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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACTGTCGGTGGTGATGGTTCTCATCGGGGTGCTCCGCTATTTCGTCTCCAAGCTCATGCGATCCTCTCAAGTGCCCGATTCCAAAATCGTTAGAGAAGGgttagaaaccctagctcctgcatgttagcgtaatctaatcctgtgatttcatgtgtctgatttgattttttttttttttaatttcag

Basic information

species Vitis vinifera
transcript Vv00s0187g00170.t01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0187g00170.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: LOC_Os09g32220.1 (Oryza sativa), 5'ss of exon 1
CACTGTCGGTGGTGATGGTTCTCATCGGGGTGCTCCGCTATTTCGTCTCCAAGCTCATGCGATCCTCTCAAGTG---------CCCGATTCCAAAATCGTTAGAGAAGGgttagaaaccct---agctcctgcatgttagcgtaatctaatcctgtgatttcatgt-gtctgatttgattttttttttttttaatttcag----------
         |||||||||| |||||||| ||||||||||| |||||| ||||||| ||||| ||| |    | |         |||||  ||||  |||| |  || ||||| |   |  |   | |||  | ||  |  ||  ||||  |  ||       || | |   ||| |||            |  ||               
---------TGGTGATGGTGCTCATCGGCGTGCTCCGCTACTTCGTCGCCAAGCTGATGCGCTCCCCGTCGGCGTCGCCCTCCCCCGACCCCAAGCTCGTCAAGGAGGGgttcgttgcttttccaactctcg-atcctgccgcgatctgtttttgctcgccgatttcgctcgatctgacgccgcgagacctagatccggaggcctcaccg

upper sequence: Vv00s0187g00170.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GRMZM2G014313_T02 (Zea mays), 5'ss of exon 1
CACTGTCGGTGGTGATGGTTCTCATCGGGGTGCTCCGCTATTTCGTCTCCAAGCTCATGCGATCC---------TCTCAAGTGCCCGATTCCAAAATCGTTAGAGAAGGgttagaaaccctagctcctgcatgttagcgtaatctaatcctg-tgatttcatgtgtct-gatttgatttttttttttttta-atttcag-------------
         |||| ||||| |||||||| ||||||||||| || ||||||||||||||||| |||         ||||     |||||  ||||  ||||||  |||||||  |||||      || | |    || |  |||    ||| | | |     |||  |  | |||| |       ||   |  || | ||             
---------TGGTTATGGTCCTCATCGGCGTGCTCCGCTACTTTGTCTCCAAGCTCATGCGCTCCCCGGCGACCTCTCCGTCTCCCGACCCCAAGCTCGTTAAGGAAGGgtaggaaacttctcttcatcc---ctaccccaattccctcccgatcacgatctgttccccggtttgctcggagggttcgctggatctgagcgatctagatcca

upper sequence: Vv00s0187g00170.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: EFJ16947 (Selaginella moellendorffii), 5'ss of exon 1
CACTGTCGGTGGTGATGGTTCTCATCGGGGTGCTCCGCTATTTCGTCTCCAAGCTCATGCGATCCTCTCAAGTGCCCGATTCCAAAATCGTTAGAGAAGGgttagaaaccctagctcctgcatgttagcgtaatctaatcctgtgatttcatgtgtctgatttgattttttttttttttaatttcag
| |||||| ||||||||||||||||||| ||||| ||| | ||||||||||||   |||   ||    |  | ||||||  ||||     | | ||||   |    |    |   | ||   | || ||| |   |  || | | || ||     | | | ||  ||                    
CGCTGTCGCTGGTGATGGTTCTCATCGGCGTGCTGCGCCACTTCGTCTCCAAGTGTATGTCCTCGCAGCCGGAGCCCGACGCCAAGGCTCTCAAAGAA---TCgtgagtttttttttctttgttttggcg-agcttcttcttctcatctcgctcttgtaactttcttcaag----------------

upper sequence: Vv00s0187g00170.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: EFJ16068 (Selaginella moellendorffii), 5'ss of exon 1
CACTGTCGGTGGTGATGGTTCTCATCGGGGTGCTCCGCTATTTCGTCTCCAAGCTCATGCGATCCTCTCAAGTGCCCGATTCCAAAATCGTTAGAGAAGGgttagaaaccctagctcctgcatgttagcgtaatctaatcctgtgatttcatgtgtctgatttgattttttttttttttaatttcag
| |||||| ||||||||||||||||||| ||||| ||| | ||||||||||||   |||   ||    |  | ||||||  ||||     | | ||||   |    |    |   | ||   | |  ||  |   |  || | | || ||     | | | ||  ||                    
CGCTGTCGCTGGTGATGGTTCTCATCGGCGTGCTGCGCCACTTCGTCTCCAAGTGTATGTCCTCGCAGCCGGAGCCCGACGCCAAGGCTCTCAAAGAA---TCgtgagtttttttttctttgtttcggccgagcttcttcttctcatctcgctcttgtaacttccttcaag----------------

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|30132459|gb|CB917798.1|CB917798
EST:     AAGCTCATGCGATCCTCTCAAGTGCCCGATTCCAAAATCGTTAGAGAAGG                         GCAGGTGATTGTTAGGGCTCGAAACTTGCGGGCGGCGGCGAATTACATTCC
genomic: AAGCTCATGCGATCCTCTCAAGTGCCCGATTCCAAAATCGTTAGAGAAGGgttagaaacc ... ttaatttcagGCAGGTGATTGTTAGGGCTCGAAACTTGCGGGCGGCGGCGAATTACATTCC
EST: gi|30136299|gb|CB921637.1|CB921637
EST:     AAGCTCATGCGATCCTCTCAAGTGCCCGATTCCAAAATCGTTAGAGAAGG                         GCAGGTGATTGTTAGGGCTCGAAACTTGCGGGCGGCGGCGAATTACATTCC
genomic: AAGCTCATGCGATCCTCTCAAGTGCCCGATTCCAAAATCGTTAGAGAAGGgttagaaacc ... ttaatttcagGCAGGTGATTGTTAGGGCTCGAAACTTGCGGGCGGCGGCGAATTACATTCC
EST: gi|294966792|gb|GW837811.1|GW837811
EST:     AAGCTCATGCGATCCTCTCAAGTGCCCGATTCCAAAATCGTTAGAGAAGG                         GCAGGTGATTGTTAGGGCTCGAAACTTGCGGGCGGCGGCGAATTACATTCC
genomic: AAGCTCATGCGATCCTCTCAAGTGCCCGATTCCAAAATCGTTAGAGAAGGgttagaaacc ... ttaatttcagGCAGGTGATTGTTAGGGCTCGAAACTTGCGGGCGGCGGCGAATTACATTCC
EST: gi|32250235|gb|CD716054.1|CD716054
EST:     AAGCTCATGCGATCCTCTCAAGTGCCCGATTCCAAAATCGTTAGAGAAGG                         GCAGGTGATTGTTAGGGCTCGAAACTTGCGGGCGGCGGCGAATTACATTCC
genomic: AAGCTCATGCGATCCTCTCAAGTGCCCGATTCCAAAATCGTTAGAGAAGGgttagaaacc ... ttaatttcagGCAGGTGATTGTTAGGGCTCGAAACTTGCGGGCGGCGGCGAATTACATTCC
EST: gi|30135330|gb|CB920668.1|CB920668
EST:     AAGCTCATGCGATCCTCTCAAGTGCCCGATTCCAAAATCGTTAGAGAAGG                         GCAGGTGATTGTTAGGGCTCGAAACTTGCGGGCGGCGGCGAATTACATTCC
genomic: AAGCTCATGCGATCCTCTCAAGTGCCCGATTCCAAAATCGTTAGAGAAGGgttagaaacc ... ttaatttcagGCAGGTGATTGTTAGGGCTCGAAACTTGCGGGCGGCGGCGAATTACATTCC
EST: gi|110407602|gb|EC973208.1|EC973208
EST:     CTCAAGTGCCCGATTCCAAAATCGTTAGAGAAGG                         GCAGGTGATTGTTAGGGCTCGAAACTTGCGGGCGGCGGCGAATTACATTCC
genomic: CTCAAGTGCCCGATTCCAAAATCGTTAGAGAAGGgttagaaacc ... ttaatttcagGCAGGTGATTGTTAGGGCTCGAAACTTGCGGGCGGCGGCGAATTACATTCC
EST: gi|110417816|gb|EC983901.1|EC983901
EST:     CATGCGATCCTCTCAAGTGCCCGATTCCAAAATCGTTAGAGAAGG                         GCAGGTGATTGTTAGGGCTCGAAACTTGCGGGCGGCGGCGAATTACATTCC
genomic: CATGCGATCCTCTCAAGTGCCCGATTCCAAAATCGTTAGAGAAGGgttagaaacc ... ttaatttcagGCAGGTGATTGTTAGGGCTCGAAACTTGCGGGCGGCGGCGAATTACATTCC
EST: gi|110712100|gb|EE089333.1|EE089333
EST:     AAGCTCATGCGATCCTCTCAAGTGCCCGATTCCAAAATCGTTAGAGAAGG                         GCAGGTGATTGTTAGGGCTCGAAACTTGCGGGCGGCGGCGAATTACATTCC
genomic: AAGCTCATGCGATCCTCTCAAGTGCCCGATTCCAAAATCGTTAGAGAAGGgttagaaacc ... ttaatttcagGCAGGTGATTGTTAGGGCTCGAAACTTGCGGGCGGCGGCGAATTACATTCC
EST: gi|110429192|gb|EC995681.1|EC995681
EST:     AAGCTCATGCGATCCTCTCAAGTGCCCGATTCCAAAATCGTTAGAGAAGG                         GCAGGTGATTGTTAGGGCTCGAAACTTGCGGGCGGCGGCGAATTACATTCC
genomic: AAGCTCATGCGATCCTCTCAAGTGCCCGATTCCAAAATCGTTAGAGAAGGgttagaaacc ... ttaatttcagGCAGGTGATTGTTAGGGCTCGAAACTTGCGGGCGGCGGCGAATTACATTCC
EST: gi|27580483|gb|CB003178.1|CB003178
EST:     CTCAAGTGCCCGATTCCAAAATCGTTAGAGAAGG                         GCAGGTGATTGTTAGGGCTCGAAACTTGCGGGCGGCGGCGAATTACATTCC
genomic: CTCAAGTGCCCGATTCCAAAATCGTTAGAGAAGGgttagaaacc ... ttaatttcagGCAGGTGATTGTTAGGGCTCGAAACTTGCGGGCGGCGGCGAATTACATTCC
EST: gi|110728851|gb|EE104791.1|EE104791
EST:     AAGCTCATGCGATCCTCTCAAGTGCCCGATTCCAAAATCGTTAGAGAAGG                         GCAGGTGATTGTTAGGGCTCGAAACTTGCGGGCGGCGGCGAATTACATTCC
genomic: AAGCTCATGCGATCCTCTCAAGTGCCCGATTCCAAAATCGTTAGAGAAGGgttagaaacc ... ttaatttcagGCAGGTGATTGTTAGGGCTCGAAACTTGCGGGCGGCGGCGAATTACATTCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACTGTCGGTGGTGATGGTTCTCATCGGGGTGCTCCGCTATTTCGTCTCCAAGCTCATGCGATCCTCTCAAGTGCCCGATTCCAAAATCGTTAGAGAAGGgttagaaaccctagctcctgcatgttagcgtaatctaatcctgtgatttcatgtgtctgatttgattttttttttttttaatttcag

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