Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttactggaatcactggctgtcaagacgaatccaataatgtaaatttgggtttctgtgcttgtacagatatattttggtaactgtgttatctggtgtatagGGATTTGCAGAGCCAGTCAAGTGGCTGAGCTATTTCCAACGGTGTTGCCCGAGATTGTCGTTCGGGAGGCCAGGTTAGAGGACTGTTGGGAAGTGGCTGA

Basic information

species Vitis vinifera
transcript Vv13s0019g04360.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g04360.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA20G32020.2 (Glycine max), 3'ss of exon 1
-ttactggaatcactggctgtcaagacgaatccaataatgtaaatttgggtttctgtgcttgtacagatatattttggtaac-tgtgttatctggtgtatagGGATTTGCAGAGCCAGTCAAGTGGCTGAGCTATTTCCAACGGTGTTGCCCGAGATTGTCGTTCGGGAGGCCAGGTTAGAGGACTGTTGGGAAGTGGCTGA
  | ||   | ||  |  | |   ||    |   ||   ||||| ||||       |    ||    |  |   | || | | |||| | | |||  | ||||  | |||||||| |||||||| | |||  | || ||||| ||||  || || ||| | || ||||||||||||||||||||||||||||||||||| ||
aatccttccaacatagtatattttgagatgtgtcatcg-gtaaagttggtggatactctaagtgttaacttgggtaggaaccctgtggtgtttgg-atgtagGATTATGCAGAGCGAGTCAAGTTGTTGATTTGTTCCCAACTGTGTCTCCTGAAATTATTGTGCGGGAGGCCAGGTTAGAGGACTGTTGGGAAGTGGCAGA

upper sequence: Vv13s0019g04360.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA10G35500.1 (Glycine max), 3'ss of exon 1
--ttactggaatcactggctgtcaagacgaatccaataatgtaaatttgggtttctg-tgcttgtacagatatattttggtaactgtgttatctggtgtatagGGATTTGCAGAGCCAGTCAAGTGGCTGAGCTATTTCCAACGGTGTTGCCCGAGATTGTCGTTCGGGAGGCCAGGTTAGAGGACTGTTGGGAAGTGGCTGA
  ||  ||||    | |    ||||    |     | ||   || ||    | |  | || |      | ||     |      |||| | | |||  | ||||  | || ||||| |||||||| | |||  | || || || ||||  || || ||| | ||||||||||||||| |||||||||||||||||||||| ||
aattgatggatattccg--catcaatgttatggtgacaaaaaaagttatattctgagatgttaacttgggtaggaactaaagggtgtggtgtttgg-atgtagGATTATGTAGAGCAAGTCAAGTTGTTGATTTGTTCCCGACTGTGTCTCCTGAAATTATTGTTCGGGAGGCCAGGCTAGAGGACTGTTGGGAAGTGGCAGA
















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|18459514|gb|BM437792.1|BM437792
EST:     TCTCACCACCATCAAGAAACCGTCTAGGGTTTCTAATTTCCCCAAATCAG                         GGATTTGCAGAGCCAGTCAAGTGGCTGAGCTATTTCCAACGGTGTTGCCCG
genomic: TCTCACCACCATCAAGAAACCGTCTAGGGTTTCTAATTTCCCCAAATCAGgtatcacttt ... tggtgtatagGGATTTGCAGAGCCAGTCAAGTGGCTGAGCTATTTCCAACGGTGTTGCCCG
EST: gi|32249196|gb|CD715015.1|CD715015
EST:     TCTCACCACCATCAAGAAACCGTCTAGGGTTTCTAATTTCCCCAAATCAG                         GGATTTGCAGAGCCAGTCAAGTGGCTGAGCTATTTCCAACGGTGTTGCCCG
genomic: TCTCACCACCATCAAGAAACCGTCTAGGGTTTCTAATTTCCCCAAATCAGgtatcacttt ... tggtgtatagGGATTTGCAGAGCCAGTCAAGTGGCTGAGCTATTTCCAACGGTGTTGCCCG
EST: gi|32248451|gb|CD714270.1|CD714270
EST:     TCTCACCACCATCAAGAAACCGTCTAGGGTTTCTAATTTCCCCAAATCAG                         GGATTTGCAGAGCCAGTCAAGTGGCTGAGCTATTTCCAACGGTGTTGCCCG
genomic: TCTCACCACCATCAAGAAACCGTCTAGGGTTTCTAATTTCCCCAAATCAGgtatcacttt ... tggtgtatagGGATTTGCAGAGCCAGTCAAGTGGCTGAGCTATTTCCAACGGTGTTGCCCG
EST: gi|110401396|gb|EC968006.1|EC968006
EST:     TTTCCCCAAATCAG                         GGATTTGCAGAGCCAGTCAAGTGGGTGAGCTATTTCCAACGGTGTTGCCCG
genomic: TTTCCCCAAATCAGgtatcacttt ... tggtgtatagGGATTTGCAGAGCCAGTCAAGTGGCTGAGCTATTTCCAACGGTGTTGCCCG
EST: gi|32265414|gb|CD716267.1|CD716267
EST:     TCTCACCACCATCAAGAAACCGTCTAGGGTTTCTAATTTCCCCAAATCAG                         GGATTTGCAGAGCCAGTCAAGTGGCTGAGCTATTTCCAACGGTGTTGCCCG
genomic: TCTCACCACCATCAAGAAACCGTCTAGGGTTTCTAATTTCCCCAAATCAGgtatcacttt ... tggtgtatagGGATTTGCAGAGCCAGTCAAGTGGCTGAGCTATTTCCAACGGTGTTGCCCG
EST: gi|349825461|gb|FQ419378.1|FQ419378
EST:     TCTCACCACCATCAAGAAACCGTCTAGGGTTTCTAATTTCCCCAAATCAG                         GGATTTGCAGAGCCAGTCAAGTGGCTGAGCTATTTCCAACGGTGTTGCCCG
genomic: TCTCACCACCATCAAGAAACCGTCTAGGGTTTCTAATTTCCCCAAATCAGgtatcacttt ... tggtgtatagGGATTTGCAGAGCCAGTCAAGTGGCTGAGCTATTTCCAACGGTGTTGCCCG
EST: gi|30322468|gb|CD005730.1|CD005730
EST:     TCTCACCACCATCAAGAAACCGTCTAGGGTTTCTAATTTCCCCAAATCAG                         GGATTTGCAGAGCCAGTCAAGTGGCTGAGCTATTTCCAACGGTGTTGCCCG
genomic: TCTCACCACCATCAAGAAACCGTCTAGGGTTTCTAATTTCCCCAAATCAGgtatcacttt ... tggtgtatagGGATTTGCAGAGCCAGTCAAGTGGCTGAGCTATTTCCAACGGTGTTGCCCG
EST: gi|294965198|gb|GW837029.1|GW837029
EST:     TCTCACCACCATCAAGAAACCGTCTAGGGTTTCTAATTTCCCCAAATCAG                         GGATTTGCAGAGCCAGTCAAGTGGTTGAGCTATTTCCAACAGTGTTGCCCG
genomic: TCTCACCACCATCAAGAAACCGTCTAGGGTTTCTAATTTCCCCAAATCAGgtatcacttt ... tggtgtatagGGATTTGCAGAGCCAGTCAAGTGGCTGAGCTATTTCCAACGGTGTTGCCCG
EST: gi|32269110|gb|CD718269.1|CD718269
EST:     TCTCACCACCATCAAGAAACCGTCTAGGGTTTCTAATTTCCCCAAATCAG                         GGATTTGCAGAGCCAGTCAAGTGGCTGAGCTATTTCCAACGGTGTTGCCCG
genomic: TCTCACCACCATCAAGAAACCGTCTAGGGTTTCTAATTTCCCCAAATCAGgtatcacttt ... tggtgtatagGGATTTGCAGAGCCAGTCAAGTGGCTGAGCTATTTCCAACGGTGTTGCCCG
EST: gi|351046898|gb|FQ454508.1|FQ454508
EST:     TCTCACCACCATCAAGAAACCGTCTAGGGTTTCTAATTTCCCCAAATCAG                         GGATTTGCAGAGCCAGTCAAGTGGCTGAGCTATTTCCAACGGTGTTGCCCG
genomic: TCTCACCACCATCAAGAAACCGTCTAGGGTTTCTAATTTCCCCAAATCAGgtatcacttt ... tggtgtatagGGATTTGCAGAGCCAGTCAAGTGGCTGAGCTATTTCCAACGGTGTTGCCCG
EST: gi|32269034|gb|CD718193.1|CD718193
EST:     TCTCACCACCATCAAGAAACCGTCTAGGGTTTCTAATTTCCCCAAATCAG                         GGATTTGCAGAGCCAGTCAAGTGGCTGAGCTATTTCCAACGGTGTTGCCCG
genomic: TCTCACCACCATCAAGAAACCGTCTAGGGTTTCTAATTTCCCCAAATCAGgtatcacttt ... tggtgtatagGGATTTGCAGAGCCAGTCAAGTGGCTGAGCTATTTCCAACGGTGTTGCCCG
EST: gi|26257461|gb|CA808524.1|CA808524
EST:     TCTCACCACCATCAAGAAACCGTCTAGGGTTTCTAATTTCCCCAAATCAG                         GGATTTGCAGAGCCAGTCAAGTGGCTGAGCTATTTCCAACGGTGTTGCCCG
genomic: TCTCACCACCATCAAGAAACCGTCTAGGGTTTCTAATTTCCCCAAATCAGgtatcacttt ... tggtgtatagGGATTTGCAGAGCCAGTCAAGTGGCTGAGCTATTTCCAACGGTGTTGCCCG
EST: gi|30131664|gb|CB917003.1|CB917003
EST:     TCTCACCACCATCAAGAAACCGTCTAGGGTTTCTAATTTCCCCAAATCAG                         GGATTTGCAGAGCCAGTCAAGTGGCTGAGCTATTTCCAACGGTGTTGCCCG
genomic: TCTCACCACCATCAAGAAACCGTCTAGGGTTTCTAATTTCCCCAAATCAGgtatcacttt ... tggtgtatagGGATTTGCAGAGCCAGTCAAGTGGCTGAGCTATTTCCAACGGTGTTGCCCG
EST: gi|110701724|gb|EE079624.1|EE079624
EST:     TCTCACCACCATCAAGAAACCGTCTAGGGTTTCTAATTTCCCCAAATCAG                         GGATTTGCAGAGCCAGTCAAGTGGCTGAGCTATTTCCAACGGTGTTGCCCG
genomic: TCTCACCACCATCAAGAAACCGTCTAGGGTTTCTAATTTCCCCAAATCAGgtatcacttt ... tggtgtatagGGATTTGCAGAGCCAGTCAAGTGGCTGAGCTATTTCCAACGGTGTTGCCCG
EST: gi|32249014|gb|CD714833.1|CD714833
EST:     TCTCACCACCATCAAGAAACCGTCTAGGGTTTCTAATTTCCCCAAATCAG                         GGATTTGCAGAGCCAGTCAAGTGGCTGAGCTATTTCCAACGGTGTTGCCCG
genomic: TCTCACCACCATCAAGAAACCGTCTAGGGTTTCTAATTTCCCCAAATCAGgtatcacttt ... tggtgtatagGGATTTGCAGAGCCAGTCAAGTGGCTGAGCTATTTCCAACGGTGTTGCCCG
EST: gi|30322577|gb|CD005839.1|CD005839
EST:     TCTCACCACCATCAAGAAACCGTCTAGGGTTTCTAATTTCCCCAAATCAG                         GGATTTGCAGAGCCAGTCAAGTGGCTGAGCTATTTCCAACGGTGTTGCCCG
genomic: TCTCACCACCATCAAGAAACCGTCTAGGGTTTCTAATTTCCCCAAATCAGgtatcacttt ... tggtgtatagGGATTTGCAGAGCCAGTCAAGTGGCTGAGCTATTTCCAACGGTGTTGCCCG
EST: gi|30325587|gb|CD008849.1|CD008849
EST:     TCTCACCACCATCAAGAAACCGTCTAGGGTTTCTAATTTCCCCAAATCAG                         GGATTTGCAGAGCCAGTCAAGTGGCTGAGCTATTTCCAACGGTGTTGCCCG
genomic: TCTCACCACCATCAAGAAACCGTCTAGGGTTTCTAATTTCCCCAAATCAGgtatcacttt ... tggtgtatagGGATTTGCAGAGCCAGTCAAGTGGCTGAGCTATTTCCAACGGTGTTGCCCG
EST: gi|351036439|gb|FQ457152.1|FQ457152
EST:     TCTCACCACCATCAAGAAACCGTCTAGGGTTTCTAATTTCCCCAAATCAG                         GGATTTGCAGAGCCAGTCAAGTGGCTGAGCTATTTCCAACGGTGTTGCCCG
genomic: TCTCACCACCATCAAGAAACCGTCTAGGGTTTCTAATTTCCCCAAATCAGgtatcacttt ... tggtgtatagGGATTTGCAGAGCCAGTCAAGTGGCTGAGCTATTTCCAACGGTGTTGCCCG
EST: gi|110708111|gb|EE085280.1|EE085280
EST:     TCTCACCACCATCAAGAAACCGTCTAGGGTTTCTAATTTCCCCAAATCAG                         GGATTTGCAGAGCCAGTCAAGTGGCTGAGCTATTTCCAACGGTGTTGCCCG
genomic: TCTCACCACCATCAAGAAACCGTCTAGGGTTTCTAATTTCCCCAAATCAGgtatcacttt ... tggtgtatagGGATTTGCAGAGCCAGTCAAGTGGCTGAGCTATTTCCAACGGTGTTGCCCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgggtttctgtgcttgtacagatatattttggtaactgtgttatctggtgtatagGGATTTGCAGAGCCAGTCAAGTGGCTGAGCTATTTCCAACGGTGTTGCCCGAGATTGTCGTTCGGGAGGCCAGGTTAGAGGACTGTTGGGAAGTGGCTGA
                             tggtaac  putative branch site (score: 2)
                tacagatatatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttactggaatcactggctgtcaagacgaatccaataatgtaaatttgggtttctgtgcttgtacagatatattttggtaactgtgttatctggtgtatagGGATTTGCAGAGCCAGTCAAGTGGCTGAGCTATTTCCAACGGTGTTGCCCGAGATTGTCGTTCGGGAGGCCAGGTTAGAGGACTGTTGGGAAGTGGCTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
ttactgg
- - - - - - - - ctgtcaa
- - - - - - - - - - - - - -aatccaa
- - - - - - - - - - - - - - - - - -aatgtaaa