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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagagctctctctctctctctcattctttttctttgggatcccattttttgttttcccatttcctgattgggggctattgttttgactgtttattcaagATGCGAGTCTCAGCAATCATCTCTAATGCTCCTTACCTACTGAACGTGGACTGTGATCACTATATAAACAACAGTAAGGCCCTTCGTGAAGCCATGTGCT

Basic information

species Vitis vinifera
transcript Vv18s0072g00370.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0072g00370.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA10G36790.1 (Glycine max), 3'ss of exon 9
gtagagctctctctctctctctcattctttttctttgggatcccattttttgttttcccatttc-ctgattgggggctat--tgttttgactgtttat---tcaagATGCGAGTCTCAGCAATCATCTCTAATGCTCCTTACCTACTGAACGTGGACTGTGATCACTATATAAACAACAGTAAGGCCCTTCGTGAAGCCATGTGCT
||||||  |  || ||||  || |       | | |   ||  |   || ||| || ||||||  ||||        |||  ||| ||| ||| |||    ||||| |||||||||||||| |||| || ||||||||||||||||| || || || ||||||||||| ||||||||||| || || |||||||||||||||||||
gtagagtcccttccctcttgcttacataaact-tctaatatttc---ttgtgtctttccattttactgaccaatttttatgatgtgttggctgattaattgtcaagGTGCGAGTCTCAGCAGTCATATCAAATGCTCCTTACCTACTCAATGTTGATTGTGATCACTACATAAACAACAGCAAAGCACTTCGTGAAGCCATGTGCT

upper sequence: Vv18s0072g00370.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA16G28080.1 (Glycine max), 3'ss of exon 8
gtagagc-tctctctctctctctcattc---tttttctttgggatcccattttttgttttcccatttcctgattgggggctattgttttgactgtttattcaagATGCGAGTCTCAGCAATCATCTCTAATGCTCCTTACCTACTGAACGTGGACTGTGATCACTATATAAACAACAGTAAGGCCCTTCGTGAAGCCATGTGCT
||||||  ||  |||| |  |   |||     ||||||  |   ||   | | |   ||| || |  | |  ||       ||||||  || || || |  ||| || ||||||||||||| ||| | |||||||| ||  ||||||| || || ||||||||||| ||||| |||||||||||||||||||||||||||||||
gtagagtgtccttctcacaataaaattgaaaattttctcagttttcttctgtctccattttccttaccatttttctaatgcattgtt--gattgattgtg-aagGTGAGAGTCTCAGCAATAATCACCAATGCTCCCTATGTACTGAATGTTGATTGTGATCACTACATAAATAACAGTAAGGCCCTTCGTGAAGCCATGTGCT

upper sequence: Vv18s0072g00370.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA02G08920.1 (Glycine max), 3'ss of exon 9
gtagagc-tctctctctctctctcattctttttctttgggatcccattttttgttttcccatttcctgattgggggctattgttttgactgtttattcaagATGCGAGTCTCAGCAATCATCTCTAATGCTCCTTACCTACTGAACGTGGACTGTGATCACTATATAAACAACAGTAAGGCCCTTCGTGAAGCCATGTGCT
||||||  ||  |||| || |   | |    ||  |  |  | |   ||| |   ||    || ||   ||      |  | | |||| || || |  ||| || ||||||| ||||| ||| | |||||||||||  ||||||| || || ||||||||||| ||||| |||||||||||||||||||||||||||||||
gtagagtgtccttctcactataaaactgaactttctcagttttcttctttctccatttttcttaccatttttctaa-tgctttgttgattgattgtg-aagGTGAGAGTCTCGGCAATAATCACCAATGCTCCTTATGTACTGAATGTTGATTGTGATCACTACATAAATAACAGTAAGGCCCTTCGTGAAGCCATGTGCT

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|351019334|gb|FQ429494.1|FQ429494
EST:     AGAGACCGGGATTTGATCACCACAAAAAAGCTGGGGCAATGAATGCTTTG                         ATGCGAGTCTCAGCAATCATCTCTAATGCTCCTTACCTACTGAACGTGGAC
genomic: AGAGACCGGGATTTGATCACCACAAAAAAGCTGGGGCAATGAATGCTTTGgtagagctct ... tttattcaagATGCGAGTCTCAGCAATCATCTCTAATGCTCCTTACCTACTGAACGTGGAC
EST: gi|351026053|gb|FQ428065.1|FQ428065
EST:     AGAGACCGGGATTTGATCACCACAAAAAAGCTGGGGCAATGAATGCTTTG                         ATGCGAGTCTCAGCAATCATCTCTAATGCTCCTTACCTACTGAACGTGGAC
genomic: AGAGACCGGGATTTGATCACCACAAAAAAGCTGGGGCAATGAATGCTTTGgtagagctct ... tttattcaagATGCGAGTCTCAGCAATCATCTCTAATGCTCCTTACCTACTGAACGTGGAC
EST: gi|351025958|gb|FQ427970.1|FQ427970
EST:     AGAGACCGGGATTTGATCACCACAAAAAAGCTGGGGCAATGAATGCTTTG                         ATGCGAGTCTCAGCAATCATCTCTAACGCTCCTTACCTACTGAACGTGGAC
genomic: AGAGACCGGGATTTGATCACCACAAAAAAGCTGGGGCAATGAATGCTTTGgtagagctct ... tttattcaagATGCGAGTCTCAGCAATCATCTCTAATGCTCCTTACCTACTGAACGTGGAC
EST: gi|351024090|gb|FQ423513.1|FQ423513
EST:     AGAGACCGGGATTTGATCACCACAAAAAAGCTGGGGCAATGAATGCTTTG                         ATGCGAGTCTCAGCAATCATCTCTAATGCTCCTTACCTACTGAACGTGGAC
genomic: AGAGACCGGGATTTGATCACCACAAAAAAGCTGGGGCAATGAATGCTTTGgtagagctct ... tttattcaagATGCGAGTCTCAGCAATCATCTCTAATGCTCCTTACCTACTGAACGTGGAC
EST: gi|349826424|gb|FQ418515.1|FQ418515
EST:     AGAGACCGGGATTTGATCACCACAAAAAAGCTGGGGCAATGAATGCTTTG                         ATGCGAGTCTCAGCAATCATCTCTAATGCTCCTTACCTACTGAACGTGGAC
genomic: AGAGACCGGGATTTGATCACCACAAAAAAGCTGGGGCAATGAATGCTTTGgtagagctct ... tttattcaagATGCGAGTCTCAGCAATCATCTCTAATGCTCCTTACCTACTGAACGTGGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttgttttcccatttcctgattgggggctattgttttgactgtttattcaagATGCGAGTCTCAGCAATCATCTCTAATGCTCCTTACCTACTGAACGTGGACTGTGATCACTATATAAACAACAGTAAGGCCCTTCGTGAAGCCATGTGCT
                                    ttttgac  putative branch site (score: 3)
                                             tttattc  putative PPT
                               tattgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagagctctctctctctctctcattctttttctttgggatcccattttttgttttcccatttcctgattgggggctattgttttgactgtttattcaagATGCGAGTCTCAGCAATCATCTCTAATGCTCCTTACCTACTGAACGTGGACTGTGATCACTATATAAACAACAGTAAGGCCCTTCGTGAAGCCATGTGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC