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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caaaaatcactctgtatttttatctgcttggtgatccttgtagatgttgtagctgtgaatcctaatttcattttttttattggattattttccttcttagGTTGAACAAGTGCATAAGATATTCAAGTTATGTGGCTCCCCATCTGAAGAATATTGGAAGAAATCCAAACTGCCACATGCAACAATCTTTAAGCCGCAAC

Basic information

species Vitis vinifera
transcript Vv17s0000g00620.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g00620.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA05G38410.2 (Glycine max), 3'ss of exon 3
caaaaatcactctgtatttttat-ctgcttggtgatccttgtagatgttgtagctgtgaatcctaatttcattttttttattggattattttccttcttagGTTGAACAAGTGCATAAGATATTCAAGTTATGTGGCTCCCCATCTGAAGAATATTGGAAGAAATCCAAACTGCCACATGCAACAATCTTTAAGCCGCAAC------
    |   | | | | |||  || ||| ||  |    |||| |     | |      |||  |  || | | |  |||| |   ||  |   |||    ||||||| ||  |||| || ||||| |||||||||||||| |||||||| ||||| ||||||||||  | | ||||| |||| ||| ||| |||||| || |      
---tatcaaatttatgtttcgattctgtttcctatatcttgcaatgcctattttctggaagacacatatgactgattttttaaaatcttggacct----aggttgagCAGCTGCACAAAATATTTAAGTTATGTGGCTCTCCATCTGATGAATACTGGAAGAAATATAGATTGCCAAATGCTACACTCTATAAGCCTCAGCAACCAT

upper sequence: Vv17s0000g00620.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA05G38410.1 (Glycine max), 3'ss of exon 3
---caaaaatcactctgtatttttat-ctgcttggtgatccttgtagatgttgtagctgtgaatcctaatttcattttttttattggattattttccttcttagGTTGAACAAGTGCATAAGATATTCAAGTTATGTGGCTCCCCATCTGAAGAATATTGGAAGAAATCCAAACTGCCACATGCAACAATCTTTAAGCCGCAAC
    |  |   | | | | |||  || ||| ||  |    |||| |     | |      |||  |  || | | |  |||| |   ||  |   |||    ||||||| ||  |||| || ||||| |||||||||||||| |||||||| ||||| ||||||||||  | | ||||| |||| ||| ||| |||||| || |
ctatagtatcaaatttatgtttcgattctgtttcctatatcttgcaatgcctattttctggaagacacatatgactgattttttaaaatcttggacct----agGTTGAGCAGCTGCACAAAATATTTAAGTTATGTGGCTCTCCATCTGATGAATACTGGAAGAAATATAGATTGCCAAATGCTACACTCTATAAGCCTCAGC

upper sequence: Vv17s0000g00620.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA06G17460.1 (Glycine max), 3'ss of exon 3
-caaaaatcactctgtatttttatctgcttggtgatccttgtagatgttgtagc-tgtgaatcctaatttcattttttttattggattattttccttcttagGTTGAACAAGTGCATAAGATATTCAAGTTATGTGGCTCCCCATCTGAAGAATATTGGAAGAAATCCAAACTGCCACATGCAACAATCTTTAAGCCGCAAC
    |  |   |||| |||   || | | |  |  ||||| || |  | |||   | |  |   | ||       |   | |||| ||  ||     |  ||||||||||| |||| || ||||| ||||| || ||||| |||||||| ||||| |||| ||| |  | | ||||| |||| || ||||||||||| || |
atgtatctttatctgcattccaatatccctttttttccttttaaaattagtattattttcaggatgatacatgactaacttttgggttgcttgggacc--agGTTGAACAACTGCACAAAATATTTAAGTTGTGCGGCTCTCCATCTGAGGAATACTGGAGGAAGTATAGATTGCCAAATGCTACTATCTTTAAGCCACAGC

upper sequence: Vv17s0000g00620.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA04G37630.1 (Glycine max), 3'ss of exon 3
caaaaatcactctgtatttttat---ctgcttggtgatccttgtagatgttgtagc-tgtgaatcctaatttcattttttttattggattattttccttcttagGTTGAACAAGTGCATAAGATATTCAAGTTATGTGGCTCCCCATCTGAAGAATATTGGAAGAAATCCAAACTGCCACATGCAACAATCTTTAAGCCGCAAC
   |  |   |||| |||   ||   |  |||  |  ||||| || |  | |||   | |  |   | ||       |   | | || ||  ||     |  ||||||||||| |||| || ||||| ||||| || ||||| |||||||| ||||| |||| ||| |  | | ||||| |||| || ||||||||||| || |
--catctttatctgcattccaatatcccccttttttttccttttaaaattagtattattttcaggatgatacatgactaactttcgggttgcttggggcc--agGTTGAACAACTGCACAAAATATTTAAGTTGTGCGGCTCTCCATCTGAGGAATACTGGAGGAAGTATAGATTGCCAAATGCTACTATCTTTAAGCCCCAGC

upper sequence: Vv17s0000g00620.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: EFJ35595 (Selaginella moellendorffii), 3'ss of exon 2
caaaaatcactctgtatttttatctgcttggtgatccttgtagatgttgtagctgtgaatcctaatttcattttttttattggattattttccttcttagGTTGAACAAGTGCATAAGATATTCAAGTTATGTGGCTCCCCATCTGAAGAATATTGGAAGAAATCCAAACTGCCACATGCAACAATCTTTAAGCCGCAAC
                      | |||| | || |  ||||   |    |   |   ||  |     |  || || ||||||    |           |||| || ||| | || ||||| || ||| |||||||||| ||||| ||||| |||||||| ||||||||||| || || || || || ||||||||||| |
---------------------gtatgctcgttggtttttgttt-tacgatgtttagtaacgcctgcct--ttcttcttattgatcgaac---------agGTGGAGCAATTACACAAGATTTTTAAGCTATGTGGCTCGCCATCGGAAGAGTATTGGAAAAAATCCAAACTTCCTCACGCTACGATTTTTAAGCCGCAGC

upper sequence: Vv17s0000g00620.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: EFJ24328 (Selaginella moellendorffii), 3'ss of exon 4
caaaaatcactctgtatttttatctgcttggtgatccttgtagatgttgtagctgtgaatcctaatttcattttttttattggattattttccttcttagGTTGAACAAGTGCATAAGATATTCAAGTTATGTGGCTCCCCATCTGAAGAATATTGGAAGAAATCCAAACTGCCACATGCAACAATCTTTAAGCCGCAAC
                              ||   |    | | | || |   |  ||    || |  |   |   ||  |   | ||    |     |||| || ||| | || ||||| || ||| |||||||||| ||||| ||||| |||||||| ||||||||||| || || || || || ||||||||||| |
------------------------------gtatgctccttggtttttatt-ttacgatgtttagtaacgcctgcctttcttattgatcgaac-----agGTGGAGCAATTACACAAGATTTTTAAGCTATGTGGCTCGCCATCGGAAGAGTATTGGAAAAAATCCAAACTTCCTCACGCTACGATTTTTAAGCCGCAGC

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|352795543|gb|FQ480131.1|FQ480131
EST:     TTTTGGCGGAGTTGCTTGGTGGGAAGCCAATAATGCCTGGACGAACAGAG                         GTTGAACAAGTGCATAAGATATTCAAGTTATGTGGCTCCCCATCTGAAGAA
genomic: TTTTGGCGGAGTTGCTTGGTGGGAAGCCAATAATGCCTGGACGAACAGAGgtgatctatt ... tccttcttagGTTGAACAAGTGCATAAGATATTCAAGTTATGTGGCTCCCCATCTGAAGAA
EST: gi|351046377|gb|FQ452993.1|FQ452993
EST:     TTTTGGCGGAGTTGCTTGGTGGGAAGCCAATAATGCCTGGACGAACAGAG                         GTTGAACAAGTGCATAAGATATTCAAGTTATGTGGCTCCCCATCTGAAGAA
genomic: TTTTGGCGGAGTTGCTTGGTGGGAAGCCAATAATGCCTGGACGAACAGAGgtgatctatt ... tccttcttagGTTGAACAAGTGCATAAGATATTCAAGTTATGTGGCTCCCCATCTGAAGAA
EST: gi|351055934|gb|FQ453395.1|FQ453395
EST:     TTTTGGCGGAGTTGCTTGGTGGGAAGCCAATAATGCCTGGACGAACAGAG                         GTTGAACAAGTGCATAAGATATTCAAGTTATGTGGCTCCCCATCTGAAGAA
genomic: TTTTGGCGGAGTTGCTTGGTGGGAAGCCAATAATGCCTGGACGAACAGAGgtgatctatt ... tccttcttagGTTGAACAAGTGCATAAGATATTCAAGTTATGTGGCTCCCCATCTGAAGAA
EST: gi|352786901|gb|FQ481276.1|FQ481276
EST:     TTTTGGCGGAGTTGCTTGGTGGGAAGCCAATAATGCCTGGACGAACAGAG                         GTTGAACAAGTGCATAAGATATTCAAGTTATGTGGCTCCCCATCTGAAGAA
genomic: TTTTGGCGGAGTTGCTTGGTGGGAAGCCAATAATGCCTGGACGAACAGAGgtgatctatt ... tccttcttagGTTGAACAAGTGCATAAGATATTCAAGTTATGTGGCTCCCCATCTGAAGAA
EST: gi|351043417|gb|FQ451469.1|FQ451469
EST:     TTTTGGCGGAGTTGCTTGGTGGGAAGCCAATAATGCCTGGACGAACAGAG                         GTTGAACAAGTGCATAAGATATTCAAGTTATGTGGCTCCCCATCTGAAGAA
genomic: TTTTGGCGGAGTTGCTTGGTGGGAAGCCAATAATGCCTGGACGAACAGAGgtgatctatt ... tccttcttagGTTGAACAAGTGCATAAGATATTCAAGTTATGTGGCTCCCCATCTGAAGAA
EST: gi|351043887|gb|FQ452681.1|FQ452681
EST:     TTTTGGCGGAGTTGCTTGGTGGGAAGCCAATAATGCCTGGACGAACAGAG                         GTTGAACAAGTGCATAAGATATTCAAGTTATGTGGCTCCCCATCTGAAGAA
genomic: TTTTGGCGGAGTTGCTTGGTGGGAAGCCAATAATGCCTGGACGAACAGAGgtgatctatt ... tccttcttagGTTGAACAAGTGCATAAGATATTCAAGTTATGTGGCTCCCCATCTGAAGAA
EST: gi|351038967|gb|FQ457642.1|FQ457642
EST:     TTTTGGCGGAGTTGCTTGGTGGGAAGCCAATAATGCCTGGACGAACAGAG                         GTTGAACAAGTGCATAAGATATTCAAGTTATGTGGCTCCCCATCTGAAGAA
genomic: TTTTGGCGGAGTTGCTTGGTGGGAAGCCAATAATGCCTGGACGAACAGAGgtgatctatt ... tccttcttagGTTGAACAAGTGCATAAGATATTCAAGTTATGTGGCTCCCCATCTGAAGAA
EST: gi|351055161|gb|FQ440500.1|FQ440500
EST:     TTTTGGCGGAGTTGCTTGGTGGGAAGCCAATAATGCCTGGACGAACAGAG                         GTTGAACAAGTGCATAAGATATTCAAGTTATGTGGCTCCCCATCTGAAGAA
genomic: TTTTGGCGGAGTTGCTTGGTGGGAAGCCAATAATGCCTGGACGAACAGAGgtgatctatt ... tccttcttagGTTGAACAAGTGCATAAGATATTCAAGTTATGTGGCTCCCCATCTGAAGAA
EST: gi|351032086|gb|FQ460343.1|FQ460343
EST:     TTTTGGCGGAGTTGCTTGGTGGGAAGCCAATAATGCCTGGACGAACAGAG                         GTTGAACAAGTGCATAAGATATTCAAGTTATGTGGCTCCCCATCTGAAGAA
genomic: TTTTGGCGGAGTTGCTTGGTGGGAAGCCAATAATGCCTGGACGAACAGAGgtgatctatt ... tccttcttagGTTGAACAAGTGCATAAGATATTCAAGTTATGTGGCTCCCCATCTGAAGAA
EST: gi|351043841|gb|FQ452635.1|FQ452635
EST:     TTTTGGCGGAGTTGCTTGGTGGGAAGCCAATAATGCCTGGACGAACAGAG                         GTTGAACAAGTGCATAAGATATTCAAGTTATGTGGCTCCCCATCTGAAGAA
genomic: TTTTGGCGGAGTTGCTTGGTGGGAAGCCAATAATGCCTGGACGAACAGAGgtgatctatt ... tccttcttagGTTGAACAAGTGCATAAGATATTCAAGTTATGTGGCTCCCCATCTGAAGAA
EST: gi|349824254|gb|FQ417641.1|FQ417641
EST:     TTTTGGCGGAGTTGCTTGGTGGGAAGCCAATAATGCCTGGACGAACAGAG                         GTTGAACAAGTGCATAAGATATTCAAGTTATGTGGCTCCCCATCTGAAGAA
genomic: TTTTGGCGGAGTTGCTTGGTGGGAAGCCAATAATGCCTGGACGAACAGAGgtgatctatt ... tccttcttagGTTGAACAAGTGCATAAGATATTCAAGTTATGTGGCTCCCCATCTGAAGAA
EST: gi|351013309|gb|FQ425014.1|FQ425014
EST:     TTTTGGCGGAGTTGCTTGGTGGGAAGCCAATAATGCCTGGACGAACAGAG                         GTTGAACAAGTGCATAAGATATTCAAGTTATGTGGCTCCCCATCTGAAGAA
genomic: TTTTGGCGGAGTTGCTTGGTGGGAAGCCAATAATGCCTGGACGAACAGAGgtgatctatt ... tccttcttagGTTGAACAAGTGCATAAGATATTCAAGTTATGTGGCTCCCCATCTGAAGAA
EST: gi|352795551|gb|FQ480139.1|FQ480139
EST:     TTTTGGCGGAGTTGCTTGGTGGGAAGCCAATAATGCCTGGACGAACAGAG                         GTTGAACAAGTGCATAAGATATTCAAGTTATGTGGCTCCCCATCTGAAGAA
genomic: TTTTGGCGGAGTTGCTTGGTGGGAAGCCAATAATGCCTGGACGAACAGAGgtgatctatt ... tccttcttagGTTGAACAAGTGCATAAGATATTCAAGTTATGTGGCTCCCCATCTGAAGAA
EST: gi|351034440|gb|FQ463253.1|FQ463253
EST:     TTTTGGCGGAGTTGCTTGGTGGGAAGCCAATAATGCCTGGACGAACAGAG                         GTTGAACAAGTGCATAAGATATTCAAGTTATGTGGCTCCCCATCTGAAGAA
genomic: TTTTGGCGGAGTTGCTTGGTGGGAAGCCAATAATGCCTGGACGAACAGAGgtgatctatt ... tccttcttagGTTGAACAAGTGCATAAGATATTCAAGTTATGTGGCTCCCCATCTGAAGAA
EST: gi|352790536|gb|FQ478176.1|FQ478176
EST:     TTTTGGCGGAGTTGCTTGGTGGGAAGCCAATAATGCCTGGACGAACAGAG                         GTTGAACAAGTGCATAAGATATTCAAGTTATGTGGCTCCCCATCTGAAGAA
genomic: TTTTGGCGGAGTTGCTTGGTGGGAAGCCAATAATGCCTGGACGAACAGAGgtgatctatt ... tccttcttagGTTGAACAAGTGCATAAGATATTCAAGTTATGTGGCTCCCCATCTGAAGAA
EST: gi|352791008|gb|FQ480001.1|FQ480001
EST:     TTTTGGCGGAGTTGCTTGGTGGGAAGCCAATAATGCCTGGACGAACAGAG                         GTTGAACAAGTGCATAAGATATTCAAGTTATGTGGCTCCCCATCTGAAGAA
genomic: TTTTGGCGGAGTTGCTTGGTGGGAAGCCAATAATGCCTGGACGAACAGAGgtgatctatt ... tccttcttagGTTGAACAAGTGCATAAGATATTCAAGTTATGTGGCTCCCCATCTGAAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgtagctgtgaatcctaatttcattttttttattggattattttccttcttagGTTGAACAAGTGCATAAGATATTCAAGTTATGTGGCTCCCCATCTGAAGAATATTGGAAGAAATCCAAACTGCCACATGCAACAATCTTTAAGCCGCAAC
              tcctaat  putative branch site (score: 2)
                                       ttattttccttctt  putative PPT
            aatcctaatttcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caaaaatcactctgtatttttatctgcttggtgatccttgtagatgttgtagctgtgaatcctaatttcattttttttattggattattttccttcttagGTTGAACAAGTGCATAAGATATTCAAGTTATGTGGCTCCCCATCTGAAGAATATTGGAAGAAATCCAAACTGCCACATGCAACAATCTTTAAGCCGCAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
-aaaaatc
- - - - -ctctgta
- - - - - - - - - - - - tgcttgg
- - - - - - - - - - - - - - - - - -ccttgta
- - - - - - - - - - - - - - - - - - - - - - - -tgtagct
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tgaatcc