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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCATCCAGAAAGCTGGAACCCAATGTGGTCTGTATCAAGgtaagacagagccaagatttcttatacacgacacttgttttatgttatcttttctgttatttaatatagcctttttgaactaacatggttgtatgttacaaatacag

Basic information

species Vitis vinifera
transcript Vv09s0002g00280.t01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g00280.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA07G05170.1 (Glycine max), 5'ss of exon 7
TTCATCCAGAAAGCTGGAACCCAATGTGGTCTGTATCAAGgtaagacag----agccaagat-ttcttatacacg-acacttgttttatgttatcttttctgttatttaatatagccttt----ttgaactaacatggttgtatgttacaaatacag-------------------------------------------------------------
||||||||||||| ||||| || ||||||||||||||||||| ||| ||    ||  | ||  ||||| ||     |||||| |  |||||| | |||| |  | ||| || || |||||    ||    | |     |  ||| |   ||  ||||                                                             
TTCATCCAGAAAGTTGGAATCCCATGTGGTCTGTATCAAGgtcagaaagttttagttatgaagttcttttatttatacactt-tactatgttttgttttttactgttttatttaccctttgacttttgcatgaggaattgatatctgtgaataacagtaaatgtggattattattgctttatagctttatactaatgttttcaattttttgaatgcag

upper sequence: Vv09s0002g00280.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA16G01680.1 (Glycine max), 5'ss of exon 7
TTCATCCAGAAAGCTGGAACCCAATGTGGTCTGTATCAAGgtaagacaga-------gccaagatttcttatacacgacacttgttttatg--ttatc--------ttttctgttatttaatatagcctt-----tttgaactaaca-tggttgtatgttacaaatacag----------------------------------------------------------
||||||||||||| ||||| || ||||||||||||||||||| ||| ||        |  ||| | | ||||  |    |  || || |||  ||| |        |||| |  | ||| || || ||||     |||| |  |  | | | | | ||| |  || |                                                             
TTCATCCAGAAAGTTGGAATCCCATGTGGTCTGTATCAAGgtcagaaagttttagttgtgaagttcttttatttatattatatggttaatggtttaccatgtttggttttttacttttttatttatcctttgacttttgcatgaggaattgatatctgtgaataacaataaatgtggattattattactttatagctttatactgatgttttcaatttccgaatgcag

upper sequence: Vv09s0002g00280.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: AT1G17280.1 (Arabidopsis thaliana), 5'ss of exon 7
TTCATCCAGAAAGCTGGAACCCAATGTGGTCTGTATCAAGgta-agacagagccaagatttcttatacacgacacttgttttatgttatcttttctgttatttaatatagcctttttgaactaacatggttgtatgttacaaatacag
||||||||||||||||||| || |||||||||||||||||||| |||      |   | || |   | | |||| | | | ||           | |||  | |  |   | |||||  |  ||    |                   
TTCATCCAGAAAGCTGGAATCCGATGTGGTCTGTATCAAGgtatagattctttctttacttttggaagatgacaatcgatatac----------ccgttgataacca--actttttttcatgaatgcag-------------------

upper sequence: Vv09s0002g00280.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: AT5G50430.2 (Arabidopsis thaliana), 5'ss of exon 7
TTCATCCAGAAAGCTGGAACCCAATGTGGTCTGTATCAAGgtaagacagagccaagatttcttatacacgacacttgt-tttatgttatcttttctgttatt-taatatagcctttttgaactaacatggttgtatgttacaaatacag
||||||||||||||||||| ||||||||||| || ||||||||          ||||| |  | ||||    | |||| || | |||||          |   ||||  | |||| ||  || ||  || ||   ||     ||  |||
TTCATCCAGAAAGCTGGAATCCAATGTGGTCAGTGTCAAGgta---------taagatctgatgtacattcaaattgtgttcaagttattaaaataaacagagtaatggatccttatttgaccaatttgtttccctg-----aacgcag

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|34543477|gb|CF511709.1|CF511709
EST:     TTCATCCAGAAAGCTGGAACCCAATGTGGTCTGTATCAAG                         CATACTTACAGGGCTTCTGTCATTTATG
genomic: TTCATCCAGAAAGCTGGAACCCAATGTGGTCTGTATCAAGgtaagacaga ... acaaatacagCATACTTACAGGGCTTCTGTCATTTATG
EST: gi|161715609|gb|FC068353.1|FC068353
EST:     TTCATCCAGAAAGCTGGAACCCAATGTGGTCTGTATCAAG                         CATACTTACAGGGCTTCTGTCATTTATG
genomic: TTCATCCAGAAAGCTGGAACCCAATGTGGTCTGTATCAAGgtaagacaga ... acaaatacagCATACTTACAGGGCTTCTGTCATTTATG
EST: gi|110693874|gb|EE070489.1|EE070489
EST:     TTCATCCAGAAAGCTGGAACCCAATGTGGTCTGTATCAAG                         CATACTTACAGGGCTTCTGTCATTTATG
genomic: TTCATCCAGAAAGCTGGAACCCAATGTGGTCTGTATCAAGgtaagacaga ... acaaatacagCATACTTACAGGGCTTCTGTCATTTATG
EST: gi|110730040|gb|EE106668.1|EE106668
EST:     TTCATCCAGAAAGCTGGAACCCAATGTGGTCTGTATCAAG                         CATACTTACAGGGCTTCTGTCATTTATG
genomic: TTCATCCAGAAAGCTGGAACCCAATGTGGTCTGTATCAAGgtaagacaga ... acaaatacagCATACTTACAGGGCTTCTGTCATTTATG
EST: gi|294966722|gb|GW837741.1|GW837741
EST:     TTCATCCAGAAAGCTGGAACCCAATGTGGTCTGTATCAAG                         CATACTTACAGGGCTTCTGTCATTTATG
genomic: TTCATCCAGAAAGCTGGAACCCAATGTGGTCTGTATCAAGgtaagacaga ... acaaatacagCATACTTACAGGGCTTCTGTCATTTATG
EST: gi|26257010|gb|CA808073.1|CA808073
EST:     TTCATCCAGAAAGCTGGAACCCAATGTGGTCTGTACCAAG                         CATACTTACAGGGCTTCTGTCATTTATG
genomic: TTCATCCAGAAAGCTGGAACCCAATGTGGTCTGTATCAAGgtaagacaga ... acaaatacagCATACTTACAGGGCTTCTGTCATTTATG
EST: gi|110728958|gb|EE104982.1|EE104982
EST:     TTCATCCAGAAAGCTGGAACCCAATGTGGTCTGTATCAAG                         CATACTTACAGGGCTTCTGTCATTTATG
genomic: TTCATCCAGAAAGCTGGAACCCAATGTGGTCTGTATCAAGgtaagacaga ... acaaatacagCATACTTACAGGGCTTCTGTCATTTATG
EST: gi|110713617|gb|EE089696.1|EE089696
EST:     TTCATCCAGAAAGCTGGAACCCAATGTGGTCTGTATCAAG                         CATACTTACAGGGCTTCTGTCATTTATG
genomic: TTCATCCAGAAAGCTGGAACCCAATGTGGTCTGTATCAAGgtaagacaga ... acaaatacagCATACTTACAGGGCTTCTGTCATTTATG
EST: gi|110726385|gb|EE102119.1|EE102119
EST:     TTCATCCAGAAAGCTGGAACCCAATGTGGTCTGTATCAAG                         CATACTTACAGGGCTTCTGTCATTTATG
genomic: TTCATCCAGAAAGCTGGAACCCAATGTGGTCTGTATCAAGgtaagacaga ... acaaatacagCATACTTACAGGGCTTCTGTCATTTATG
EST: gi|77587429|gb|DV222858.1|DV222858
EST:     TTCATCCAGAAAGCTGGAACCCAATGTGGTCTGTATCAAG                         CATACTTACAGGGCTTCTGTCATTTATG
genomic: TTCATCCAGAAAGCTGGAACCCAATGTGGTCTGTATCAAGgtaagacaga ... acaaatacagCATACTTACAGGGCTTCTGTCATTTATG
EST: gi|34543563|gb|CF511795.1|CF511795
EST:     TTCATCCAGAAAGCTGGAACCCAATGTGGTCTGTATCAAG                         CATACTTACAGGGCTTCTGTCATTTATG
genomic: TTCATCCAGAAAGCTGGAACCCAATGTGGTCTGTATCAAGgtaagacaga ... acaaatacagCATACTTACAGGGCTTCTGTCATTTATG
EST: gi|110732339|gb|EE107537.1|EE107537
EST:     TTCATCCAGAAAGCTGGAACCCAATGTGGTCTGTATCAAG                         CATACTTACAGGGCTTCTGTCATTTATG
genomic: TTCATCCAGAAAGCTGGAACCCAATGTGGTCTGTATCAAGgtaagacaga ... acaaatacagCATACTTACAGGGCTTCTGTCATTTATG
EST: gi|110721123|gb|EE097761.1|EE097761
EST:     TTCATCCAGAAAGCTGGAACCCAATGTGGTCTGTATCAAG                         CATACTTACAGGGCTTCTGTCATTTATG
genomic: TTCATCCAGAAAGCTGGAACCCAATGTGGTCTGTATCAAGgtaagacaga ... acaaatacagCATACTTACAGGGCTTCTGTCATTTATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCATCCAGAAAGCTGGAACCCAATGTGGTCTGTATCAAGgtaagacagagccaagatttcttatacacgacacttgttttatgttatcttttctgttatttaatatagcctttttgaactaacatggttgtatgttacaaatacag

- - - - - AAGCTG
- - - - - - GCTGGA