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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGAAGAAAACCTGGTGCACTGGAGAAAGTAGTAGAGAGAAGGCAGAGAAGGATGATTAAAAACAGAGAATCAGCCGCAAGATCACGAGCTCGTAAGCAGgtgaatatccatcatacatcttttagtggttccacactatttattttgtgttgcttgtgatgctcttgtagtttctttgtgatacttcaagctaatcaaa...

Basic information

species Vitis vinifera
transcript Vv03s0063g00310.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0063g00310.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA02G14880.1 (Glycine max), 5'ss of exon 1
GGGAAGAAAACCTGGTGCACTGGAGAAAGTAGTAGAGAGAAGGCAGAGAAGGATGATTAAAAACAGAGAATCAGCCGCAAGATCACGAGCTCGTAAGCAGgtgaatatccatcatacatcttttagtggttccacactatttattttgtgttgcttgtgatgctcttgtagtttc----tttgtgatacttcaagctaatcaaa
|||||| |||    ||||  | |||||||| || ||||| || || || || ||||||||||| ||||||||||| || |||||| | ||||||||||||||   || ||||| ||||  |  |  |  |    ||| | ||| ||    |   || | |  |      ||| |       ||||| | |  || | | |    
GGGAAGGAAATTCAGTGCCATAGAGAAAGTGGTTGAGAGGAGACAAAGGAGAATGATTAAAAATAGAGAATCAGCAGCGAGATCAAGGGCTCGTAAGCAGgt---tagccatcttacaattagtcattttaatgcaccagttagttccactgttttatta-acataaaaagtattaacacatgtgacattgtaaacaactttct

upper sequence: Vv03s0063g00310.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: AT4G34000.1 (Arabidopsis thaliana), 5'ss of exon 3
GGGAAGAAAACCTGGTGCACTGGAGAAAGTAGTAGAGAGAAGGCAGAGAAGGATGATTAAAAACAGAGAATCAGCCGCAAGATCACGAGCTCGTAAGCAGgtgaatatccatcatacatcttttagtggttccacac-tatttattttgtgttgcttgtgat--gctcttgtagtttctt-tgtgatacttcaagctaatcaaa
| ||| || |  ||  |  |||||||||||  | ||||||||||| | ||||||||| || || || |||||||| |||||||| || ||||| ||||| |||| | |   |     |  |||| | | ||  | |    || |   ||||   | ||| ||   || ||  | ||||||   ||| |                
GAGAAAAACAGGTGCAGTTCTGGAGAAAGTGATTGAGAGAAGGCAAAAAAGGATGATAAAGAATAGGGAATCAGCTGCAAGATCCCGCGCTCGCAAGCAAgtgagtgtttgtt---taaattttggagattaaagaaaccttaaaactgtgac-catgttatttactttttcactttcttgcttgacag---------------
















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|110359889|gb|EC922177.1|EC922177
EST:     CGAGCTCGTAAGCAG                         GCTTATACCTTGGAACTTGAAATGGAAGTTGCAAAACTGAAAGAGGCGAAT
genomic: CGAGCTCGTAAGCAGgtgaatatcc ... tttctgccagGCTTATACCTTGGAACTTGAAATGGAAGTTGCAAAACTGAAAGAGGCGAAT
EST: gi|18459306|gb|BM437584.1|BM437584
EST:     GGATGATTAAAAACAGAGAATCAGCTGCAAGATCACGAGCTCGTAAGCAG                         GCTTATACCTTGGAACTTGAAATGGAAGTTGCAAAACTGAAAGAGGCGAAT
genomic: GGATGATTAAAAACAGAGAATCAGCCGCAAGATCACGAGCTCGTAAGCAGgtgaatatcc ... tttctgccagGCTTATACCTTGGAACTTGAAATGGAAGTTGCAAAACTGAAAGAGGCGAAT
EST: gi|352781564|gb|FQ468408.1|FQ468408
EST:     GGATGATTAAAAACAGAGAATCAGCCGCAAGATCACGAGCTCGTAAGCAG                         GCTTATACCTTGGAACTTGAAATGGAAGTTGCAAAACTGANAGAGGCGAAT
genomic: GGATGATTAAAAACAGAGAATCAGCCGCAAGATCACGAGCTCGTAAGCAGgtgaatatcc ... tttctgccagGCTTATACCTTGGAACTTGAAATGGAAGTTGCAAAACTGAAAGAGGCGAAT
EST: gi|71882440|gb|DT031495.1|DT031495
EST:     GGATGATTAAAAACAGAGAATCAGCTGCAAGATCACGAGCTCGTAAGCAG                         GCTTATACCTTGGAACTTGAAATGGAAGTTGCAAAACTGAAAGAGGTGAAT
genomic: GGATGATTAAAAACAGAGAATCAGCCGCAAGATCACGAGCTCGTAAGCAGgtgaatatcc ... tttctgccagGCTTATACCTTGGAACTTGAAATGGAAGTTGCAAAACTGAAAGAGGCGAAT
EST: gi|110362700|gb|EC926250.1|EC926250
EST:     GGATGATTAAAAACAGAGAATCAGCTGCAAGATCACGAGCTCGTAAGCAG                         GCTTATACCTTGGAACTTGAAATGGAAGTTGCAAAACTGAAAGAGGCGAAT
genomic: GGATGATTAAAAACAGAGAATCAGCCGCAAGATCACGAGCTCGTAAGCAGgtgaatatcc ... tttctgccagGCTTATACCTTGGAACTTGAAATGGAAGTTGCAAAACTGAAAGAGGCGAAT
EST: gi|71883659|gb|DT032714.1|DT032714
EST:     GGATGATTAAAAACAGAGAATCAGCTGCAAGATCACGAGCTCGTAAGCAG                         GCTTATACCTTGGAACTTGAAATGGAAGTTGCAAAACTGAAAGAGGTGAAT
genomic: GGATGATTAAAAACAGAGAATCAGCCGCAAGATCACGAGCTCGTAAGCAGgtgaatatcc ... tttctgccagGCTTATACCTTGGAACTTGAAATGGAAGTTGCAAAACTGAAAGAGGCGAAT
EST: gi|71886572|gb|DT035627.1|DT035627
EST:     GGATGATTAAAAACAGAGAATCAGCTGCAAGATCACGAGCTCGTAAGCAG                         GCTTATACCTTGGAACTTGAAATGGAAGTTGCAAAACTGAAAGAGGTGAAT
genomic: GGATGATTAAAAACAGAGAATCAGCCGCAAGATCACGAGCTCGTAAGCAGgtgaatatcc ... tttctgccagGCTTATACCTTGGAACTTGAAATGGAAGTTGCAAAACTGAAAGAGGCGAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGAAGAAAACCTGGTGCACTGGAGAAAGTAGTAGAGAGAAGGCAGAGAAGGATGATTAAAAACAGAGAATCAGCCGCAAGATCACGAGCTCGTAAGCAGgtgaatatccatcatacatcttttagtggttccacactatttattttgtgttgcttgtgatgctcttgtagtttctttgtgatacttcaagctaatcaaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA