGACTCTGGAACTGCAATGCTTGGAGTGGGGGTTTCTTCCAGCAAAAACC
  ||| |   |||| |||| |    |  |  |  |||    |  | | | |  ||  || |||||||   |  |||      ||| ||  | |  |    | |||| |||||||| || || || ||||| |||||||||||||| |||||||||||||| || ||||||||||||||||| || || || |||||||||||||||||||
-gtgagtc--tatg-tattgtataaagcacataacaagttggttgatgaatgcttattgattgatccccaaagattctgaggaaacagtatatattttgttctttttcagATACCTGGACTAGTCAATGTAGATTTTGCAGATGTGAAGGCAGTCATGAAAGATTCTGGAACTGCAATGCTCGGGGTAGGTGTTTCTTCCAGCAAAAACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatctttgctgttgatcctatataatttaaaatagcgtgtccttgttttgcagATACCCGGGCTGGTAAATGTTGATTTTGCAGATGTAAAGGCAGTCATGAAGGACTCTGGAACTGCAATGCTTGGAGTGGGGGTTTCTTCCAGCAAAAACC
           tgttgat  putative branch site (score: 4)
                                         tccttgtttt  putative PPT
             ttgatcctatataatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actgatttattatgatattttcctgattaatttccaatactgaagtttatctttgctgttgatcctatataatttaaaatagcgtgtccttgttttgcagATACCCGGGCTGGTAAATGTTGATTTTGCAGATGTAAAGGCAGTCATGAAGGACTCTGGAACTGCAATGCTTGGAGTGGGGGTTTCTTCCAGCAAAAACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - -ttcctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - taaaata