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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGGACCCAACAGATGAGAGATATGCTAGAAGCAAGGAAGCGTGGGGACTTTGCATTCCGTGACAAGGATTTTAAAACTGCCATTGATTGTTATTCTCAGgtatgatttctatctcttccaatggaaagtatgatgctgtgcaaatgctaaggtgtatctccataggttacactataagtcataaaaggcaaaaggggta...

Basic information

species Vitis vinifera
transcript Vv03s0038g03270.t01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0038g03270.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: LOC_Os10g39670.1 (Oryza sativa), 5'ss of exon 8
ATGGACCCAACAGATGAGAGATATGCTAGAAGCAAGGAAGCGTGGGGACTTTGCATTCCGTGACAAGGATTTTAAAACTGCCATTGATTGTTATTCTCAGgtatgat----ttctatctcttcca----atggaaagtatgatgctgtgcaaatgctaaggtgtat--------------ctccataggtta-cactataagtcataaaa-ggcaaaaggggta-----------
|||||| |||||||||||||||||| | || || ||||| ||||| || |||||||| || |||||  |||| ||    ||||| ||||||||  |||||||| ||     |  ||| |||||      |||  |  |   ||| | |  || | | |   |  ||              |||     |||| || | |   || | |||   |   | || ||           
ATGGACTCAACAGATGAGAGATATGTTGGATGCTAGGAAACGTGGTGATTTTGCATTTCGAGACAAAAATTTCAAGCAAGCCATAGATTGTTACACTCAGgtaggaggctgtattatttcttctttatcatgagaccttcaatgttctaaaattaccacttttcatgtagttcattcatcctctgctcgttatcattttccttcttgaaacatctgcatggttattgtttcacag

upper sequence: Vv03s0038g03270.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GRMZM2G127050_T01 (Zea mays), 5'ss of exon 8
ATGGACCCAACAGATGAGAGATATGCTAGAAGCAAGGAAGCGTGGGGACTTTGCATTCCGTGACAAGGATTTTAAAACTGCCATTGATTGTTATTCTCAGgta--tgatttctatctcttccaatggaaagtatgatgctgtgcaaatgctaaggtgtatctccataggttacactataagtcataaaaggcaaaaggggta
|||||| || |||||||| || ||||| ||||| ||||| |||||||||||||| ||||||||||| ||||| ||  | ||||| || || ||  | |||||   |    | ||  |  |   | |   | | || |  | |  | | |||       |       |  | ||  | | |    |  | |    |       
ATGGACGCAGCAGATGAGGGACATGCTGGAAGCTAGGAAACGTGGGGACTTTGCTTTCCGTGACAAAGATTTCAAGGCAGCCATAGACTGCTACACGCAGgtgcctcgactttagttaatatcaggagcactttggtattctagaga-gctgctagaaacgcagccaactcactgtgtcacctcttcatgctgcag------

upper sequence: Vv03s0038g03270.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GRMZM2G099598_T01 (Zea mays), 5'ss of exon 8
ATGGACCCAACAGATGAGAGATATGCTAGAAGCAAGGAAGCGTGGGGACTTTGCATTCCGTGACAAGGATTTTAAAACTGCCATTGATTGTTATTCTCAGgtatgat--ttctatctcttccaatggaaagtatgatg--ctgtgcaaatgctaaggtgtatctccataggttacactataagtcataaaaggcaaaaggggta
|||||| || |||||||| || ||||| ||||| ||||||||||||||||| || || || || || ||||| ||  | ||||| ||||| ||  | |||||    |  |  || || |  ||  | | | | || ||  ||   ||| |||||   |  ||   |     | || ||   |    |  | |    |       
ATGGACGCAGCAGATGAGGGACATGCTGGAAGCTAGGAAGCGTGGGGACTTCGCCTTTCGCGATAAAGATTTCAAGGCAGCCATAGATTGCTACACGCAGgtggcttcatcttagctatatcag-gaacactttgttgttctagacaactgctagaata-atgcacccgattcactctgctacctcttcatgctgcag------

upper sequence: Vv03s0038g03270.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA02G48030.1 (Glycine max), 5'ss of exon 6
ATGGACCCAACAGATGAGAGATATGCTAGAAGCAAGGAAGCGTGGGGACTTTGCATTCCGTGACAAGGATTTTAAAACTGCCATTGATTGTTATTCTCAGgtatgatttc-tatctcttc--caatggaaagtatgat-gctgtgcaaatgctaaggtg--tatctccataggttacactataagtcataaaaggcaaaaggggta
 ||||| |||||||||||||||||||| || |||||||||||||| |||| |||||||||||||||||| ||||| || |||||||||   ||||| |||||   |||    |  | ||   || || ||| |||  | ||| ||| |     | | |   ||| |  | | | | |   ||   |  | |       | |  |  
GTGGACTCAACAGATGAGAGATATGCTGGAGGCAAGGAAGCGTGGAGACTATGCATTCCGTGACAAGGACTTTAAGACAGCCATTGATAACTATTCCCAGgtgcaattcagcacttgtttgacattgtaaattattgtagctttgctatgagcacgctaattattttgagatgcttctgcattgtttgttattcattcatgcag--

upper sequence: Vv03s0038g03270.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA14G00540.1 (Glycine max), 5'ss of exon 6
ATGGACCCAACAGATGAGAGATATGCTAGAAGCAAGGAAGCGTGGGGACTTTGCATTCCGTGACAAGGATTTTAAAACTGCCATTGATTGTTATTCTCAGgtatgatttc-tatctcttc--caatggaaagtatgat------gctgtgcaaatgctaaggtgtatctccataggt-tacactataagtcataaaaggcaaaaggggta
 ||||| |||||||||||||||||||| |||||||||||||| || |||  |||||||||||||||||| ||||  || |||||||||   ||||| |||||   |||    |  | ||   || || ||| |||  |      ||| ||   | || ||  | | |    ||   | | || | | | ||||  |              
GTGGACTCAACAGATGAGAGATATGCTGGAAGCAAGGAAGCGCGGAGACCATGCATTCCGTGACAAGGACTTTAGGACAGCCATTGATAACTATTCCCAGgtgcaattctgcacttgtttgacattgtaaactattgtagctttgctatgtgcacgccaat-tattttgagatgcttctgcattgttattcatgcag-------------

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|110714728|gb|EE091969.1|EE091969
EST:     AGGATTTTAAAACTGCCATTGATTGTTATTCTCAG                         TTTGTAGATGTGGGAACCATGGTGTCCCCAACTGTTTATGCACGGCGCAGT
genomic: AGGATTTTAAAACTGCCATTGATTGTTATTCTCAGgtatgatttc ... tctggagcagTTTGTAGATGTGGGAACCATGGTGTCCCCAACTGTTTATGCACGGCGCAGT
EST: gi|33405170|gb|CF210797.1|CF210797
EST:     TTGCATTCCGTGACAAGGATTTTAAAACTGCCATTGATTGTTATTCTCAG                         TTTGTAGATGTGGGAACCATGGTGTCCCCAACTGTTTATGCACGGCGCAGT
genomic: TTGCATTCCGTGACAAGGATTTTAAAACTGCCATTGATTGTTATTCTCAGgtatgatttc ... tctggagcagTTTGTAGATGTGGGAACCATGGTGTCCCCAACTGTTTATGCACGGCGCAGT
EST: gi|110396180|gb|EC961861.1|EC961861
EST:     TTGCATTCCGTGACAAGGATTTTAAAACTGCCATTGATTGTTATTCTCAG                         TTTGTAGATGTGGGAACCATGGTGTCCCCAACTGTTTATGCACGGCGCAGT
genomic: TTGCATTCCGTGACAAGGATTTTAAAACTGCCATTGATTGTTATTCTCAGgtatgatttc ... tctggagcagTTTGTAGATGTGGGAACCATGGTGTCCCCAACTGTTTATGCACGGCGCAGT
EST: gi|110358197|gb|EC922241.1|EC922241
EST:     TTGCATTCCGTGACAGGGATTTTAAAACTGCCATTGATTGTTATTCTCAG                         TTGGTAGATGTGGGAACCATGGTGTCCCCAACTGTTTATGCACGGCGCAGT
genomic: TTGCATTCCGTGACAAGGATTTTAAAACTGCCATTGATTGTTATTCTCAGgtatgatttc ... tctggagcagTTTGTAGATGTGGGAACCATGGTGTCCCCAACTGTTTATGCACGGCGCAGT
EST: gi|110386358|gb|EC950948.1|EC950948
EST:     TTGCATTCCGTGACAAGGATTTTAAAACTGCCATTGATTGTTATTCTCAG                         TTTGTAGATGTGGGAACCATGGTGTCCCCAACTGTTTATGCACGGCGCAGT
genomic: TTGCATTCCGTGACAAGGATTTTAAAACTGCCATTGATTGTTATTCTCAGgtatgatttc ... tctggagcagTTTGTAGATGTGGGAACCATGGTGTCCCCAACTGTTTATGCACGGCGCAGT
EST: gi|110368581|gb|EC932568.1|EC932568
EST:     TTGCATTCCGTGACAAGGATTTTAAAACTGCCATTGATTGTTATTCTCAG                         TTTGTAGATGTGGGAACCATGGTGTCCCCAACTGTTTATGCACGGCGCAGT
genomic: TTGCATTCCGTGACAAGGATTTTAAAACTGCCATTGATTGTTATTCTCAGgtatgatttc ... tctggagcagTTTGTAGATGTGGGAACCATGGTGTCCCCAACTGTTTATGCACGGCGCAGT
EST: gi|22014191|gb|BQ799225.1|BQ799225
EST:     TTGCATTCCGTGACAAGGATTTTAAAACTGCCATTGATTGTTATTCTCAG                         TTTGTAGATGTGGGAACCATGGTGTCCCCAACTGTTTATGCACGGCGCAGT
genomic: TTGCATTCCGTGACAAGGATTTTAAAACTGCCATTGATTGTTATTCTCAGgtatgatttc ... tctggagcagTTTGTAGATGTGGGAACCATGGTGTCCCCAACTGTTTATGCACGGCGCAGT
EST: gi|33405090|gb|CF210717.1|CF210717
EST:     TTGCATTCCGTGACAAGGATTTTAAAACTGCCATTGATTGTTATTCTCAG                         TTTGTAGATGTGGGAACCATGGTGTCCCCAACTGTTTATGCACGGCGCAGT
genomic: TTGCATTCCGTGACAAGGATTTTAAAACTGCCATTGATTGTTATTCTCAGgtatgatttc ... tctggagcagTTTGTAGATGTGGGAACCATGGTGTCCCCAACTGTTTATGCACGGCGCAGT
EST: gi|30136281|gb|CB921619.1|CB921619
EST:     TTGCATTCCGTGACAAGGATTTTAAAACTGCCATTGATTGTTATTCTCAG                         TTTGTAGATGTGGGAACCATGGTGTCCCCAACTGTTTATGCACGGCGCAGT
genomic: TTGCATTCCGTGACAAGGATTTTAAAACTGCCATTGATTGTTATTCTCAGgtatgatttc ... tctggagcagTTTGTAGATGTGGGAACCATGGTGTCCCCAACTGTTTATGCACGGCGCAGT
EST: gi|46918835|gb|CN548164.1|CN548164
EST:     TTGCATTCCGTGACAAGGATTTTAAAACTGCCATTGATTGTTATTCTCAG                         TTTGTAGATGTGGGAACCATGGTGTCCCCAACTGTTTATGCACGGCGCAGT
genomic: TTGCATTCCGTGACAAGGATTTTAAAACTGCCATTGATTGTTATTCTCAGgtatgatttc ... tctggagcagTTTGTAGATGTGGGAACCATGGTGTCCCCAACTGTTTATGCACGGCGCAGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGGACCCAACAGATGAGAGATATGCTAGAAGCAAGGAAGCGTGGGGACTTTGCATTCCGTGACAAGGATTTTAAAACTGCCATTGATTGTTATTCTCAGgtatgatttctatctcttccaatggaaagtatgatgctgtgcaaatgctaaggtgtatctccataggttacactataagtcataaaaggcaaaaggggta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcttcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atggaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aggcaaa