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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttaactttttccgaggtcattctcattgacccacaatcaggcttgcctgattattcttgaatttttgtgtatgtgatgaggcatgtgcatgtgttacagGTACAACATGGTGAAACAAGGTCTTGTTAAGGAGCCAGTATTTTCATTCTGGCTCAACCGCAAGACAGATGATGATGAAGGGGGTGAACTTGTGTTTGGT

Basic information

species Vitis vinifera
transcript Vv10s0116g01210.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0116g01210.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os01g47410.2 (Oryza sativa), 3'ss of exon 5
tttaactttttccgaggtcattct-cattgacccacaatcaggcttgcctgattattc----ttgaat----ttttgtgtatgtgatgaggcatgtgcatgtgttacagGTACAACATGGTGAAACAAGGTCTTGTTAAGGAGCCAGTATTTTCATTCTGGCTCAACCGCAAGACAGATGATGATGAAGGGGGTGAACTTGTGTTTGGT
              ||  |||| |  |  |  | ||   ||   ||  || ||  |||     ||||     |||  |||   |||    |||   |||    | | |||||||||||||||| |||||||||||||   || || || || ||||||||| |||||||  |  | ||||| |   | || || ||| |||||||||| 
-------aaaatgaagaccattttgtaccgggctacctgcatatttctctcatccttcgaatgtgaagcagatttcctgtcactgacattgcaaa-gcaaac-tcatagGTACAACATGGTGAGACAAGGTCTTGTTGTTGATCCTGTTTTCTCATTCTGGTTCAACCGGCATGCTGATGAAGGGCAGGGAGGCGAAATTGTGTTTGGA

upper sequence: Vv10s0116g01210.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA17G01500.1 (Glycine max), 3'ss of exon 5
tttaactttttccgaggtcattctcattgacccacaatcaggcttgcctgattattcttgaatttttgtg-------tatgtgatgaggcatgtgcatgtgttacagGTACAACATGGTGAAACAAGGTCTTGTTAAGGAGCCAGTATTTTCATTCTGGCTCAACCGCAAGACAGATGATGATGAAGGGGGTGAACTTGTGTTTGGT
     |||  |     |  | ||| || || |||     |  ||||    ||| || || || |||| |         ||||| | |         |  ||| ||||||||||||||||  | ||||||||| ||||||| |||||||||||||| ||| ||||||||||  |||| || || |||||||||||  |||| || |||
----tcttcctatagtgagagtcttatagaacca-ggctacccttgtt--attgtttttaaaattttattgaatccccatgtgtttatctgatcttacctgtcacagGTACAACATGGTTGACCAAGGTCTTCTTAAGGAACCAGTATTTTCATTTTGGTTCAACCGCAATCCAGAGGAAGAGGAAGGGGGTGAGATTGTTTTCGGT

upper sequence: Vv10s0116g01210.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA07G39240.2 (Glycine max), 3'ss of exon 5
tttaactttttccgaggtcattctcattgacccacaatcaggcttgcctgattattcttgaatttttgtg-------tatgtgatgaggcatgtgcatgtgttacagGTACAACATGGTGAAACAAGGTCTTGTTAAGGAGCCAGTATTTTCATTCTGGCTCAACCGCAAGACAGATGATGATGAAGGGGGTGAACTTGTGTTTGGT
     |||  |     |  | ||| || || |||   |   ||     | ||| ||||| ||  ||| |         ||||| | |   || |  |  |||  |||||||||||||||  | ||||||||| ||||||| |||||||||||||| ||| ||||||||||  | || || || |||||||||||  |||| ||||||
---ctcttcctatagtgagagtcttatagaaccaggct---gcccttgttattgttcttaaaagtttattgaatccccatgtgcttattgatct-tacctgtcgcagGTACAACATGGTTGACCAAGGTCTTATTAAGGAACCAGTATTTTCATTTTGGTTCAACCGCAAACCGGAGGAAGAGGAAGGGGGTGAGATTGTTTTTGGT

upper sequence: Vv10s0116g01210.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA09G00810.1 (Glycine max), 3'ss of exon 4
tttaactttttccgaggtcattctcatt-gacccacaatcaggcttgcctgattattcttgaatttttgtgtatgtgatgaggcatgtgcatgtgttacagGTACAACATGGTGAAACAAGGTCTTGTTAAGGAGCCAGTATTTTCATTCTGGCTCAACCGCAAGACAGATGATGATGAAGGGGGTGAACTTGTGTTTGGT
             |       ||  |||  | |    | |  || |  ||| |  |  || | | | | |||   | |||||||   | | |||   |||||||||  |||||  ||||||||||||| ||||| |||||||||||||| ||||| || || ||  |||| || ||  | ||||| || ||||| ||||| 
-------------gtatctgctcatatttaaacttttagctagcatttctgttattattttattctctatgt-cattatgaggccctttcctgt--cacagGTACAGTATGGTTGAACAAGGTCTTGTAAAGGATCCAGTATTTTCATTTTGGCTAAATCGGAAACCAGAAGAAGAGAATGGGGGGGAGCTTGTTTTTGGA

upper sequence: Vv10s0116g01210.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA15G11670.1 (Glycine max), 3'ss of exon 4
tttaactttttccgaggtcattctcattgacccacaatcaggcttgcctgattattcttgaatttttgtgtatgtga---tgaggcatgtgcatgtgttacagGTACAACATGGTGAAACAAGGTCTTGTTAAGGAGCCAGTATTTTCATTCTGGCTCAACCGCAAGACAGATGATGATGAAGGGGGTGAACTTGTGTTTGGT
             |   |   ||  ||| |  |    |   ||| || |   | || ||   || |||| | ||| |   |||||||  | | |||   |||||||||  |||||  ||||||||||||| ||||| |||||||||||||| ||||| || || ||  |||| || ||  | || || || ||||| ||||||
-------------gtatttgctcatatttaaact---tttagctagcatttctgttattattttattgtctctgtcaatttgaggcactttcctgt--cacagGTACACTATGGTTGAACAAGGTCTTGTAAAGGATCCAGTATTTTCATTTTGGCTAAATCGGAAACCAGAAGAAGAGAATGGTGGGGAGCTTGTTTTTGGT

upper sequence: Vv10s0116g01210.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT1G11910.1 (Arabidopsis thaliana), 3'ss of exon 5
tttaactttttccgaggtcattctcattgacccacaatcaggcttgcctgattattcttgaatttttgtgtatgtgatgaggcatgtgcatgtgttacagGTACAACATGGTGAAACAAGGTCTTGTTAAGGAGCCAGTATTTTCATTCTGGCTCAACCGCAAGACAGATGATGATGAAGGGGGTGAACTTGTGTTTGGT
             |    | | | ||||   |     |  ||  ||  | | ||   |     | | ||||   || | |    | |   | | |||||||||||||||| | || ||||| ||| | |||||||| || |||||||| ||||| ||||| ||  ||||||| || ||||| ||||||||||| ||||| 
-------------gtatgcctgcacattcttctcttgtttggactgagttactacattc---ctgtagtgttaatgctaatatgtct-tgttttttacagGTACAACATGCTCAAGCAAGGCCTTATCAAGGAGCCGGTTTTTTCATTTTGGCTTAACCGTAATGCAGATGAAGAAGAAGGTGGTGAACTTGTATTTGGA

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|110723374|gb|EE100612.1|EE100612
EST:     TTAAGACTTGGATTTCAAGAGATTTCAGTTGGAAATGCCGTCCCGGTGTG                         GTACAACATGGTGAAACAAGGTCTTGTTTAGGAGCCATTATTTTCATTCTG
genomic: TTAGGACTTGGATTTCAAGAGATTTCAGTTGGAAATGCCGTCCCAGTGTGgtatgttgga ... tgtgttacagGTACAACATGGTGAAACAAGGTCTTGTTAAGGAGCCAGTATTTTCATTCTG
EST: gi|352794761|gb|FQ475259.1|FQ475259
EST:     TTAGGACTTGGATTTCAAGAGATTTCAGTTGGAAATGCCGTCCCAGTGTG                         GTACAACATGGTGAAACAAGGTCTTGTTAAGGAGCCAGTATTTTCATTCTG
genomic: TTAGGACTTGGATTTCAAGAGATTTCAGTTGGAAATGCCGTCCCAGTGTGgtatgttgga ... tgtgttacagGTACAACATGGTGAAACAAGGTCTTGTTAAGGAGCCAGTATTTTCATTCTG
EST: gi|110703507|gb|EE080413.1|EE080413
EST:     TTAGGACTTGGATTTCAAGAGATTTCAGTTGGAAATGCCGTCCCGGTGTG                         GTACAACATGGTGAAACAANGTCTTGTTAANGAGCCAGTATTTTCATTCTG
genomic: TTAGGACTTGGATTTCAAGAGATTTCAGTTGGAAATGCCGTCCCAGTGTGgtatgttgga ... tgtgttacagGTACAACATGGTGAAACAAGGTCTTGTTAAGGAGCCAGTATTTTCATTCTG
EST: gi|110726583|gb|EE102492.1|EE102492
EST:     TTAGGACTTGGATTTCAAGAGATTTCAGTTGGAAATGCCGTCCCGGTGTG                         GTACAACATGGTGAAACAAGGTCTTGTTAANGAGCCAGTATTTTCATTCCG
genomic: TTAGGACTTGGATTTCAAGAGATTTCAGTTGGAAATGCCGTCCCAGTGTGgtatgttgga ... tgtgttacagGTACAACATGGTGAAACAAGGTCTTGTTAAGGAGCCAGTATTTTCATTCTG
EST: gi|110723213|gb|EE100267.1|EE100267
EST:     TTANGACTTGGATTTCAAGAGATTTCAGTTGGAAATGCCGTCCCGGTGTG                         GTACAACATGGTGAAACAAGGTCTTGTTAANGAGCCAGTATTTTCATTCTG
genomic: TTAGGACTTGGATTTCAAGAGATTTCAGTTGGAAATGCCGTCCCAGTGTGgtatgttgga ... tgtgttacagGTACAACATGGTGAAACAAGGTCTTGTTAAGGAGCCAGTATTTTCATTCTG
EST: gi|34549541|gb|CF517773.1|CF517773
EST:     GGACTTGGATTTCAAGAGATTTCAGTTGGAAATGCCGTCCCAGTGTG                         GTACAACATGGTGAAACAAGGTCTTGTTAAGGAGCCAGTATTTTCATTCTG
genomic: GGACTTGGATTTCAAGAGATTTCAGTTGGAAATGCCGTCCCAGTGTGgtatgttgga ... tgtgttacagGTACAACATGGTGAAACAAGGTCTTGTTAAGGAGCCAGTATTTTCATTCTG
EST: gi|110724471|gb|EE100330.1|EE100330
EST:     TTANGACTTGGATTTCAAGAGATTTCAGTTGGAAATGCCGTCCCAGTGTG                         GTACAACATGGTGAAACAAAGTCTTGTTAAGGAGCCAGTATTTTCATTCTG
genomic: TTAGGACTTGGATTTCAAGAGATTTCAGTTGGAAATGCCGTCCCAGTGTGgtatgttgga ... tgtgttacagGTACAACATGGTGAAACAAGGTCTTGTTAAGGAGCCAGTATTTTCATTCTG
EST: gi|161719906|gb|FC066714.1|FC066714
EST:     TTAGGACTTGGATTTCAAGAGATTTCAGTTGGAAATGCCGTCCCAGTGTG                         GTACAACATGGTGAAACAAGGTCTTGTTAAGGAGCCAGTATTTTCATTCTG
genomic: TTAGGACTTGGATTTCAAGAGATTTCAGTTGGAAATGCCGTCCCAGTGTGgtatgttgga ... tgtgttacagGTACAACATGGTGAAACAAGGTCTTGTTAAGGAGCCAGTATTTTCATTCTG
EST: gi|110709179|gb|EE084415.1|EE084415
EST:     TTANGACTTGGATTTCAAGAGATTTCAGTTGGAAATGCCGTCCCAGTGTG                         GTACAACATGGTTGAAAAAAGGTCTTTGTAAAGGA-CCAGTATTTTCCATT
genomic: TTAGGACTTGGATTTCAAGAGATTTCAGTTGGAAATGCCGTCCCAGTGTGgtatgttgga ... tgtgttacagGTACAACATGGT-GAAACAAGGTCTT-GTTAAGGAGCCAGTATTTTC-ATT
EST: gi|110724332|gb|EE100065.1|EE100065
EST:     TTAGGACTTGGATTTCAAGAGATTTCAGTTGGAAATGCCGTCCCGGTGTG                         GTACAACATGGTGAAACAAGGTCTTGTTAAGGAGCCAGTATTTTCATTCTG
genomic: TTAGGACTTGGATTTCAAGAGATTTCAGTTGGAAATGCCGTCCCAGTGTGgtatgttgga ... tgtgttacagGTACAACATGGTGAAACAAGGTCTTGTTAAGGAGCCAGTATTTTCATTCTG
EST: gi|110710072|gb|EE086085.1|EE086085
EST:     TTAAGACTTGGATTTCAAGAGATTTCAGTTGGAAATGCCGTCCCAGTGTG                         GTACAACATGGTGAAACAAAGTCTTGTTAAGGAGCCAGTATTTTCATTCTG
genomic: TTAGGACTTGGATTTCAAGAGATTTCAGTTGGAAATGCCGTCCCAGTGTGgtatgttgga ... tgtgttacagGTACAACATGGTGAAACAAGGTCTTGTTAAGGAGCCAGTATTTTCATTCTG
EST: gi|110724931|gb|EE101189.1|EE101189
EST:     TTAGGACTTGGATTTCAAGAGATTTCAGTTGGAAATGCCGTCCCAGTGTG                         GTACAACATGGTGAAACAAGGTCTTGTTAAGGAGCCAGTATTTTCATTCTG
genomic: TTAGGACTTGGATTTCAAGAGATTTCAGTTGGAAATGCCGTCCCAGTGTGgtatgttgga ... tgtgttacagGTACAACATGGTGAAACAAGGTCTTGTTAAGGAGCCAGTATTTTCATTCTG
EST: gi|110708151|gb|EE085368.1|EE085368
EST:     TTAAGACTTGGATTTCAAGAAATTTCAGTTGGAAATGCCGTCCCGGTGTG                         GTACAACATGGGTGAA
genomic: TTAGGACTTGGATTTCAAGAGATTTCAGTTGGAAATGCCGTCCCAGTGTGgtatgttgga ... tgtgttacagGTACAACATGG-TGAA
EST: gi|110723066|gb|EE099952.1|EE099952
EST:     TTAGGACTTGGATTTCAAGAGATTTCAGTTGGAAATGCCGTCCCAGTGTG                         GTACAACATGGTGAAACAAGGTCTTGTTAAGGAGCCAGTATTTTCATTCTG
genomic: TTAGGACTTGGATTTCAAGAGATTTCAGTTGGAAATGCCGTCCCAGTGTGgtatgttgga ... tgtgttacagGTACAACATGGTGAAACAAGGTCTTGTTAAGGAGCCAGTATTTTCATTCTG
EST: gi|110709842|gb|EE085666.1|EE085666
EST:     TTANGACTTGGATTTCAAGAGATTTCAGTTGGAAATGCCGTCCCGGTGTG                         GTACAACATGGTGAAACAAAGTCTTGTTAAGGAGCCAGTATTTTCATTCTG
genomic: TTAGGACTTGGATTTCAAGAGATTTCAGTTGGAAATGCCGTCCCAGTGTGgtatgttgga ... tgtgttacagGTACAACATGGTGAAACAAGGTCTTGTTAAGGAGCCAGTATTTTCATTCTG
EST: gi|71865136|gb|DT014191.1|DT014191
EST:     TTAGGACTTGGATTTCAAGAGATTTCAGTTGGAAATGCTGTCCCAGTGTG                         GTACAACATGGTGAAACAAGGTCTTGTTAAGGAGCCAGTATTTTCATTCTG
genomic: TTAGGACTTGGATTTCAAGAGATTTCAGTTGGAAATGCCGTCCCAGTGTGgtatgttgga ... tgtgttacagGTACAACATGGTGAAACAAGGTCTTGTTAAGGAGCCAGTATTTTCATTCTG
EST: gi|110697801|gb|EE075199.1|EE075199
EST:     TTANGACTTGGATTTCAAGAGATTTCAGTTGGAAATGCCGTNCCAGTGTG                         GTACAACATGGTGAAACAAGGTCTTNGT-AANGAGCCAGTATTTTCATTCT
genomic: TTAGGACTTGGATTTCAAGAGATTTCAGTTGGAAATGCCGTCCCAGTGTGgtatgttgga ... tgtgttacagGTACAACATGGTGAAACAAGGTCTT-GTTAAGGAGCCAGTATTTTCATTCT
EST: gi|110723493|gb|EE100867.1|EE100867
EST:     TTANGACTTGGATTTCAAGAGATTTCAGTTGGAAATGCCGTCCCGGTGTG                         GTACAACATGGTGAAACAAAGTCTTGTTAAAGAGCCAGTATTTTCATTCTG
genomic: TTAGGACTTGGATTTCAAGAGATTTCAGTTGGAAATGCCGTCCCAGTGTGgtatgttgga ... tgtgttacagGTACAACATGGTGAAACAAGGTCTTGTTAAGGAGCCAGTATTTTCATTCTG
EST: gi|30299773|gb|CB976567.1|CB976567
EST:     TTAGGACTTGGATTTCAAGAGATTTCAGTTGGAAATGCCGTCCCAGTGTG                         GTACAACATGGTGAAACAAGGTCTTGTTAAGGAGCCAGTATTTTCATTCTG
genomic: TTAGGACTTGGATTTCAAGAGATTTCAGTTGGAAATGCCGTCCCAGTGTGgtatgttgga ... tgtgttacagGTACAACATGGTGAAACAAGGTCTTGTTAAGGAGCCAGTATTTTCATTCTG
EST: gi|352789600|gb|FQ476198.1|FQ476198
EST:     TTAGGACTTGGATTTCAAGAGATTTCAGTTGGAAATGCCGTCCCAGTGTG                         GTACAACATGGTGAAACAGGGTCTTGTTAAGGAGCCAGTATTTTCATTCTG
genomic: TTAGGACTTGGATTTCAAGAGATTTCAGTTGGAAATGCCGTCCCAGTGTGgtatgttgga ... tgtgttacagGTACAACATGGTGAAACAAGGTCTTGTTAAGGAGCCAGTATTTTCATTCTG
EST: gi|110684973|gb|EE062864.1|EE062864
EST:     TTAGGACTTGGATTTCAAGAGATTTCAGTTGGAAATGCCGTCCCAGTGTG                         GTACAACATGGTGAAACAAGGTCTTGTTAAGGAGCCAGTATTTTCATTCTG
genomic: TTAGGACTTGGATTTCAAGAGATTTCAGTTGGAAATGCCGTCCCAGTGTGgtatgttgga ... tgtgttacagGTACAACATGGTGAAACAAGGTCTTGTTAAGGAGCCAGTATTTTCATTCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcctgattattcttgaatttttgtgtatgtgatgaggcatgtgcatgtgttacagGTACAACATGGTGAAACAAGGTCTTGTTAAGGAGCCAGTATTTTCATTCTGGCTCAACCGCAAGACAGATGATGATGAAGGGGGTGAACTTGTGTTTGGT
 gcctgat  putative branch site (score: 4)
     attattcttgaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttaactttttccgaggtcattctcattgacccacaatcaggcttgcctgattattcttgaatttttgtgtatgtgatgaggcatgtgcatgtgttacagGTACAACATGGTGAAACAAGGTCTTGTTAAGGAGCCAGTATTTTCATTCTGGCTCAACCGCAAGACAGATGATGATGAAGGGGGTGAACTTGTGTTTGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - cattctc
- - - - - - - - - - - - - - - cccacaa
- - - - - - - - - - - - - - - - - - - - - cttgcct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgtgc