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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaatacttttaaactttaggtattctttcctgtcctaagttatcatatttctaatcatgtaattctgttttcttctcttctgaaacagGTCTTTCAGAGTGCTGCACTTTTTGATTCTTTAACTGTTCGTGAAAATGTTGGTTTCCTTTT

Basic information

species Vitis vinifera
transcript Vv04s0023g00290.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g00290.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os03g46740.1 (Oryza sativa), 3'ss of exon 5
-------gtaaaatacttttaaactttaggtattctttcctgtcctaagttatcatatttctaatcatgtaa-ttctgttttcttctcttctgaaacagGTCTTTCAGAGTGCTGCACTTTTTGATTCTTTAACTGTTCGTGAAAATGTTGGTTTCCTTTT
        |  |||   || |||  |   | ||   | ||      |  |||||      ||  ||  | || ||||    |  ||| | |  |   |||| ||||| ||||| ||  | ||||||||| | || ||||||||||||||||| ||||||||
gtatactctttaattacttcaaatctgccgaataaataccatgataattttatcgaccaactgttctcgaaaattctaaaatggtctttgcctatgaagGTGTTTCAAAGTGCAGCTTTGTTTGATTCTCTCACGGTTCGTGAAAATGTTGGATTCCTTTT

upper sequence: Vv04s0023g00290.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM5G889923_T02 (Zea mays), 3'ss of exon 2
gtaaaatacttttaaactttaggtattctttcctgtcctaagttatcatatttcta----atcatgtaattctgttttctt-----ctcttctgaaacagGTCTTTCAGAGTGCTGCACTTTTTGATTCTTTAACTGTTCGTGAAAATGTTGGTTTCCTTTT
||| |      ||   ||||      ||| | ||     | |  || || |   |      || |||   |     ||||       | || ||| |||||||||||| ||||||||||||||||||||| | || ||||||||||||||||| ||||||||
gtacatattccttgtgctttgttgcatctgtactaagaaatggcatgatttccttgtagcttcttgtgcctgaacattctgatgtggtgttgtgatacagGTCTTTCAAAGTGCTGCACTTTTTGATTCTCTCACAGTTCGTGAAAATGTTGGATTCCTTTT

upper sequence: Vv04s0023g00290.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM5G868168_T04 (Zea mays), 3'ss of exon 5
gtaaaatacttttaaactttaggtattctttcctgtcctaagttatcatatttcta----atcatgtaattctgttttctt-----ctcttctgaaacagGTCTTTCAGAGTGCTGCACTTTTTGATTCTTTAACTGTTCGTGAAAATGTTGGTTTCCTTTT
||| |     |||   ||||      ||| | ||     | |  || || |   |      || |||   |  |  ||||       | || ||| |||||||||||| ||||||||||||||||||||| | || ||||||||||||||||| ||||||||
gtacatattctttgtgctttgttgcatctgtactaagaaatggcatgatttccttgtagcttcttgtgcctgagcattctgatgtggtgttgtgatacagGTCTTTCAAAGTGCTGCACTTTTTGATTCTCTCACAGTTCGTGAAAATGTTGGATTCCTTTT

upper sequence: Vv04s0023g00290.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA18G47600.1 (Glycine max), 3'ss of exon 4
gtaaaatacttttaaactttaggtattctttcctgtcctaagttatcatatttctaatcatgtaattctgttttcttctcttctg-aaacagGTCTTTCAGAGTGCTGCACTTTTTGATTCTTTAACTGTTCGTGAAAATGTTGGTTTCCTTTT
     |   ||   |    || | | | |      || || ||||      || ||||  ||||||| | |||| || |  |||| |||||||| || || ||||||||||| ||||||||||| ||||||||||||||||||||||| || | 
--ggtaagtttcagagtaatatgcaatatgctaattcttaggttacg----ttttaat--tgtaattttattttatttttatctgtaaacaGGTTTTCCAAAGTGCTGCACTCTTTGATTCTTTGACTGTTCGTGAAAATGTTGGTTTTCTCT-

upper sequence: Vv04s0023g00290.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA09G38730.1 (Glycine max), 3'ss of exon 4
gtaaaatacttttaaactttag-gtattctttcctgtcctaagttatcatatttctaatcatgtaattctgttttcttctcttctgaaacagGTCTTTCAGAGTGCTGCACTTTTTGATTCTTTAACTGTTCGTGAAAATGTTGGTTTCCTTTT
            |||  || || ||||| |    | | |||| || | || ||  |    | |||| | | |||| ||   |    ||| |||| || || ||||| ||||| ||||||||||| ||||||||||||||||||||||| || ||
-----------gtaagtttcagagtattatgcaatatactaa-ttcttattttgttttcaacgtaact-tattttttttaatctgtaaatagGTTTTCCAAAGTGCAGCACTCTTTGATTCTTTGACTGTTCGTGAAAATGTTGGTTTTCTCTT

upper sequence: Vv04s0023g00290.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT1G65410.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaaaatacttttaaactttaggtattctttcctgtcctaagttatcatatttctaatcatgtaattctgttttcttctcttctgaaacagGTCTTTCAGAGTGCTGCACTTTTTGATTCTTTAACTGTTCGTGAAAATGTTGGTTTCCTTTT
|||   | || ||   ||  || | |  ||     || |||||  |    ||| ||   |  |   | | | || |     ||    |||||| ||||||||||| || || ||||||||  || | |||||||||||||||||||| ||  |
gtagg-tgctgtt---ctggagatgtatttc----tcataagtcgttgagtttgtatctaaatggctttttgttttctgtctc----acagGTATTTCAGAGTGCAGCTCTCTTTGATTCACTATCAGTTCGTGAAAATGTTGGTTTTCTACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctaagttatcatatttctaatcatgtaattctgttttcttctcttctgaaacagGTCTTTCAGAGTGCTGCACTTTTTGATTCTTTAACTGTTCGTGAAAATGTTGGTTTCCTTTT
               ttctaat  putative branch site (score: 2)
                          taattctgttttcttc  putative PPT
      ttatcatatttctaat  TA-rich tract