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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attggttataaaatggttatccaaaaaaagaattggtaaaatggctaactgcatcttttattctattattaaagccttggggtgcttgtttaatttgcagGCAAAAAGTGCAGTAAAGCTCCCAAGATACAGAGGTTGGTTACTCCTTTGACCTTGCAGAGGAAGCGAGCCAGGATTGCAGAGAAGAAGAAGAGAATTGC

Basic information

species Vitis vinifera
transcript Vv18s0001g06290.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g06290.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA13G24630.1 (Glycine max), 3'ss of exon 5
--attggttataaaatggttatccaaaaaaagaattggtaaaatggctaactgcatctt--ttattctattattaaagccttgg-ggtgcttgtttaatttgcagGCAAAAAGTGCAGTAAAGCTCCCAAGATACAGAGGTTGGTTACTCCTTTGACCTTGCAGAGGAAGCGAGCCAGGATTGCAGAGAAGAAGAAGAGAATTGC
  | |  |||   ||   ||||  |      |   |||  |      ||| |   || |  ||| |     |||| || ||  |   ||  |  ||  |||||||| |||||    || |||||||| ||||| ||  | ||||| |||||||||||  | || ||||| ||||| |||||||| || |||||||||||||||||
acactt-ttactcaacatttatggactctttg---tggacatccaattaatttggtcatgattagtggtgaattatagtctgagtaatgaataattg-tttgcagGGAAAAAAGTGAGCAAAGCTCCAAAGATTCAACGATTGGTCACTCCTTTGACACTCCAAAGGAAACGAGCAAGGATTGCCGACAAGAAGAAGAGAATTGC

upper sequence: Vv18s0001g06290.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA07G31840.3 (Glycine max), 3'ss of exon 4
--------attggttataaaatggttatccaaaaaaagaattggtaaaatggctaactgcatcttttattctattattaaagccttggggtgcttgtttaatttgcagGCAAAAAGTGCAGTAAAGCTCCCAAGATACAGAGGTTGGTTACTCCTTTGACCTTGCAGAGGAAGCGAGCCAGGATTGCAGAGAAGAAGAAGAGAATTGC
        | |    ||  |  |  | | ||   | |       | ||||   |  |      ||    |  |||||  |  |   |   ||  |  ||  |||||||| |||||    || |||||||| ||||| ||  |  | || |||||||||||  | || ||||| ||||| |||||||| || |||||||||||||||||
acacttttactcaacatttatggactcttcatggacat--ccaattaaat---tggccatgatttgagatgaattat--agtctgagtaatgaatacttg-tttgcagGGAAAAAAGTGAGCAAAGCTCCAAAGATTCAACGACTAGTCACTCCTTTGACACTCCAAAGGAAACGAGCAAGGATTGCCGACAAGAAGAAGAGAATTGC

upper sequence: Vv18s0001g06290.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA15G08210.1 (Glycine max), 3'ss of exon 5
attggttataaaatggttatccaaaaaaagaattggtaaaatggctaactgcatcttttattct-attattaaagccttggggtgcttgt-ttaatttgcagGCAAAAAGTGCAGTAAAGCTCCCAAGATACAGAGGTTGGTTACTCCTTTGACCTTGCAGAGGAAGCGAGCCAGGATTGCAGAGAAGAAGAAGAGAATTGC
  |  ||||    | |||        |          ||   |  ||  |       | ||| | || |||       || | | | | | ||   ||| ||| ||||||   || |||||||| ||||||||  || |||| |||||  ||||| | || || ||| | || ||||||||||| |||||||||||||||||
--tatttatgctgttgtttgatgggtaggacccattgaaggagattatttttggacatgattgtgatgatttctagtctgagttacatatgtttggttgtagGGAAAAAGGTGAGCAAAGCTCCTAAGATACAACGGCTGGTCACTCCCCTGACCCTCCAAAGAAAGAGGGCAAGGATTGCAGATAAGAAGAAGAGAATTGC

upper sequence: Vv18s0001g06290.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA13G31130.1 (Glycine max), 3'ss of exon 6
------attggttataaaatggttatccaaaaaaagaattggtaaaatggctaactgcatcttttattctattattaaagccttggggtgcttgtttaatttgcagGCAAAAAGTGCAGTAAAGCTCCCAAGATACAGAGGTTGGTTACTCCTTTGACCTTGCAGAGGAAGCGAGCCAGGATTGCAGAGAAGAAGAAGAGAATTGC
        || || |  |  |   | |||   || ||  |      ||   |   |  |    || |  |  | |  || |   |       |||||  || ||||| ||||||   || |||||||| ||||||||  |  |||| |||||  ||||| | || || ||| | || ||||||||||| |||||||||||||||||
atttatgctgttttttgatggaggacccattgaaggagatt-----atttttggatatacaaattgtgatggtttctaatctgagttacatatgtttggtt-gcagGGAAAAAGGTGAGCAAAGCTCCGAAGATACAACGACTGGTCACTCCCCTGACCCTCCAAAGAAAGAGGGCAAGGATTGCAGATAAGAAGAAGAGAATTGC

upper sequence: Vv18s0001g06290.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT5G10360.1 (Arabidopsis thaliana), 3'ss of exon 5
attggttataaaatgg---ttatccaaaaaaagaattggtaaaatggctaactgcatcttttattctattattaaagccttggggtgcttgtttaatttgcagGCAAAAAGTGCAGTAAAGCTCCCAAGATACAGAGGTTGGTTACTCCTTTGACCTTGCAGAGGAAGCGAGCCAGGATTGCAGAGAAGAAGAAGAGAATTGC
    || | |||||     | |   ||| | | |||||  ||| ||  ||  | |   |  |  | || || || |    || ||      ||  || ||||||||| |||   || || ||||| ||||| |||||| | || ||||| |||||| | ||||||||| |||| || ||||| || |||||||||||||| ||
----gtaagaaaattagattcacttaaagagataattga-aaactgttta--tacgattgatgatttactaatata----tgaggc-----ttccatgtgcagGCAAGAAGGTTAGCAAGGCTCCTAAGATCCAGAGGCTTGTGACTCCATTGACCCTCCAGAGGAAGAGAGCTAGAATTGCTGACAAGAAGAAGAGAATCGC

upper sequence: Vv18s0001g06290.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT5G10360.2 (Arabidopsis thaliana), 3'ss of exon 5
attggttataaaatggttatccaaaaaaagaattggtaaaatggctaactgc--atcttttattctattattaaagccttggggtgcttg--tttaatttgcagGCAAAAAGTGCAGTAAAGCTCCCAAGATACAGAGGTTGGTTACTCCTTTGACCTTGCAGAGGAAGCGAGCCAGGATTGCAGAGAAGAAGAAGAGAATTGC
       | || | || ||   ||||  ||| |   | |||  | ||| ||   |   ||||| | |||  | |     |    |    |  ||  || ||||||||| |||   || || ||||| ||||| |||||| | || ||||| |||||| | ||||||||| |||| || ||||| || |||||||||||||| ||
---acaaacaagaagggtaag-aaaattagattcacttaaagagataattgaaaactgtttatacgattgatgatttactaatatatgaggcttccatgtgcagGCAAGAAGGTTAGCAAGGCTCCTAAGATCCAGAGGCTTGTGACTCCATTGACCCTCCAGAGGAAGAGAGCTAGAATTGCTGACAAGAAGAAGAGAATCGC

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|110710093|gb|EE086127.1|EE086127
EST:     TGTCCGAAAGTATGTCAACACATACCGCAGATCATTCACAACCAAATCTG                         GCAAAAAGTGCAGTAAAGCTCCCAAGATACAGAGGTTGGTTACTCCTTTGA
genomic: TGTCCGAAAGTATGTCAACACATACCGCAGATCATTCACAACCAAATCTGgtaggttttt ... taatttgcagGCAAAAAGTGCAGTAAAGCTCCCAAGATACAGAGGTTGGTTACTCCTTTGA
EST: gi|110731210|gb|EE109174.1|EE109174
EST:     TGTCCGAAAGTATGTCAACACATACCGCAGATCATTCACAACCAAATCTG                         GCAAAAAGTGCAGTAAAGCTCCCAAGATACAGAGGTTGGTTACTCCTTTGA
genomic: TGTCCGAAAGTATGTCAACACATACCGCAGATCATTCACAACCAAATCTGgtaggttttt ... taatttgcagGCAAAAAGTGCAGTAAAGCTCCCAAGATACAGAGGTTGGTTACTCCTTTGA
EST: gi|110398664|gb|EC965135.1|EC965135
EST:     TGTCCGAAAGTATGTCAACACATACCGCAGATCATTCACAACCAAATCTG                         GCAAAAAGTGCAGTAAAGCTCCCAAGATACAGAGGTTGGTTACTCCTTTGA
genomic: TGTCCGAAAGTATGTCAACACATACCGCAGATCATTCACAACCAAATCTGgtaggttttt ... taatttgcagGCAAAAAGTGCAGTAAAGCTCCCAAGATACAGAGGTTGGTTACTCCTTTGA
EST: gi|110369359|gb|EC933517.1|EC933517
EST:     TGTCCGAAAGTATGTCAACACATACCGCAGATCATTCACAACCAAATCTG                         GCAAAAAGTGCAGTAAAGCTCCCAAGATACAGAGGTTGGTTACTCCTTTGA
genomic: TGTCCGAAAGTATGTCAACACATACCGCAGATCATTCACAACCAAATCTGgtaggttttt ... taatttgcagGCAAAAAGTGCAGTAAAGCTCCCAAGATACAGAGGTTGGTTACTCCTTTGA
EST: gi|29782562|gb|CB347995.2|CB347995
EST:     TGTCCGAAAGTATGTCAACACATACCGCAGATCATTCACAACCAAATCTG                         GCAAAAAGTGCAGTAAAGCTCCCAAGATACAGAGGTTGGTTACTCCTTTGA
genomic: TGTCCGAAAGTATGTCAACACATACCGCAGATCATTCACAACCAAATCTGgtaggttttt ... taatttgcagGCAAAAAGTGCAGTAAAGCTCCCAAGATACAGAGGTTGGTTACTCCTTTGA
EST: gi|110724727|gb|EE100810.1|EE100810
EST:     TGTCCGAAAGTATGTCAACACATACCGCAGATCATTCACAACCAAATCTG                         GCAAAAAGTGCAGTAAAGCTCCCAAGATACAGAGGTTGGTTACTCCTTTGA
genomic: TGTCCGAAAGTATGTCAACACATACCGCAGATCATTCACAACCAAATCTGgtaggttttt ... taatttgcagGCAAAAAGTGCAGTAAAGCTCCCAAGATACAGAGGTTGGTTACTCCTTTGA
EST: gi|110694354|gb|EE071389.1|EE071389
EST:     TGTCCGAAAGTATGTCAACACATACCGCAGATCATTCACAACCAAATCTG                         GCAAAAAGTGCAGTAAAGCTCCCAAGATACAGAGGTTGGTTACTCCTTTGA
genomic: TGTCCGAAAGTATGTCAACACATACCGCAGATCATTCACAACCAAATCTGgtaggttttt ... taatttgcagGCAAAAAGTGCAGTAAAGCTCCCAAGATACAGAGGTTGGTTACTCCTTTGA
EST: gi|110701201|gb|EE078523.1|EE078523
EST:     TGTCCGAAAGTATGTCAACACATACCGCAGATCATTCACAACCAAATCTG                         GCAAAAAGTGCAGTAAAGCTCCCAAGATACAGAGGTTGGTTACTCCTTTGA
genomic: TGTCCGAAAGTATGTCAACACATACCGCAGATCATTCACAACCAAATCTGgtaggttttt ... taatttgcagGCAAAAAGTGCAGTAAAGCTCCCAAGATACAGAGGTTGGTTACTCCTTTGA
EST: gi|30124734|gb|CB910073.1|CB910073
EST:     TGTCCGAAAGTATGTCAACACATACCGCAGATCATTCACAACCAAATCTG                         GGCAAAA-GTGCAGTAAAGCTCCCAAGATACAGAGGTTGGTTACTCCTTTG
genomic: TGTCCGAAAGTATGTCAACACATACCGCAGATCATTCACAACCAAATCTGgtaggttttt ... taatttgcagG-CAAAAAGTGCAGTAAAGCTCCCAAGATACAGAGGTTGGTTACTCCTTTG
EST: gi|110426639|gb|EC993054.1|EC993054
EST:     TGTCCGAAAGTATGTCAACACATACCGCAGATCATTCACAACCAAATCTG                         GCAAAAAGTGCAGTAAAGCTCCCAAGATACAGAGGTTGGTTACTCCTTTGA
genomic: TGTCCGAAAGTATGTCAACACATACCGCAGATCATTCACAACCAAATCTGgtaggttttt ... taatttgcagGCAAAAAGTGCAGTAAAGCTCCCAAGATACAGAGGTTGGTTACTCCTTTGA
EST: gi|110422092|gb|EC988404.1|EC988404
EST:     TGTCCGAAAGTATGTCAACACATACCGCAGATCATTCACAACCAAATCTG                         GCAAAAAGTGCAGTAAAGCTCCCAAGATACAGAGGTTGGTTACTCCTTTGA
genomic: TGTCCGAAAGTATGTCAACACATACCGCAGATCATTCACAACCAAATCTGgtaggttttt ... taatttgcagGCAAAAAGTGCAGTAAAGCTCCCAAGATACAGAGGTTGGTTACTCCTTTGA
EST: gi|28962095|gb|CB341128.1|CB341128
EST:     TGTCCGAAAGTATGTCAACACATACCGCAGATCATTCACAACCAAATCTG                         GCAAAAAGTGCAGTAAAGCTCCCAAGATACAGAGGTTGGTTACTCCTTTGA
genomic: TGTCCGAAAGTATGTCAACACATACCGCAGATCATTCACAACCAAATCTGgtaggttttt ... taatttgcagGCAAAAAGTGCAGTAAAGCTCCCAAGATACAGAGGTTGGTTACTCCTTTGA
EST: gi|110729833|gb|EE106221.1|EE106221
EST:     TGTCCGAAAGTATGTCAACACATACCGCAGATCATTCACAACCAAATCTG                         GCAAAAAGTGCAGTAAAGCTCCCAAGATACAGAGGTTGGTTACTCCTTTGA
genomic: TGTCCGAAAGTATGTCAACACATACCGCAGATCATTCACAACCAAATCTGgtaggttttt ... taatttgcagGCAAAAAGTGCAGTAAAGCTCCCAAGATACAGAGGTTGGTTACTCCTTTGA
EST: gi|110698432|gb|EE075922.1|EE075922
EST:     TGTCCGAAAGTATGTCAACACATACCGCAGATCATTCACAACCAAATCTG                         GCAAAAAGTGCAGTAAAGCTCCCAAGATACAGAGGTTGGTTACTCCTTTGA
genomic: TGTCCGAAAGTATGTCAACACATACCGCAGATCATTCACAACCAAATCTGgtaggttttt ... taatttgcagGCAAAAAGTGCAGTAAAGCTCCCAAGATACAGAGGTTGGTTACTCCTTTGA
EST: gi|30132967|gb|CB918306.1|CB918306
EST:     TGTCCGAAAGTATGTCAACACATACCGCAGATCATTCACAACCAAATCTG                         GCAAAAAGTGCAGTAAAGCTCCCAAGATACAGAGGTTGGTTACTCCTTTGA
genomic: TGTCCGAAAGTATGTCAACACATACCGCAGATCATTCACAACCAAATCTGgtaggttttt ... taatttgcagGCAAAAAGTGCAGTAAAGCTCCCAAGATACAGAGGTTGGTTACTCCTTTGA
EST: gi|110730616|gb|EE107900.1|EE107900
EST:     TGTCCGAAAGTATGTCAACACATACCGCAGATCATTCACAACCAAATCTG                         GCAAAAAGTGCAGTAAAGCTCCCAAGATACAGAGGTTGGTTACTCCTTTGA
genomic: TGTCCGAAAGTATGTCAACACATACCGCAGATCATTCACAACCAAATCTGgtaggttttt ... taatttgcagGCAAAAAGTGCAGTAAAGCTCCCAAGATACAGAGGTTGGTTACTCCTTTGA
EST: gi|110708627|gb|EE086388.1|EE086388
EST:     TGTCCGAAAGTATGTCAACACATACCGCAGATCATTCACAACCAAATCTG                         GCAAAAAGTGCAGTAAAGCTCCCAAGATACAGAGGTTGGTTACTCCTTTGA
genomic: TGTCCGAAAGTATGTCAACACATACCGCAGATCATTCACAACCAAATCTGgtaggttttt ... taatttgcagGCAAAAAGTGCAGTAAAGCTCCCAAGATACAGAGGTTGGTTACTCCTTTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taactgcatcttttattctattattaaagccttggggtgcttgtttaatttgcagGCAAAAAGTGCAGTAAAGCTCCCAAGATACAGAGGTTGGTTACTCCTTTGACCTTGCAGAGGAAGCGAGCCAGGATTGCAGAGAAGAAGAAGAGAATTGC
                                       cttgttt  CT-rich tract
       atcttttattctatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attggttataaaatggttatccaaaaaaagaattggtaaaatggctaactgcatcttttattctattattaaagccttggggtgcttgtttaatttgcagGCAAAAAGTGCAGTAAAGCTCCCAAGATACAGAGGTTGGTTACTCCTTTGACCTTGCAGAGGAAGCGAGCCAGGATTGCAGAGAAGAAGAAGAGAATTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - -ataaaat
- - - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - ggtaaaa
- - - - - - - - - - - - - - - - - - - - - - - aactgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -taaagcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgcttg