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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGGTCCAAGATTTTGTTTGAATCCCATCAAGATATTTGGTGGCAGCTTTGGAGGCCCAACATTATATGAGAATCCATTTTACATATCACCGAATGAGgttataaactccttcatgttcctgtagaatgtttccatttcgtaaattttgtttgatgttctggggatcctgatgtgtgcattgatggtagaggttactgcagctccttttctctgttacaatagtcttactggtgcattgttcttatgctatttatgcttccag

Basic information

species Vitis vinifera
transcript Vv07s0005g04550.t01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0005g04550.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA08G28320.1 (Glycine max), 5'ss of exon 8
GTTGGTCCAAGATTTTGTTTGAATCCCATCAAGATATTTGGTGGCAGCTTTGGAGGCCCAACATTATATGAGAATCCATTTTACATATCACCGAATGAGgttataaactccttcatgttcctgtagaatgtttccatttcgtaaattttgt-ttgatgttctggggatcctgatgtgtgcattgatggtagaggttactgcagctccttttctctgttacaatagtcttactggtgcattgttcttatgctatttatgcttccag
||||||||  |||| || ||||| || || || |||||||||||||| |||||||||||||| ||||||||||||||  | ||  | ||||| ||| |||| |    |   |  || ||||      || ||   |||||  ||  |||    |||   | |    |  ||   ||    |||| | |  ||  |   |  ||                                                              
GTTGGTCCGCGATTCTGCTTGAACCCAATTAAAATATTTGGTGGCAGTTTTGGAGGCCCAACTTTATATGAGAATCCGCTCTATGTGTCACCAAATCAGgt-actggccaatatattttccatctatat-ttataatttcccaagctttccactgacaatata---actctatcgt---tattggttgctga--tccttatag--------------------------------------------------------------

upper sequence: Vv07s0005g04550.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA18G51310.1 (Glycine max), 5'ss of exon 7
GTTGGTCCAAGATTTTGTTTGAATCCCATCAAGATATTTGGTGGCAGCTTTGGAGGCCCAACATTATATGAGAATCCATTTTACATATCACCGAATGAGgttataaactccttcatgttcctgtagaatgtttccatttcgtaaattttgtttgatgttctggggatcctgatgtgtgcattgatggtagaggttactgcagctccttttctctgttacaatagtcttactggtgcattgttcttatgctatttatgcttccag
|| || ||  |||| || ||||| || || || |||||||||||||| |||||||||||||| ||||| ||||||||| | ||  | ||||||||| |||| |   ||   |  || ||||      || ||   |||||  ||  |||     |  ||||    ||     | |   ||||| | |  |  |||  |  ||                                                              
GTCGGCCCGCGATTCTGCTTGAACCCAATTAAAATATTTGGTGGCAGTTTTGGAGGCCCAACTTTATACGAGAATCCACTCTATGTGTCACCGAATCAGgt-acttaccaatatattttccatctatat-ttataatttcccaagctttcc---actttctaactat----gtatcatcattggttgctg--gttcttatag--------------------------------------------------------------

upper sequence: Vv07s0005g04550.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA02G12700.2 (Glycine max), 5'ss of exon 9
GTTGGTCCAAGATTTTGTTTGAATCCCATCAAGATATTTGGTGGCAGCTTTGGAGGCCCAACATTATATGAGAATCCATTTTACATATCACCGAATGAGgttataaactccttcatgttcctgtagaatgtttccatttcgtaaattttgtttgatgttctggggatcctgatgtgtgcattgatggtagaggttactgcagctccttttctctgttacaatagtcttactggtgcattgttcttatgctatttatgcttccag
||||||||  |||| || ||||| || || || ||||||||||| || |||||||| ||||| ||||||||||||||||| ||  | || || ||| |||| | | ||   |  || || |  |  |   ||   |||||  || |||| |        |||   ||    || |   ||||| | || |  |||  | |||                                                              
GTTGGTCCGCGATTCTGCTTGAACCCAATTAAAATATTTGGTGGAAGTTTTGGAGGGCCAACTTTATATGAGAATCCATTCTATGTGTCCCCAAATCAGgtaa-agaccaataaat-ttaccatctatacttataatttcccaagttttcta-------ctgaaaataacaatatcatcattggttgttg--gttcttacag--------------------------------------------------------------

upper sequence: Vv07s0005g04550.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: AT3G15460.1 (Arabidopsis thaliana), 5'ss of exon 7
GTTGGTCCAAGATTTTGTTTGAATCCCATCAAGATATTTGGTGGCAGCTTTGGAGGCCCAACATTATATGAGAATCCATTTTACATATCACCGAATGAGgttataaactccttcatgttcctgtagaatgtttccatttcgtaaattttgtttgatgttctggggatcctgatgtgtgcattgatggtagaggttactgcagctccttttctctgttacaatagtcttactggtgcattgttcttatgctatttatgcttccag
||||||||||| |||||||| ||||| || ||||||||||| ||||||||||||||  ||||  | || ||||| ||||| ||  |||| || ||  ||||  |    || |  ||   |   | ||  | |  |||| | || || |  ||   |||     |  | || || | | |     |  |     |||                                                                    
GTTGGTCCAAGGTTTTGTTTAAATCCAATTAAGATATTTGGAGGCAGCTTTGGAGGTACAACGCTTTACGAGAACCCATTCTATGTATCTCCAAACCAGgtacttggttcttctataagcaacttgatagatcacattgc-tatatatgattatctgtc---agagttctcatatattccaatttcctgccttttag-------------------------------------------------------------------

upper sequence: Vv07s0005g04550.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: AT1G52930.1 (Arabidopsis thaliana), 5'ss of exon 6
GTTGGTCCAAGATTTTGTTTGAATCCCATCAAGATATTTGGTGGCAGCTTTGGAGGCCCAACATTATATGAGAATCCATTTTACATATCACCGAATGAGgttataaactccttcatgttcctgtagaatgtttccatttcgtaaattttgtttgatgttctggggatcctgatgtgtgcattgatggtagaggttactgcagctccttttctctgttacaatagtcttactggtgcattgttcttatgctatttatgcttccag
||||||||||| |||||| ||||||| ||||||||||| |  |||||||||||||| || ||  | |||||||| || || ||| |||| || ||  ||||       || || ||    || |    | ||| ||      | || |      |||       || | |    |  |||   ||  || |  | | || |  |                                                            
GTTGGTCCAAGGTTTTGTCTGAATCCAATCAAGATATTCGCGGGCAGCTTTGGAGGTCCTACTCTTTATGAGAACCCGTTATACGTATCTCCAAACCAGgta------tcattgattaatctct----tatttgcaagcaaaagatataaccaaatgaatcttagaactttccttaagca--aattttaaa--tcaatgtatttag----------------------------------------------------------

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|34544827|gb|CF513059.1|CF513059
EST:     TTGGAGGCCCAACATTATATGAGAATCCATTTTACATATCACCGAATGAG                         ATTCGAGCACTAAAG
genomic: TTGGAGGCCCAACATTATATGAGAATCCATTTTACATATCACCGAATGAGgttataaact ... atgcttccagATTCGAGCACTAAAG
EST: gi|110417096|gb|EC983122.1|EC983122
EST:     TTGGAGGCCCAACATTATATGAGAATCCATTTTACATATCACCGAATGAG                         ATTCGAGCACTAAAGAAGAGGAAAGCGGCTGGCAAGTATGCAAAGAAAGTG
genomic: TTGGAGGCCCAACATTATATGAGAATCCATTTTACATATCACCGAATGAGgttataaact ... atgcttccagATTCGAGCACTAAAGAAGAGGAAGGCGGCTGGCAAGTATGCAAAGAAAGTG
EST: gi|30329834|gb|CD013096.1|CD013096
EST:     TTGGAGGCCCAACATTATATGAGAATCCATTTTACATATCACCGAATGAG                         ATTCGAGCACTAAAGAAGAGGAAGGCGGCTGGCAAGTATGCAAAGAAAGTG
genomic: TTGGAGGCCCAACATTATATGAGAATCCATTTTACATATCACCGAATGAGgttataaact ... atgcttccagATTCGAGCACTAAAGAAGAGGAAGGCGGCTGGCAAGTATGCAAAGAAAGTG
EST: gi|110373531|gb|EC937775.1|EC937775
EST:     TTGGAGGCCCAACATTATATGAGAATCCATTTTACATATCACCGAATGAG                         ATTCGAGCACTAAAAAAGAGGAAGGCGGCTGGCAAGTATGCAAAGAAAGT
genomic: TTGGAGGCCCAACATTATATGAGAATCCATTTTACATATCACCGAATGAGgttataaact ... atgcttccagATTCGAGCACTAAAGAAGAGGAAGGCGGCTGGCAAGTATGCAAAGAAAGT
EST: gi|110425852|gb|EC992246.1|EC992246
EST:     TTGGAGGCCCAACATTATATGAGAATCCATTTTACATATCACCGAATGAG                         ATTCGAGCACTAAAGAAGAGGAAGGCGGCTGGCAAGTATGCAAAGAAAGTG
genomic: TTGGAGGCCCAACATTATATGAGAATCCATTTTACATATCACCGAATGAGgttataaact ... atgcttccagATTCGAGCACTAAAGAAGAGGAAGGCGGCTGGCAAGTATGCAAAGAAAGTG
EST: gi|30330375|gb|CD013637.1|CD013637
EST:     TTGGAGGCCCAACATTATATGAGAATCCATTTTACATATCACCGAATGAG                         ATTCGAGCACTAAAGAAGAGGAAGGCGGCTGGCAAGTATGCAAAGAAAGTG
genomic: TTGGAGGCCCAACATTATATGAGAATCCATTTTACATATCACCGAATGAGgttataaact ... atgcttccagATTCGAGCACTAAAGAAGAGGAAGGCGGCTGGCAAGTATGCAAAGAAAGTG
EST: gi|30252991|gb|CB970542.1|CB970542
EST:     TTGGAGGCCCAACATTATATGAGAATCCATTTTACATATCACCGAATGAG                         ATTCGAGCACTAAAGAAGAGGAAGGCGGCTGGCAAGTATGCAAAGAAAGTG
genomic: TTGGAGGCCCAACATTATATGAGAATCCATTTTACATATCACCGAATGAGgttataaact ... atgcttccagATTCGAGCACTAAAGAAGAGGAAGGCGGCTGGCAAGTATGCAAAGAAAGTG
EST: gi|110685111|gb|EE063162.1|EE063162
EST:     TTGGAGGCCCCACATTATATGAGAATCCATTTTACATATCACCGAATGAG                         ATTCGAGCACTAA
genomic: TTGGAGGCCCAACATTATATGAGAATCCATTTTACATATCACCGAATGAGgttataaact ... atgcttccagATTCGAGCACTAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGGTCCAAGATTTTGTTTGAATCCCATCAAGATATTTGGTGGCAGCTTTGGAGGCCCAACATTATATGAGAATCCATTTTACATATCACCGAATGAGgttataaactccttcatgttcctgtagaatgtttccatttcgtaaattttgtttgatgttctggggatcctgatgtgtgcattgatggtagaggttactgcagctccttttctctgttacaatagtcttactggtgcattgttcttatgctatttatgcttccag

- - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG