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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGTGGAAGTGGAGGTAAATGGAGTCAAGCAAAGAAGTGGAGTCCTTATAAAAAAGTGCAGgtagatgtcttacttctttacatatgctttggaactgaaatgatctgttgtatctgaattcatcttgcatcattctggttcctttttcattttcttggga...

Basic information

species Vitis vinifera
transcript Vv02s0025g02640.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g02640.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA13G10340.1 (Glycine max), 5'ss of exon 4
GTTGTGGAAGTGGAGGTAAATGGAGTCAAGCAAAGAAGTGGAGTCCTTATAAAAAAGTGCAGgtagatgtcttacttctttacatatgctttggaactgaaatgatctgttgtatctgaattcatcttgcatcattctggttcctttttcattttcttggga---
||||||||||| ||| |||||||||| ||||||| |||||| || | |||||| |||||||||||||| || |   | || | ||  |   | ||||  |   |    ||   ||||| |||    ||  | |||   | |      ||||| ||   ||     
GTTGTGGAAGTAGAGATAAATGGAGTGAAGCAAAAAAGTGGCGTGCATATAAAGAAGTGCAGgtagatttcatgtct-ttgagattggtaattgaacatatgcgtaaagtc--atctgtatttcaattcaaacatgtagatattaaattcatatttggggccctg

upper sequence: Vv02s0025g02640.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA02G09680.2 (Glycine max), 5'ss of exon 4
GTTGTGGAAGTGGAGGTAAATGGAGTCAAGCAAAGAAGTGGAGTCCTTATAAAAAAGTGCAGgtagatgtcttacttctttacatatgctttggaac---tgaa-atgatctgttgtatctgaattcat-cttgcatcattctggttcctttttcattttcttggga
||| ||||||| ||| |||||||||| ||||||| |||||| || | |||||| |||||||||||||| || |   | || | ||  |   | ||||   ||   |   ||   ||||| | ||||||  | || || ||  | | | | | ||     |||||   
GTTATGGAAGTAGAGATAAATGGAGTGAAGCAAAAAAGTGGCGTGCATATAAAGAAGTGCAGgtagatttcatgtct-ttgagattggtaattgaacatttgcgcaaagtcatctgtatttcaattcaaacatgtat-atattagattcatctttggggtcttg---
















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|18459168|gb|BM437446.1|BM437446
EST:     GAGGTAAATGGAATCAAGCAAAGAAGTGGAGTCCTTATAAAAAAGTGCAG                         GTACCTGGAGAACAGTGGGTGTGTGGGAATGTGCGTGAATATGTGCAAAAT
genomic: GAGGTAAATGGAGTCAAGCAAAGAAGTGGAGTCCTTATAAAAAAGTGCAGgtagatgtct ... tcctatcaagGTACCTGGAGAACAGTGGGTGTGTGGGAATGTGCGTGAATATGTGCAAAAT
EST: gi|110384986|gb|EC949461.1|EC949461
EST:     GAGGTAAATGGAGTCAAGCAAAGAAGTGGAGTCCTTATAAAAAAGTGCAG                         GTACCTGGAGAACAGTGGGTGTGTGGGAATGTGCGTGAATATGTGCAAAAT
genomic: GAGGTAAATGGAGTCAAGCAAAGAAGTGGAGTCCTTATAAAAAAGTGCAGgtagatgtct ... tcctatcaagGTACCTGGAGAACAGTGGGTGTGTGGGAATGTGCGTGAATATGTGCAAAAT
EST: gi|110374326|gb|EC939496.1|EC939496
EST:     GAGGTAAATGGAGTCAAGCAAAGAAGTGGAGTCCTTATAAAAAAGTGCAG                         GTACCTGGAGAACAGTGGGTGTGTGGGAATGTGCGTGAATATGTGCAAAAT
genomic: GAGGTAAATGGAGTCAAGCAAAGAAGTGGAGTCCTTATAAAAAAGTGCAGgtagatgtct ... tcctatcaagGTACCTGGAGAACAGTGGGTGTGTGGGAATGTGCGTGAATATGTGCAAAAT
EST: gi|110379290|gb|EC944475.1|EC944475
EST:     GAGGTAAATGGAGTCAAGCAAAGAAGTGGAGTCCTTATAAAAAAGTGCAG                         GTACCTGGAGAACAGTGGGTGTGTGGGAATGTGCGTGAATATGTGCAAAAT
genomic: GAGGTAAATGGAGTCAAGCAAAGAAGTGGAGTCCTTATAAAAAAGTGCAGgtagatgtct ... tcctatcaagGTACCTGGAGAACAGTGGGTGTGTGGGAATGTGCGTGAATATGTGCAAAAT
EST: gi|110376860|gb|EC941936.1|EC941936
EST:     GAGGTAAATGGAGTCAAGCAAAGAAGTGGAGTCCTTATAAAAAAGTGCAG                         GTACCTGGAGAACAGTGGGTGTGTGGGAATGTGCGTGAATATGTGCAAAAT
genomic: GAGGTAAATGGAGTCAAGCAAAGAAGTGGAGTCCTTATAAAAAAGTGCAGgtagatgtct ... tcctatcaagGTACCTGGAGAACAGTGGGTGTGTGGGAATGTGCGTGAATATGTGCAAAAT
EST: gi|110372636|gb|EC936820.1|EC936820
EST:     GAGGTAAATGGAGTCAAGCAAAGAAGTGGAGTCCTTATAAAAAAGTGCAG                         GTACCTGGAGAACAGTGGGTGTGTGGGAATGTGCGTGAATATGTGCAAAAT
genomic: GAGGTAAATGGAGTCAAGCAAAGAAGTGGAGTCCTTATAAAAAAGTGCAGgtagatgtct ... tcctatcaagGTACCTGGAGAACAGTGGGTGTGTGGGAATGTGCGTGAATATGTGCAAAAT
EST: gi|27755371|gb|CB036126.1|CB036126
EST:     GAGGTAAATGGAATCAAGCAAAGAAGTGGAGTCCTTATAAAAAAGTGCAG                         GTACCTGGAGAACAGTGGGTGTGTGGGAATGTGCGTGAATATGTGCAAAAT
genomic: GAGGTAAATGGAGTCAAGCAAAGAAGTGGAGTCCTTATAAAAAAGTGCAGgtagatgtct ... tcctatcaagGTACCTGGAGAACAGTGGGTGTGTGGGAATGTGCGTGAATATGTGCAAAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGTGGAAGTGGAGGTAAATGGAGTCAAGCAAAGAAGTGGAGTCCTTATAAAAAAGTGCAGgtagatgtcttacttctttacatatgctttggaactgaaatgatctgttgtatctgaattcatcttgcatcattctggttcctttttcattttcttggga

- - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaatga