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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aattgacttgctctttgcttatttgacaagtttatctatttggatttcacatctatactgctgaagcttggttggtaattacgttgtttgaactttgcagGGAGATGCTGACAGTGCCCTTGATAGGCTCTGGCAAAAGAAGAAAGCCGAAGTCCGGCAACAGTAGTTCCAGTCTCTTTAAACATTTTCCTTCATGATAG

Basic information

species Vitis vinifera
transcript Vv14s0060g02110.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0060g02110.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: EFJ24774 (Selaginella moellendorffii), 3'ss of exon 2
aattgacttgctctttgcttatttgacaagtttatctatttggatttcacatctatactgctgaagcttggttggtaattacgttgtttgaactttgcagGGAGATGCTGACAGTGCCCTTGATAGGCTCTGGCAAAAGAAGAAAGCCGAAGTCCGGCAACAGTAGTTCCAGTCTCTTTAAACATTTTCCTTCATGATAG
                             ||  ||||    |  |||| | |||   || |   ||||  |     | ||   ||   ||  |||| ||||||||||  |||||||| || ||| |||| ||||| ||||||||||||||  ||  |||  ||  |       |     | |  |      ||||| |  
-----------------------------gtaaatctccgcgactttctcttct---cttcgagagctctg-----agttctttttcgtgctctttccagGGAGATGTGGACAGTGCGCTGGATCGGCTATGGCAGAAGAAGAAAGCCGAGCTCAAGCAGTAGCGGCGGTGAACCACCAAGAACTCGCTTCTCATGTTTT

upper sequence: Vv14s0060g02110.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: EFJ15472 (Selaginella moellendorffii), 3'ss of exon 2
aattgacttgctctttgcttatttgacaagtttatctatttggatttcacatctatactgctgaagcttggttggtaattacgttgtttgaactttgcagGGAGATGCTGACAGTGCCCTTGATAGGCTCTGGCAAAAGAAGAAAGCCGAAGTCCGGCAACAGTAGTTCCAGTCTCTTTAAACATTTTCCTTCATGATAG
                             ||  ||||    |  |||| | ||| |           |  ||| ||| ||    |   ||  |||| ||||||||||  |||||||| || ||| |||| ||||| ||||||||||||||  ||  |||  ||  |       |     | |  |      ||||| |  
-----------------------------gtaaatctccgcgactttctcttctct-----------tgagttagtagttcttcttcgtgctctttccagGGAGATGTGGACAGTGCGCTGGATCGGCTATGGCAGAAGAAGAAAGCCGAGCTCAAGCAGTAGCGGCGGTGAACCACCAAGAACTCGCTTCTCATGTTTT
















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|77584391|gb|DV221265.1|DV221265
EST:     ACACCGGTCAATTTACTACCTTTGCTCTTTGCGGCTTTGTCCGGGCTCAG                         GGAGATGCTGACAGTGCCCTTGATAGGCTCTGGCAAAAGAAGAAAGCCGAA
genomic: ACACCGGTCAATTTACTACCTTTGCTCTTTGCGGCTTTGTCCGGGCTCAGgttatttttc ... aactttgcagGGAGATGCTGACAGTGCCCTTGATAGGCTCTGGCAAAAGAAGAAAGCCGAA
EST: gi|34320516|gb|CF373270.1|CF373270
EST:     ACACCGGTCAATTTACTACCTTTGCTCTTTGCGGCTTTGTCCGGGCTCAG                         GGAGATGCTGACAGTGCCCTTGATAGGCTCTGGCAAAAGAAGAAAGCCGAA
genomic: ACACCGGTCAATTTACTACCTTTGCTCTTTGCGGCTTTGTCCGGGCTCAGgttatttttc ... aactttgcagGGAGATGCTGACAGTGCCCTTGATAGGCTCTGGCAAAAGAAGAAAGCCGAA
EST: gi|77587917|gb|DV223161.1|DV223161
EST:     ACACCGGTCAATTTACTACCTTTGCTCTTTGCGGCTTTGTCCGGGCTCAG                         GGAGATGCTGACAGTGCCCTTGATAGGCTCTGGCAAAAGAAGAAAGCCGAA
genomic: ACACCGGTCAATTTACTACCTTTGCTCTTTGCGGCTTTGTCCGGGCTCAGgttatttttc ... aactttgcagGGAGATGCTGACAGTGCCCTTGATAGGCTCTGGCAAAAGAAGAAAGCCGAA
EST: gi|110372534|gb|EC936710.1|EC936710
EST:     ACACCGGTCAATTTACTACCTTTGCTCTTTGCGGCTTTGTCCGGGCTCAG                         GGAGATGCTGACAGTGCCCTTGATAGGCTCTGGCAAAAGAAGAAAGCCGAA
genomic: ACACCGGTCAATTTACTACCTTTGCTCTTTGCGGCTTTGTCCGGGCTCAGgttatttttc ... aactttgcagGGAGATGCTGACAGTGCCCTTGATAGGCTCTGGCAAAAGAAGAAAGCCGAA
EST: gi|110691741|gb|EE070187.1|EE070187
EST:     ACACCGGTCAATTTACTACCTTTGCTCTTTGCGGCTTTGTCCGGGCTCAG                         GGAGATGCTGACAGTGCCCTTGATAGGCTCTGGCAAAAGAAGAAAGCCGAA
genomic: ACACCGGTCAATTTACTACCTTTGCTCTTTGCGGCTTTGTCCGGGCTCAGgttatttttc ... aactttgcagGGAGATGCTGACAGTGCCCTTGATAGGCTCTGGCAAAAGAAGAAAGCCGAA
EST: gi|110401045|gb|EC967638.1|EC967638
EST:     GGTCAATTTACTACCTTTGCTCTTTGCGGCTTTGTCCGGGCTCAG                         GGAGATGCTGACAGTGCCCTTGATAGGCTCTGGCAAAAGAAGAAAGCCGAA
genomic: GGTCAATTTACTACCTTTGCTCTTTGCGGCTTTGTCCGGGCTCAGgttatttttc ... aactttgcagGGAGATGCTGACAGTGCCCTTGATAGGCTCTGGCAAAAGAAGAAAGCCGAA
EST: gi|110385849|gb|EC950405.1|EC950405
EST:     ACACCGGTCAATTTACTACCTTTGCTCTTTGCGGCTTTGTCCGGGCTCAG                         GGAGATGCTGACAGTGCCCTTGATAGGCTCTGGCAAAAGAAGAAAGCCGAA
genomic: ACACCGGTCAATTTACTACCTTTGCTCTTTGCGGCTTTGTCCGGGCTCAGgttatttttc ... aactttgcagGGAGATGCTGACAGTGCCCTTGATAGGCTCTGGCAAAAGAAGAAAGCCGAA
EST: gi|71879577|gb|DT028632.1|DT028632
EST:     ACACCGGTCAATTTACTACCTTTGCTCTTTGCGGCTTTGTCCGGGCTCAG                         GGAGATGCTGACAGTGCCCTTGATAGGCTCTGGCAAAAGAAGAAAGCCGAA
genomic: ACACCGGTCAATTTACTACCTTTGCTCTTTGCGGCTTTGTCCGGGCTCAGgttatttttc ... aactttgcagGGAGATGCTGACAGTGCCCTTGATAGGCTCTGGCAAAAGAAGAAAGCCGAA
EST: gi|34416942|gb|CF415696.1|CF415696
EST:     ACACCGGTCAATTTACTACCTTTGCTCTTTGCGGCTTTGTCCGGGCTCAG                         GGAGATGCTGACAGTGCCCTTGATAGGCTCTGGCAAAAGAAGAAAGCCGAA
genomic: ACACCGGTCAATTTACTACCTTTGCTCTTTGCGGCTTTGTCCGGGCTCAGgttatttttc ... aactttgcagGGAGATGCTGACAGTGCCCTTGATAGGCTCTGGCAAAAGAAGAAAGCCGAA
EST: gi|110696100|gb|EE074877.1|EE074877
EST:     ACACCGGTCAATTTACTACCTTTGCTCTTTGCGGCTTTGTCCGGGCTCAA                         GGAGATGCTGACAGTGCCCTTGATAGGCTCTGGCAAAAGAAGAAAGCCGAA
genomic: ACACCGGTCAATTTACTACCTTTGCTCTTTGCGGCTTTGTCCGGGCTCAGgttatttttc ... aactttgcagGGAGATGCTGACAGTGCCCTTGATAGGCTCTGGCAAAAGAAGAAAGCCGAA
EST: gi|110396771|gb|EC962470.1|EC962470
EST:     ACACCGGTCAATTTACTACCTTTGCTCTTTGCGGCTTTGTCCGGGCTCAG                         GGAGATGCTGACAGTGCCCTTGATAGGCTCTGGCAAAAGAAGAAAGCCGAA
genomic: ACACCGGTCAATTTACTACCTTTGCTCTTTGCGGCTTTGTCCGGGCTCAGgttatttttc ... aactttgcagGGAGATGCTGACAGTGCCCTTGATAGGCTCTGGCAAAAGAAGAAAGCCGAA
EST: gi|110425492|gb|EC991877.1|EC991877
EST:     ACACCGGTCAATTTACTACCTTTGCTCTTTGCGGCTTTGTCCGGGCTCAG                         GGAGATGCTGACAGTGCCCTTGATAGGCTCTGGCAAAAGAAGAAAGCCGAA
genomic: ACACCGGTCAATTTACTACCTTTGCTCTTTGCGGCTTTGTCCGGGCTCAGgttatttttc ... aactttgcagGGAGATGCTGACAGTGCCCTTGATAGGCTCTGGCAAAAGAAGAAAGCCGAA
EST: gi|110692217|gb|EE071207.1|EE071207
EST:     ACACCGGTCAATTTACTACCTTTGCTCTTTGCGGCTTTGTCCGGGCTCAG                         GGAGATGCTGACAGTGCCCTTGATAGGCTCTGGCAAAAGAAGAAAGCCGAA
genomic: ACACCGGTCAATTTACTACCTTTGCTCTTTGCGGCTTTGTCCGGGCTCAGgttatttttc ... aactttgcagGGAGATGCTGACAGTGCCCTTGATAGGCTCTGGCAAAAGAAGAAAGCCGAA
EST: gi|110693060|gb|EE068961.1|EE068961
EST:     ACACCGGTCAATTTACTACCTTTGCTCTTTGCGGCTTTGTCCGGGCTCAG                         GGAGATGCTGACAGTGCCCTTGATAGGCTCTGGCAAAAGAAGAAAGCCGAA
genomic: ACACCGGTCAATTTACTACCTTTGCTCTTTGCGGCTTTGTCCGGGCTCAGgttatttttc ... aactttgcagGGAGATGCTGACAGTGCCCTTGATAGGCTCTGGCAAAAGAAGAAAGCCGAA
EST: gi|34416577|gb|CF415331.1|CF415331
EST:     ACACCGGTCAATTTACTACCTTTGCTCTTTGCGGCTTTGTCCGGGCTCAG                         GGAGATGCTGACAGTGCCCTTGATAGGCTCTGGCAAAAGAAGAAAGCCGAA
genomic: ACACCGGTCAATTTACTACCTTTGCTCTTTGCGGCTTTGTCCGGGCTCAGgttatttttc ... aactttgcagGGAGATGCTGACAGTGCCCTTGATAGGCTCTGGCAAAAGAAGAAAGCCGAA
EST: gi|34415798|gb|CF414552.1|CF414552
EST:     ACACCGGTCAATTTACTACCTTTGCTCTTTGCGGCTTTGTCCGGGCTCAG                         GGAGATGCTGACAGTGCCCTTGATAGGCTCTGGCAAAAGAAGAAAGCCGAA
genomic: ACACCGGTCAATTTACTACCTTTGCTCTTTGCGGCTTTGTCCGGGCTCAGgttatttttc ... aactttgcagGGAGATGCTGACAGTGCCCTTGATAGGCTCTGGCAAAAGAAGAAAGCCGAA
EST: gi|110428421|gb|EC994893.1|EC994893
EST:     ACACCGGTCAATTTACTACCTTTGCTCTTTGCGGCTTTGTCCGGGCTCAG                         GGAGATGCTGACAGTGCCCTTGATAGGCTCTGGCAAAAGAAGAAAGCCGAA
genomic: ACACCGGTCAATTTACTACCTTTGCTCTTTGCGGCTTTGTCCGGGCTCAGgttatttttc ... aactttgcagGGAGATGCTGACAGTGCCCTTGATAGGCTCTGGCAAAAGAAGAAAGCCGAA
EST: gi|110695764|gb|EE074157.1|EE074157
EST:     ACACCGGTCAATTTACTACCTTTGCTCTTTGCGGCTTTGTCCGGGCTCAG                         GGAGATGCTGACAGTGCCCTTGATAGGCTCTGGCAAAAGAAGAAAGCCGAA
genomic: ACACCGGTCAATTTACTACCTTTGCTCTTTGCGGCTTTGTCCGGGCTCAGgttatttttc ... aactttgcagGGAGATGCTGACAGTGCCCTTGATAGGCTCTGGCAAAAGAAGAAAGCCGAA
EST: gi|110412806|gb|EC978567.1|EC978567
EST:     ACACCGGTCAATTTACTACCTTTGCTCTTTGCGGCTTTGTCCGGGCTCAG                         GGAGATGCTGACAGTGCCCTTGATAGGCTCTGGCAAAAGAAGAAAGCCGAA
genomic: ACACCGGTCAATTTACTACCTTTGCTCTTTGCGGCTTTGTCCGGGCTCAGgttatttttc ... aactttgcagGGAGATGCTGACAGTGCCCTTGATAGGCTCTGGCAAAAGAAGAAAGCCGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcacatctatactgctgaagcttggttggtaattacgttgtttgaactttgcagGGAGATGCTGACAGTGCCCTTGATAGGCTCTGGCAAAAGAAGAAAGCCGAAGTCCGGCAACAGTAGTTCCAGTCTCTTTAAACATTTTCCTTCATGATAG
                              taatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aattgacttgctctttgcttatttgacaagtttatctatttggatttcacatctatactgctgaagcttggttggtaattacgttgtttgaactttgcagGGAGATGCTGACAGTGCCCTTGATAGGCTCTGGCAAAAGAAGAAAGCCGAAGTCCGGCAACAGTAGTTCCAGTCTCTTTAAACATTTTCCTTCATGATAG

- - - cttgctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - actgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggttgg