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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTGGTTACACCAAAAAGCAAGAGGAAAGGCATTTCCGTGGTGTCATCACTTTAGAGgtatggattgcaataaataccaataaccagaattttttgtcctgttgtggccaaaattttaaccattgtaaatattgaaagcaaagttgggtttatattg...

Basic information

species Vitis vinifera
transcript Vv18s0089g00350.t01
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0089g00350.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: LOC_Os08g32920.1 (Oryza sativa), 5'ss of exon 16
CTTGGTTACACCAAAAAGCAAGAGGAAAGGCATTTCCGTGGTGTCATCACTTTAGAGgtatggattgcaataaataccaataaccagaattttttgtcctgttgtggccaaaatttt---aaccattgtaa--atattgaaagcaaagttgggtttatattg
|||||||||||||| || |||||||| |||||||| || || ||||||| ||| ||||||   ||     | | | |   |  |  |   || || || |     |   ||  || |    |  | ||| |  || |      |  || ||| ||       
CTTGGTTACACCAAGAAACAAGAGGAGAGGCATTTTCGAGGCGTCATCAATTTGGAGgtacatatct---tcagtgctctttgcttgtgattcttctcatcgctcgagtaactttctcgagatgaatgtgatgatgtcatgcacgtagatggattctcgg--

upper sequence: Vv18s0089g00350.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: GLYMA12G37100.1 (Glycine max), 5'ss of exon 16
CTTGGTTACACCAAAAAGCAAGAGGAAAGGCATTTCCGTGGTGTCATCACTTTAGAGgtatggattgcaataaataccaataaccagaattttttgtcctgttgtggccaaaattttaaccattgtaaatattgaaagcaaagttgggtttat--attg-
||||| || |||||||| ||||||||||| ||||| || ||||| || || ||||||||||||| | |  |    |  ||| |     |||   | |    |       | | |  |     |||| |||  |  ||   | |||||  || |  |||  
CTTGGATATACCAAAAAACAAGAGGAAAGACATTTTCGCGGTGTTATTACATTAGAGgtatggagtacttt---cattaatcatgtacattcaatatttgataaattttacagtactgtgttttgtgaatcatataaattatgttggaattctcaattaa

upper sequence: Vv18s0089g00350.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: GLYMA09G00430.2 (Glycine max), 5'ss of exon 16
CTTGGTTACACCAAAAAGCAAGAGGAAAGGCATTTCCGTGGTGTCATCACTTTAGAGgtatggattgcaataaata--ccaataaccagaattttttgtcctgttgtggccaaaattttaaccattgtaaatattgaaag-caaagttgggtttatattg-
||||| ||||||||||| ||||||||||  ||||| || ||||| || || ||||||||||||| |||  | | ||  |   ||     |||  ||||      | |   |   | | |  |  ||||  || ||| ||  |  |  |  ||   |  || 
CTTGGGTACACCAAAAAACAAGAGGAAAAACATTTTCGCGGTGTTATTACATTAGAGgtatggagtgctttcattaatcttgtacgttcaataatttgataaacttta--cggtactgtgtc--ttgtgcatgttggaattcttaactaagtaattcatga

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|161719802|gb|FC065762.1|FC065762
EST:     ACACCAAAAAGCAAGAGGAAAGGCATTTCCGTGGTGTCATCACTTTAGAG                         GAATGTAACGTAGAGGAGGTTTCAGATGAGGAAGAACCTCCCCGAAAAAGT
genomic: ACACCAAAAAGCAAGAGGAAAGGCATTTCCGTGGTGTCATCACTTTAGAGgtatggattg ... tgccgtgcagGAATGTAACGTAGAGGAGGTTTCAGATGAGGAAGAACCTCCCCGAAAAAGT
EST: gi|32270986|gb|CD720145.1|CD720145
EST:     ACACCAAAAAGCAAGAGGAAAGGCATTTCCGTGGTGTGATCACTTTAGAG                         GAATGTAACGTAGAGGAGGTTTCAGATGAGGAAGAACCTCCCCGAAAAAGT
genomic: ACACCAAAAAGCAAGAGGAAAGGCATTTCCGTGGTGTCATCACTTTAGAGgtatggattg ... tgccgtgcagGAATGTAACGTAGAGGAGGTTTCAGATGAGGAAGAACCTCCCCGAAAAAGT
EST: gi|161714373|gb|FC063214.1|FC063214
EST:     ACACCAAAAAGCAAGAGGAAAGACATTTCCGTGGTGTCATCACTTTAGAG                         GAATGTAACGTAGAAGAGGTTTCAGATGAGGAAGAACCTCCCCGAAAAAGT
genomic: ACACCAAAAAGCAAGAGGAAAGGCATTTCCGTGGTGTCATCACTTTAGAGgtatggattg ... tgccgtgcagGAATGTAACGTAGAGGAGGTTTCAGATGAGGAAGAACCTCCCCGAAAAAGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTGGTTACACCAAAAAGCAAGAGGAAAGGCATTTCCGTGGTGTCATCACTTTAGAGgtatggattgcaataaataccaataaccagaattttttgtcctgttgtggccaaaattttaaccattgtaaatattgaaagcaaagttgggtttatattg

- - - - - - -  AAGCAA
- - - - - - - - AGCAAG
- - - - - - - -  GCAAGA
- - - - - - - - -  AAGAGG
- - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaccagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gccaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagcaaa