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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGCAAACAGATGGGTTAGCGGGATTCACCAAGCGCTCGGAGAGTGAATATGACTGCTTTGGAACCGGCCACAGTTCTACTACCATCTCAGCAGGCTTGGgtaattctctcttccatctccaattgaatatggaaaaatattgaacttagacaaagagtaccaaaatttgatatgtactgaagcccaaacttttccaagt...

Basic information

species Vitis vinifera
transcript Vv05s0020g02130.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g02130.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os05g33840.1 (Oryza sativa), 5'ss of exon 3
AGGCAAACAGATGGGTTAGCGGGATTCACCAAGCGCTCGGAGAGTGAATATGACTGCTTTGGAACCGGCCACAGTTCTACTACCATCTCAGCAGGCTTGGgtaattctctcttccatctccaat-tgaatatggaaaaatattgaa-cttagacaaagagtaccaaaatttgatatgtactgaagcccaaacttttccaagt
 | || ||  | || ||  |||||||||||||||| |||||||| || || |||| ||| || ||||||||||| || || |||||||| || | | | |||||    ||||||   ||||| | |   |      |  | |  |  ||  |  |||  |  | | |    |   |    |||       |           
CGTCAGACCAACGGCTTGTCGGGATTCACCAAGCGGTCGGAGAGCGAGTACGACTCCTTCGGCACCGGCCACAGCTCCACCACCATCTCCGCCGCCCTCGgtaacctcctcttcttcctccagtctctctgcatcgagctgtaaattctctgtgaaactgacctacaggccggcgtacg-tgagattggcag----------
















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|352777281|gb|FQ473915.1|FQ473915
EST:     TGACTGCTTTGGAACCGGCCACAGTTCTACTACCATCTCAGCAGGCTTGG                         GAATGGCGGTCGGCCGGGATCT
genomic: TGACTGCTTTGGAACCGGCCACAGTTCTACTACCATCTCAGCAGGCTTGGgtaattctct ... gtgtgaacagGAATGGCGGTCGGCCGGGATCT
EST: gi|352781778|gb|FQ469076.1|FQ469076
EST:     TGACTGCTTTGGAACCGGCCACAGTTCTACTACCATCTCAGCAGGCTTGG                         GAATGGCGGTCGGCCGGGATCTAAAAAGGAAAAA-CAACAACGTTATTGCT
genomic: TGACTGCTTTGGAACCGGCCACAGTTCTACTACCATCTCAGCAGGCTTGGgtaattctct ... gtgtgaacagGAATGGCGGTCGGCCGGGATCTAAAA-GGAAAAAACAACAACGTTATTGCT
EST: gi|161713384|gb|FC063376.1|FC063376
EST:     TGACTGCTTTGGAACCGGCCACAGTTCTACTACCATCTCAGCAGGCTTGG                         GAATGGCGGTCGGCCGGGATCTAAAAGGAAAAAACAACAACGTCATTGCTG
genomic: TGACTGCTTTGGAACCGGCCACAGTTCTACTACCATCTCAGCAGGCTTGGgtaattctct ... gtgtgaacagGAATGGCGGTCGGCCGGGATCTAAAAGGAAAAAACAACAACGTTATTGCTG
EST: gi|352768724|gb|FQ467936.1|FQ467936
EST:     TGACTGCTTTGGAACCGGCCACAGTTCTACTACCATCTCAGCAGGCTTGG                         GAATGGCGGTCGGCCGGGATCTAAAAGGAAAAAACAACAACGTTATTGCTG
genomic: TGACTGCTTTGGAACCGGCCACAGTTCTACTACCATCTCAGCAGGCTTGGgtaattctct ... gtgtgaacagGAATGGCGGTCGGCCGGGATCTAAAAGGAAAAAACAACAACGTTATTGCTG

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGCAAACAGATGGGTTAGCGGGATTCACCAAGCGCTCGGAGAGTGAATATGACTGCTTTGGAACCGGCCACAGTTCTACTACCATCTCAGCAGGCTTGGgtaattctctcttccatctccaattgaatatggaaaaatattgaacttagacaaagagtaccaaaatttgatatgtactgaagcccaaacttttccaagt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctcttcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gacaaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -accaaaa