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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcagtgtattttcttcttttcattttaaacagtgaacttcatgtttatgggcactccagagatatgtttaatttgtgtattgcataatggtaacagGTACTTGGAGTATTTGAATGGTCTGGCAATAATCCTCTGCCCCCTGAAATATGGCTTCTTCCCTATATCCTACCAGTCCATCCAG

Basic information

species Vitis vinifera
transcript Vv11s0065g00640.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0065g00640.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA01G00430.2 (Glycine max), 3'ss of exon 5
gttcagtgtattttcttcttttcattttaaacagtgaacttcatgtttatgggcactccagagatatgtttaatttgtgtattgcataatggt--aacagGTACTTGGAGTATTTGAATGGTCTGGCAATAATCCTCTGCCCCCTGAAATATGGCTTCTTCCCTATATCCTACCAGTCCATCCAG
                          ||||    | ||| | || || |||     |   |   | || |  |||| | | |    |  | ||   | ||||||||||||| | |||||||||||| |||||||| ||||||||||| |||||||| ||||| || || || ||| | |||||||
-------------------------gttaagatctcaaccttattttgatgatagatatggcattgtggtatatttatttctaattttgttgtgggatagGTACTTGGAGTGTATGAATGGTCTGGAAATAATCCCCTGCCCCCTGAGATATGGCTCCTTCCATACATGCTTCCATTTCATCCAG

upper sequence: Vv11s0065g00640.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT2G07050.1 (Arabidopsis thaliana), 3'ss of exon 4
gt-tcagtgtattttcttcttttcattttaaacagtgaactt--catgtttatgggcactccagagatatgtttaatttgtgtattgcataatggtaaca--gGTACTTGGAGTATTTGAATGGTCTGGCAATAATCCTCTGCCCCCTGAAATATGGCTTCTTCCCTATATCCTACCAGTCCATCCAG
||   |  || ||  | ||| |   |  |  | ||| | | |   |   ||   |  |||  |   || | |||  || |        ||| ||  || |  |||||||||||  ||||||||||| || ||||| || ||||| ||||| ||||||||||| || ||| |||| ||| | |||||||
gtactaaagttttgacctctatctgtcctttaaagttatcgtatgaaaatttctgttacttgactcatctttttgcttggatctgctaatactgtaaataaagGTACTTGGAGCTTTTGAATGGTCCGGAAATAACCCACTGCCACCTGAGATATGGCTTCTCCCATATTTCCTGCCAATACATCCAG

upper sequence: Vv11s0065g00640.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: PP1S33_211V6.1 (Physcomitrella patens), 3'ss of exon 4
gttcagtgtattttcttcttttcattttaaacagtgaact-tcatgtttatgggcactccagagatatgtttaatttgtgtattgcataa--------tggtaacagGTACTTGGAGTATTTGAATGGTCTGGCAATAATCCTCTGCCCCCTGAAATATGGCTTCTTCCCTATATCCTACCAGTCCATCCAG
       |||||     ||       ||  | ||| | |   |||| |   |  |  |    | ||||| ||||| |   |    | |          || |  ||||| |||||||||||||||||||| || || ||||| ||||| |||||||  ||| | || || ||| | || ||  | |||||||
-------gtattcaagactcgggtgcttgtatagttatcaaccatgctgtggaacggtttgaatatatgattaatctccttgcaaccttcggtttatctgatgccagGTTCTTGGAGTATTTGAATGGTCAGGAAACAATCCCCTGCCTCCTGAAACTTGGATACTGCCGTATTTTCTTCCTATGCATCCAG

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|110419266|gb|EC985479.1|EC985479
EST:     ATCATGGTGGTGCAACTGCAATAACCTCATGGGGAAAAATGTGGCTTTCA                         GTACTTGGAGTATTTGAATGGTCTGGCAATAATCCTCTGCCCCCTGAAATA
genomic: ATCATGGTGGTGCAACTGCAATAACCTCATGGGGAAAAATGTGGCTTTCAgttcagtgta ... atggtaacagGTACTTGGAGTATTTGAATGGTCTGGCAATAATCCTCTGCCCCCTGAAATA
EST: gi|30299627|gb|CB976421.1|CB976421
EST:     ATCATGGTGGTGCAACTGCAATAACCTCATGGGGAAAAATGTGGCTTTCA                         GTACTTGGAGTATTTGAATGGTCTGGCAATAATCCTCTGCCCCCTGAAATA
genomic: ATCATGGTGGTGCAACTGCAATAACCTCATGGGGAAAAATGTGGCTTTCAgttcagtgta ... atggtaacagGTACTTGGAGTATTTGAATGGTCTGGCAATAATCCTCTGCCCCCTGAAATA
EST: gi|161719373|gb|FC064852.1|FC064852
EST:     ATCATGGTGGTGCAACTGCAATAACCTCATGGGGAAAAATGTGGCTTTCA                         GTACTTGGAGTATTTGAATGGTCTGGCAATAATCCTCTGCCCCCTGAAATA
genomic: ATCATGGTGGTGCAACTGCAATAACCTCATGGGGAAAAATGTGGCTTTCAgttcagtgta ... atggtaacagGTACTTGGAGTATTTGAATGGTCTGGCAATAATCCTCTGCCCCCTGAAATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttatgggcactccagagatatgtttaatttgtgtattgcataatggtaacagGTACTTGGAGTATTTGAATGGTCTGGCAATAATCCTCTGCCCCCTGAAATATGGCTTCTTCCCTATATCCTACCAGTCCATCCAG
                        gtttaat  putative branch site (score: 4)
                  agatatgtttaattt  TA-rich tract