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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTACAATATCTAAGGACGATACTGTTATCCTTGATGGGGCTGGTGACAAGAAGGCCATTGAGGAACGGTGTGAGCAGgtccatattactttcttctcacatgttatttagaatctcctgattctttattctttttctttcttttcttctctggatgattgatctgtcgattggtttttccttcattgcgaagcaaatgccaaattttatatatttttttcatgttgtaattggattcatttggttacattgggatggcag

Basic information

species Vitis vinifera
transcript Vv05s0051g00340.t01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0051g00340.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: LOC_Os10g32550.1 (Oryza sativa), 5'ss of exon 12
GTTACAATATCTAAGGACGATACTGTTATCCTTGATGGGGCTGGTGACAAGAAGGCCATTGAGGAACGGTGTGAGCAGgtccatattactttcttctcacatgttatttagaatctcctgattctttattctttttctttcttttcttctctggatgattgatctgtcgattggtttttccttcattgcgaagcaaatgccaaattttatatatttttttcatgttgtaattggattcatttggttacattgggatggcag
|| ||  ||||||||||||| |||||||| |||||||| ||||| ||||||||  ||||||| ||  ||  ||||||||| | ||  || ||  |       |||| |   | |    |  ||    | || |  |  ||  |   || | |  |||  ||   ||  |                                                                                            
GTAACTGTATCTAAGGACGACACTGTTATTCTTGATGGAGCTGGAGACAAGAAATCCATTGAAGAGAGGGCTGAGCAGgttcgtacaacattaattcattgcgttact---agtgcattattttgaaaatcgtggttgttgatagattatataaatg-ctgtgttgcag--------------------------------------------------------------------------------------------

upper sequence: Vv05s0051g00340.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: LOC_Os03g04970.1 (Oryza sativa), 5'ss of exon 12
GTTACAATATCTAAGGACGATACTGTTATCCTTGATGGGGCTGGTGACAAGAAGGCCATTGAGGAACGGTGTGAGCAGgtccatattactttcttctcacatgttatttagaatctcctgattctttattctttttctttcttttcttctctggatgattgatctgtcgattggtttttccttcattgcgaagcaaatgccaaattttatatatttttttcatgttgtaattggattcatttggttacattgggatggcag
|||||| |||||||||| || || || ||||||||||| ||||| || |||||||||||||| ||  |   ||||||||| |||  ||   |  | |    |   ||  ||   |   ||  ||  ||   ||||    |  |  |  | ||| |  |||  | |  | |  |                                                                                        
GTTACAGTATCTAAGGATGACACAGTCATCCTTGATGGAGCTGGAGATAAGAAGGCCATTGAAGAGAGAGCTGAGCAGgttcattctatgctagtttacttttacatgaagccacgtgtgtctcactaaatttttctaatggtgacaccactgtaaaattctttttccaacag----------------------------------------------------------------------------------------

upper sequence: Vv05s0051g00340.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: AT3G23990.1 (Arabidopsis thaliana), 5'ss of exon 10
GTTACAATATCTAAGGACGATACTGTTATCCTTGATGGGGCTGGTGACAAGAAGGCCATTGAGGAACGGTGTGAGCAGgtccatattactttcttctcacatgttatttagaatctcctgattctttattctttttctttcttttcttctctggatgattgatctgtcgattggtttttccttcattgcgaagcaaatgccaaattttatatatttttttcatgttgtaattggattcatttggttacattgggatggcag
|||||| | || |||||||| |||||||| |||||||||||||| |||||||| |  ||||||||| | ||||| |||||       | ||| |   |  ||    |    |||    || ||  | ||    ||| | |         | || |   |      || | || ||| |   | | | |    |||| |  ||                                                           
GTTACAGTCTCCAAGGACGACACTGTTATTCTTGATGGGGCTGGCGACAAGAAAGGAATTGAGGAAAGATGTGAACAGgt-------aatttttaaccttataccctgataaat----tggttagtaataaaatttgtatgcaagaaattatgaagtgtatgaaagtag-ttcgttctaattgcttggtattgcaactaacag----------------------------------------------------------

upper sequence: Vv05s0051g00340.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: AT2G33210.1 (Arabidopsis thaliana), 5'ss of exon 11
GTTACAATATCTAAGGACGATACTGTTATCCTTGATGGGGCTGGTGACAAGAAGGCCATTGAGGAACGGTGTGAGCAGgtccatattactttcttctcacatgttatttagaatctcctgattctttattctttttctttcttttcttctctggatgattgatctgtcgattggtttttccttcattgcgaagcaaatgccaaattttatatatttttttcatgttgtaattggattcatttggttacattgggatggcag
|| ||  |||| || || ||||||||| | || |||||||||||||||||| | || |||| |||||| ||||| |||||     |   |||   ||    | | ||||||    ||    |    ||| | ||| |  | |||||      | |   || || |||   |   |||||  |  |   || ||                                                                    
GTAACGGTATCCAAAGATGATACTGTTGTTCTCGATGGGGCTGGTGACAAGCAAGCAATTGGGGAACGATGTGAACAGgttagcgt-gtttttcgcttttttatcatttagtggttc--agtgtcatatacctttgcccttttttccaactggtagttttaatatgttt-tgaatttttattaaaccacgcag--------------------------------------------------------------------

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|110686767|gb|EE064783.1|EE064783
EST:     TCCTTGATGGGGCTGGTGACNAGAAGGCCATTGAGGAACGGTGTGAGCAG                         ATTANGTCAGCCATTGAATCGAGCACTTCTGATTATGACAAGGAAAAGTTT
genomic: TCCTTGATGGGGCTGGTGACAAGAAGGCCATTGAGGAACGGTGTGAGCAGgtccatatta ... gggatggcagATTAGGTCAGCCATTGAATTGAGCACTTCTGATTATGACAAGGAAAAGTT-
EST: gi|34542276|gb|CF510508.1|CF510508
EST:     TCCTTGATGGGGCTGGTGACAAGAAGGCCATTGAGGAACGGTGTGAGCAG                         ATTAGGTCAGCCATTGAATCGAGCACTTCTGATTATGACAAGGAAAAGTTG
genomic: TCCTTGATGGGGCTGGTGACAAGAAGGCCATTGAGGAACGGTGTGAGCAGgtccatatta ... gggatggcagATTAGGTCAGCCATTGAATTGAGCACTTCTGATTATGACAAGGAAAAGTTG
EST: gi|110691710|gb|EE070124.1|EE070124
EST:     TCCTTGATGGGGCTGGTGACAN-AAGGCCATTGAGGAACGGTGTGACCAG                         ATAAG-TCACCCATTGAATCCAGCACTTCTGAT-ATGAAAAGGAAAAGTTG
genomic: TCCTTGATGGGGCTGGTGACAAGAAGGCCATTGAGGAACGGTGTGAGCAGgtccatatta ... gggatggcagATTAGGTCAGCCATTGAATTGAGCACTTCTGATTATGACAAGGAAAAGTTG
EST: gi|71873742|gb|DT022797.1|DT022797
EST:     TCCTTGATGGGGCTGGTGACAAGAAGGCCATTGAGGAACGGTGTGAGCAG                         ATTAGGTCAGCCATTGAAT
genomic: TCCTTGATGGGGCTGGTGACAAGAAGGCCATTGAGGAACGGTGTGAGCAGgtccatatta ... gggatggcagATTAGGTCAGCCATTGAAT
EST: gi|77586617|gb|DV222437.1|DV222437
EST:     TCCTTGATGGGGCTGGTGACAAGAAGGCCATTGAGGAACGGTGTGAGCAG                         ATTAGGTCAGCCATTGAATCGAGCACTTCTGATTATGACAAGGAAAAGTTG
genomic: TCCTTGATGGGGCTGGTGACAAGAAGGCCATTGAGGAACGGTGTGAGCAGgtccatatta ... gggatggcagATTAGGTCAGCCATTGAATTGAGCACTTCTGATTATGACAAGGAAAAGTTG
EST: gi|110700181|gb|EE077929.1|EE077929
EST:     TCCTTGATGGGGCTGGTGACAAGAAGGCCATTGAGGAACGGTGTGAGCAG                         ATTAGGTCAGCCATTGAATTGAGCTCTTCTGATTATGACAAGGAAAAGTTG
genomic: TCCTTGATGGGGCTGGTGACAAGAAGGCCATTGAGGAACGGTGTGAGCAGgtccatatta ... gggatggcagATTAGGTCAGCCATTGAATTGAGCACTTCTGATTATGACAAGGAAAAGTTG
EST: gi|77587495|gb|DV222914.1|DV222914
EST:     TCCTTGATGGGGCTGGTGACAAGAAGGCCATTGAGGAACGGTGTGAGCAG                         ATTAGGTCAGCCATTGAATCGAGCACTTCTGATTATGACAAGGAAAAGTTG
genomic: TCCTTGATGGGGCTGGTGACAAGAAGGCCATTGAGGAACGGTGTGAGCAGgtccatatta ... gggatggcagATTAGGTCAGCCATTGAATTGAGCACTTCTGATTATGACAAGGAAAAGTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTACAATATCTAAGGACGATACTGTTATCCTTGATGGGGCTGGTGACAAGAAGGCCATTGAGGAACGGTGTGAGCAGgtccatattactttcttctcacatgttatttagaatctcctgattctttattctttttctttcttttcttctctggatgattgatctgtcgattggtttttccttcattgcgaagcaaatgccaaattttatatatttttttcatgttgtaattggattcatttggttacattgggatggcag

- - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG