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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgccctcatttttctaccaagccaatcttttcgtcattttaatgttgagaggcatgcgagaattttctttctcttgctgataaatttctttgacttctgtttggaaattgaattataattttgtcatcacctgctaaatcctttactttttcagGGTTAAGCTTCCTTCATGGGCGATGTTTGAACTTGGGAGGGCTCCTGTCTACTGGAAGACCATGAATGGCCTTCCTCCTAGTTCT

Basic information

species Vitis vinifera
transcript Vv09s0002g06980.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g06980.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA07G03360.2 (Glycine max), 3'ss of exon 2
gtatgtgccctcatttttctaccaagccaatcttttcgtcattttaatgttgagaggcatgcgagaattttctttctcttgctgataaatttctttgacttctgtttggaaattgaattataattttgtcatcacctgctaaatcctttactttttcagGGTTAAGCTTCCTTCATGGGCGATGTTTGAACTTGGGAGGGCTCCTGTCTACTGGAAGACCATGAATGGCCTTCCTCCTAGTTCT
                                             |||  |||   |  || ||  || |||  | | |  | ||  ||        | ||   |||||| |    ||||| |   |  ||| | || |  |||| ||    | | ||||   |||||||| |||||||| | ||||||| ||||||||||| ||||||| ||||| |||||||||||||| ||||||| ||| 
--------------------------------------------aaataatgaatag-gtgggatgatgttcaatgtttcccagaataa-------aagttaattttggataac--attattacaataccattatctac--aatcattg---tctacagGTACAAGCTTCCATCATGGGCTAAGTTTGAAATTGGGAGGGCTGCTGTCTATTGGAAAACCATGAATGGCCTCCCTCCTACTTCA

upper sequence: Vv09s0002g06980.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA08G22740.1 (Glycine max), 3'ss of exon 2
gtatgtgccctcatttttctaccaagccaatcttttcgtcattttaatgttgagaggcatgcgagaattttctttctcttgctgataaatttctttgacttctgtttggaaattgaattataattttgtcatcacctgctaaatcctttactttttcagGGTTAAGCTTCCTTCATGGGCGATGTTTGAACTTGGGAGGGCTCCTGTCTACTGGAAGACCATGAATGGCCTTCCTCCTAGTTCT
                                         || || ||||        |   |||||||| | | |||     |||||        | ||   |||||| |    ||||| |   |  ||| | || |  |||| ||    ||| ||||   |||||||| |||||||| | ||||||| | ||||||||| ||||||| ||||| |||||||||||||| ||||||  ||| 
-----------------------------------------ttgtagtgtttgtgc---tttaagaattttttgtttctccagaataaa--------agttaattttggataac--attattacaataccattatctac--aatcattg---tttacagGTACAAGCTTCCATCATGGGCTAAGTTTGAAATAGGGAGGGCTGCTGTCTATTGGAAAACCATGAATGGCCTCCCTCCTTCTTCA

upper sequence: Vv09s0002g06980.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT3G15840.1 (Arabidopsis thaliana), 3'ss of exon 2
gtatgtgccctcatttttctaccaagccaatcttttcgtcattttaatgttgagaggcatgcgagaattttctttctcttgctgataa-atttctttgacttctgtttggaaattgaattataattttgtcatcacctgctaaatcctttactttttcagGGTTAAGCTTCCTTCATGGGCGATGTTTGAACTTGGGAGGGCTCCTGTCTACTGGAAGACCATGAATGGCCTTCCTCCTAGTTCT
                                                                |  | |  ||  | | | | ||    || |||||   ||  | |    ||   | ||||||  |      |  |  | | |   ||| |||   ||    ||||||||||||||||| ||||| ||  | || |  |||||||| |||||||| ||||||||||| ||||| || |  || 
----------------------------------------------------------------gtctgtctttattttagttcatcgtgttgctttgg--tcgatataactatatgaatataataataaacatagttcatga-ttgattattttgatagATACAAGCTTCCTTCATGGGCCATGTTCGAGATGGGTACTGCTCCTGTGTACTGGAAAACCATGAATGGTCTTCCACCAACCTCA

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|110377543|gb|EC942616.1|EC942616
EST:     AAAGTAAGTGCTGCTGCTGTCGCAACAACTCCTGTTGAGGAAACCAAAGA                         GGTTAAGCTTCCTTCATGGGCGATGTTTGAACTTGGGAGGGCTCCTGTCTA
genomic: AAAGTAAGTGCTGCTGCTGTCGCAACAACTCCTGTTGAGGAAACCAAAGAgtatgtgccc ... actttttcagGGTTAAGCTTCCTTCATGGGCGATGTTTGAACTTGGGAGGGCTCCTGTCTA
EST: gi|26256962|gb|CA808025.1|CA808025
EST:     AAAGTAAGTGCTGCTGCTGTCGCAGCAACTCCTGTTGAGGAAACCAAAGA                         GGTTAAGCTTCCTTCATGGGCGATGTTTGAACTTGGGAGGGCTCCTGTCTA
genomic: AAAGTAAGTGCTGCTGCTGTCGCAACAACTCCTGTTGAGGAAACCAAAGAgtatgtgccc ... actttttcagGGTTAAGCTTCCTTCATGGGCGATGTTTGAACTTGGGAGGGCTCCTGTCTA
EST: gi|28961921|gb|CB340979.1|CB340979
EST:     GTGCTGCTGCTGTTGCAACAACTCCTGTTGAGGAAACCAAAGA                         GGTTAAGCTTCCTTCATGGGCGATGTTTGAACTTGGGAGGGCTCCTGTCTA
genomic: GTGCTGCTGCTGTCGCAACAACTCCTGTTGAGGAAACCAAAGAgtatgtgccc ... actttttcagGGTTAAGCTTCCTTCATGGGCGATGTTTGAACTTGGGAGGGCTCCTGTCTA
EST: gi|110385730|gb|EC950281.1|EC950281
EST:     AAAGTAAGTGCTGCTGCTGTTGCAACAACTCCTGTTGAGGAAACCAAAGA                         GGTTAAGCTTCCTTCATGGGCGATGTTTGAACTTGGGAGGGCTCCTGTCTA
genomic: AAAGTAAGTGCTGCTGCTGTCGCAACAACTCCTGTTGAGGAAACCAAAGAgtatgtgccc ... actttttcagGGTTAAGCTTCCTTCATGGGCGATGTTTGAACTTGGGAGGGCTCCTGTCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttggaaattgaattataattttgtcatcacctgctaaatcctttactttttcagGGTTAAGCTTCCTTCATGGGCGATGTTTGAACTTGGGAGGGCTCCTGTCTACTGGAAGACCATGAATGGCCTTCCTCCTAGTTCT
                                tgctaaa  putative branch site (score: 2)
                                       tcctttactttttc  CT-rich tract
     aaattgaattataatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgccctcatttttctaccaagccaatcttttcgtcattttaatgttgagaggcatgcgagaattttctttctcttgctgataaatttctttgacttctgtttggaaattgaattataattttgtcatcacctgctaaatcctttactttttcagGGTTAAGCTTCCTTCATGGGCGATGTTTGAACTTGGGAGGGCTCCTGTCTACTGGAAGACCATGAATGGCCTTCCTCCTAGTTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA