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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAACATGGTTGGGACACTAATTTATATGGCACCTGAAATATTGAGGAAGGAGATACATACTGAAAAATCAGATGTATACAGTTTTGGAGTATCAATTAAgtaagaatcttgagcaagttgaggatttgtgctatataacttcaatgatttccgatatcttgactcaagggaaaattaaaattcagttacttgctagtat...

Basic information

species Vitis vinifera
transcript Vv08s0040g00760.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0040g00760.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: LOC_Os01g36080.4 (Oryza sativa), 5'ss of exon 4
AGAACATGGTTGGGACACTAATTTATATGGCACCTGAAATATTGAGGAAGGAGATACATACTGAAAAATCAGATGTATACAGTTTTGGAGTATCAATTAAgtaagaatcttgagcaagttgaggatttgtgctatataacttcaatgatttccgatat---cttgact-caagggaaaattaaaattcagttacttgctagtat
||||||||||||||||| |||| || |||||||| ||||| ||||| ||||| |||||||| || |||||||||||||| || |||| | |||| || |||||||    ||       |||    |   |||  | |  | |||   | |||  || |   ||  | | |  | ||||||     |    || |||| | ||  
AGAACATGGTTGGGACATTAATATACATGGCACCAGAAATTTTGAGAAAGGACATACATACAGAGAAATCAGATGTATATAGCTTTGCAATATCTATCAAgtaagccatttctctc--ttggtattaactgcagtttggcctcatatacttcaaatgtgtactccattgcctgagaaaatacgtttgtgttttcttggtggt--
















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|349826751|gb|FQ418842.1|FQ418842
EST:     GAGATACATACTGAAAAATCAGATGTATACAGTTTTGGAGTATCAATTAA                         TGAGCTACTTACTGGTGTTGTGCCATATACTGATCTTCGAGCAGAAGCTCA
genomic: GAGATACATACTGAAAAATCAGATGTATACAGTTTTGGAGTATCAATTAAgtaagaatct ... catattgcagTGAGCTACTTACTGGTGTTGTGCCATATACTGATCTTCGAGCAGAAGCTCA
EST: gi|351033000|gb|FQ461889.1|FQ461889
EST:     GAGATACATACTGAAAAATCAGATGTATACAGTTTTGGAGTATCAATTAA                         TGAGCTACTTACTGGTGTTGTGCCATATACTGATCTTCGAGCAGAAGCTCA
genomic: GAGATACATACTGAAAAATCAGATGTATACAGTTTTGGAGTATCAATTAAgtaagaatct ... catattgcagTGAGCTACTTACTGGTGTTGTGCCATATACTGATCTTCGAGCAGAAGCTCA
EST: gi|351051800|gb|FQ455214.1|FQ455214
EST:     GAGATACATACTGAAAAATCAGATGTATACAGTTTTGGAGTATCAATTAA                         TGAGCTACTTACTGGTGTTGTGCCATATACTGATCTTCGAGCAGAAGCTCA
genomic: GAGATACATACTGAAAAATCAGATGTATACAGTTTTGGAGTATCAATTAAgtaagaatct ... catattgcagTGAGCTACTTACTGGTGTTGTGCCATATACTGATCTTCGAGCAGAAGCTCA
EST: gi|349827660|gb|FQ422528.1|FQ422528
EST:     GAGATACATACTGAAAAATCAGATGTATACAGTTTTGGAGTATCAATTAA                         TGAGCTACTTACTGGTGTTGTGCCATATACTGATCTTCGAGCAGAAGCTCA
genomic: GAGATACATACTGAAAAATCAGATGTATACAGTTTTGGAGTATCAATTAAgtaagaatct ... catattgcagTGAGCTACTTACTGGTGTTGTGCCATATACTGATCTTCGAGCAGAAGCTCA
EST: gi|349829925|gb|FQ422238.1|FQ422238
EST:     GAGATACATACTGAAAAATCAGATGTATACAGTTTTGGAGTATCAATTAA                         TGAGCTACTTACTGGTGTTGTGCCATATACTGATCTTCGAGCAGAAGCTCA
genomic: GAGATACATACTGAAAAATCAGATGTATACAGTTTTGGAGTATCAATTAAgtaagaatct ... catattgcagTGAGCTACTTACTGGTGTTGTGCCATATACTGATCTTCGAGCAGAAGCTCA
EST: gi|351039168|gb|FQ457843.1|FQ457843
EST:     GAGATACATACTGAAAAATCAGATGTATACAGTTTTGGAGTATCAATTAA                         TGAGCTACTTACTGGTGTTGTGCCATATACTGATCTTCGAGCAGAAGCTCA
genomic: GAGATACATACTGAAAAATCAGATGTATACAGTTTTGGAGTATCAATTAAgtaagaatct ... catattgcagTGAGCTACTTACTGGTGTTGTGCCATATACTGATCTTCGAGCAGAAGCTCA
EST: gi|351025853|gb|FQ427865.1|FQ427865
EST:     GAGATACATACTGAAAAATCAGATGTATACAGTTTTGGAGTATCAATTAA                         TGAGCTACTTACTGGTGTTGTGCCATATACTGATCTTCGAGCAGAAGCTCA
genomic: GAGATACATACTGAAAAATCAGATGTATACAGTTTTGGAGTATCAATTAAgtaagaatct ... catattgcagTGAGCTACTTACTGGTGTTGTGCCATATACTGATCTTCGAGCAGAAGCTCA
EST: gi|351019117|gb|FQ429277.1|FQ429277
EST:     GAGATACATACTGAAAAATCAGATGTATACAGTTTTGGAGTATCAATTAA                         TGAGCTACTTACTGGTGTTGTGCCATATACTGATCTTCGAGCAGAAGCTCA
genomic: GAGATACATACTGAAAAATCAGATGTATACAGTTTTGGAGTATCAATTAAgtaagaatct ... catattgcagTGAGCTACTTACTGGTGTTGTGCCATATACTGATCTTCGAGCAGAAGCTCA
EST: gi|351038320|gb|FQ461012.1|FQ461012
EST:     GAGATACATACTGAAAAATCAGATGTATACAGTTTTGGAGTATCAATTAA                         TGAGCTACTTACTGGTGTTGTGCCATATACTGATCTTCGAGCAGAAGCTCA
genomic: GAGATACATACTGAAAAATCAGATGTATACAGTTTTGGAGTATCAATTAAgtaagaatct ... catattgcagTGAGCTACTTACTGGTGTTGTGCCATATACTGATCTTCGAGCAGAAGCTCA
EST: gi|352798467|gb|FQ480492.1|FQ480492
EST:     GAGATACATACTGAAAAATCAGATGTATACAGTTTTGGAGTATCAATTAA                         TGAGCTACTTACTGGTGTTGTGCCATATACTGATCTTCGAGCAGAAGCTCA
genomic: GAGATACATACTGAAAAATCAGATGTATACAGTTTTGGAGTATCAATTAAgtaagaatct ... catattgcagTGAGCTACTTACTGGTGTTGTGCCATATACTGATCTTCGAGCAGAAGCTCA
EST: gi|352790239|gb|FQ481438.1|FQ481438
EST:     GAGATACATACTGAAAAATCAGATGTATACAGTTTTGGAGTATCAATTAA                         TGAGCTACTTACTGGTGTTGTGCCATATACTGATCTTCGAGCAGAAGCTCA
genomic: GAGATACATACTGAAAAATCAGATGTATACAGTTTTGGAGTATCAATTAAgtaagaatct ... catattgcagTGAGCTACTTACTGGTGTTGTGCCATATACTGATCTTCGAGCAGAAGCTCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAACATGGTTGGGACACTAATTTATATGGCACCTGAAATATTGAGGAAGGAGATACATACTGAAAAATCAGATGTATACAGTTTTGGAGTATCAATTAAgtaagaatcttgagcaagttgaggatttgtgctatataacttcaatgatttccgatatcttgactcaagggaaaattaaaattcagttacttgctagtat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gggaaaa