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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACTAGGGTTCAATTTCATCACGATCAGATACATTTACTGGCAGTTCATGAAACGCAGATAGCCATATTTGAGGCATCCAAACTTGAGTGCCTTAGGCAGgtgtgccagattttttctgctcatttcagtatgtgtacatgcatatgttgatgttacttacagttcgaaggttttcctttaaggattgctgtttttctcctttgttgccttcacagtcaacaactctatttttctgttaaaactattgactttatgaaattatgttcctcaaatag

Basic information

species Vitis vinifera
transcript Vv11s0016g05620.t01
intron # 24
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g05620.t01 (Vitis vinifera), 5'ss of exon 24
lower sequence: GLYMA17G12110.2 (Glycine max), 5'ss of exon 24
TACTAGGGTTCAATTTCATCACGATCAGATACATTTACTGGCAGTTCATGAAACGCAGATAGCCATATTTGAGGCATCCAAACTTGAGTGCCTTAGGCAGgtgtgccagattttttctgctcatttcagtatgtgtacatgcatatgttgatgttacttacagttcgaaggttttcctttaaggattgctgtttttc--tcctttgttgccttcacagtcaacaactctatttttctgttaaaactattgactttatgaaattatgttcctcaaatag
|||| |||| ||||||||||  || |||| |||||||||||| ||||||||||| || |||||| ||| ||||||| | ||  | || ||  | | |||||||||| ||     || |    | || | | |||   |     |  | |    | ||||  |  ||   | |    | |  | | ||    || | |  | ||||  |   |  |   |||                                                         
TACTCGGGTCCAATTTCATCTAGACCAGACACATTTACTGGCTGTTCATGAAACTCAAATAGCCTTATATGAGGCACCAAAGTTGGAATGTATAAAGCAGgtgtgctag-----ttataaataatttaat-tgtcagctcaatttggctttcttcacttcaatgtcatcgatcaagcctgcaagcttaaccttgtgccgtgctttactttttgtatgatcag--------------------------------------------------------

upper sequence: Vv11s0016g05620.t01 (Vitis vinifera), 5'ss of exon 24
lower sequence: GLYMA13G22720.1 (Glycine max), 5'ss of exon 24
TACTAGGGTTCAATTTCATCACGATCAGATACATTTACTGGCAGTTCATGAAACGCAGATAGCCATATTTGAGGCATCCAAACTTGAGTGCCTTAGGCAGgtgtgccagattttttctgctcatttcagt----atgtgtacatgcatatgttgatgttacttacagttcgaaggttttcctttaaggattgctgtttttctcctttgttgccttcacagtcaacaactctatttttctgttaaaactattgactttatgaaattatgttcctcaaatag
|||| |||| ||||||||||  || |||| |||||||||||| ||||||||||| || |||||| | |  |||||| | ||  | || ||  | | |||||||||| || || | | |  | | || | |    |  | ||  ||  | | || || | | |   |  || |       |||  ||| ||  |  | |   || ||| |||  |   |||                                                            
TACTCGGGTCCAATTTCATCTAGACCAGACACATTTACTGGCTGTTCATGAAACCCAAATAGCCTTGTACGAGGCACCAAAGTTGGAATGTATAAAGCAGgtgtgctag-ttatatatatttaatttaattgccagctctatttggctttcttcatttcaatgtgatctctagctcaagcctgcaagcataacattgtgcttcattttttgtatgatcag------------------------------------------------------------
















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|30134210|gb|CB919548.1|CB919548
EST:     AAACGCAGATAGCCATATTTGAGGCATCCAAACTTGAGTGCCTTAGGCAG                         TGGGTTCCCCGGGAAGCAAGTGGCTCAATTACACATGCTACTTATTCGTGT
genomic: AAACGCAGATAGCCATATTTGAGGCATCCAAACTTGAGTGCCTTAGGCAGgtgtgccaga ... cctcaaatagTGGGTTCCCCGGGAAGCAAGTGGCTCAATTACACATGCTACTTATTCGTGT
EST: gi|161719514|gb|FC067700.1|FC067700
EST:     AAACGCAGATAGCCATATTTGAGGCATCCAAACTTGAGTGCCTTAGGCAG                         TGGGTTCCCCGGGAAGCAAGTGGCTCAATTACACATGCTACTTATTCGTGT
genomic: AAACGCAGATAGCCATATTTGAGGCATCCAAACTTGAGTGCCTTAGGCAGgtgtgccaga ... cctcaaatagTGGGTTCCCCGGGAAGCAAGTGGCTCAATTACACATGCTACTTATTCGTGT
EST: gi|30131041|gb|CB916380.1|CB916380
EST:     AAACGCAGATAGCCATATTTGAGGCATCCAAACTTGAGTGCCTTAGGCAGG                         T
genomic: AAACGCAGATAGCCATATTTGAGGCATCCAAACTTGAGTGCCTTAGGCA-Ggtgtgccaga ... cctcaaatag-
EST: gi|30131041|gb|CB916380.1|CB916380
EST:     AAACGCAGATAGCCATATTTGAGGCATCCAAACTTGAGTGCCTTAGGCAGG                         T
genomic: AAACGCAGATAGCCATATTTGAGGCATCCAAACTTGAGTGCCTTAGGCA-Ggtgtgccaga ... cctcaaatag-

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TACTAGGGTTCAATTTCATCACGATCAGATACATTTACTGGCAGTTCATGAAACGCAGATAGCCATATTTGAGGCATCCAAACTTGAGTGCCTTAGGCAGgtgtgccagattttttctgctcatttcagtatgtgtacatgcatatgttgatgttacttacagttcgaaggttttcctttaaggattgctgtttttctcctttgttgccttcacagtcaacaactctatttttctgttaaaactattgactttatgaaattatgttcctcaaatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT