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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttgcttaatatcaagaacaagaaagctattacttccagcctgtcaaatcttttgctttgaatttgatattaacctttagaacactgggctgaatgtcttctaatttgctgtaatcttttatcagGTACTTCCTCAACCTGTTCGGATTAAGGGGTTTATTTAGTCTCATTCTGGGAGAAGAAAATG

Basic information

species Vitis vinifera
transcript Vv00s0187g00170.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0187g00170.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA08G44410.1 (Glycine max), 3'ss of exon 6
gtacttgcttaatatcaagaacaagaaagctattacttccagcctgtcaaatcttttgctttgaatttgatattaacctttagaacac-tgggctgaatgtcttctaatttgctgtaatcttttatcagGTACTTCCTCAACCTGTTCGGATTAAGGGGTTTATTTAGTCTCATTCTGGGAGAAGAAAATG
                                                 ||||||    |||    | ||| || |||| |   || | |   |||   || |  || |     |  ||    | |||||||||||||||| ||||| |||||||| || || |||||||||||  |||| ||||||||||
-----------------------------------------------gtaatcttcattttta---tggatcttcacctgtttcactcatactctg---gtttaatagtcaaaag--attgcatttcagGTACTTCCTCAATCTGTTTGGATTAAGAGGATTCTTTAGTCTCATCTTGGGTGAAGAAAATG

upper sequence: Vv00s0187g00170.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA18G08370.1 (Glycine max), 3'ss of exon 3
gtacttgcttaatatcaagaacaagaaagctattacttccagcctgtcaaatcttttgctttgaatttgatattaacctttagaacactgggctgaatgtcttctaatttgctgtaatcttttat--cagGTACTTCCTCAACCTGTTCGGATTAAGGGGTTTATTTAGTCTCATTCTGGGAGAAGAAAATG
                                                 ||||||    |||    | |||||| ||||     || ||    |   ||  ||   | ||| || ||  || |||  ||||||||||||||| ||||| |||||||| || || |||||||||||  |||| ||||||||| 
----------------------------------------------ggtaatcttcattttta---tggatatttacctgcttcactct---ttctctggttt---aattgttgaaagattgtattacaGGTACTTCCTCAATCTGTTTGGATTAAGAGGATTGTTTAGTCTCATATTGGGTGAAGAAAAT-

upper sequence: Vv00s0187g00170.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT4G12590.1 (Arabidopsis thaliana), 3'ss of exon 5
gtacttgcttaatatcaagaacaagaaagctattacttccag-cctgtcaaatcttttgctttgaatttgatattaacctttagaacactgggctgaatgtcttctaatttgctgtaatcttttatc-------agGTACTTCCTCAACCTGTTCGGATTAAGGGGTTTATTTAGTCTCATTCTGGGAGAAGAAAATG
|||  | || || || |   | ||| |   | |    ||| | ||| |  |   |||   | ||    | |||||  | | | ||    ||  ||   | | || |  |||  ||   | || | ||       ||||||||| | ||| |||| |||||||| || || || ||||||||||| ||||| |||||||
gtaagtactcaa-attacaca-aaggactttgtgttatccggtcctcttcagattttcagtatgctaatcatatttgcttctggatatttgccctttctcttttttttttttatgagtttttctttcgctcttcagGTACTTCTTGAACTTGTTTGGATTAAGAGGCTTGTTCAGTCTCATTCTCGGAGATGAAAATG

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|30132459|gb|CB917798.1|CB917798
EST:     GGAATTGATTTGAGCACTGTAGATGTTAGCTATGTCAGCAGTCGCTCATG                         GTACTTCCTCAACCTGTTCGGATTAAGGGGTTTATTTAGTCTCATTCTG
genomic: GGAATTGATTTGAGCACTGTAGATGTTAGCTATGTCAGCAGTCGCTCATGgtacttgctt ... cttttatcagGTACTTCCTCAACCTGTTCGGATTAAGGGGTTTATTTAGTCTCATTCTG
EST: gi|30136299|gb|CB921637.1|CB921637
EST:     GGAATTGATTTGAGCACTGTAGATGTTAGCTATGTCAGCAGTCGCTCATG                         GTACTTCCTCAACCTGTTCGGATTAAGGGGTTTATTTAGTCTCATTCTGGG
genomic: GGAATTGATTTGAGCACTGTAGATGTTAGCTATGTCAGCAGTCGCTCATGgtacttgctt ... cttttatcagGTACTTCCTCAACCTGTTCGGATTAAGGGGTTTATTTAGTCTCATTCTGGG
EST: gi|294966792|gb|GW837811.1|GW837811
EST:     GGAATTGATTTGAGCACTGTAGATGTTAGCTATGTCAGCAGTCGCTCATG                         GTACTTCCTCAACCTGTTCGGATTAAGGGGTTTATTTAGTCTCATTCTGGG
genomic: GGAATTGATTTGAGCACTGTAGATGTTAGCTATGTCAGCAGTCGCTCATGgtacttgctt ... cttttatcagGTACTTCCTCAACCTGTTCGGATTAAGGGGTTTATTTAGTCTCATTCTGGG
EST: gi|32250235|gb|CD716054.1|CD716054
EST:     GGAATTGATTTGAGCACTGTAGATGTTAGCTATGTCAGCAGTCGCTCATG                         GTACTTCCTCAACCTGTTCGGATTAAGGGGTTTATTTAGTCTCATTCTGGG
genomic: GGAATTGATTTGAGCACTGTAGATGTTAGCTATGTCAGCAGTCGCTCATGgtacttgctt ... cttttatcagGTACTTCCTCAACCTGTTCGGATTAAGGGGTTTATTTAGTCTCATTCTGGG
EST: gi|30135330|gb|CB920668.1|CB920668
EST:     GGAATTGATTTGAGCACTGTAGATGTTAGCTATGTCAGCAGTCGCTCATG                         GTACTTCCTCAACCTGTTCGGATTAAGGGGTTTATTTAGTCTCATTCTGGG
genomic: GGAATTGATTTGAGCACTGTAGATGTTAGCTATGTCAGCAGTCGCTCATGgtacttgctt ... cttttatcagGTACTTCCTCAACCTGTTCGGATTAAGGGGTTTATTTAGTCTCATTCTGGG
EST: gi|110407602|gb|EC973208.1|EC973208
EST:     GGAATTGATTTGAGCACTGTAGATGTTAGCTATGTCAGCAGTCGCTCATG                         GTACTTCCTCAACCTGTTCGGATTAAGGGGTTTATTTAGTCTCATTCTGGG
genomic: GGAATTGATTTGAGCACTGTAGATGTTAGCTATGTCAGCAGTCGCTCATGgtacttgctt ... cttttatcagGTACTTCCTCAACCTGTTCGGATTAAGGGGTTTATTTAGTCTCATTCTGGG
EST: gi|110428045|gb|EC994506.1|EC994506
EST:     GGAATTGATTTGAGCACTGTAGATGTTAGCTATGTCAGCAGTCGCTCATG                         GTACTTCCTCAACCTGTTCGGATTAAGGGGTTTATTTAGTCTCATTCTGGG
genomic: GGAATTGATTTGAGCACTGTAGATGTTAGCTATGTCAGCAGTCGCTCATGgtacttgctt ... cttttatcagGTACTTCCTCAACCTGTTCGGATTAAGGGGTTTATTTAGTCTCATTCTGGG
EST: gi|110417816|gb|EC983901.1|EC983901
EST:     GGAATTGATTTGAGCACTGTAGATGTTAGCTATGTCAGCAGTCGCTCATG                         GTACTTCCTCAACCTGTTCGGATTAAGGGGTTTATTTAGTCTCATTCTGGG
genomic: GGAATTGATTTGAGCACTGTAGATGTTAGCTATGTCAGCAGTCGCTCATGgtacttgctt ... cttttatcagGTACTTCCTCAACCTGTTCGGATTAAGGGGTTTATTTAGTCTCATTCTGGG
EST: gi|110712100|gb|EE089333.1|EE089333
EST:     GGAATTGATTTGAGCACTGTAGATGTTAGCTATGTCAGCAGTCGCTCATG                         GTACTTCCTCAACCTGTTCGGATTAAGGGGTTTATTTAGTCTCATTCTGGG
genomic: GGAATTGATTTGAGCACTGTAGATGTTAGCTATGTCAGCAGTCGCTCATGgtacttgctt ... cttttatcagGTACTTCCTCAACCTGTTCGGATTAAGGGGTTTATTTAGTCTCATTCTGGG
EST: gi|32457083|gb|CD798257.1|CD798257
EST:     AATTGATTTGAGCACTGTAGATGTTAGCTATGTCACAGCAGTCGCTCATG                         GTACTTCCTCAACCTGTTCGGATTAAGGGGTTTATTTAGTCTCATTCTGGG
genomic: AATTGATTTGAGCACTGTAGATGTTAGCTATGT--CAGCAGTCGCTCATGgtacttgctt ... cttttatcagGTACTTCCTCAACCTGTTCGGATTAAGGGGTTTATTTAGTCTCATTCTGGG
EST: gi|110428615|gb|EC995092.1|EC995092
EST:     GGAATTGATTTGAGCACTGTAGATGTTAGCTATGTCAGCAGTCGCTCATG                         GTACTTCCTCAACCTGTTCGGATTAAGGGGTTTATTTAGTCTCATTCTGGG
genomic: GGAATTGATTTGAGCACTGTAGATGTTAGCTATGTCAGCAGTCGCTCATGgtacttgctt ... cttttatcagGTACTTCCTCAACCTGTTCGGATTAAGGGGTTTATTTAGTCTCATTCTGGG
EST: gi|352764273|gb|FQ471253.1|FQ471253
EST:     GGAATTGATTTGAGCACTGTAGATGTTAGCTATGTCAGCAGTCGCTCATG                         GTACTTCCTCAACCTGTTCGGATTAAGGGGTTTATTTAGTCTCATTCTGGG
genomic: GGAATTGATTTGAGCACTGTAGATGTTAGCTATGTCAGCAGTCGCTCATGgtacttgctt ... cttttatcagGTACTTCCTCAACCTGTTCGGATTAAGGGGTTTATTTAGTCTCATTCTGGG
EST: gi|110429192|gb|EC995681.1|EC995681
EST:     GGAATTGATTTGAGCACTGTAGATGTTAGCTATGTCAGCAGTCGCTCATG                         GTACTTCCTCAACCTGTTCGGATTAAGGGGTTTATTTAGTCTCATTCTGGG
genomic: GGAATTGATTTGAGCACTGTAGATGTTAGCTATGTCAGCAGTCGCTCATGgtacttgctt ... cttttatcagGTACTTCCTCAACCTGTTCGGATTAAGGGGTTTATTTAGTCTCATTCTGGG
EST: gi|27580483|gb|CB003178.1|CB003178
EST:     GGAATTGATTTGAGCACTGTAGATGTTAGCTATGTCAGCAGTCGCTCATG                         GTACTTCCTCAACCTGTTCGGATTAAGGGGTTTATTTAGTCTCATTCTGGG
genomic: GGAATTGATTTGAGCACTGTAGATGTTAGCTATGTCAGCAGTCGCTCATGgtacttgctt ... cttttatcagGTACTTCCTCAACCTGTTCGGATTAAGGGGTTTATTTAGTCTCATTCTGGG
EST: gi|110728851|gb|EE104791.1|EE104791
EST:     GGAATTGATTTGAGCACTGTAGATGTTAGCTATGTCAGCAGTCGCTCATG                         GTACTTCCTCAACCTGTTCGGATTAAGGGGTTTATTTAGTCTCATTCTGGG
genomic: GGAATTGATTTGAGCACTGTAGATGTTAGCTATGTCAGCAGTCGCTCATGgtacttgctt ... cttttatcagGTACTTCCTCAACCTGTTCGGATTAAGGGGTTTATTTAGTCTCATTCTGGG
EST: gi|30125541|gb|CB910880.1|CB910880
EST:     GGAATTGATTTGAGCACTGTAGATGTTAGCTATGTCAGCAGTCGCTCATG                         GTACTTCCTCAACCTGTTCGGATTAAGGGGTTTATTTAGTCTCATTCTGGG
genomic: GGAATTGATTTGAGCACTGTAGATGTTAGCTATGTCAGCAGTCGCTCATGgtacttgctt ... cttttatcagGTACTTCCTCAACCTGTTCGGATTAAGGGGTTTATTTAGTCTCATTCTGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taacctttagaacactgggctgaatgtcttctaatttgctgtaatcttttatcagGTACTTCCTCAACCTGTTCGGATTAAGGGGTTTATTTAGTCTCATTCTGGGAGAAGAAAATG
                                            tcttttatc  CT-rich tract
                                         taatcttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacttgcttaatatcaagaacaagaaagctattacttccagcctgtcaaatcttttgctttgaatttgatattaacctttagaacactgggctgaatgtcttctaatttgctgtaatcttttatcagGTACTTCCTCAACCTGTTCGGATTAAGGGGTTTATTTAGTCTCATTCTGGGAGAAGAAAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA