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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCAGCCTTGTGTTGGGATATGGAGTGACAAGTGCTCTTCAAAATATGGAAGAAGACGACCATTTATTCTTGCTGGGTCTCTAATGATCTCAGTTGCTgtaagcataaaaaagtttcttatatgaatttttttaagtgattatatatttttatttatattgactaaaacaaagttttggaatttag

Basic information

species Vitis vinifera
transcript Vv01s0026g01960.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0026g01960.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GRMZM2G145107_T03 (Zea mays), 5'ss of exon 3
GTTCAGCCTTGTGTTGGGATATGGAGTGACAAGTGCTCTTCAAAATATGGAAGAAGACGACCATTTATTCTTGCTGGGTCTCTAATGATCTCAGTTGCTgtaagcataaaaaagtttcttatatgaatttttttaagtgattatatatttttatttatattgactaaaacaaagttttggaatttag
||||| |||||||||||  | |||||||| ||||||  |||||| ||||| || ||| ||||||||||| | ||||| |   ||||||| |  | |||||| ||    |  ||||||| |||   | | | |||       | |    |   |||   ||   |||| | |  |  |    |  |||
GTTCAACCTTGTGTTGGTGTTTGGAGTGATAAGTGCCGTTCAAAGTATGGGAGGAGAAGACCATTTATTTTGGCTGGATGCATAATGATATGTGCTGCTgtgagttagatgaagtttcatatgccattgtatttc-----ctgttctctgcaattcgcatgttctaatagatggactccatacgtag

upper sequence: Vv01s0026g01960.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT2G02860.1 (Arabidopsis thaliana), 5'ss of exon 3
GTTCAGCCTTGTGTTGGGATATGGAGTGACAAGTGCTCTTCAAAATATGGAAGAAGACGACCATTTATTCTTGCTGGGTCTCTAATGATCTCAGTTGCTgtaagc----ataaaaaa----gtttcttatatgaatttttttaagtgatta------tatatttttatttatattgactaaaacaaagttttggaatttag
|| ||||||| |||||| || |||||||| || ||  ||||||| |||||||||||||||||||||||||| | ||| ||  | ||||||||| | || |||||     ||| || |     |||||  | ||| ||| ||| ||    ||      || ||| |  |||||||   ||||| ||||   ||| |||||||
GTCCAGCCTTTTGTTGGCATTTGGAGTGATAAATGTACTTCAAAGTATGGAAGAAGACGACCATTTATTCTAGTTGGATCATTCATGATCTCAATAGCAgtaagtgccaatagaagatatgatttctgttttgattttcttttaggagatagctggctacattgtgttttatataagctaaa-caaaagcttgcaatttag

upper sequence: Vv01s0026g01960.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT2G02860.2 (Arabidopsis thaliana), 5'ss of exon 3
GTTCAGCCTTGTGTTGGGATATGGAGTGACAAGTGCTCTTCAAAATATGGAAGAAGACGACCATTTATTCTTGCTGGGTCTCTAATGATCTCAGTTGCTgtaagc----ataaaaaa----gtttcttatatgaatttttttaagtgatta------tatatttttatttatattgactaaaacaaagttttggaatttag-------------------------
|| ||||||| |||||| || |||||||| || ||  ||||||| |||||||||||||||||||||||||| | ||| ||  | ||||||||| | || |||||     ||| || |     |||||  | ||| ||| ||| ||    ||      || ||| |  |||||||   ||||| ||||   ||| |||||||                         
GTCCAGCCTTTTGTTGGCATTTGGAGTGATAAATGTACTTCAAAGTATGGAAGAAGACGACCATTTATTCTAGTTGGATCATTCATGATCTCAATAGCAgtaagtgccaatagaagatatgatttctgttttgattttcttttaggagatagctggctacattgtgttttatataagctaaa-caaaagcttgcaatttaggtgataataatcggattttctgcag

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|352778247|gb|FQ465557.1|FQ465557
EST:     GAAGAAGACGACCATTTATTCTTGCTGGGTCTCTAATGATCTCAGTTGCT                         GTGACAATTATTGGGTTTTCTGCAGACATTGGATATTTATTAGGAGATACC
genomic: GAAGAAGACGACCATTTATTCTTGCTGGGTCTCTAATGATCTCAGTTGCTgtaagcataa ... tggaatttagGTGACAATTATTGGGTTTTCTGCAGACATTGGATATTTATTAGGAGATACC
EST: gi|110698594|gb|EE076268.1|EE076268
EST:     GAAGAAGACGACCATTTATTCTTGCTGGGTCTCTAATGATCTCAGTTGCT                         GTGACAATTATTGGGTTTTCTGCAGACATTGGATATTTATTAGGAGATACC
genomic: GAAGAAGACGACCATTTATTCTTGCTGGGTCTCTAATGATCTCAGTTGCTgtaagcataa ... tggaatttagGTGACAATTATTGGGTTTTCTGCAGACATTGGATATTTATTAGGAGATACC
EST: gi|352776811|gb|FQ472698.1|FQ472698
EST:     GAAGAAGACGACCATTTATTCTTGCTGGGTCTCTAATGATCTCAGTTGCT                         GTGACAATTATTGGGTTTTCTGCAGACATTGGATATTTATTAGGAGATACC
genomic: GAAGAAGACGACCATTTATTCTTGCTGGGTCTCTAATGATCTCAGTTGCTgtaagcataa ... tggaatttagGTGACAATTATTGGGTTTTCTGCAGACATTGGATATTTATTAGGAGATACC
EST: gi|110723267|gb|EE100385.1|EE100385
EST:     AAAGAAGACGACCATTTATTCTTGCTGGGTCTCTAATGATCTCAGTTGCT                         GTGACAATTATTGGGTTTTCTGCAGACATTGGATATTTACTAGGAGATACC
genomic: GAAGAAGACGACCATTTATTCTTGCTGGGTCTCTAATGATCTCAGTTGCTgtaagcataa ... tggaatttagGTGACAATTATTGGGTTTTCTGCAGACATTGGATATTTATTAGGAGATACC
EST: gi|352764959|gb|FQ473607.1|FQ473607
EST:     GAAGAAGACGACCATTTATTCTTGCTGGGTCTCTAATGATCTCAGTTGCT                         GTGACAATTATTGGGTTTTCTGCAGACATTGGATATTTATTAGGAGATACC
genomic: GAAGAAGACGACCATTTATTCTTGCTGGGTCTCTAATGATCTCAGTTGCTgtaagcataa ... tggaatttagGTGACAATTATTGGGTTTTCTGCAGACATTGGATATTTATTAGGAGATACC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCAGCCTTGTGTTGGGATATGGAGTGACAAGTGCTCTTCAAAATATGGAAGAAGACGACCATTTATTCTTGCTGGGTCTCTAATGATCTCAGTTGCTgtaagcataaaaaagtttcttatatgaatttttttaagtgattatatatttttatttatattgactaaaacaaagttttggaatttag

- - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG