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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgaatctgagatctgtttatgataaacatattggtgaaatattttacaattaattttgtctctaactgaaatggacatcatccttgagaaaattgcagGTTCTTTTACTAGATGAAGTGACAGTTGATCTTGATGTTGTGGCAAGGATGGATTTACTTGAATTCTTCAAGGAAGAATGTGATCAG

Basic information

species Vitis vinifera
transcript Vv07s0005g03680.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0005g03680.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os02g56550.1 (Oryza sativa), 3'ss of exon 4
tttgaatctgagatctgttta-tgataaacatattggtgaaatattttacaattaattttgtctctaa--ctgaaatgga--catcatccttgagaaaattgcagGTTCTTTTACTAGATGAAGTGACAGTTGATCTTGATGTTGTGGCAAGGATGGATTTACTTGAATTCTTCAAGGAAGAATGTGATCAG
    || ||    | |||||    | |   ||  |  ||    | |||    ||| | | ||  | ||  |||  ||| |   || |  | |||||  | | ||||| || || || |||||| | || |||||||||||||||||| | || |||||| | ||||| ||||| |||||||| ||||| |||
----aaactaccttatgtttggctagaggtattctcatggttaaatttgtg-ttagtgtagtgccaaagactgctatgaaactatgacacctgagatcaatacagGTACTCTTGCTTGATGAAATCACCGTTGATCTTGATGTTGTGACTAGAATGGATCTCCTTGACTTCTTTAAGGAAGAGTGTGAACAG

upper sequence: Vv07s0005g03680.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT1G03905.1 (Arabidopsis thaliana), 3'ss of exon 4
--------------------------------------------------------------------------------------------------tttgaatctgagatctgtttatgataaacatattggtga-aatattttacaattaattttgtctctaactgaaatggacatcatccttgagaaaattgcagGTTCTTTTACTAGATGAAGTGACAGTTGATCTTGATGTTGTGGCAAGGATGGATTTACTTGAATTCTTCAAGGAAGAATGTGATCAG
                                                                                                     ||| ||    |||| || || ||     |||| |||   || |||  |  | |||||    | ||||    |  | |||   | ||     ||  |||||  | ||||| ||||| || || ||||| || || || || |||||||||||||| || ||||||||||| |||||||||||||||
gtgaaaacaatactgtttcagagaggctgattattctgcatcctctaaaatctcacatgattcattgtcagttatgttctcctctggctttaagcaaaaaagaacctcgtttctgattgtgttatcatcattgctgacgctaattttaatctgatttta---caaacttct-tataaatctctcatgctctgatcacagGTGTTATTACTCGATGAGGTCACTGTTGACCTAGACGTCGTTGCAAGGATGGATTTGCTGGAATTCTTCAAAGAAGAATGTGATCAG
















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|33406635|gb|CF212262.1|CF212262
EST:     GACAGCGGCGTCGAGTCCAAATATGCATGGGTCTTCTTCATCCGTTCCAG                         GTTCTTTTACTAGATGAAGTGACAGTTGATCTTGATGTTGTGGCAAGGATG
genomic: GACAGCGGCGTCGAGTCCAAATATGCATGGGTCTTCTTCATCCGTTCCAGgtaatttccc ... aaaattgcagGTTCTTTTACTAGATGAAGTGACAGTTGATCTTGATGTTGTGGCAAGGATG
EST: gi|71890478|gb|DT039533.1|DT039533
EST:     GACAGCGGCGTCGAGTCCAAATATGCATGGGTCTTCTTCATCCGTTCCAG                         GTTCTTTTACTAGATGAAGTGACAGTTGATCTTGATGTTGTGGCAAGGATG
genomic: GACAGCGGCGTCGAGTCCAAATATGCATGGGTCTTCTTCATCCGTTCCAGgtaatttccc ... aaaattgcagGTTCTTTTACTAGATGAAGTGACAGTTGATCTTGATGTTGTGGCAAGGATG
EST: gi|349812583|gb|FQ407202.1|FQ407202
EST:     GACAGCGGCGTCGAGTCCAAATATGCATGGGTCTTCTTCATCCGTTCCAG                         GTTCTTTT-CTAGATGAAGTGACAGTTGATCTTGATGTTGTGGCAAGGATG
genomic: GACAGCGGCGTCGAGTCCAAATATGCATGGGTCTTCTTCATCCGTTCCAGgtaatttccc ... aaaattgcagGTTCTTTTACTAGATGAAGTGACAGTTGATCTTGATGTTGTGGCAAGGATG
EST: gi|351029239|gb|FQ435439.1|FQ435439
EST:     GACAGCGGCGTCGAGTCCAAATATGCATGGGTCTTCTTCATCCGTTCCAA                         GTTCTTTTACTAGATGAAGTGACA
genomic: GACAGCGGCGTCGAGTCCAAATATGCATGGGTCTTCTTCATCCGTTCCAGgtaatttccc ... aaaattgcagGTTCTTTTACTAGATGAAGTGACA
EST: gi|351045986|gb|FQ441369.1|FQ441369
EST:     GACAGCGGCGTCGAGTCCAAATATGCATGGGTCTTCTTCATCCGTTCCAG                         GTTCTTTTACTAGATGAAGTGACAGTTGATCTTGATGTTGTGGCAAGGATG
genomic: GACAGCGGCGTCGAGTCCAAATATGCATGGGTCTTCTTCATCCGTTCCAGgtaatttccc ... aaaattgcagGTTCTTTTACTAGATGAAGTGACAGTTGATCTTGATGTTGTGGCAAGGATG
EST: gi|110403165|gb|EC964426.1|EC964426
EST:     GACAGCGGCGTCGAGTCCAAATATGCATGGGTCTTCTTCATCCGTTCCAG                         GTTCTTTTACTAGATGAAGTTACAGTTGATCTTGATGTTGTGGCAAGGATG
genomic: GACAGCGGCGTCGAGTCCAAATATGCATGGGTCTTCTTCATCCGTTCCAGgtaatttccc ... aaaattgcagGTTCTTTTACTAGATGAAGTGACAGTTGATCTTGATGTTGTGGCAAGGATG
EST: gi|351027875|gb|FQ448445.1|FQ448445
EST:     GACAGCGGCGTCGAGTCCAAATATGCATGGGTCTTCTTCATCCGTTCCAG                         GTTCTTTTACTAGATGAAGTGACAGTTGGTCTTGATGTTGTGGCAAGGATG
genomic: GACAGCGGCGTCGAGTCCAAATATGCATGGGTCTTCTTCATCCGTTCCAGgtaatttccc ... aaaattgcagGTTCTTTTACTAGATGAAGTGACAGTTGATCTTGATGTTGTGGCAAGGATG
EST: gi|110383570|gb|EC947949.1|EC947949
EST:     GACAGCGGCGTCGAGTCCAAATATGCATGGGTCTTCTTCATCCGTTCCAG                         GTTCTTTTACTAGATGAAGTTACAGTTGATCTTGATGTTGTGGCAAGGATG
genomic: GACAGCGGCGTCGAGTCCAAATATGCATGGGTCTTCTTCATCCGTTCCAGgtaatttccc ... aaaattgcagGTTCTTTTACTAGATGAAGTGACAGTTGATCTTGATGTTGTGGCAAGGATG
EST: gi|71867051|gb|DT016106.1|DT016106
EST:     GACAGCGGCGTCGAGTCCAAATATGCATGGGTCTTCTTCATCCGTTCCAG                         GTTCTTTTACTAGATGAAGTGACAGTTGATCTTGATGTTGTGGCAAGGATG
genomic: GACAGCGGCGTCGAGTCCAAATATGCATGGGTCTTCTTCATCCGTTCCAGgtaatttccc ... aaaattgcagGTTCTTTTACTAGATGAAGTGACAGTTGATCTTGATGTTGTGGCAAGGATG
EST: gi|33401651|gb|CF207278.1|CF207278
EST:     GACAGCGGCGTCGAGTCCAAATATGCATGGGTCTTCTTCATCCGTTCCAG                         GTTCTTTTACTAGATGAAGTTACAGTTGATCTTGATGTTGTGGCAAGGATG
genomic: GACAGCGGCGTCGAGTCCAAATATGCATGGGTCTTCTTCATCCGTTCCAGgtaatttccc ... aaaattgcagGTTCTTTTACTAGATGAAGTGACAGTTGATCTTGATGTTGTGGCAAGGATG
EST: gi|351045639|gb|FQ440824.1|FQ440824
EST:     GACAGCGGCGTCGAGTCCAAATATGCATGGGTCTTCTTCATCCGTTCCAG                         GTTCTTTTACTAGATGAAGTGACAGTTGATCTTGATGTTGTGGCAAGGATG
genomic: GACAGCGGCGTCGAGTCCAAATATGCATGGGTCTTCTTCATCCGTTCCAGgtaatttccc ... aaaattgcagGTTCTTTTACTAGATGAAGTGACAGTTGATCTTGATGTTGTGGCAAGGATG
EST: gi|71867344|gb|DT016399.1|DT016399
EST:     GACAGCGGCGTCGAGTCCAAATATGCATGGGTCTTCTTCATCCGTTCCAG                         GTTCTTTTACTAGATGAAGTGACAGTTGATCTTGATGTTGTGGCAAGGATG
genomic: GACAGCGGCGTCGAGTCCAAATATGCATGGGTCTTCTTCATCCGTTCCAGgtaatttccc ... aaaattgcagGTTCTTTTACTAGATGAAGTGACAGTTGATCTTGATGTTGTGGCAAGGATG
EST: gi|71869053|gb|DT018108.1|DT018108
EST:     GACAGCGGCGTCGAGTCCAAATATGCATGGGTCTTCTTCATCCGTTCCAG                         GTTCTTTTACTAGATGAAGTGACAGTTGATCTTGATGTTGTGGCAAGGATG
genomic: GACAGCGGCGTCGAGTCCAAATATGCATGGGTCTTCTTCATCCGTTCCAGgtaatttccc ... aaaattgcagGTTCTTTTACTAGATGAAGTGACAGTTGATCTTGATGTTGTGGCAAGGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttacaattaattttgtctctaactgaaatggacatcatccttgagaaaattgcagGTTCTTTTACTAGATGAAGTGACAGTTGATCTTGATGTTGTGGCAAGGATGGATTTACTTGAATTCTTCAAGGAAGAATGTGATCAG
                ctctaac  putative branch site (score: 2)
     attaattttgt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgaatctgagatctgtttatgataaacatattggtgaaatattttacaattaattttgtctctaactgaaatggacatcatccttgagaaaattgcagGTTCTTTTACTAGATGAAGTGACAGTTGATCTTGATGTTGTGGCAAGGATGGATTTACTTGAATTCTTCAAGGAAGAATGTGATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - gataaac
- - - - - - - - - - - - - - - - - - tgaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaatgga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catcatc