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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCATCGATTGGAGCAGTGTACATGGACCCCAACAGGAGCCCAGATCAAGTTGTGGACGAGAGCTGTTGGAGTGATCTTGAATTCTGCAAGAACACCAAGgtcttcccacctatctttttttcttcaacactatttacccctaattttcatcattttttttcaacattttcgcttcttcttcaacctataatcatcagacttgtctttcatgtcccaaaggtaacggaacggcactaaaataaaatttgactcacccaaaaacaagatttttgattaactgagaggaaaatgcag

Basic information

species Vitis vinifera
transcript Vv09s0070g00240.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0070g00240.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GRMZM2G017285_T01 (Zea mays), 5'ss of exon 3
ATCATCGATTGGAGCAGTGTACATGGACCCCAACAGGAGCCCAGATCAAGTTGTGGACGAGAGCTGTTGGAGTGATCTTGAATTCTGCAAGAACACCAAGgtcttcccacctatctttttttcttcaacactatttacccctaattttcatcattttttttcaacattttcgcttcttcttcaacctataatcatcagacttgtctttcatgtcccaaaggtaacggaacggcactaaaataaaatttgactcacccaaaaacaagatttttgattaactgagaggaaaatgcag
 |||||    || || ||  ||||| |||| ||||||  ||| ||||     ||||||||||| ||||||||||| ||||||||||||||| | ||  |||||  |           |  | |||| || ||||| |  | |  ||||  |     ||||| |   |       |    ||  |   |||||   || ||| ||     || |                                                                                  
CTCATCCTACGGGGCTGTCCACATGAACCCTAACAGGGACCCTGATCGGACAGTGGACGAGAGTTGTTGGAGTGACCTTGAATTCTGCAAGCAAACACAGgtccac-----------tgctacttctacgctattcaagcatttttttggtaggaatttttaagtttcagtctctaacgttggagagataata--catactagttaagaattt----------------------------------------------------------------------------------

upper sequence: Vv09s0070g00240.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA13G44700.1 (Glycine max), 5'ss of exon 3
ATCATCGATTGGAGCAGTGTACATGGACCCCAACAGGAGCCCAGATCAAGTTGTGGACGAGAGCTGTTGGAGTGATCTTGAATTCTGCAAGAACACCAAGgtcttcccacctatctttttttcttcaacactatttacccctaattttcatcattttttttcaacattttcgcttcttcttcaacctataatcatcagacttgtctttcatgtcccaaaggtaacggaacggcactaaaataaaatttgactcacccaaaaacaagatttttgattaactgagaggaaaatgcag
 ||||| ||||| || || |||||||||||||| ||||||   |||   || || ||||||  ||||||||||||| | ||||| |||||||||||||||||        | || ||  | | |   |   |  | ||    | |||   | | || || | |     |     | |  |      |  |                                                                                                         
CTCATCCATTGGTGCCGTTTACATGGACCCCAAAAGGAGCATCGATTTGGTGGTTGACGAGTCCTGTTGGAGTGATTTAGAATTTTGCAAGAACACCAAGgtt-------ccattttaatatataataattttctaacataaagtttgagtaagttattataagtgcgtgtatgtttgatattgattgcag--------------------------------------------------------------------------------------------------------

upper sequence: Vv09s0070g00240.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT1G15950.2 (Arabidopsis thaliana), 5'ss of exon 3
ATCATCGATTGGAGCAGTGTACATGGACCCCAACAGGAGCCCAGATCAAGTTGTGGACGAGAGCTGTTGGAGTGATCTTGAATTCTGCAAGAACACCAAGgtcttcccacctatctttttttcttcaacactatttacccctaattttcatcattttttttcaacattttcgcttcttcttcaacctataatcatcagacttgtctttcatgtcccaaaggt---aacggaacggcactaaaataaaatttgactcacccaaaaacaagattt-ttgattaactgagaggaaaatgcag
 || || ||||| || || ||||||||||| ||| |   ||| ||    || || ||||| || ||||||||||||||||| |||||||| |||||||||||||| |   ||  |||  ||| || ||             || ||| |||  | ||  || ||||| ||    || | || ||     |||    | |    | ||| |||||  |||  |   ||      ||  |||   | ||||   | |  |    |    || | | |||| ||  ||   |     || ||
CTCCTCCATTGGTGCCGTCTACATGGACCCGAACCGTGACCCTGAGGCTGTCGTTGACGAAAGTTGTTGGAGTGATCTTGACTTCTGCAAAAACACCAAGgtcttgcactcttgcttcgtttttttaaa------------tattttgcatt-tgttaattaaacatgttta--tcatgttaaaa----aattgaaaaa----tatttaatgtctaaaaaatgtgaattttttggttctattgtgaaatagtattatctttgatgttaggtctattgaatatttgtatgtgttttgtag

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|161714382|gb|FC063223.1|FC063223
EST:     TTGTGGACGAGAGCTGTTGGAGTGATCTTGAATTCTGCAAGAACACCAAG                         AATTGGTATTGTTACGGAAAGGCGGTGGCGGAGCAGGCGGCATGGGAGGTT
genomic: TTGTGGACGAGAGCTGTTGGAGTGATCTTGAATTCTGCAAGAACACCAAGgtcttcccac ... gaaaatgcagAATTGGTATTGTTACGGAAAGGCGGTGGCGGAGCAGGCGGCATGGGAGGTT
EST: gi|161714058|gb|FC063794.1|FC063794
EST:     TTGTGGACGAGAGCTGTTGGAGTGATCTTGAATTCTGCAAGAACACCAAG                         AATTGGTATTGTTACGGAAAGGCGGTGGCGGAGCAGGCGGCATGGGAGGTT
genomic: TTGTGGACGAGAGCTGTTGGAGTGATCTTGAATTCTGCAAGAACACCAAGgtcttcccac ... gaaaatgcagAATTGGTATTGTTACGGAAAGGCGGTGGCGGAGCAGGCGGCATGGGAGGTT
EST: gi|161717599|gb|FC067886.1|FC067886
EST:     TTGTGGACGAGAGCTGTTGGAGTGATCTTGAATTCTGCAAGAACACCAAG                         AATTGGTATTGTTACGGAAAGGCGGTGGCGGAGCAGGCGGCATGGGAGGTT
genomic: TTGTGGACGAGAGCTGTTGGAGTGATCTTGAATTCTGCAAGAACACCAAGgtcttcccac ... gaaaatgcagAATTGGTATTGTTACGGAAAGGCGGTGGCGGAGCAGGCGGCATGGGAGGTT
EST: gi|71873555|gb|DT022610.1|DT022610
EST:     TTGTGGACGAGAGCTGTTGGAGTGATCTTGAATTCTGCAAGAACACCAAG                         AATTGGTATTGTTACGGAAAGGCGGTGGCGGAGCAGGCGGCATGGGAGGTT
genomic: TTGTGGACGAGAGCTGTTGGAGTGATCTTGAATTCTGCAAGAACACCAAGgtcttcccac ... gaaaatgcagAATTGGTATTGTTACGGAAAGGCGGTGGCGGAGCAGGCGGCATGGGAGGTT
EST: gi|161714328|gb|FC062629.1|FC062629
EST:     TTGTGGACGAGAGCTGTTGGAGTGATCTTGAATTCTGCAAGAACACCAAG                         AATTGGTATTGTTACGGAAAGGCGGTGGCGGAGCAGGCGGCATGGGAGGTT
genomic: TTGTGGACGAGAGCTGTTGGAGTGATCTTGAATTCTGCAAGAACACCAAGgtcttcccac ... gaaaatgcagAATTGGTATTGTTACGGAAAGGCGGTGGCGGAGCAGGCGGCATGGGAGGTT
EST: gi|110383896|gb|EC948301.1|EC948301
EST:     TTGTGGACGAGAGCTGTTGGAGTGATCTTGAATTCTGCAAGAACACCAAG                         AATTGGTATTGTTACGGAAAGGCGGTGGCGGAGCAGGCGGCATGGGAGGTT
genomic: TTGTGGACGAGAGCTGTTGGAGTGATCTTGAATTCTGCAAGAACACCAAGgtcttcccac ... gaaaatgcagAATTGGTATTGTTACGGAAAGGCGGTGGCGGAGCAGGCGGCATGGGAGGTT
EST: gi|110710498|gb|EE086896.1|EE086896
EST:     TTGTGGACGAGAGCTGTTGGAGTGATCTTGAATTCTGCAAGAACACCAAG                         AATTGGTATTGTTACGGAAAGGCGGTGGCGGAGCAGGCGGCATGGGAGGTT
genomic: TTGTGGACGAGAGCTGTTGGAGTGATCTTGAATTCTGCAAGAACACCAAGgtcttcccac ... gaaaatgcagAATTGGTATTGTTACGGAAAGGCGGTGGCGGAGCAGGCGGCATGGGAGGTT
EST: gi|71856625|gb|DT005680.1|DT005680
EST:     TTGTGGACGAGAGCTGTTGGAGTGATCTTGAATTCTGCAAGAACACCAAG                         AATTGGTATTGTTACGGAAAGGCGGTGGCGGAGCAGGCGGCATGGGAGGTT
genomic: TTGTGGACGAGAGCTGTTGGAGTGATCTTGAATTCTGCAAGAACACCAAGgtcttcccac ... gaaaatgcagAATTGGTATTGTTACGGAAAGGCGGTGGCGGAGCAGGCGGCATGGGAGGTT
EST: gi|71866385|gb|DT015440.1|DT015440
EST:     TTGTGGACGAGAGCTGTTGGAGTGATCTTGAATTCTGCAAGAACACCAAG                         AATTGGTATTGTTACGGAAAGGCGGTGGCGGAGCAGGCGGCATGGGAGGTT
genomic: TTGTGGACGAGAGCTGTTGGAGTGATCTTGAATTCTGCAAGAACACCAAGgtcttcccac ... gaaaatgcagAATTGGTATTGTTACGGAAAGGCGGTGGCGGAGCAGGCGGCATGGGAGGTT
EST: gi|161719483|gb|FC066419.1|FC066419
EST:     TTGTGGACGAGAGCTGTTGGAGTGATCTTGAATTCTGCAAGAACACCAAG                         AATTGGTATTGTTACGGAAAGGCGGTGGCGGAGCAGGCGGCATGGGAGGTT
genomic: TTGTGGACGAGAGCTGTTGGAGTGATCTTGAATTCTGCAAGAACACCAAGgtcttcccac ... gaaaatgcagAATTGGTATTGTTACGGAAAGGCGGTGGCGGAGCAGGCGGCATGGGAGGTT
EST: gi|110686121|gb|EE063440.1|EE063440
EST:     TTGTGGACGAGAGCTGTTGGAGTGATCTTGAATTCTGCAAGAACACCAAG                         AATTGGTATTGTTACGGAAAGGCGGTGGCGGAGCANGCGGCATGGGAGGTT
genomic: TTGTGGACGAGAGCTGTTGGAGTGATCTTGAATTCTGCAAGAACACCAAGgtcttcccac ... gaaaatgcagAATTGGTATTGTTACGGAAAGGCGGTGGCGGAGCAGGCGGCATGGGAGGTT
EST: gi|71854899|gb|DT003954.1|DT003954
EST:     TTGTGGACGAGAGCTGTTGGAGTGATCTTGAATTCTGCAAGAACACCAAG                         AATTGGTATTGTTACGGAAAGGCGGTGGCGGAGCAGGCGGCATGGGAGGTT
genomic: TTGTGGACGAGAGCTGTTGGAGTGATCTTGAATTCTGCAAGAACACCAAGgtcttcccac ... gaaaatgcagAATTGGTATTGTTACGGAAAGGCGGTGGCGGAGCAGGCGGCATGGGAGGTT
EST: gi|161713112|gb|FC062476.1|FC062476
EST:     TTGTGGACGAGAGCTGTTGGAGTGATCTTGAATTCTGCAAGAACACCAAG                         AATTGGTATTGTTACGGAAAGGCGGTGGCGGAGCAGGCGGCATGGGAGGTT
genomic: TTGTGGACGAGAGCTGTTGGAGTGATCTTGAATTCTGCAAGAACACCAAGgtcttcccac ... gaaaatgcagAATTGGTATTGTTACGGAAAGGCGGTGGCGGAGCAGGCGGCATGGGAGGTT
EST: gi|161717105|gb|FC066553.1|FC066553
EST:     TTGTGGACGAGAGCTGTTGGAGTGATCTTGAATTCTGCAAGAACACCAAG                         AATTGGTATTGTTACGGAAAGGCGGTGGCGGAGCAGGCGGCATGGGAGGTT
genomic: TTGTGGACGAGAGCTGTTGGAGTGATCTTGAATTCTGCAAGAACACCAAGgtcttcccac ... gaaaatgcagAATTGGTATTGTTACGGAAAGGCGGTGGCGGAGCAGGCGGCATGGGAGGTT
EST: gi|110385089|gb|EC949581.1|EC949581
EST:     TTGTGGACGAGAGCTGTTGGAGTGATCTTGAATTCTGCAAGAACACCAAG                         AATTGGTATTGTTACGGAAAGGCGGTGGCGGAGCAGGCGGCATGGGAGGTT
genomic: TTGTGGACGAGAGCTGTTGGAGTGATCTTGAATTCTGCAAGAACACCAAGgtcttcccac ... gaaaatgcagAATTGGTATTGTTACGGAAAGGCGGTGGCGGAGCAGGCGGCATGGGAGGTT
EST: gi|110708939|gb|EE083965.1|EE083965
EST:     TTGTGGACGAGAGCTGTTGGAGTGATCTTGAATTCTGCAAGAACACCAAG                         AATTGGTATTGTTACGGAAAGGCGGTGGCGGAGCAGGCGGCATGGGAGGTT
genomic: TTGTGGACGAGAGCTGTTGGAGTGATCTTGAATTCTGCAAGAACACCAAGgtcttcccac ... gaaaatgcagAATTGGTATTGTTACGGAAAGGCGGTGGCGGAGCAGGCGGCATGGGAGGTT
EST: gi|110372072|gb|EC936216.1|EC936216
EST:     TTGTGGACGAGAGCTGTTGGAGTGATCTTGAATTCTGCAAGAACACCAAG                         AATTGGTATTGTTACGGAAAGGCGGTGGCGGAGCAGGCGGCATGGGAGGTT
genomic: TTGTGGACGAGAGCTGTTGGAGTGATCTTGAATTCTGCAAGAACACCAAGgtcttcccac ... gaaaatgcagAATTGGTATTGTTACGGAAAGGCGGTGGCGGAGCAGGCGGCATGGGAGGTT
EST: gi|110398867|gb|EC965343.1|EC965343
EST:     TTGTGGACGAGAGCTGTTGGAGTGATCTTGAATTCTGCAAGAACACCAAG                         AATTGGTATTGTTACGGAAAGGCGGTGGCGGAGCAGGCGGCATGGGAGGTT
genomic: TTGTGGACGAGAGCTGTTGGAGTGATCTTGAATTCTGCAAGAACACCAAGgtcttcccac ... gaaaatgcagAATTGGTATTGTTACGGAAAGGCGGTGGCGGAGCAGGCGGCATGGGAGGTT
EST: gi|161712542|gb|FC061847.1|FC061847
EST:     TTGTGGACGAGAGCTGTTGGAGTGATCTTGAATTCTGCAAGAACACCAAG                         AATTGGTATTGTTACGGAAAGGCGGTGGCGGAGCAGGCGGCATGGGAGGTT
genomic: TTGTGGACGAGAGCTGTTGGAGTGATCTTGAATTCTGCAAGAACACCAAGgtcttcccac ... gaaaatgcagAATTGGTATTGTTACGGAAAGGCGGTGGCGGAGCAGGCGGCATGGGAGGTT
EST: gi|161717252|gb|FC067258.1|FC067258
EST:     TTGTGGACGAGAGCTGTTGGAGTGATCTTGAATTCTGCAAGAACACCAAG                         AATTGGTATTGTTACGGAAAGGCGGTGGCGGAGCAGGCGGCATGGGAGGTT
genomic: TTGTGGACGAGAGCTGTTGGAGTGATCTTGAATTCTGCAAGAACACCAAGgtcttcccac ... gaaaatgcagAATTGGTATTGTTACGGAAAGGCGGTGGCGGAGCAGGCGGCATGGGAGGTT
EST: gi|110384860|gb|EC949326.1|EC949326
EST:     TTGTGGACGAGAGCTGTTGGAGTGATCTTGAATTCTGCAAGAACACCAAG                         AATTGGTATTGTTACGGAAAGGCGGTGGCAGAGCAGGCGGCATGGGAGGTT
genomic: TTGTGGACGAGAGCTGTTGGAGTGATCTTGAATTCTGCAAGAACACCAAGgtcttcccac ... gaaaatgcagAATTGGTATTGTTACGGAAAGGCGGTGGCGGAGCAGGCGGCATGGGAGGTT
EST: gi|110685724|gb|EE062693.1|EE062693
EST:     TTGTGGACGAGAGCTGTTGGAGTGATCTTGAATTCTGCAAGAACACCAAG                         AATTGGTATTGTTACGGAAAGGCGGTGGCGGAGCAGGCGGCATGGGAGGTT
genomic: TTGTGGACGAGAGCTGTTGGAGTGATCTTGAATTCTGCAAGAACACCAAGgtcttcccac ... gaaaatgcagAATTGGTATTGTTACGGAAAGGCGGTGGCGGAGCAGGCGGCATGGGAGGTT
EST: gi|110732417|gb|EE107684.1|EE107684
EST:     TTGTGGACGAGAGCTGTTGGAGTGATCTTGAATTCTGCAAGAACACCAAG                         AATTGGTATTGTTACGGAAAGGCGGTGGCGGAGCAGGCGGCATGGGAGGTT
genomic: TTGTGGACGAGAGCTGTTGGAGTGATCTTGAATTCTGCAAGAACACCAAGgtcttcccac ... gaaaatgcagAATTGGTATTGTTACGGAAAGGCGGTGGCGGAGCAGGCGGCATGGGAGGTT
EST: gi|110365510|gb|EC928612.1|EC928612
EST:     TTGTGGACGAGAGCTGTTGGAGTGATCTTGAATTCTGCAAGAACACCAAG                         AATTGGTATTGTTACGGAAAGGCGGTGGCGGAGCAGGCGGCATGGGAGGTT
genomic: TTGTGGACGAGAGCTGTTGGAGTGATCTTGAATTCTGCAAGAACACCAAGgtcttcccac ... gaaaatgcagAATTGGTATTGTTACGGAAAGGCGGTGGCGGAGCAGGCGGCATGGGAGGTT
EST: gi|77582495|gb|DV220225.1|DV220225
EST:     TTGTGGACGAGAGCTGTTGGAGTGATCTTGAATTCTGCAAGAACACCAAG                         AATTGGTATTGTTACGGAAAGGCGGTGGCGGAGCAGGCGGCATGGGAGGTT
genomic: TTGTGGACGAGAGCTGTTGGAGTGATCTTGAATTCTGCAAGAACACCAAGgtcttcccac ... gaaaatgcagAATTGGTATTGTTACGGAAAGGCGGTGGCGGAGCAGGCGGCATGGGAGGTT
EST: gi|110383367|gb|EC947736.1|EC947736
EST:     TTGTGGACGAGAGCTGTTGGAGTGATCTTGAATTCTGCAAGAACACCAAG                         AATTGGTATTGTTACGGAAAGGCGGTGGCGGAGCAGGCGGCATGGGAGGTT
genomic: TTGTGGACGAGAGCTGTTGGAGTGATCTTGAATTCTGCAAGAACACCAAGgtcttcccac ... gaaaatgcagAATTGGTATTGTTACGGAAAGGCGGTGGCGGAGCAGGCGGCATGGGAGGTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCATCGATTGGAGCAGTGTACATGGACCCCAACAGGAGCCCAGATCAAGTTGTGGACGAGAGCTGTTGGAGTGATCTTGAATTCTGCAAGAACACCAAGgtcttcccacctatctttttttcttcaacactatttacccctaattttcatcattttttttcaacattttcgcttcttcttcaacctataatcatcagacttgtctttcatgtcccaaaggtaacggaacggcactaaaataaaatttgactcacccaaaaacaagatttttgattaactgagaggaaaatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC