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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTGACCCTGTGAAATTAAAGAAGCTCCGACCCAGTTTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAGgtatattatcttatttatacttctgttcatctttatttacttattgtttgatgccagtaccttcttgtgtttatggtccttgttgccggtataaactcac...

Basic information

species Vitis vinifera
transcript Vv12s0057g01200.t01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0057g01200.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: LOC_Os09g07830.1 (Oryza sativa), 5'ss of exon 9
TTTGACCCTGTGAAATTAAAGAAGCTCCGACCCAGTTTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAGgtatattatcttatttatacttctgttcatctttatttacttattgtttgatgc--cagtaccttcttgtgtttatggtccttgttgccggtataaactcac
|||||||| |||||| | ||||||||||| || ||||| ||||||||||| ||| |||| ||||| || ||||||||||| |||||||   |  | | |    || ||   || || ||||   | || |    |  | |   ||||| |  || |    |    |  ||||  | | | |     | 
TTTGACCCAGTGAAACTGAAGAAGCTCCGTCCTAGTTTCAAGGAGAATGGTGGTACTGTTACTGCTGGGAATGCTTCTAGTATAAGgtgcttgctttgacacttattttaatttatttttaag-atttgtgaggtatttctgtagtacatggttttagg-actacctatgttagcagaacagttgtat

upper sequence: Vv12s0057g01200.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GRMZM5G866758_T02 (Zea mays), 5'ss of exon 9
TTTGACCCTGTGAAATTAAAGAAGCTCCGACCCAGTTTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAGgtatattatcttatttatacttctgttcatct-ttatttacttattgtttgatgccagtaccttcttgtgtttatggtccttgttgccggtat-aaactcac
|||||||| || ||| ||||||| || || || ||||| ||||||||||| ||| | || || || || ||||||||||| ||||||||   |   | |  |||   |  |  | | | |  |  |     | | |||  ||      |||     | | | ||     |  | | ||| ||   || 
TTTGACCCAGTAAAACTAAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGTGGTACAGTTACAGCTGGAAATGCTTCTAGTATAAGgta-gctgcttgaaatatttctgaggccttttgtcctacaaagtctttctgagaccttgtttttcggccatatgttgtttagctgacagatatgaaggaca-

upper sequence: Vv12s0057g01200.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA02G47860.1 (Glycine max), 5'ss of exon 8
TTTGACCCTGTGAAATTAAAGAAGCTCCGACCCAGTTTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAGgtatattatcttatttatacttctgttcatctttatttacttattgtttgatgccagtaccttcttgtgtttatggtccttgttgccggtataaactcac
|||||  |||  || |||   || || || || ||||| ||||||| |||||||||||| ||||| ||||||||||| |||||||||| || ||| ||||| | | ||  | | | |||| ||  | || ||| ||      ||   |     ||   ||| || ||| |  | |           
TTTGATGCTGCCAAGTTACGCAAACTTCGGCCAAGTTTCAAGGAGACTGGAGGTTCTGTTACTGCTGGCAATGCTTCCAGCATAAGgt-taatatattattgaaattt--gcttaactttttt--cctagtgtgtgt-----gtgtgtgtgaatgaaaatgctc-ttgctaacag-----------

upper sequence: Vv12s0057g01200.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA14G00760.1 (Glycine max), 5'ss of exon 8
TTTGACCCTGTGAAATTAAAGAAGCTCCGACCCAGTTTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAGgtatattatcttatttatacttctgttcatctttatttacttattgtttgatgccagtaccttcttgt-gtttatggtccttgttgccggtataaactcac-
|||||  |||  || |||   || || || || ||||| ||||||| |||||||||||| || || ||||||||||| |||||||||| || ||| || |  | | || | |  |  |||   ||| ||  | ||  |    | |    ||||| | ||||  |  |         |||| |   |  
TTTGATGCTGCCAAGTTACGCAAACTTCGGCCAAGTTTCAAGGAGACTGGAGGTTCTGTTACAGCTGGCAATGCTTCCAGCATAAGgt-taatatattttcgaaatttgt-taaactttttcctacataacgatttgtatttggatgcccttgtcgattattttgttataaaatactatatatatata

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|110398909|gb|EC965389.1|EC965389
EST:     TTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAG                         TGATGGTGCTGCTGCTTTAGTTTTGGTCAGTGGAAAGAAGGCACTTCAACT
genomic: TTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAGgtatattatc ... tcatcgacagTGATGGTGCTGCTGCTTTAGTTTTGGTAAGTGGAGAGAAGGCACTTCAACT
EST: gi|352790687|gb|FQ475445.1|FQ475445
EST:     CAGGCAATGCTTCTAGCATAAG                         TGATGGTGCTGCTGCTTTAGTTTCGGTCAGTGGAGAGAAGGCACTTCAACT
genomic: CAGGCAATGCTTCTAGCATAAGgtatattatc ... tcatcgacagTGATGGTGCTGCTGCTTTAGTTTTGGTAAGTGGAGAGAAGGCACTTCAACT
EST: gi|30126694|gb|CB912033.1|CB912033
EST:     TTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAG                         TGATGGTGCTGCTGCTTTAGTTTTGGTAAGTGGAGAGAAGGCACTTCAACT
genomic: TTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAGgtatattatc ... tcatcgacagTGATGGTGCTGCTGCTTTAGTTTTGGTAAGTGGAGAGAAGGCACTTCAACT
EST: gi|30133903|gb|CB919242.1|CB919242
EST:     TTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAG                         TGATGGTGCTGCTGCTTTAGTTTTGGTAAGTGGAGAGAAGGCACTTCAACT
genomic: TTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAGgtatattatc ... tcatcgacagTGATGGTGCTGCTGCTTTAGTTTTGGTAAGTGGAGAGAAGGCACTTCAACT
EST: gi|71876405|gb|DT025460.1|DT025460
EST:     TTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAG                         TGATGGTGCTGCTGCTTTAGTTTTGGTAAGTGGAGAGAAGGCACTTCAACT
genomic: TTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAGgtatattatc ... tcatcgacagTGATGGTGCTGCTGCTTTAGTTTTGGTAAGTGGAGAGAAGGCACTTCAACT
EST: gi|110699364|gb|EE076300.1|EE076300
EST:     TTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAG                         TGATGGTGCTGCTGCTTTAGTTTTGGTAAGTGGAGAGAAG-CACTTCAACT
genomic: TTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAGgtatattatc ... tcatcgacagTGATGGTGCTGCTGCTTTAGTTTTGGTAAGTGGAGAGAAGGCACTTCAACT
EST: gi|110403296|gb|EC964774.1|EC964774
EST:     TTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAG                         TGATGGTGCTGCTGCTTTAGTTTTGGTCAGTGGAGAGAAGGCACTTCAACT
genomic: TTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAGgtatattatc ... tcatcgacagTGATGGTGCTGCTGCTTTAGTTTTGGTAAGTGGAGAGAAGGCACTTCAACT
EST: gi|161716985|gb|FC066530.1|FC066530
EST:     TTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAG                         TGATGGTGCTGCTG
genomic: TTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAGgtatattatc ... tcatcgacagTGATGGTGCTGCTG
EST: gi|30129594|gb|CB914933.1|CB914933
EST:     TTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAG                         TGATGGTGCTGCTGCTTTAGTTTTGGTAAGTGGAGAGAAGGCACTTCAACT
genomic: TTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAGgtatattatc ... tcatcgacagTGATGGTGCTGCTGCTTTAGTTTTGGTAAGTGGAGAGAAGGCACTTCAACT
EST: gi|110385906|gb|EC950465.1|EC950465
EST:     TTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAG                         TGATGGTGCTGCTGCTTTAGTTTTGGTAAGTGGAGAGAAGGCACTTCAACT
genomic: TTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAGgtatattatc ... tcatcgacagTGATGGTGCTGCTGCTTTAGTTTTGGTAAGTGGAGAGAAGGCACTTCAACT
EST: gi|30128765|gb|CB914104.1|CB914104
EST:     TTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAG                         TGATGGTGCTGCTGCTTTAGTTTTGGTAAGTGGAGAGAAGGCACTTCAACT
genomic: TTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAGgtatattatc ... tcatcgacagTGATGGTGCTGCTGCTTTAGTTTTGGTAAGTGGAGAGAAGGCACTTCAACT
EST: gi|110700654|gb|EE077500.1|EE077500
EST:     TTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAG                         TGATGGTGCTGCTGCTTTAGTTTTGGTAAGTGGAGAGAAGGCACTTCAACT
genomic: TTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAGgtatattatc ... tcatcgacagTGATGGTGCTGCTGCTTTAGTTTTGGTAAGTGGAGAGAAGGCACTTCAACT
EST: gi|110398035|gb|EC964108.1|EC964108
EST:     TTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAG                         TGATGGTGCTGCTGCTTTAGTTTT
genomic: TTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAGgtatattatc ... tcatcgacagTGATGGTGCTGCTGCTTTAGTTTT
EST: gi|30254555|gb|CB971300.1|CB971300
EST:     TTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAG                         TGATGGTGCTGCTGCTTTAGTTTTGGTCAGTGGAGAGAAGGCACTTCAACT
genomic: TTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAGgtatattatc ... tcatcgacagTGATGGTGCTGCTGCTTTAGTTTTGGTAAGTGGAGAGAAGGCACTTCAACT
EST: gi|30130051|gb|CB915390.1|CB915390
EST:     TTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAG                         TGATGGTGCTGCTGCTTTAGTTTTGGTAAGTGGAGAGAAGGCACTTCAAC
genomic: TTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAGgtatattatc ... tcatcgacagTGATGGTGCTGCTGCTTTAGTTTTGGTAAGTGGAGAGAAGGCACTTCAAC
EST: gi|30129595|gb|CB914934.1|CB914934
EST:     TTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAG                         TGATGGTGCTGCTGCTTTAGTTTTGGTAAGTGGAGAGAAGGCACTTCAACT
genomic: TTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAGgtatattatc ... tcatcgacagTGATGGTGCTGCTGCTTTAGTTTTGGTAAGTGGAGAGAAGGCACTTCAACT
EST: gi|349833317|gb|FQ416695.1|FQ416695
EST:     TTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAG                         TGATGGTGCTGCTGCTTTAGTTTTGGTAAGTGGAGAGAAGGCACTTCAACT
genomic: TTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAGgtatattatc ... tcatcgacagTGATGGTGCTGCTGCTTTAGTTTTGGTAAGTGGAGAGAAGGCACTTCAACT
EST: gi|110723249|gb|EE100343.1|EE100343
EST:     TTTAAGGAGAATGGANGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAG                         TGATGGTGCTGCTGCTTTAGTTTTGGTAAGTGGAGAGAAG-CACTTCAACT
genomic: TTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAGgtatattatc ... tcatcgacagTGATGGTGCTGCTGCTTTAGTTTTGGTAAGTGGAGAGAAGGCACTTCAACT
EST: gi|110368276|gb|EC932247.1|EC932247
EST:     TTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAG                         TGATGGTGCTGCTGCTTTAGTTTTGGTCAGTGGAGAGAAGGCACTTCAACT
genomic: TTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAGgtatattatc ... tcatcgacagTGATGGTGCTGCTGCTTTAGTTTTGGTAAGTGGAGAGAAGGCACTTCAACT
EST: gi|110371396|gb|EC935385.1|EC935385
EST:     TTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAG                         TGATGGTGCTGCTGCTTTAGTTTTGGTCAGTGGAGAGAAGGCACTTCAACT
genomic: TTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAGgtatattatc ... tcatcgacagTGATGGTGCTGCTGCTTTAGTTTTGGTAAGTGGAGAGAAGGCACTTCAACT
EST: gi|27584750|gb|CB007445.1|CB007445
EST:     TTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAG                         TGATGGTGCTGCTGCTTTAGTTTTGGTAAGTGGAGAGAAGGCACTTCAACT
genomic: TTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAGgtatattatc ... tcatcgacagTGATGGTGCTGCTGCTTTAGTTTTGGTAAGTGGAGAGAAGGCACTTCAACT
EST: gi|33402805|gb|CF208432.1|CF208432
EST:     TTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAG                         TGATGGTGCTGCTGCTTTAGTTTTGGTCAGTGGAGAGAAGGCACTTCAACT
genomic: TTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAGgtatattatc ... tcatcgacagTGATGGTGCTGCTGCTTTAGTTTTGGTAAGTGGAGAGAAGGCACTTCAACT
EST: gi|34543095|gb|CF511327.1|CF511327
EST:     TTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAG                         TGATGGTGCTGCTGCTTTAGTTTTGGTCAGTGGAGAGAAGGCACTTCAACT
genomic: TTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAGgtatattatc ... tcatcgacagTGATGGTGCTGCTGCTTTAGTTTTGGTAAGTGGAGAGAAGGCACTTCAACT
EST: gi|110361968|gb|EC925474.1|EC925474
EST:     TTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAG                         TGATGGTGCTGCTGCTTTAGTTTTGGTCAGTGGAGAGAAGGCACTTCAACT
genomic: TTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAGgtatattatc ... tcatcgacagTGATGGTGCTGCTGCTTTAGTTTTGGTAAGTGGAGAGAAGGCACTTCAACT
EST: gi|30133750|gb|CB919089.1|CB919089
EST:     TTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAG                         TGATGGTGCTGCTGCTTTAGTTTTGGTAAGTGGAGAGAAGGCACTTCAACT
genomic: TTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAGgtatattatc ... tcatcgacagTGATGGTGCTGCTGCTTTAGTTTTGGTAAGTGGAGAGAAGGCACTTCAACT
EST: gi|30299187|gb|CB975981.1|CB975981
EST:     TTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAG                         TGATGGTGCTGCTGCTTTAGTTTTGGTCAGTGGAGAGAAGGCACTTCAACT
genomic: TTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAGgtatattatc ... tcatcgacagTGATGGTGCTGCTGCTTTAGTTTTGGTAAGTGGAGAGAAGGCACTTCAACT
EST: gi|110361336|gb|EC924802.1|EC924802
EST:     TTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAG                         TGATGGTGCTGCTGCTTTAGTTTTGGTCAGTGGAGAGAAGGCACTTCAACT
genomic: TTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAGgtatattatc ... tcatcgacagTGATGGTGCTGCTGCTTTAGTTTTGGTAAGTGGAGAGAAGGCACTTCAACT
EST: gi|110362059|gb|EC925566.1|EC925566
EST:     TTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAG                         TGATGGTGCTGCTGCTTTAGTTTTGGTAAGTGGAGAGAAGGCACTTCAACT
genomic: TTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAGgtatattatc ... tcatcgacagTGATGGTGCTGCTGCTTTAGTTTTGGTAAGTGGAGAGAAGGCACTTCAACT
EST: gi|110357331|gb|EC920800.1|EC920800
EST:     TTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAG                         TGATGGTGCTGCTGCTTTAGTTTTGGTAAGTGGAGAGAAGGCACTTCAACT
genomic: TTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAGgtatattatc ... tcatcgacagTGATGGTGCTGCTGCTTTAGTTTTGGTAAGTGGAGAGAAGGCACTTCAACT
EST: gi|33403297|gb|CF208924.1|CF208924
EST:     TTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAG                         TGATGGTGCTGCTGCTTTAGTTTTGGTCAGTGGAGAGAAGGCACTTCAACT
genomic: TTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAGgtatattatc ... tcatcgacagTGATGGTGCTGCTGCTTTAGTTTTGGTAAGTGGAGAGAAGGCACTTCAACT
EST: gi|71858509|gb|DT007564.1|DT007564
EST:     TTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAG                         TGATGGTGCTGCTGCTTTAGTTTTGGTAAGTGGAGAGAAGGC
genomic: TTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAGgtatattatc ... tcatcgacagTGATGGTGCTGCTGCTTTAGTTTTGGTAAGTGGAGAGAAGGC
EST: gi|110723122|gb|EE100072.1|EE100072
EST:     TTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAG                         TGATGGTGCTGCTGCTTTAGTTTTGGTAAGTGGAGAGAAGGCACTTCAACT
genomic: TTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAGgtatattatc ... tcatcgacagTGATGGTGCTGCTGCTTTAGTTTTGGTAAGTGGAGAGAAGGCACTTCAACT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTGACCCTGTGAAATTAAAGAAGCTCCGACCCAGTTTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAGgtatattatcttatttatacttctgttcatctttatttacttattgtttgatgccagtaccttcttgtgtttatggtccttgttgccggtataaactcac

- - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG