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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgtcttgatttatggtaccattcacatttttgcacaacatgcaaatcaagttctccttatgagaggctggtggctaactttttcaattttttgagcagAGGCTGTTGCTGATGCAAACAGAGCAATTGAGTTGGACCCATCAATGTCTAAAGCATTCTTGCGGAAAGG

Basic information

species Vitis vinifera
transcript Vv16s0050g01510.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0050g01510.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA16G29450.2 (Glycine max), 3'ss of exon 1
------tttgtcttg-atttatggtaccattcacatttttgcacaacatgcaaatcaagttctccttatgagaggctggtggctaactttttcaattttttgagcagAGGCTGTTGCTGATGCAAACAGAGCAATTGAGTTGGACCCATCAATGTCTAAAGCATTCTTGCGGAAAGG
      ||| | |||  || ||||   | |  | |  | ||      |||         | ||  |||  | |   |||   |||| ||||     |||| | |||||||||||||||||||| |||| ||||||||| ||| |  | ||  |  | |||||||  |||||||||||
atggtgtttattttgtgttcatggcgtcctgtagacatgtggttgtaatgttt------tactaattactaaattttgggaactaaattttcttgctttt-gtgcagAGGCTGTTGCTGATGCTAACAAAGCAATTGAATTGAATTCTTCTCTACCAAAAGCATATTTGCGGAAAGG

upper sequence: Vv16s0050g01510.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA09G23980.1 (Glycine max), 3'ss of exon 1
--------tttgtcttg-atttatggtaccattcacatttttgcacaacatgca-aatcaagttctccttatgagaggctggtggctaactttttcaattttttgagcagAGGCTGTTGCTGATGCAAACAGAGCAATTGAGTTGGACCCATCAATGTCTAAAGCATTCTTGCGGAAAGG
        ||| | ||| ||| ||||  || | || |  | ||      |||    |  || | ||  || || ||         |||| ||| |     ||||| ||||||||||| |||||||| |||| ||||||||| ||| | || ||  |  | |||||||  |||||||||||
atatggtgtttattttgtattcatggcgccctgcagacatgtggttgtaatgtttgactaattactaattttgggaa--------ctaattttcttg--cttttgtgcagAGGCTGTGGCTGATGCTAACAAAGCAATTGAATTGAATCCTTCTCTACCAAAAGCATATTTGCGGAAAGG
















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|110712988|gb|EE088514.1|EE088514
EST:     GCTCTATGTTGAACGATCTCAGGCCAACATCAAACTCAACAACTTCACTG                         AGGCTGTTGCTGATGCAAACAGAGCAATTGAGTTGGACCCATCAATGTCTA
genomic: GCTCTATGTTGAACGATCTCAGGCCAACATCAAACTCAACAACTTCACTGgtatcgatca ... ttttgagcagAGGCTGTTGCTGATGCAAACAGAGCAATTGAGTTGGACCCATCAATGTCTA
EST: gi|71859342|gb|DT008397.1|DT008397
EST:     CCAACATCAAACTCAACAACTTCACTG                         AGGCTGTTGCTGATGCAAACAGAGCAATTGAGTTGGACCCATCAATGTCTA
genomic: CCAACATCAAACTCAACAACTTCACTGgtatcgatca ... ttttgagcagAGGCTGTTGCTGATGCAAACAGAGCAATTGAGTTGGACCCATCAATGTCTA
EST: gi|161710647|gb|FC059030.1|FC059030
EST:     GCTCTATGTTGAACGATCTCAGGCCAACATCAAACTCAACAACTTCACTG                         AGGCTGTTGCTGATGCAAACAGAGCAATTGAGTTGGACCCATCAATGTCTA
genomic: GCTCTATGTTGAACGATCTCAGGCCAACATCAAACTCAACAACTTCACTGgtatcgatca ... ttttgagcagAGGCTGTTGCTGATGCAAACAGAGCAATTGAGTTGGACCCATCAATGTCTA
EST: gi|110733197|gb|EE109180.1|EE109180
EST:     GCTCTATGTTGAACGATCTCAGGCCAACATCAAACTCAACAACTTCACTG                         AGGCTGTTGCTGATGCAAACAGAGCAATTGAGTTGGACCCATCAATGTCTA
genomic: GCTCTATGTTGAACGATCTCAGGCCAACATCAAACTCAACAACTTCACTGgtatcgatca ... ttttgagcagAGGCTGTTGCTGATGCAAACAGAGCAATTGAGTTGGACCCATCAATGTCTA
EST: gi|29782866|gb|CB348559.2|CB348559
EST:     GCTCTATGTTGAACGATCTCAGGCCAACATCAAACTCAACAACTTCACTG                         AGGCTGTTGCTGATGCAAACAGAGCAATTGAGTTGGACCCATCAATGTCTA
genomic: GCTCTATGTTGAACGATCTCAGGCCAACATCAAACTCAACAACTTCACTGgtatcgatca ... ttttgagcagAGGCTGTTGCTGATGCAAACAGAGCAATTGAGTTGGACCCATCAATGTCTA
EST: gi|29783203|gb|CB349232.2|CB349232
EST:     GCTCTATGTTGAACGATCTCAGGCCAACATCAAACTCAACAACTTCACTG                         AGGCTGTTGCTGATGCAAACAGAGCAATTGAGTTGGACCCATCAATGTCTA
genomic: GCTCTATGTTGAACGATCTCAGGCCAACATCAAACTCAACAACTTCACTGgtatcgatca ... ttttgagcagAGGCTGTTGCTGATGCAAACAGAGCAATTGAGTTGGACCCATCAATGTCTA
EST: gi|110694395|gb|EE071465.1|EE071465
EST:     GCTCTATGTTGAACGATCTCAGGCCAACATCAAACTCAACAACTTCACTG                         AGGCTGTTGCTGATGCAAACAGAGCAATTGAGTTGGACCCATCAATGTCTA
genomic: GCTCTATGTTGAACGATCTCAGGCCAACATCAAACTCAACAACTTCACTGgtatcgatca ... ttttgagcagAGGCTGTTGCTGATGCAAACAGAGCAATTGAGTTGGACCCATCAATGTCTA
EST: gi|161712354|gb|FC061928.1|FC061928
EST:     GCTCTATGTTGAACGATCTCAGGCCAACATCAAACTCAACAACTTCACTG                         AGGCTGTTGCTGATGCAAACAGAGCAATTGAGTTGGACCCATCAATGTCTA
genomic: GCTCTATGTTGAACGATCTCAGGCCAACATCAAACTCAACAACTTCACTGgtatcgatca ... ttttgagcagAGGCTGTTGCTGATGCAAACAGAGCAATTGAGTTGGACCCATCAATGTCTA
EST: gi|110686508|gb|EE064228.1|EE064228
EST:     GCTCTATGTTGAACGATCTCAGGCCAACATCAAACTCAACAACTTCACTG                         AGGCTGTTGCTGATGCAAACAGAGCAATTGAGTTGGACCCATCAATGTCTA
genomic: GCTCTATGTTGAACGATCTCAGGCCAACATCAAACTCAACAACTTCACTGgtatcgatca ... ttttgagcagAGGCTGTTGCTGATGCAAACAGAGCAATTGAGTTGGACCCATCAATGTCTA
EST: gi|37187277|gb|CF606630.1|CF606630
EST:     GCTCTATGTTGAACGATCTCAGGCCAACATCAAACTCAACAACTTCACTG                         AGGCTGTTGCTGATGCAAACAGAGCAATTGAGTTGGACCCATCAATGTCTA
genomic: GCTCTATGTTGAACGATCTCAGGCCAACATCAAACTCAACAACTTCACTGgtatcgatca ... ttttgagcagAGGCTGTTGCTGATGCAAACAGAGCAATTGAGTTGGACCCATCAATGTCTA
EST: gi|46917631|gb|CN546960.1|CN546960
EST:     CGATCTCAGGCCAACATCAAACTCAACAACTTCACTG                         AGGCTGTTGCTGATGCAAACAGAGCAATTGAGTTGGACCCATCAATGTCTA
genomic: CGATCTCAGGCCAACATCAAACTCAACAACTTCACTGgtatcgatca ... ttttgagcagAGGCTGTTGCTGATGCAAACAGAGCAATTGAGTTGGACCCATCAATGTCTA
EST: gi|294964470|gb|GW838273.1|GW838273
EST:     GCTCTATGTTGAACGATCTCAGGCCAACATCAAACTCAACAACTGCACTG                         AGGCTGTTGCTGATGCAAACAGAGCAATTGAGTTGGACCCATCAATGTCTA
genomic: GCTCTATGTTGAACGATCTCAGGCCAACATCAAACTCAACAACTTCACTGgtatcgatca ... ttttgagcagAGGCTGTTGCTGATGCAAACAGAGCAATTGAGTTGGACCCATCAATGTCTA
EST: gi|110729024|gb|EE105164.1|EE105164
EST:     GCTCTATGTTGAACGATCTCAGGCCAACATCAAACTCAACAACTTCACTG                         AGGCTGTTGCTGATGCAAACAGAGCAATTGAGTTGGACCCATCAATGTCTA
genomic: GCTCTATGTTGAACGATCTCAGGCCAACATCAAACTCAACAACTTCACTGgtatcgatca ... ttttgagcagAGGCTGTTGCTGATGCAAACAGAGCAATTGAGTTGGACCCATCAATGTCTA
EST: gi|28969441|gb|CB348474.1|CB348474
EST:     GCTCTATGTTGAACGATCTCAGGCCAACATCAAACTCAACAACTTCACTG                         AGGCTGTTGCTGATGCAAACAGAGCAATTGAGTTGGACCCATCAATGTCTA
genomic: GCTCTATGTTGAACGATCTCAGGCCAACATCAAACTCAACAACTTCACTGgtatcgatca ... ttttgagcagAGGCTGTTGCTGATGCAAACAGAGCAATTGAGTTGGACCCATCAATGTCTA
EST: gi|71863962|gb|DT013017.1|DT013017
EST:     GCTCTATGTTGAACGATCTCAGGCCAACATCAAACTCAACAACTTCACTG                         AGGCTGTTGCTGATGCAAACAGAGCAATTGAGTTGGACCCATCAATGTCTA
genomic: GCTCTATGTTGAACGATCTCAGGCCAACATCAAACTCAACAACTTCACTGgtatcgatca ... ttttgagcagAGGCTGTTGCTGATGCAAACAGAGCAATTGAGTTGGACCCATCAATGTCTA
EST: gi|71859797|gb|DT008852.1|DT008852
EST:     GCTCTATGTTGAACGATCTCAGGCCAACATCAAACTCAACAACTTCACTG                         AGGCTGTTGCTGATGCAAACAGAGCAATTGAGTTGGACCCATCAATGTCTA
genomic: GCTCTATGTTGAACGATCTCAGGCCAACATCAAACTCAACAACTTCACTGgtatcgatca ... ttttgagcagAGGCTGTTGCTGATGCAAACAGAGCAATTGAGTTGGACCCATCAATGTCTA
EST: gi|161707617|gb|FC057397.1|FC057397
EST:     GCTCTATGTTGAACGATCTCAGGCCAACATCAAACTCAACAACTTCACTG                         AGGCTGTTGCTGATGCAAACAGAGCAATTGAGTTGGACCCATCAATGTCTA
genomic: GCTCTATGTTGAACGATCTCAGGCCAACATCAAACTCAACAACTTCACTGgtatcgatca ... ttttgagcagAGGCTGTTGCTGATGCAAACAGAGCAATTGAGTTGGACCCATCAATGTCTA
EST: gi|110687406|gb|EE064790.1|EE064790
EST:     GCTCTATGTTGAACGATCTCAGGCCAACATCAAACTCAACAACTTCACTG                         AGGCTGTTGCTGATGCAAACAGAGCAATTGAGTTGGACCCATCAATGTCTA
genomic: GCTCTATGTTGAACGATCTCAGGCCAACATCAAACTCAACAACTTCACTGgtatcgatca ... ttttgagcagAGGCTGTTGCTGATGCAAACAGAGCAATTGAGTTGGACCCATCAATGTCTA
EST: gi|110693950|gb|EE070628.1|EE070628
EST:     GCTCTATGTTGAACGATCTCAGGCCAACATCAAACTCAACAACTTCACTG                         AGGCTGTTGCTGATGCAAACAGAGCAATTGAGTTGGACCCATCAATGTCTA
genomic: GCTCTATGTTGAACGATCTCAGGCCAACATCAAACTCAACAACTTCACTGgtatcgatca ... ttttgagcagAGGCTGTTGCTGATGCAAACAGAGCAATTGAGTTGGACCCATCAATGTCTA
EST: gi|110711614|gb|EE088295.1|EE088295
EST:     GCTCTATGTTGAACGATCTCAGGCCAACATCAAACTCAACAACTTCACTG                         AGGCTGTTGCTGATGCAAACAGAGCAATTGAGTTGGACCCATCAATGTCTA
genomic: GCTCTATGTTGAACGATCTCAGGCCAACATCAAACTCAACAACTTCACTGgtatcgatca ... ttttgagcagAGGCTGTTGCTGATGCAAACAGAGCAATTGAGTTGGACCCATCAATGTCTA
EST: gi|161711760|gb|FC058309.1|FC058309
EST:     GCTCTATGTTGAACGATCTCAGGCCAACATCAAACTCAACAACTTCACTG                         AGGCTGTTGCTGATGCAAACAGAGCAATTGAGTTGGACCCATCAATGTCTA
genomic: GCTCTATGTTGAACGATCTCAGGCCAACATCAAACTCAACAACTTCACTGgtatcgatca ... ttttgagcagAGGCTGTTGCTGATGCAAACAGAGCAATTGAGTTGGACCCATCAATGTCTA
EST: gi|110732977|gb|EE108734.1|EE108734
EST:     GCTCTATGTTGAACGATCTCAGGCCAACATCAAACTCAACAACTTCACTG                         AGGCTGTTGCTGATGCAAACAGAGCAATTGAGTTGGACCCATCAATGTCTA
genomic: GCTCTATGTTGAACGATCTCAGGCCAACATCAAACTCAACAACTTCACTGgtatcgatca ... ttttgagcagAGGCTGTTGCTGATGCAAACAGAGCAATTGAGTTGGACCCATCAATGTCTA
EST: gi|161708929|gb|FC060472.1|FC060472
EST:     GCTCTATGTTGAACGATCTCAGGCCAACATCAAACTCAACAACTTCACTG                         AGGCTGTTGCTGATGCAAACAGAGCAATTGAGTTGGACCCATCAATGTCT
genomic: GCTCTATGTTGAACGATCTCAGGCCAACATCAAACTCAACAACTTCACTGgtatcgatca ... ttttgagcagAGGCTGTTGCTGATGCAAACAGAGCAATTGAGTTGGACCCATCAATGTCT
EST: gi|110723197|gb|EE100235.1|EE100235
EST:     GCTCTATGTTGAACGATCTCAGGCCAACATCAAACTCAACAACTTCACTG                         AGGCTGTTGCTGATGCAAACAGAGCAATTGAGTTGGACCCATCAATGTCTA
genomic: GCTCTATGTTGAACGATCTCAGGCCAACATCAAACTCAACAACTTCACTGgtatcgatca ... ttttgagcagAGGCTGTTGCTGATGCAAACAGAGCAATTGAGTTGGACCCATCAATGTCTA
EST: gi|161718657|gb|FC067946.1|FC067946
EST:     GCTCTATGTTGAACGATCTCAGGCCAACATCAAACTCAACAACTTCACTG                         AGGCTGTTGCTGATGCAAACAGAGCAATTGAGTTGGACCCATCAATGTCTA
genomic: GCTCTATGTTGAACGATCTCAGGCCAACATCAAACTCAACAACTTCACTGgtatcgatca ... ttttgagcagAGGCTGTTGCTGATGCAAACAGAGCAATTGAGTTGGACCCATCAATGTCTA
EST: gi|71857115|gb|DT006170.1|DT006170
EST:     GCTCTATGTTGAACGATCTCAGGCCAACATCAAACTCAACAACTTCACTG                         AGGCTGTTGCTGATGCAAACAGAGCAATTGAGTTGGACCCATCAATGTCTA
genomic: GCTCTATGTTGAACGATCTCAGGCCAACATCAAACTCAACAACTTCACTGgtatcgatca ... ttttgagcagAGGCTGTTGCTGATGCAAACAGAGCAATTGAGTTGGACCCATCAATGTCTA
EST: gi|71873209|gb|DT022264.1|DT022264
EST:     GCTCTATGTTGAACGATCTCAGGCCAACATCAAACTCAACAACTTCACTG                         AGGCTGTTGCTGATGCAAACAGAGCAATTGAGTTGGACCCATCAATGTCTA
genomic: GCTCTATGTTGAACGATCTCAGGCCAACATCAAACTCAACAACTTCACTGgtatcgatca ... ttttgagcagAGGCTGTTGCTGATGCAAACAGAGCAATTGAGTTGGACCCATCAATGTCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatcaagttctccttatgagaggctggtggctaactttttcaattttttgagcagAGGCTGTTGCTGATGCAAACAGAGCAATTGAGTTGGACCCATCAATGTCTAAAGCATTCTTGCGGAAAGG
                            ggctaac  putative branch site (score: 2)
                                  ctttttcaatttttt  CT-rich tract
                               taactttttcaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgtcttgatttatggtaccattcacatttttgcacaacatgcaaatcaagttctccttatgagaggctggtggctaactttttcaattttttgagcagAGGCTGTTGCTGATGCAAACAGAGCAATTGAGTTGGACCCATCAATGTCTAAAGCATTCTTGCGGAAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- tgtcttg
- - - - - - - - - -ccattca
- - - - - - - - - - - - - - -ttttgca
- - - - - - - - - - - - - - - - - - caacatg
- - - - - - - - - - - - - - - - - - - - - - aaatcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aggctgg