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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttaaatgcgatacatgtgtaagattgtaatatttgagtgtgtattgctgttatcctttctattcatataactaaagatttataatctattttgttcagTTCTAAGGATGGAGCAAGACATCGAGAAGTTCATTCATGATCCTACTCAACAGCAACTAGAGTTTCAACAGTTGCCTACCTCCTATCTACGGTTGGCTGC

Basic information

species Vitis vinifera
transcript Vv13s0106g00640.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0106g00640.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os09g39462.1 (Oryza sativa), 3'ss of exon 1
----atttaaatgcgatacatgtgtaagattgtaatatttgagtgtgtattgctgttatcctttctattcatataactaaagatttataatctattttgttcagTTCTAAGGATGGAGCAAGACATCGAGAAGTTCATTCATGATCCTACTCAACAGCAACTAGAGTTTCAACAGTTGCCTACCTCCTATCTACGGTTGGCTGC
     ||  |     ||   ||  ||   || |||        |||   |||       | |      |  ||      |  | |  ||    ||| |    ||| ||||||||||||||||||||   ||||||||||||||| ||||| ||     |  | || || ||     | ||||| || || || ||  | |||||
tactgttgtatcttcatgattgactacctttctaactacaagttgtaagttgagaaatgcttcgtggcttgtaccttacagcagtcttatctcattgt----agTGCTAAGGATGGAGCAAGACATTTTGAAGTTCATTCATGACCCTACGCAGACAGAGTTTGACTTCCATGGTCTTCCTACTTCTTACCTGCGTCTTGCTGC

upper sequence: Vv13s0106g00640.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA10G34810.3 (Glycine max), 3'ss of exon 1
-----atttaaatgcgatacatgtgtaagattgtaatatttgagtgtgtattgctgttatcctttctattcatataactaaagatttataatctattttgttcagTTCTAAGGATGGAGCAAGACATCGAGAAGTTCATTCATGATCCTACTCAACAGCAACTAGAGTTTCAACAGTTGCCTACCTCCTATCTACGGTTGGCTGC
     ||||  |||  ||   | |   ||||   |  |  ||  ||| | ||    | ||   |  |   ||  | | ||| | ||  |||| |  |   ||||||  | ||||||||||||||  | ||||| || |||| |||||||||||||||||| || || ||| | ||| | || || |||||| || || |||| ||
gcattatttgtatgttatttgttt---agatctaataagctgtatgt-tcttagaatgatatatcttgcccaactgattaaggcttc-taatttgatgaattcagTCTTGAGGATGGAGCAAGATGTTGAGAATTTTATTCGTGATCCTACTCAACAGCAGCTTGAATTTAAGCAGCTTCCAACATCCTATTTAAGGCTGGCCGC

upper sequence: Vv13s0106g00640.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA20G32800.2 (Glycine max), 3'ss of exon 1
-----atttaaatgcgatacatgtgtaagattgtaatatttgagtgtgtattgctgttatcctttctattcatataactaaagatttataatctattttgttcagTTCTAAGGATGGAGCAAGACATCGAGAAGTTCATTCATGATCCTACTCAACAGCAACTAGAGTTTCAACAGTTGCCTACCTCCTATCTACGGTTGGCTGC
     ||||  |||  ||   | |   |  |  |||  |||  ||   ||    ||||||   ||     ||  | | ||| | ||  |||| |  |   ||||||  | ||||||||||||||  | ||||| || |||| |||||||||||||||||| || || ||| | ||| | || || |||||| || || |||||||
gcattatttgtatgttatttgttta-gatctaataagctttatgttcttag-attgttatatctt--gcccaactgattaaggcttc-taatttgataaattcagTCTTGAGGATGGAGCAAGATGTTGAGAATTTTATTCGTGATCCTACTCAACAGCAGCTTGAATTTAAGCAGCTTCCAACATCCTATTTAAGGCTGGCTGC

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|352774074|gb|FQ474597.1|FQ474597
EST:     GGATCAGTTTCTTCGTGAGGCTCTGCAGAATCCGCGTGAGCGGCTGTCAA                         TTCTAAGGATGGAGCAAGACATCGAGAAGTTCATTCATGATCCTACTCAAC
genomic: GGATCAGTTTCTTCGTGAGGCTCTGCAGAATCCGCGTGAGCGGCTGTCAAgtgagttgcc ... ttttgttcagTTCTAAGGATGGAGCAAGACATCGAGAAGTTCATTCATGATCCTACTCAAC
EST: gi|352769755|gb|FQ468683.1|FQ468683
EST:     GGATCAGTTTCTTCGTGAGGCTCTGCAGAATCCGCGTGAGCGGCTGTCAA                         TTCTAAGGATGGAGCAAGACATCGAGAAGTTCATTCATGATCCTACTCAAC
genomic: GGATCAGTTTCTTCGTGAGGCTCTGCAGAATCCGCGTGAGCGGCTGTCAAgtgagttgcc ... ttttgttcagTTCTAAGGATGGAGCAAGACATCGAGAAGTTCATTCATGATCCTACTCAAC
EST: gi|352774082|gb|FQ474605.1|FQ474605
EST:     GGATCAGTTTCTTCGTGAGGCTCTGCAGAATCCGCGTGAGCGGCTGTCAA                         TTCTAAGGATGGAGCAAGACATCGAGAAGTTCATTCATGATCCTACTCAAC
genomic: GGATCAGTTTCTTCGTGAGGCTCTGCAGAATCCGCGTGAGCGGCTGTCAAgtgagttgcc ... ttttgttcagTTCTAAGGATGGAGCAAGACATCGAGAAGTTCATTCATGATCCTACTCAAC
EST: gi|352781936|gb|FQ469233.1|FQ469233
EST:     GGATCAGTTTCTTCGTGAGGCTCTGCAGAATCCGCGTGAGCGGCTGTCAA                         TTCTAAGGATGGAGCAAGACATCGAGAAGTTCATTCATGATCCTACTCAAC
genomic: GGATCAGTTTCTTCGTGAGGCTCTGCAGAATCCGCGTGAGCGGCTGTCAAgtgagttgcc ... ttttgttcagTTCTAAGGATGGAGCAAGACATCGAGAAGTTCATTCATGATCCTACTCAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgctgttatcctttctattcatataactaaagatttataatctattttgttcagTTCTAAGGATGGAGCAAGACATCGAGAAGTTCATTCATGATCCTACTCAACAGCAACTAGAGTTTCAACAGTTGCCTACCTCCTATCTACGGTTGGCTGC
                         aactaaa  putative branch site (score: 2)
                                         tctatttt  putative PPT
            tttctattcatataac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttaaatgcgatacatgtgtaagattgtaatatttgagtgtgtattgctgttatcctttctattcatataactaaagatttataatctattttgttcagTTCTAAGGATGGAGCAAGACATCGAGAAGTTCATTCATGATCCTACTCAACAGCAACTAGAGTTTCAACAGTTGCCTACCTCCTATCTACGGTTGGCTGC

- - - - - - - catgtgt
- - - - - - - - - - - - - - - - - -tgagtgt
- - - - - - - - - - - - - - - - - - - - - - attgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aactaaa