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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTACAACTACCCCAGCCCTTGCAATACCAAAAGCTATTTCTAATGCTGGCCTGAAGGCTTCTCAAATTGATTACTATGAAATAAATGAGGCTTTCGCCgtaaggatttattcttgtgcttgttatacttctaccatctcttttatcaagtaacagtttatgctaattttatgatctcatttgttttctgcag

Basic information

species Vitis vinifera
transcript Vv00s0531g00050.t01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0531g00050.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: LOC_Os09g07830.2 (Oryza sativa), 5'ss of exon 11
GTTTACAACTACCCCAGCCCTTGCAATACCAAAAGCTATTTCTAATGCTGGCCTGAAGGCTTCTCAAATTGATTACTATGAAATAAATGAGGCTTTCGCCgtaaggatttattcttgtgcttgttatacttctaccatctcttttatcaagtaacagtttatgctaatt-ttatgatctcatttgttttctgcag----------
 ||||| |||| ||| || ||||| ||||| || ||| || ||||||||||| || || ||||||   |||||||||||||||| ||||| || ||  | ||| |   ||  || | ||  | ||  |||| |    | | |||| |  | | | | ||| | | ||   || | ||   |||| ||||   |            
ATTTACCACTAGCCCGGCACTTGCCATACCTAAGGCTCTTGCTAATGCTGGCTTGGAGTCTTCTCGTGTTGATTACTATGAAATTAATGAAGCCTTTTCAgtatga--ttgatcatctg--tattcaacttattagtttttttttttgtaatcataatttgttccaaaaattctaatggtatttatttttgacttatcaatacag

upper sequence: Vv00s0531g00050.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GLYMA07G39870.2 (Glycine max), 5'ss of exon 11
GTTTACAACTACCCCAGCCCTTGCAATACCAAAAGCTATTTCTAATGCTGGCCTGAAGGCTTCTCAAATTGATTACTATGAAATAAATGAGGCTTTCGCCgtaaggatttattcttgtgcttgttatacttctaccatctcttttatcaagtaacagtttatgctaattttatgatctcatttgttttctgcag
 ||||||||| | ||  |||||||||||||||||||||| || |||||||| ||  | ||||||||||||||||| |||||||||||||| |||||  | ||||||| | |     |  | | || | ||  |             || ||| |     ||||| |||  |||  ||  | || || | |||||
ATTTACAACTGCTCCTTCCCTTGCAATACCAAAAGCTATATCAAATGCTGGTCTTGATGCTTCTCAAATTGATTATTATGAAATAAATGAAGCTTTTTCAgtaaggaataaa----gcacatattttgctcat-------------tctagtgaa----tatgccaatggtat--tccaacttcttctgtgcag

upper sequence: Vv00s0531g00050.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GLYMA17G00910.2 (Glycine max), 5'ss of exon 11
GTTTACAACTACCCCAGCCCTTGCAATACCAAAAGCTATTTCTAATGCTGGCCTGAAGGCTTCTCAAATTGATTACTATGAAATAAATGAGGCTTTCGCCgtaaggatttattcttgtgcttgttatacttctaccatctcttttatcaagtaacagtttatgctaattttatgatctcatttgttttctgcag
 ||||||||| | ||  |||||||||||||||||||||| || |||||||| ||  | ||||||||||| ||||| |||||||||||||| |||||  | ||||||| |       |  | | || | ||  |             |||||| |     |||||||||| | |  ||    || ||   |||||
ATTTACAACTGCTCCTTCCCTTGCAATACCAAAAGCTATATCAAATGCTGGTCTTGATGCTTCTCAAATAGATTATTATGAAATAAATGAAGCTTTTTCGgtaaggaata----cagcacatattttgctcat-------------tcaagtgaa----tatgctaattgtgt--tccaccttcttcaatgcag

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|30301836|gb|CB978630.1|CB978630
EST:     GCCTGAAGGCTTCTCAAATTGATTACTATGAAATAAATGAGGCTTTCGCC                         GTTGTAGCTCTTGCCAATCAAAAGTTGCTTGGTCTTGATCCT
genomic: GCCTGAAGGCTTCTCAAATTGATTACTATGAAATAAATGAGGCTTTCGCCgtaaggattt ... ttttctgcagGTTGTAGCTCTTGCCAATCAAAAGTTGCTTGGTCTTGATCCT
EST: gi|30301768|gb|CB978562.1|CB978562
EST:     GCCTGAAGGCTTCTCAAATTGATTACTATGAAATAAATGAGGCTTTCGCC                         GTTGTAGCTCTTGCCAATCAAAAGTTGCTTGGTCTTGATCCT
genomic: GCCTGAAGGCTTCTCAAATTGATTACTATGAAATAAATGAGGCTTTCGCCgtaaggattt ... ttttctgcagGTTGTAGCTCTTGCCAATCAAAAGTTGCTTGGTCTTGATCCT
EST: gi|30329769|gb|CD013031.1|CD013031
EST:     GCCTGAAGGCTTCTCAAATTGATTACTATGAAATAAATGAGGCTTTCGCC                         GTTGTAGCTCTTGCCAATCAAAAGTTGCTTGGTCTTGATCCT
genomic: GCCTGAAGGCTTCTCAAATTGATTACTATGAAATAAATGAGGCTTTCGCCgtaaggattt ... ttttctgcagGTTGTAGCTCTTGCCAATCAAAAGTTGCTTGGTCTTGATCCT
EST: gi|34362568|gb|CF404153.1|CF404153
EST:     GCCTGAAGGCTTCTCAAATTGATTACTATGAAATAAATGAGGCTTTCGCC                         GTTGTAGCTCTTGCCAATCAAAAGTTGCTTGGTCTTGATCCT
genomic: GCCTGAAGGCTTCTCAAATTGATTACTATGAAATAAATGAGGCTTTCGCCgtaaggattt ... ttttctgcagGTTGTAGCTCTTGCCAATCAAAAGTTGCTTGGTCTTGATCCT
EST: gi|110358833|gb|EC923335.1|EC923335
EST:     GCCTGAAGGCTTCTCAAATTGATTACTATGAAATAAATGAGGCTTTCGCC                         GTTGTAGCTCTTGCCAATCAAAAGTTGCTTGGTCTTGATCCT
genomic: GCCTGAAGGCTTCTCAAATTGATTACTATGAAATAAATGAGGCTTTCGCCgtaaggattt ... ttttctgcagGTTGTAGCTCTTGCCAATCAAAAGTTGCTTGGTCTTGATCCT
EST: gi|110381509|gb|EC934651.1|EC934651
EST:     GCCTGAAGGCTTCTCAAATTGATTACTATGAAATAAATGAGGCTTTCGCC                         GTTGTAGCTCTTGCCAATCAAAAGTTGCTTGGTCTTGATCCT
genomic: GCCTGAAGGCTTCTCAAATTGATTACTATGAAATAAATGAGGCTTTCGCCgtaaggattt ... ttttctgcagGTTGTAGCTCTTGCCAATCAAAAGTTGCTTGGTCTTGATCCT
EST: gi|30298600|gb|CB975394.1|CB975394
EST:     GCCTGAAGGCTCCTCAAATTGATTACTATGAAATAAATGAGGCTTTCGCC                         GTTGTAGCTCTTGCCAATCAAAAGTTGCTTGGTCTTGATCCT
genomic: GCCTGAAGGCTTCTCAAATTGATTACTATGAAATAAATGAGGCTTTCGCCgtaaggattt ... ttttctgcagGTTGTAGCTCTTGCCAATCAAAAGTTGCTTGGTCTTGATCCT
EST: gi|110376548|gb|EC941608.1|EC941608
EST:     GCCTGAAGGCTTCTCAAATTGATTACTATGAAATAAATGAGGCTTTCGCC                         GTTGTAGCTCTTGCCAATCAAAAGTTGCTTGGTCTTGATCCT
genomic: GCCTGAAGGCTTCTCAAATTGATTACTATGAAATAAATGAGGCTTTCGCCgtaaggattt ... ttttctgcagGTTGTAGCTCTTGCCAATCAAAAGTTGCTTGGTCTTGATCCT
EST: gi|27585769|gb|CB008464.1|CB008464
EST:     GCCTGAAGGCTTCTCAAATTGATTACTATGAAATAAATGAGGCTTTCGCC                         GTTGTAGCTCTTGCCAATCAAAAGTTGCTTGGTCTTGATCCT
genomic: GCCTGAAGGCTTCTCAAATTGATTACTATGAAATAAATGAGGCTTTCGCCgtaaggattt ... ttttctgcagGTTGTAGCTCTTGCCAATCAAAAGTTGCTTGGTCTTGATCCT
EST: gi|110378421|gb|EC943552.1|EC943552
EST:     GCCTGAAGGCTTCTCAAATTGATTACTATGAAATAAATGAGGCTTTCGCC                         GTTGTAGCTCTTGCCAATCAAAAGTTGCTTGGTCTTGATCCT
genomic: GCCTGAAGGCTTCTCAAATTGATTACTATGAAATAAATGAGGCTTTCGCCgtaaggattt ... ttttctgcagGTTGTAGCTCTTGCCAATCAAAAGTTGCTTGGTCTTGATCCT
EST: gi|110395476|gb|EC961142.1|EC961142
EST:     GCCTGAAGGCTTCTCAAATTGATTACTATGAAATAAATGAGGCTTTCGCC                         GTTGTAGCTCTTGCCAATCAAAAGTTGCTTGGTCTTGATCCT
genomic: GCCTGAAGGCTTCTCAAATTGATTACTATGAAATAAATGAGGCTTTCGCCgtaaggattt ... ttttctgcagGTTGTAGCTCTTGCCAATCAAAAGTTGCTTGGTCTTGATCCT
EST: gi|110361851|gb|EC925352.1|EC925352
EST:     GCCTGAAGGCTTCTCAAATTGATTACTATGAAATAAATGAGGCTTTCGCC                         GTTGTAGCTCTTGCCAATCAAAAGTTGCTTGGTCTTGATCCT
genomic: GCCTGAAGGCTTCTCAAATTGATTACTATGAAATAAATGAGGCTTTCGCCgtaaggattt ... ttttctgcagGTTGTAGCTCTTGCCAATCAAAAGTTGCTTGGTCTTGATCCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTACAACTACCCCAGCCCTTGCAATACCAAAAGCTATTTCTAATGCTGGCCTGAAGGCTTCTCAAATTGATTACTATGAAATAAATGAGGCTTTCGCCgtaaggatttattcttgtgcttgttatacttctaccatctcttttatcaagtaacagtttatgctaattttatgatctcatttgttttctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG