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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACGCACTGTGAGAGTGGAGAAGCGAATAAATGAGATAGTTAATAGATTGAACAGGACAAAAGTAGAAAGGAAACCAGATTTAAAAGgtaatcttgcaacctcagctttctttataacatgttaattgaatttctcttgaatctttaatttggtatagacttcatatcaaactcagcccttttcaac...

Basic information

species Vitis vinifera
transcript Vv04s0008g03810.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g03810.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA06G08640.1 (Glycine max), 5'ss of exon 4
GTACGCACTGTGAGAGTGGAGAAGCGAATAAATGAGATAGTTAATAGATTGAACAGGACAAAAGTAGAAAGGAAACCAGATTTAAAAGgtaat-------cttgcaacct------------cagctttctttataacatgttaattgaatttctcttgaatctttaatttggtatagactt-catatcaaactcagcccttttcaac-------------------------------------------------------------
|| || ||||||||||| |||||||| ||||||||||| ||||| ||  | |||| ||||||||| ||||||||||| ||||| ||||||| |        ||||   ||            ||| |||||||  ||||| | | ||  | |      |||| | || ||   ||||  ||| || |    | |   |   |   | |                                                             
GTTCGAACTGTGAGAGTTGAGAAGCGGATAAATGAGATTGTTAACAGGCTAAACAAGACAAAAGTGGAAAGGAAACCTGATTTGAAAGgtacttcataagtttgccctctttccgttgaatacagttttcttttgaacatttaagttttaatagctaagaat-tctatttctttatatgcttacaaacttgatttgacttatccgatcttgatatgtaataatatgcttacaaatctcatgtatattaaatatacccaatgtgctgcag

upper sequence: Vv04s0008g03810.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA04G08530.3 (Glycine max), 5'ss of exon 5
GTACGCACTGTGAGAGTGGAGAAGCGAATAAATGAGATAGTTAATAGATTGAACAGGACAAAAGTAGAAAGGAAACCAGATTTAAAAGgtaatcttgcaacctcagctttctttataacatgttaattgaatttctcttgaatctttaa--tttggta--tagacttcatatcaaactcagcccttttcaac-
|| || ||||| ||||| |||||| | ||||||||||| ||||| ||  | |||| ||||||||| ||||||||||| ||||| |||||||  |||   |  |  ||| |||||        |  | |   ||||| ||||   |||||  |||  ||  ||    |  |||       |    |   |||| 
GTTCGAACTGTAAGAGTTGAGAAGAGGATAAATGAGATTGTTAACAGGCTAAACAAGACAAAAGTGGAAAGGAAACCTGATTTGAAAGgta--cttaataagtttgctctctttccgttgaatatagt---tttcttttgagcatttaagttttaatagctaagaatgctatttgctggataagtaggcaact

upper sequence: Vv04s0008g03810.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT5G11500.2 (Arabidopsis thaliana), 5'ss of exon 4
GTACGCACTGTGAGAGTGGAGAAGCGAATAAATGAGATAGTTAATAGATTGAACAGGACAAAAGTAGAAAGGAAACCAGATTTAAAAGgtaatcttgcaacctcagctttctttataacatgttaattga------atttctcttgaat-ctttaatttggtatag--acttcatatcaaactcagcccttttcaac-----------------------------------------------------------------------------
|| || ||| | ||||||||||||||| | ||||| |||||||| ||| ||||||  |||||||| ||||| |  || ||| | | |||| |   |      |  |   ||||  | | ||  |||| |       |||  || || || | |   | | || ||   | ||     |  |   ||      | ||                                                                              
GTCCGGACTATCAGAGTGGAGAAGCGAGTCAATGAAATAGTTAACAGACTGAACAAAACAAAAGTTGAAAGAACCCCTGATCTGAGAGgttagtatttgttttgtgagctcttcctcagattctaataggtagaagattgatcatgcatacatctttctcgtttaacaattttcctgctgatgaagtgtcagttaagtgtctgtagtttttccagtcagtataacttcaagatctatgaaaataatttgattgttcataactgtgttgatgaag

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|56409227|gb|CX017479.1|CX017479
EST:     AGTTAATAGATTGAACAGGACAAAAGTAGAAAGGAAACCAGATTTAAAAG                         CTGAGCGAGAAGCAGTTAATGCAGCAGAAAGAGCTGAGAGAAAACTTCAGC
genomic: AGTTAATAGATTGAACAGGACAAAAGTAGAAAGGAAACCAGATTTAAAAGgtaatcttgc ... ttaactgcagCTGAGCGAGAAGCAGTTAATGCAGCAGAAAGAGCTGAGAGAAAACTTCAGC
EST: gi|161720775|gb|FC070283.1|FC070283
EST:     AGTTAATAGATTGAACAGGACAAAAGTAGAAAGGAAACCAGATTTAAAAG                         CTGAGCGAGAAGCAGTTAATGCAGCAGAAAGAGCTGAGAGAAAACTTCAGC
genomic: AGTTAATAGATTGAACAGGACAAAAGTAGAAAGGAAACCAGATTTAAAAGgtaatcttgc ... ttaactgcagCTGAGCGAGAAGCAGTTAATGCAGCAGAAAGAGCTGAGAGAAAACTTCAGC
EST: gi|34549359|gb|CF517591.1|CF517591
EST:     AGTTAATAGATTGAACAGGACAAAAGTAGAAAGGAAACCAGATTTAAAAG                         CTGAGCGAGAAGCAGTTAATGCAGCAGAAAGAGCTGAGAGAAAACTTCAGC
genomic: AGTTAATAGATTGAACAGGACAAAAGTAGAAAGGAAACCAGATTTAAAAGgtaatcttgc ... ttaactgcagCTGAGCGAGAAGCAGTTAATGCAGCAGAAAGAGCTGAGAGAAAACTTCAGC
EST: gi|110715789|gb|EE094238.1|EE094238
EST:     AGTTAATAGATTGAACAGGACAAAAGTAGAAAGGAAACCAGATTTAAAAG                         CTGAGCGAGAAGCAGTTAATGCAGCAGAAAGAGCTGAGAGAAAACTTCAGC
genomic: AGTTAATAGATTGAACAGGACAAAAGTAGAAAGGAAACCAGATTTAAAAGgtaatcttgc ... ttaactgcagCTGAGCGAGAAGCAGTTAATGCAGCAGAAAGAGCTGAGAGAAAACTTCAGC
EST: gi|110383971|gb|EC948380.1|EC948380
EST:     AGTTAATAGATTGAACAGGACAAAAGTAGAAAGGAAACCAGATTTAAAAG                         CTGAGCGAGAAGCAGTTAATGCAGCAGAAAGAGCTGAGAGAAAACTTCAGC
genomic: AGTTAATAGATTGAACAGGACAAAAGTAGAAAGGAAACCAGATTTAAAAGgtaatcttgc ... ttaactgcagCTGAGCGAGAAGCAGTTAATGCAGCAGAAAGAGCTGAGAGAAAACTTCAGC
EST: gi|110710049|gb|EE086042.1|EE086042
EST:     AGTTAATAGATTGAACAGGACAAAAGTAGAAAGGAAACCAGATTTAAAAG                         CTGAGCGAGAAGCAGTTAATGCAGCAGAAAGAGCTGAGAGAAAACTTCAGC
genomic: AGTTAATAGATTGAACAGGACAAAAGTAGAAAGGAAACCAGATTTAAAAGgtaatcttgc ... ttaactgcagCTGAGCGAGAAGCAGTTAATGCAGCAGAAAGAGCTGAGAGAAAACTTCAGC
EST: gi|30128520|gb|CB913859.1|CB913859
EST:     AGTTAATAGATTGAACAGGACAAAAGTAGAAAGGAAACCAGATTTAAAAG                         CTGAGCGAGAAGCAGTTAATGCAGCAGAAAGAGCTGAGAGAAAACTTCAGC
genomic: AGTTAATAGATTGAACAGGACAAAAGTAGAAAGGAAACCAGATTTAAAAGgtaatcttgc ... ttaactgcagCTGAGCGAGAAGCAGTTAATGCAGCAGAAAGAGCTGAGAGAAAACTTCAGC
EST: gi|161721392|gb|FC070768.1|FC070768
EST:     AGTTAATAGATTGAACAGGACAAAAGTAGAAAGGAAACCAGATTTAAAAG                         CTGAGCGAGAAGCAGTTAATGCAGCAGAAAGAGCTGAGAGAAAACTTCAGC
genomic: AGTTAATAGATTGAACAGGACAAAAGTAGAAAGGAAACCAGATTTAAAAGgtaatcttgc ... ttaactgcagCTGAGCGAGAAGCAGTTAATGCAGCAGAAAGAGCTGAGAGAAAACTTCAGC
EST: gi|110357353|gb|EC920834.1|EC920834
EST:     AGTTAATAGATTGAACAGGACAAAAGTAGAAAGGAAACCAGATTTAAAAG                         CTGAGCGAGAAGCAGTTAATGCAGCAGAAAGAGCTGAGAGAAAACTTCAGC
genomic: AGTTAATAGATTGAACAGGACAAAAGTAGAAAGGAAACCAGATTTAAAAGgtaatcttgc ... ttaactgcagCTGAGCGAGAAGCAGTTAATGCAGCAGAAAGAGCTGAGAGAAAACTTCAGC
EST: gi|110374937|gb|EC939883.1|EC939883
EST:     AGTTAATAGATTGAACAGGACAAAAGTAGAAAGGAAACCAGATTTAAAAG                         CTGAGCGAGAAGCAGTTAATGCAGCAGAAAGAGCTGAGAGAAAACTTCAGC
genomic: AGTTAATAGATTGAACAGGACAAAAGTAGAAAGGAAACCAGATTTAAAAGgtaatcttgc ... ttaactgcagCTGAGCGAGAAGCAGTTAATGCAGCAGAAAGAGCTGAGAGAAAACTTCAGC
EST: gi|27583079|gb|CB005774.1|CB005774
EST:     AGTTAATAGATTGAACAGGACAAAAGTAGAAAGGAAACCAGATTTAAAAG                         CTGAGCGAGAAGCAGTTAATGCAGCAGAAAGAGCTGAGAGAAAACTTCAGC
genomic: AGTTAATAGATTGAACAGGACAAAAGTAGAAAGGAAACCAGATTTAAAAGgtaatcttgc ... ttaactgcagCTGAGCGAGAAGCAGTTAATGCAGCAGAAAGAGCTGAGAGAAAACTTCAGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTACGCACTGTGAGAGTGGAGAAGCGAATAAATGAGATAGTTAATAGATTGAACAGGACAAAAGTAGAAAGGAAACCAGATTTAAAAGgtaatcttgcaacctcagctttctttataacatgttaattgaatttctcttgaatctttaatttggtatagacttcatatcaaactcagcccttttcaac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccttttc