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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttgaattgcaaactttaagcttcctccatacaaaaataataggtttgggagcaatggtcttgattgctgagttgcagGTGGGAATATCTGTGGATGCGACTGGGGAGAAAGTAGGGACGTTTGCATTGGCATATGCTGCACATAAGGCTGCATCTCCTATAAGGTTCCCACCCACCG

Basic information

species Vitis vinifera
transcript Vv06s0080g01100.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0080g01100.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA11G18410.1 (Glycine max), 3'ss of exon 2
------------gtacttgaattgcaaactttaagcttcctccatacaaaaataataggtttgggagcaatggtcttgattgctgagttgcagGTGGGAATATCTGTGGATGCGACTGGGGAGAAAGTAGGGACGTTTGCATTGGCATATGCTGCACATAAGGCTGCATCTCCTATAAGGTTCCCACCCACCG
             ||     | || | | |  || |    |  | ||||||  | |  | || |||  |||    |||  || | |    ||||| ||||| ||    ||||||||||| |||||||| || || |||||||||||||||||||||||||| ||||||||||| || ||||| |||||||| |
gtgcaacacaaactaaacctaatgtagattgcaatcaaattgaaaacaaaacaatt--gcttcggattaataaa-ttgcgtgtttatcctcagGTTGGAATCTCAACTGATGCGACTGGAGAGAAAGTTGGTACCTTTGCATTGGCATATGCTGCACATAAAGCTGCATCTCCAATTAGGTTTCCACCCACAG

upper sequence: Vv06s0080g01100.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA12G09850.1 (Glycine max), 3'ss of exon 2
--------------gtacttgaattgcaaactttaagcttcctccatacaaaaataataggtttgggagcaatggtcttgattgctgagttgcagGTGGGAATATCTGTGGATGCGACTGGGGAGAAAGTAGGGACGTTTGCATTGGCATATGCTGCACATAAGGCTGCATCTCCTATAAGGTTCCCACCCACCG
               ||     | || | | |  ||  |   |  | |||||   ||| | || |||   |||    |||  || | |  | ||||| ||||| ||    ||||||||||| || ||||| || || ||||| |||||||||||||||||||| ||||||||||| || ||||| |||||||| |
gtgcaacactaaaactaaacctaatgtagattgcaatttaatttaaaacaaag-caattgcttcgggt-taataaa-ttgcgtgtttatcttcagGTTGGAATCTCAACTGATGCGACTGGCGAAAAAGTTGGTACCTTTGCTTTGGCATATGCTGCACATAAAGCTGCATCTCCAATTAGGTTTCCACCCACAG
















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|26263289|gb|CA814352.1|CA814352
EST:     GTTATGCACTAATCAATGCAGGAGTGGATGTCCAAGCTCTGTTGCAAAAG                         GTGGGAATATATGTGGATGCGACTGGGGAGAAAGTAGGGACGTTTGCATTG
genomic: GTTATGCACTAATCAATGCAGGAGTGGATGTCCAAGCTCTGTTGCAAAAGgtacttgaat ... tgagttgcagGTGGGAATATCTGTGGATGCGACTGGGGAGAAAGTAGGGACGTTTGCATTG
EST: gi|110691549|gb|EE069779.1|EE069779
EST:     GTTATGCACTAATCAATGCAGGAGTGGATGTCCAAGCTCTGTTGCAAAAG                         GTGGGAATATCTGTGGATGCGACTGGGGAGAAAGTAGGGACGTTTGCATTG
genomic: GTTATGCACTAATCAATGCAGGAGTGGATGTCCAAGCTCTGTTGCAAAAGgtacttgaat ... tgagttgcagGTGGGAATATCTGTGGATGCGACTGGGGAGAAAGTAGGGACGTTTGCATTG
EST: gi|30133576|gb|CB918915.1|CB918915
EST:     CCAAGCTCTGTTGCAAAAG                         GTGGGAATATCTGTGGATGCGACTGGGGAGAAAGTAGGGACGTTTGCATTG
genomic: CCAAGCTCTGTTGCAAAAGgtacttgaat ... tgagttgcagGTGGGAATATCTGTGGATGCGACTGGGGAGAAAGTAGGGACGTTTGCATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctccatacaaaaataataggtttgggagcaatggtcttgattgctgagttgcagGTGGGAATATCTGTGGATGCGACTGGGGAGAAAGTAGGGACGTTTGCATTGGCATATGCTGCACATAAGGCTGCATCTCCTATAAGGTTCCCACCCACCG
                                   tcttgat  putative branch site (score: 4)
     atacaaaaataata  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacttgaattgcaaactttaagcttcctccatacaaaaataataggtttgggagcaatggtcttgattgctgagttgcagGTGGGAATATCTGTGGATGCGACTGGGGAGAAAGTAGGGACGTTTGCATTGGCATATGCTGCACATAAGGCTGCATCTCCTATAAGGTTCCCACCCACCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC