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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggtagacacatgtgatgtgatttctagtgagctaaggtctcatttgtggcattgaagaggcatacctctgaggcttgcgccatttctgtaacaatactctttttttttaattttatttttatgggattacagATGATCCAAAGAATTCTCATTTGAGAGAGCTTGAAGGAGCAAAGGAGAGATTGATTTTATGCAAAGCTGATCTTATGGATTATGAGAGTCTGAAAGAGGC

Basic information

species Vitis vinifera
transcript Vv09s0070g00240.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0070g00240.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT1G15950.2 (Arabidopsis thaliana), 3'ss of exon 1
gtgggtagacacatgtg-atgtgatttctagtgagctaaggtctcatttgtggcattgaagaggcatacctctgaggcttgcgccatttctgtaacaatactctttttttttaattttatttttatgggattacagATGATCCAAAGAATTCTCATTTGAGAGAGCTTGAAGGAGCAAAGGAGAGATTGATTTTATGCAAAGCTGATCTTATGGATTATGAGAGTCTGAAAGAGGC
||   |   ||  | |  || |  ||| | |    ||   |     | | ||   |||  ||||  ||  | |     |||     |||   | |||||  |   ||| ||||   |||||||| |     | |||||||||| |||||  | ||||||||||| || ||||||| |||||||||| ||||| | |||||||| ||||||  ||| || |||  ||| || | |||
gtacttgtccatttttatatatacttttttggtcacttgtgataattatctgaagttgttgaggt-tattttta----ttgt----tttgattgacaat-ttggatttctttataattatttttct-----tgcagATGATCCGAAGAACACACATTTGAGAGAACTAGAAGGAGGAAAGGAGAGACTGATTCTGTGCAAAGCAGATCTTCAGGACTACGAGGCTCTTAAGGCGGC
















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|161714382|gb|FC063223.1|FC063223
EST:     AAAGGAACTGTTAGAAATCCAG                         ATGATCCAAAGAATTCTCATTTGAGAGAGCTTGAAGGAGCAAAGGAGAGAT
genomic: AAAGGAACTGTTAGAAATCCAGgtgggtagac ... gggattacagATGATCCAAAGAATTCTCATTTGAGAGAGCTTGAAGGAGCAAAGGAGAGAT
EST: gi|71856853|gb|DT005908.1|DT005908
EST:     GCTGCTTCTTGAAAGGGGCTATACTGTTAAAGGAACTGTTAGAAATCCAG                         ATGATCCAAAGAATTCTCATTTGAGAGAGCTTGAAGGAGCAAAGGAGAGAT
genomic: GCTGCTTCTTGAAAGGGGCTATACTGTTAAAGGAACTGTTAGAAATCCAGgtgggtagac ... gggattacagATGATCCAAAGAATTCTCATTTGAGAGAGCTTGAAGGAGCAAAGGAGAGAT
EST: gi|161714058|gb|FC063794.1|FC063794
EST:     GCTGCTTCTTGAAAGGGGCTATACTGTTAAAGGAACTGTTAGAAATCCAG                         ATGATCCAAAGAATTCTCATTTGAGAGAGCTTGAAGGAGCAAAGGAGAGAT
genomic: GCTGCTTCTTGAAAGGGGCTATACTGTTAAAGGAACTGTTAGAAATCCAGgtgggtagac ... gggattacagATGATCCAAAGAATTCTCATTTGAGAGAGCTTGAAGGAGCAAAGGAGAGAT
EST: gi|161706048|gb|FC056727.1|FC056727
EST:     GCTGCTTCTTGAAAGGGGCTATACTGTTAAAGGAACTGTTAGAAATCCAG                         ATGATCCAAAGAATTCTCATTTGAGAGAGCTTGAAGGAGCAAAGGAGAGAT
genomic: GCTGCTTCTTGAAAGGGGCTATACTGTTAAAGGAACTGTTAGAAATCCAGgtgggtagac ... gggattacagATGATCCAAAGAATTCTCATTTGAGAGAGCTTGAAGGAGCAAAGGAGAGAT
EST: gi|161717599|gb|FC067886.1|FC067886
EST:     GCTGCTTCTTGAAAGGGGCTATACTGTTAAAGGAACTGTTAGAAATCCAG                         ATGATCCAAAGAATTCTCATTTGAGAGAGCTTGAAGGAGCAAAGGAGAGAT
genomic: GCTGCTTCTTGAAAGGGGCTATACTGTTAAAGGAACTGTTAGAAATCCAGgtgggtagac ... gggattacagATGATCCAAAGAATTCTCATTTGAGAGAGCTTGAAGGAGCAAAGGAGAGAT
EST: gi|71873555|gb|DT022610.1|DT022610
EST:     GCTGCTTCTTGAAAGGGGCTATACTGTTAAAGGAACTGTTAGAAATCCAG                         ATGATCCAAAGAATTCTCATTTGAGAGAGCTTGAAGGAGCAAAGGAGAGAT
genomic: GCTGCTTCTTGAAAGGGGCTATACTGTTAAAGGAACTGTTAGAAATCCAGgtgggtagac ... gggattacagATGATCCAAAGAATTCTCATTTGAGAGAGCTTGAAGGAGCAAAGGAGAGAT
EST: gi|161714328|gb|FC062629.1|FC062629
EST:     GCTGCTTCTTGAAAGAGGCTATACTGTTAAAGGAACTGTTAGAAATCCAG                         ATGATCCAAAGAATTCTCATTTGAGAGAGCTTGAAGGAGCAAAGGAGAGAT
genomic: GCTGCTTCTTGAAAGGGGCTATACTGTTAAAGGAACTGTTAGAAATCCAGgtgggtagac ... gggattacagATGATCCAAAGAATTCTCATTTGAGAGAGCTTGAAGGAGCAAAGGAGAGAT
EST: gi|110383896|gb|EC948301.1|EC948301
EST:     GCTGCTTCTTGAAAGAGGCTATACTGTTAAAGGAACTGTTAGAAATCCAG                         ATGATCCAAAGAATTCTCATTTGAGAGAGCTTGAAGGAGCAAAGGAGAGAT
genomic: GCTGCTTCTTGAAAGGGGCTATACTGTTAAAGGAACTGTTAGAAATCCAGgtgggtagac ... gggattacagATGATCCAAAGAATTCTCATTTGAGAGAGCTTGAAGGAGCAAAGGAGAGAT
EST: gi|161712746|gb|FC061970.1|FC061970
EST:     GCTGCTTCTTGAAAGGGGCTATACTGTTAAAGGAACTGTTAGAAATCCAG                         ATGATCCAAAGAATTCTCATTTGAGAGAGCTTGAAGGAGCAAAGGAGAGAT
genomic: GCTGCTTCTTGAAAGGGGCTATACTGTTAAAGGAACTGTTAGAAATCCAGgtgggtagac ... gggattacagATGATCCAAAGAATTCTCATTTGAGAGAGCTTGAAGGAGCAAAGGAGAGAT
EST: gi|110710498|gb|EE086896.1|EE086896
EST:     GCTGCTTCTTGAAAGAGGCTATACTGTTAAAGGAACTGTTAGAAATCCAG                         ATGATCCAAAGAATTCTCATTTGAGAGAGCTTGAAGGAGCAAAGGAGAGAT
genomic: GCTGCTTCTTGAAAGGGGCTATACTGTTAAAGGAACTGTTAGAAATCCAGgtgggtagac ... gggattacagATGATCCAAAGAATTCTCATTTGAGAGAGCTTGAAGGAGCAAAGGAGAGAT
EST: gi|71866385|gb|DT015440.1|DT015440
EST:     GCTGCTTCTTGAAAGGGGCTATACTGTTAAAGGAACTGTTAGAAATCCAG                         ATGATCCAAAGAATTCTCATTTGAGAGAGCTTGAAGGAGCAAAGGAGAGAT
genomic: GCTGCTTCTTGAAAGGGGCTATACTGTTAAAGGAACTGTTAGAAATCCAGgtgggtagac ... gggattacagATGATCCAAAGAATTCTCATTTGAGAGAGCTTGAAGGAGCAAAGGAGAGAT
EST: gi|161719483|gb|FC066419.1|FC066419
EST:     GCTGCTTCTTGAAAGAGGCTATACTGTTAAAGGAACTGTTAGAAATCCAG                         ATGATCCAAAGAATTCTCATTTGAGAGAGCTTGAAGGAGCAAAGGAGAGAT
genomic: GCTGCTTCTTGAAAGGGGCTATACTGTTAAAGGAACTGTTAGAAATCCAGgtgggtagac ... gggattacagATGATCCAAAGAATTCTCATTTGAGAGAGCTTGAAGGAGCAAAGGAGAGAT
EST: gi|110686121|gb|EE063440.1|EE063440
EST:     GCTGCTTCTTGAAAGAGGCTATACTGTTAAAGGAACTGTTAGAAATCCAG                         ATGATCCAAAGAATTCTCATTTGAGAGAGCTTGAAGGAGCAAAGGAGAGAT
genomic: GCTGCTTCTTGAAAGGGGCTATACTGTTAAAGGAACTGTTAGAAATCCAGgtgggtagac ... gggattacagATGATCCAAAGAATTCTCATTTGAGAGAGCTTGAAGGAGCAAAGGAGAGAT
EST: gi|161713112|gb|FC062476.1|FC062476
EST:     GCTGCTTCTTGAAAGGGGCTATACTGTTAAAGGAACTGTTAGAAATCCAG                         ATGATCCAAAGAATTCTCATTTGAGAGAGCTTGAAGGAGCAAAGGAGAGAT
genomic: GCTGCTTCTTGAAAGGGGCTATACTGTTAAAGGAACTGTTAGAAATCCAGgtgggtagac ... gggattacagATGATCCAAAGAATTCTCATTTGAGAGAGCTTGAAGGAGCAAAGGAGAGAT
EST: gi|161717105|gb|FC066553.1|FC066553
EST:     GCTGCTTCTTGAAAGAGGCTATACTGTTAAAGGAACTGTTAGAAATCCAG                         ATGATCCAAAGAATTCTCATTTGAGAGAGCTTGAAGGAGCAAAGGAGAGAT
genomic: GCTGCTTCTTGAAAGGGGCTATACTGTTAAAGGAACTGTTAGAAATCCAGgtgggtagac ... gggattacagATGATCCAAAGAATTCTCATTTGAGAGAGCTTGAAGGAGCAAAGGAGAGAT
EST: gi|161710559|gb|FC059370.1|FC059370
EST:     GCTGCTTCTTGAAAGGGGCTATACTGTTAAAGGAACTGTTAGAAATCCAG                         ATGATCCAAAGAATTCTCATTTGAGAGAGCTTGAAGGAGCAAAGGAGAGAT
genomic: GCTGCTTCTTGAAAGGGGCTATACTGTTAAAGGAACTGTTAGAAATCCAGgtgggtagac ... gggattacagATGATCCAAAGAATTCTCATTTGAGAGAGCTTGAAGGAGCAAAGGAGAGAT
EST: gi|71858156|gb|DT007211.1|DT007211
EST:     GCTGCTTCTTGAAAGGGGCTATACTGTTAAAGGAACTGTTAGAAATCCAG                         ATGATCCAAAGAATTCTCATTTGAGAGAGCTTGAAGGAGCAAAGGAGAGAT
genomic: GCTGCTTCTTGAAAGGGGCTATACTGTTAAAGGAACTGTTAGAAATCCAGgtgggtagac ... gggattacagATGATCCAAAGAATTCTCATTTGAGAGAGCTTGAAGGAGCAAAGGAGAGAT
EST: gi|110708939|gb|EE083965.1|EE083965
EST:     GCTGCTTCTTGAAAGAGGCTATACTGTTAAAGGAACTGTTAGAAATCCAG                         ATGATCCAAAGAATTCTCATTTGAGAGAGCTTGAAGGAGCAAAGGAGAGAT
genomic: GCTGCTTCTTGAAAGGGGCTATACTGTTAAAGGAACTGTTAGAAATCCAGgtgggtagac ... gggattacagATGATCCAAAGAATTCTCATTTGAGAGAGCTTGAAGGAGCAAAGGAGAGAT
EST: gi|161712542|gb|FC061847.1|FC061847
EST:     GCTGCTTCTTGAAAGGGGCTATACTGTTAAAGGAACTGTTAGAAATCCAG                         ATGATCCAAAGAATTCTCATTTGAGAGAGCTTGAAGGAGCAAAGGAGAGAT
genomic: GCTGCTTCTTGAAAGGGGCTATACTGTTAAAGGAACTGTTAGAAATCCAGgtgggtagac ... gggattacagATGATCCAAAGAATTCTCATTTGAGAGAGCTTGAAGGAGCAAAGGAGAGAT
EST: gi|161717252|gb|FC067258.1|FC067258
EST:     GCTGCTTCTTGAAAGGGGCTATACTGTTAAAGGAACTGTTAGAAATCCAG                         ATGATCCAAAGAATTCTCATTTGAGAGAGCTTGAAGGAGCAAAGGAGAGAT
genomic: GCTGCTTCTTGAAAGGGGCTATACTGTTAAAGGAACTGTTAGAAATCCAGgtgggtagac ... gggattacagATGATCCAAAGAATTCTCATTTGAGAGAGCTTGAAGGAGCAAAGGAGAGAT
EST: gi|110384860|gb|EC949326.1|EC949326
EST:     GCTGCTTCTTGAAAGAGGCTATACTGTTAAAGGAACTGTTAGAAATCCAG                         ATGATCCAAAGAATTCTCATTTGAGAGAGCTTGAAGGAGCAAAGGAGAGAT
genomic: GCTGCTTCTTGAAAGGGGCTATACTGTTAAAGGAACTGTTAGAAATCCAGgtgggtagac ... gggattacagATGATCCAAAGAATTCTCATTTGAGAGAGCTTGAAGGAGCAAAGGAGAGAT
EST: gi|110732417|gb|EE107684.1|EE107684
EST:     GCTGCTTCTTGAAAGAGGCTATACTGTTAAAGGAACTGTTAGAAATCCAG                         ATGATCCAAAGAATTCTCATTTGAGAGAGCTTGAAGGAGCAAAGGAGAGAT
genomic: GCTGCTTCTTGAAAGGGGCTATACTGTTAAAGGAACTGTTAGAAATCCAGgtgggtagac ... gggattacagATGATCCAAAGAATTCTCATTTGAGAGAGCTTGAAGGAGCAAAGGAGAGAT
EST: gi|71856973|gb|DT006028.1|DT006028
EST:     GCTGCTTCTTGAAAGGGGCTATACTGTTAAAGGAACTGTTAGAAATCCAG                         ATGATCCAAAGAATTCTCATTTGAGAGAGCTTGAAGGAGCAAAGGAGAGAT
genomic: GCTGCTTCTTGAAAGGGGCTATACTGTTAAAGGAACTGTTAGAAATCCAGgtgggtagac ... gggattacagATGATCCAAAGAATTCTCATTTGAGAGAGCTTGAAGGAGCAAAGGAGAGAT
EST: gi|110383367|gb|EC947736.1|EC947736
EST:     GCTGCTTCTTGAAAGAGGCTATACTGTTAAAGGAACTGTTAGAAATCCAG                         ATGATCCAAAGAATTCTCATTTGAGAGAGCTTGAAGGAGCAAAGGAGAGAT
genomic: GCTGCTTCTTGAAAGGGGCTATACTGTTAAAGGAACTGTTAGAAATCCAGgtgggtagac ... gggattacagATGATCCAAAGAATTCTCATTTGAGAGAGCTTGAAGGAGCAAAGGAGAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgccatttctgtaacaatactctttttttttaattttatttttatgggattacagATGATCCAAAGAATTCTCATTTGAGAGAGCTTGAAGGAGCAAAGGAGAGATTGATTTTATGCAAAGCTGATCTTATGGATTATGAGAGTCTGAAAGAGGC
                           ttttaat  putative branch site (score: 3)
     tttctgtaacaatact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgggtagacacatgtgatgtgatttctagtgagctaaggtctcatttgtggcattgaagaggcatacctctgaggcttgcgccatttctgtaacaatactctttttttttaattttatttttatgggattacagATGATCCAAAGAATTCTCATTTGAGAGAGCTTGAAGGAGCAAAGGAGAGATTGATTTTATGCAAAGCTGATCTTATGGATTATGAGAGTCTGAAAGAGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG