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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgaactgctttggaagctatcgtttgctatttgttctttgttttctgcttgccttattgttggaatgaaccaagtccatatgctttgatatgatattagGATCCAGCTTACTATCTTCTCAAAGAAGATGCCTCCCCCTGCATTTTTGGTTCAATTGAGAAGCAGAGATGGTCCTATGCCTGTGCAAAGCAATTAATTG

Basic information

species Vitis vinifera
transcript Vv03s0017g00680.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0017g00680.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os01g73790.1 (Oryza sativa), 3'ss of exon 3
ttgaactgctttggaagctatcgtttgc-tatttgttctttgttttctgcttgccttattgttggaatgaacc--aagtccatatgcttt--gatatgatattagGATCCAGCTTACTATCTTCTCAAAGAAGATGCCTCCCCCTGCATTTTTGGTTCAATTGAGAAGCAGAGATGGTCCTATGCCTGTGCAAAGCAATTAATTG
    |  |     | ||| |  ||   | |     ||   ||| ||    |||  | |   |||      | |  |  |   | | | ||   |  |   |  |||| || |  |  ||| | || ||||||||||  |||||||||||||||||| |||||| ||| ||| ||||||| ||||| ||||| |||||  | ||||
----atggagaaaggagcaagtgtaaacctgcccattacatgtcttaattttga-tcacaattgactcttatctgatatttgtgtaccttcaaactttgaaacagGAACCTGAATTTTATGTACTGAAAGAAGATGAATCCCCCTGCATTTTTGGTCCAATTGTGAAACAGCGATGGTCTTATGCATGTGCGAAGCAGCTTATTG

upper sequence: Vv03s0017g00680.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G063949_T01 (Zea mays), 3'ss of exon 3
--ttgaactgctttggaagctatcgtttgctatttgttctttgttttctgcttgccttattgttggaatgaaccaagtccata-tgctttgatatgatat-tagGATCCAGCTTACTATCTTCTCAAAGAAGATGCCTCCCCCTGCATTTTTGGTTCAATTGAGAAGCAGAGATGGTCCTATGCCTGTGCAAAGCAATTAATTG
  ||  |   |||   | |   |   ||| || ||  | |||||| | |  | |   ||    |  | |     | ||   |  | || | ||||   |   |||| || |  |  ||| |||| ||||||||||  || ||||| ||||||||| |||| | ||| || |||||||||||||| || ||||||||| | ||||
ctttccataactt--aatgtggtgaattgataatt-ctgtttgttgtattgtggtgatacctgtccatttc-tgatgtttgtgctcctcttatatttcaaacagGAGCCTGAATTTTATGTTCTTAAAGAAGATGAGTCGCCCTGTATTTTTGGTCCAATCGTGAAACAAAGATGGTCCTATGCATGCGCAAAGCAACTTATTG

upper sequence: Vv03s0017g00680.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA12G30490.2 (Glycine max), 3'ss of exon 3
ttgaactgctttggaagctatc--gtttgctatttgttctttgttttctgcttgccttattgttggaatgaaccaagtccatatgcttt-gatatgatattagGATCCAGCTTACTATCTTCTCAAAGAAGATGCCTCCCCCTGCATTTTTGGTTCAATTGAGAAGCAGAGATGGTCCTATGCCTGTGCAAAGCAATTAATTG
 | | ||   | |||   || |  |   | | |||| |  |||  ||    ||   ||  |  || | |||   | ||     || |||  || || | | ||||||| || |||||  | || || || ||||  || || || ||||||||||||||||| |||||||||||||||||||||||||| ||||| || ||||
-ttatctaaataggatcttagcaagggagttgtttggttgttgcgtttctttt-ttttggtaatgaactgagttatgttatgttgttttcaatttggtgt-agGATCCTGCATACTACGTACTTAAGGAGGATGAGTCTCCTTGTATTTTTGGTTCAATTGAAAAGCAGAGATGGTCCTATGCCTGTGCTAAGCAGTTGATTG

upper sequence: Vv03s0017g00680.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA17G05440.1 (Glycine max), 3'ss of exon 1
--ttgaactgctttggaagctatcgtttgctatttgttctttgttttctgcttgccttattgttggaatgaaccaagtccatatgctttgatatgatattagGATCCAGCTTACTATCTTCTCAAAGAAGATGCCTCCCCCTGCATTTTTGGTTCAATTGAGAAGCAGAGATGGTCCTATGCCTGTGCAAAGCAATTAATTG
  || | |    | |||   || |    |  | |||||   |  || ||  ||   ||  |  ||   |||   |  |     || ||| |  |     |||||||| || |||||  | || || || ||||  || || || ||||||||||||||||| |||||||||||||||||||| ||||| ||||| || ||||
actttatccaaataggatcttagcaaggg--agttgtttggttgttgcttttttttttggtaatgagctgagttatattatgttgttttcaattttgtgtagGATCCTGCATACTACGTACTTAAGGAGGATGAATCTCCTTGTATTTTTGGTTCAATTGAAAAGCAGAGATGGTCCTATGCATGTGCTAAGCAGTTGATTG

upper sequence: Vv03s0017g00680.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA11G19550.1 (Glycine max), 3'ss of exon 3
ttgaactgctttggaagctatcgtttgctat-ttgttctttgttttctgcttgccttattgttggaatgaaccaagtccatatgctt-tgatatgatattagGATCCAGCTTACTATCTTCTCAAAGAAGATGCCTCCCCCTGCATTTTTGGTTCAATTGAGAAGCAGAGATGGTCCTATGCCTGTGCAAAGCAATTAATTG
  |   ||  |||| ||| |  ||| | |   ||| |  ||||||  | ||||   |    |||   |||     ||   | || ||   || |  | ||||||||| || |||||| |||| |||||||| |  || || |||||||||||||| || ||||||||||| ||||| ||||| |||||||| || || ||||
--gttttgtattgggagcaagggttggttgggttggttgttgtttctttcttgtgatgagattgagctgagatgtgttgttttgtttgcaatgttttgttagGATCCGGCATACTATGTTCTTAAAGAAGACGAATCTCCTTGCATTTTTGGTTCTATCGAGAAGCAGAGGTGGTCTTATGCATGTGCAAAACAGTTGATTG

upper sequence: Vv03s0017g00680.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA12G08930.1 (Glycine max), 3'ss of exon 3
-ttgaactgctttggaagctatcgtttgctatttgttctttgttttctgcttgccttattgttggaatgaaccaagtccatatgctttgatatgatattagGATCCAGCTTACTATCTTCTCAAAGAAGATGCCTCCCCCTGCATTTTTGGTTCAATTGAGAAGCAGAGATGGTCCTATGCCTGTGCAAAGCAATTAATTG
 | |   ||  |||| ||| |  ||| | |  |||||  ||||||  | |||    |    |||   |||     ||   | || ||  |  |  | ||||||||| || |||||| |||| |||||||| |  || || |||||||||||||| ||||| || ||||| ||||| ||||||||||| || || || ||||
ctggttttgtattgggagcaagggttggttggttgtttgttgtttctttcttctgatgggattgagctgatatgtgtt-gtttgtttgcaatttgtgttagGATCCGGCATACTATGTTCTTAAAGAAGACGAGTCTCCTTGCATTTTTGGTTCTATTGAAAAACAGAGGTGGTCTTATGCCTGTGCGAAACAGTTGATTG

upper sequence: Vv03s0017g00680.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT2G27860.1 (Arabidopsis thaliana), 3'ss of exon 3
--------ttgaactgctttggaagctatcgtttgctatttgttctttgttttctgcttgccttattgttggaatgaaccaagtccatatgctttgatatgatattagGATCCAGCTTACTATCTTCTCAAAGAAGATGCCTCCCCCTGCATTTTTGGTTCAATTGAGAAGCAGAGATGGTCCTATGCCTGTGCAAAGCAATTAATTG
        |   ||  |  | ||||||     | | |  |  || || || |   | | |  | | ||||  | |||      |   | ||| ||  ||       ||||||| |||| |||| |||| |||||||||   ||||| ||||| ||||||||||||||||||||||| ||||| ||||| |||||||||||| | ||||
ctagtctatcacacacccatagaagcttggaatagttgat-attattcgtctaaggttgggttcactgttt-actgatgttgtttgttgtgcctttctac------agGATCCTGCTTTCTATGTTCTTAAAGAAGATATTTCCCCTTGCATATTTGGTTCAATTGAGAAGCAGAGGTGGTCATATGCGTGTGCAAAGCAACTGATTG

upper sequence: Vv03s0017g00680.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT1G08200.1 (Arabidopsis thaliana), 3'ss of exon 3
ttgaactgctttggaagctatcgtttgctatttgttctttgttttctgc-ttgccttattgttggaatga--accaagtccatatgctttgatatgatattagGATCCAGCTTACTATCTTCTCAAAGAAGATGCCTCCCCCTGCATTTTTGGTTCAATTGAGAAGCAGAGATGGTCCTATGCCTGTGCAAAGCAATTAATTG
  ||  | | || |   |    | ||  ||||  | ||||  | ||||  ||   ||||| ||  | |    |||||        |  ||| | |  ||  ||||||| |  |  ||| | ||||||||||||   ||||| ||||| ||||||||||||||||||||||| ||||| ||||| |||||||||||| | ||||
-agatattcgttcgtgtcacgtggttcttattactacttttgtctctgtgttttgttattatttcactactcaccaatgatgctcgtcttgtt-tactac-agGATCCTGAATTTTATGTACTCAAAGAAGATATATCCCCTTGCATCTTTGGTTCAATTGAGAAGCAGAGGTGGTCATATGCTTGTGCAAAGCAACTTATTG

upper sequence: Vv03s0017g00680.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: EFJ07025 (Selaginella moellendorffii), 3'ss of exon 3
ttgaactgctttggaagctatcgtttgctatttgttctttgttttctgcttgccttattgttggaatgaaccaagtccatatgctttgat-atgatattagGATCCAGCTTACTATCTTCTCAAAGAAGATGCCTCCCCCTGCATTTTTGGTTCAATTGAGAAGCAGAGATGGTCCTATGCCTGTGCAAAGCAATTAATTG
                |  |||  |  | | ||  |||| || |     || |||| |  |        | |  ||   | |  | || |  ||     |||| ||   ||||||  | || || || || |  || || |||||||||||  | |||||||||||| ||||||| ||||| |||||||||||  | || |
----------------gtgatctctatccagtttctcttcgtctgac-tttaccttttcttc------tatcgtgtttttttattctgttcgtggcgacagGACCCGAGTTACTACGTCCTTAAGGAGGACGAGTCTCCTTGCATTTTTGGCCCGATTGAGAAGCAGCGATGGTCGTATGCTTGTGCAAAGCAGCTGATCG

upper sequence: Vv03s0017g00680.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: EFJ18978 (Selaginella moellendorffii), 3'ss of exon 3
ttgaactgctttggaagctatcgtttgctatttgttctttgttttctgcttgccttattgttggaatgaaccaagtccatatgctttgat-atgatattagGATCCAGCTTACTATCTTCTCAAAGAAGATGCCTCCCCCTGCATTTTTGGTTCAATTGAGAAGCAGAGATGGTCCTATGCCTGTGCAAAGCAATTAATTG
                |  |||  |  | | ||  |||| || |     || |||| |  |        | |  ||   | |  | || |  ||     |||| ||   ||||||  | || || || || |  || || |||||||||||  | |||||||||||| ||||||| ||||| |||||||||||  | || |
----------------gtgatctctatccagtttctcttcgtctgac-tttaccttttcttc------tatcgtgtttttttattctgttcgtggcgacagGACCCGAGTTACTACGTGCTTAAGGAGGACGAGTCTCCTTGCATTTTTGGCCCGATTGAGAAGCAGCGATGGTCGTATGCTTGTGCAAAGCAGCTGATCG

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|110732834|gb|EE108465.1|EE108465
EST:     ATGGGAAAACGATTGGGAGCTTTCTTCCCAAAGATTCACCTCTCCGGCAG                         GATCCAGCTTACTATCTTCTCAAAGAAGATGCCTCCCCCTGCATTTTTGGT
genomic: ATGGGAAAACGATTGGGAGCTTTCTTCCCAAAGATTCACCTCTCCGGCAGgtgagatctc ... atgatattagGATCCAGCTTACTATCTTCTCAAAGAAGATGCCTCCCCCTGCATTTTTGGT
EST: gi|71857207|gb|DT006262.1|DT006262
EST:     ATGGGAAAACGATTGGGAGCTTTCTTCCCAAAGATTCACCTCTCCGGCAG                         GATCCAGCTTACTATCTTCTCAAAGAAGATGCCTCCCCCTGCATTTTTGGT
genomic: ATGGGAAAACGATTGGGAGCTTTCTTCCCAAAGATTCACCTCTCCGGCAGgtgagatctc ... atgatattagGATCCAGCTTACTATCTTCTCAAAGAAGATGCCTCCCCCTGCATTTTTGGT
EST: gi|110387369|gb|EC952029.1|EC952029
EST:     ATGGGAAAACGATTGGGAGCTTTCTTCCCAAAGATTCACCTCTCCGGCAG                         GATCCAGCTTACTATCTTCTCAAAGAAGATGCCTCCCCCTGC
genomic: ATGGGAAAACGATTGGGAGCTTTCTTCCCAAAGATTCACCTCTCCGGCAGgtgagatctc ... atgatattagGATCCAGCTTACTATCTTCTCAAAGAAGATGCCTCCCCCTGC
EST: gi|71859790|gb|DT008845.1|DT008845
EST:     ATGGGAAAACGATTGGGAGCTTTCTTCCCAAAGATTCACCTCTCCGGCAG                         GATCCAGCTTACTATCTTCTCAAAGAAGATGCCTCCCCCTGCATTTTTGGT
genomic: ATGGGAAAACGATTGGGAGCTTTCTTCCCAAAGATTCACCTCTCCGGCAGgtgagatctc ... atgatattagGATCCAGCTTACTATCTTCTCAAAGAAGATGCCTCCCCCTGCATTTTTGGT
EST: gi|110686702|gb|EE064638.1|EE064638
EST:     ATGGGAAAACGATTGGGAGCTTTCTTCCCAAAGATTCACCTCTCCGGCAG                         GATCCAGCTTACTATCTTCTCAAAGAAGATGCCTCCCCCTGCATTTTTGGT
genomic: ATGGGAAAACGATTGGGAGCTTTCTTCCCAAAGATTCACCTCTCCGGCAGgtgagatctc ... atgatattagGATCCAGCTTACTATCTTCTCAAAGAAGATGCCTCCCCCTGCATTTTTGGT
EST: gi|110359156|gb|EC920189.1|EC920189
EST:     ATGGGAAAACGATTGGGAGCTTTCTTCCCAAAGATTCACCTCTCCGGCAG                         GATCCAGCTTACTATCTTCTCAAAGAAGATGCCTCCCCCTGCATTTTTGGT
genomic: ATGGGAAAACGATTGGGAGCTTTCTTCCCAAAGATTCACCTCTCCGGCAGgtgagatctc ... atgatattagGATCCAGCTTACTATCTTCTCAAAGAAGATGCCTCCCCCTGCATTTTTGGT
EST: gi|161710980|gb|FC060335.1|FC060335
EST:     ATGGGAAAACGATTGGGAGCTTTCTTCCCAAAGATTCACCTCTCCGGCAG                         GATCCAGCTTACTATCTTCTCAAAGAAGATGCCTCCCCCT
genomic: ATGGGAAAACGATTGGGAGCTTTCTTCCCAAAGATTCACCTCTCCGGCAGgtgagatctc ... atgatattagGATCCAGCTTACTATCTTCTCAAAGAAGATGCCTCCCCCT
EST: gi|30253074|gb|CB970625.1|CB970625
EST:     ATGGGAAAACGATTGGGAGCTTTCTTCCCAAAGATTCACCTCTCCGGCAG                         GATCCAGCTTACTATCTTCTCAAAGAAGATGCCTCCCCCTGCATTTTTGGT
genomic: ATGGGAAAACGATTGGGAGCTTTCTTCCCAAAGATTCACCTCTCCGGCAGgtgagatctc ... atgatattagGATCCAGCTTACTATCTTCTCAAAGAAGATGCCTCCCCCTGCATTTTTGGT
EST: gi|110696696|gb|EE073040.1|EE073040
EST:     AAAACGATTGGGAGCTTTCTTCCCAAAGATTCACCTCTCCGGCAG                         GATCCAGCTTACTATCTTCTCAAAGAAGATGCCTCCCCCTGCATTTTTGGT
genomic: AAAACGATTGGGAGCTTTCTTCCCAAAGATTCACCTCTCCGGCAGgtgagatctc ... atgatattagGATCCAGCTTACTATCTTCTCAAAGAAGATGCCTCCCCCTGCATTTTTGGT
EST: gi|30320980|gb|CD004242.1|CD004242
EST:     ATGGGAAAACGATTGGGAGCTTTCTTCCCAAAGATTCACCTCTCCGGCAG                         GATCCAGCTTACTATCTTCTCAAAGAAGATGCCTCCCCCTGCATTTTTGGT
genomic: ATGGGAAAACGATTGGGAGCTTTCTTCCCAAAGATTCACCTCTCCGGCAGgtgagatctc ... atgatattagGATCCAGCTTACTATCTTCTCAAAGAAGATGCCTCCCCCTGCATTTTTGGT
EST: gi|110685502|gb|EE062276.1|EE062276
EST:     ATGGGAAAACGATTGGGAGCTTTCTTCC-AA-GATTCACCTCTCCGGCAG                         GATCCAGCTTACTATCTTCTCAAAGAAGATGCCTCCCCCTGCATTTTTGGT
genomic: ATGGGAAAACGATTGGGAGCTTTCTTCCCAAAGATTCACCTCTCCGGCAGgtgagatctc ... atgatattagGATCCAGCTTACTATCTTCTCAAAGAAGATGCCTCCCCCTGCATTTTTGGT
EST: gi|71862682|gb|DT011737.1|DT011737
EST:     ATGGGAAAACGATTGGGAGCTTTCTTCCCAAAGATTCACCTCTCCGGCAG                         GATCCAGCTTACTATCTTCTCA
genomic: ATGGGAAAACGATTGGGAGCTTTCTTCCCAAAGATTCACCTCTCCGGCAGgtgagatctc ... atgatattagGATCCAGCTTACTATCTTCTCA
EST: gi|77585098|gb|DV221638.1|DV221638
EST:     ATGGGAAAACGATTGGGAGCTTTCTTCCCAAAGATTCACCTCTCCGGCAG                         GATCCAGCTTACTATCTTCTCAAAGAAGATGCCTCCCCCTGCATTTTTGGT
genomic: ATGGGAAAACGATTGGGAGCTTTCTTCCCAAAGATTCACCTCTCCGGCAGgtgagatctc ... atgatattagGATCCAGCTTACTATCTTCTCAAAGAAGATGCCTCCCCCTGCATTTTTGGT
EST: gi|71855470|gb|DT004525.1|DT004525
EST:     ATGGGAAAACGATTGGGAGCTTTCTTCCCAAAGATTCACCTCTCCGGCAG                         GATCCAGCTTACTATCTTCTCAAAGAAGATGCCTCCCCCTGCATTTTTGGT
genomic: ATGGGAAAACGATTGGGAGCTTTCTTCCCAAAGATTCACCTCTCCGGCAGgtgagatctc ... atgatattagGATCCAGCTTACTATCTTCTCAAAGAAGATGCCTCCCCCTGCATTTTTGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgcttgccttattgttggaatgaaccaagtccatatgctttgatatgatattagGATCCAGCTTACTATCTTCTCAAAGAAGATGCCTCCCCCTGCATTTTTGGTTCAATTGAGAAGCAGAGATGGTCCTATGCCTGTGCAAAGCAATTAATTG
                                      ctttgat  putative branch site (score: 5)
                                       tttgatatgatatta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgaactgctttggaagctatcgtttgctatttgttctttgttttctgcttgccttattgttggaatgaaccaagtccatatgctttgatatgatattagGATCCAGCTTACTATCTTCTCAAAGAAGATGCCTCCCCCTGCATTTTTGGTTCAATTGAGAAGCAGAGATGGTCCTATGCCTGTGCAAAGCAATTAATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - tgctttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccatatg