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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctggagttgaaaattgataaccaaaggaggttgaatactcgcttttattaaaaagaaaggggaaatggattataacctactgttcctctcatgcttgcagGACATCAGTAGATGATATCAAGTCTCTTAGGTTGATCACAGCCATCAAAACTCCATATCTTCCGGATGGCAGGTTTGATCTGGAAGCATATGATGCTTTG

Basic information

species Vitis vinifera
transcript Vv15s0048g00750.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0048g00750.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os04g18200.1 (Oryza sativa), 3'ss of exon 2
ctggagttgaaaattgataaccaaaggagg------ttgaatactcgctttta-----ttaaaaagaaaggggaaatggattataacctactgttcctctcatgcttgcagGACATCAGTAGATGATATCAAGTCTCTTAGGTTGATCACAGCCATCAAAACTCCATATCTTCCGGATGGCAGGTTTGATCTGGAAGCATATGATGCTTTG
        | || || |||| ||   ||        ||| | |   |  |||      || | |   |   |    ||   ||| | || |  ||  ||| || |  |||||||||||  || ||||||||    ||| ||  | || |||||  ||||||| |||||||| || ||||| || |||||||| |||||||||||| |  ||
--------gtaacttaataatcatgtgatcccttttttgcacatgggtatttcagtgcttgatacctatctgctgctgagatatgatcttcc-tttttctgatcc--gcagGACATCAACAGCTGATATCACTAGTCTCAGAGTAATTACAGCGGTCAAAACCCCATATCTGCCTGATGGAAGATTTGATCTTGAAGCATATGATTCACTG

upper sequence: Vv15s0048g00750.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ17013 (Selaginella moellendorffii), 3'ss of exon 1
ctggagttgaaaattgataaccaaaggaggttgaatactcgcttttattaaaaagaaaggggaaatggattataacctactgttcctctcatgcttgcagGACATCAGTAGATGATATCAAGTCTCTTAGGTTGATCACAGCCATCAAAACTCCATATCTTCCGGATGGCAGGTTTGATCTGGAAGCATATGATGCTTTG
                                   ||  |    ||   | | |     |||   |  |||     ||    |   | |    ||||||| ||  | || || || || |||   || ||| | ||| | || ||||| |||||||||||||| ||||| ||||||||||||||||| || ||| |  ||
----------------------------------gtaaccagaatttcgagagatctctgggttgtatattcgtttctctgatatatttt---cttgcagTACGCCCGTGGAAGAGATGAAGAAGCTGAGGCTCATCTCGGCTATCAAGACTCCATATCTTCCAGATGGAAGGTTTGATCTGGAAGCTTACGATTCACTG

upper sequence: Vv15s0048g00750.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ16143 (Selaginella moellendorffii), 3'ss of exon 1
ctggagttgaaaattgataaccaaaggaggttgaatactcgcttttattaaaaagaaaggggaaatggattataacctactgttcctctcatgcttgcagGACATCAGTAGATGATATCAAGTCTCTTAGGTTGATCACAGCCATCAAAACTCCATATCTTCCGGATGGCAGGTTTGATCTGGAAGCATATGATGCTTTG
                 |||||| |       ||   |||    || | | |         |   |    |||    | || |        | ||||||| ||  | || || || || |||   || ||| | ||| | || ||||| |||||||||||||| ||||| ||||||||||||||||| || ||| |  ||
----------------gtaaccagaatttcgagagatctctggattgt-agatttctcctcgcgttcttctattcgtttctctgatatattttcttgcagTACGCCCGTGGAAGAGATGAAGAAGCTGAGGCTCATCTCGGCTATCAAGACTCCATATCTTCCAGATGGAAGGTTTGATCTGGAAGCTTACGATTCACTG

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|349818845|gb|FQ409379.1|FQ409379
EST:     GTAATTCCTAATTTCCATCTCCCAATGCGTAGTTTTGAAGTTAAAAATAG                         GACATCAGTAGATGATATCAAGTCTCTTAGGTTGATCACAGCCATCAAAAC
genomic: GTAATTCCTAATTTCCATCTCCCAATGCGTAGTTTTGAAGTTAAAAATAGgtaagctatt ... atgcttgcagGACATCAGTAGATGATATCAAGTCTCTTAGGTTGATCACAGCCATCAAAAC
EST: gi|349815681|gb|FQ400837.1|FQ400837
EST:     GTAATTCCTAATTTCCATCTCCCAATGCGTAGTTTTGAAGTTAAAAATAG                         GACATCAGTAGATGATATCAAGTCTCTTAGGTTGATCACAGCCATCAAAAC
genomic: GTAATTCCTAATTTCCATCTCCCAATGCGTAGTTTTGAAGTTAAAAATAGgtaagctatt ... atgcttgcagGACATCAGTAGATGATATCAAGTCTCTTAGGTTGATCACAGCCATCAAAAC
EST: gi|349813360|gb|FQ413618.1|FQ413618
EST:     GTAATTCCTAATTTCCATCTCCCAATGCGTAGTTTTGAAGTTAAAAATAG                         GACATCAGTAGATGATATCAAGTCTCTTAGGTTGATCACAGCCATCAAAAC
genomic: GTAATTCCTAATTTCCATCTCCCAATGCGTAGTTTTGAAGTTAAAAATAGgtaagctatt ... atgcttgcagGACATCAGTAGATGATATCAAGTCTCTTAGGTTGATCACAGCCATCAAAAC
EST: gi|161711157|gb|FC061163.1|FC061163
EST:     GTAATTCCTAATTTCCATCTCCCAATGCGTAGTTTTGAAGTTAAAAATAG                         GACATCAGTAGATGATATCAAGTCTCTTAGGTTGATCACAGCCATCAAAAC
genomic: GTAATTCCTAATTTCCATCTCCCAATGCGTAGTTTTGAAGTTAAAAATAGgtaagctatt ... atgcttgcagGACATCAGTAGATGATATCAAGTCTCTTAGGTTGATCACAGCCATCAAAAC
EST: gi|349819155|gb|FQ412049.1|FQ412049
EST:     GTAATTCCTAATTTCCATCTCCCAATGCGTAGTTTTGAAGTTAAAAATAG                         GACATCAGTAGATGATATCAAGTCTCTTAGGTTGATCACAGCCATCAAAAC
genomic: GTAATTCCTAATTTCCATCTCCCAATGCGTAGTTTTGAAGTTAAAAATAGgtaagctatt ... atgcttgcagGACATCAGTAGATGATATCAAGTCTCTTAGGTTGATCACAGCCATCAAAAC
EST: gi|349813204|gb|FQ411444.1|FQ411444
EST:     GTAATTCCTAATTTCCATCTCCCAATGCGTAGTTTTGAAGTTAAAAATAG                         GACATCAGTAGATGATATCAAGTCTCTTAGGTTGATCACAGCCATCAAAAC
genomic: GTAATTCCTAATTTCCATCTCCCAATGCGTAGTTTTGAAGTTAAAAATAGgtaagctatt ... atgcttgcagGACATCAGTAGATGATATCAAGTCTCTTAGGTTGATCACAGCCATCAAAAC
EST: gi|349820595|gb|FQ404090.1|FQ404090
EST:     GTAATTCCTAATTTCCATCTCCCAATGCGTAGTTTTGAAGTTAAAAATAG                         GACATCAGTAGATGATATCAAGTCTCTTAGGTTGATCACAGCCATCAAAAC
genomic: GTAATTCCTAATTTCCATCTCCCAATGCGTAGTTTTGAAGTTAAAAATAGgtaagctatt ... atgcttgcagGACATCAGTAGATGATATCAAGTCTCTTAGGTTGATCACAGCCATCAAAAC
EST: gi|349823087|gb|FQ400066.1|FQ400066
EST:     GTAATTCCTAATTTCCATCTCCCAATGCGTAGTTTTGAAGTTAAAAATAG                         GACATCAGTAGATGATATCAAGTCTCTTAGGTTGATCACAGCCATCAAAAC
genomic: GTAATTCCTAATTTCCATCTCCCAATGCGTAGTTTTGAAGTTAAAAATAGgtaagctatt ... atgcttgcagGACATCAGTAGATGATATCAAGTCTCTTAGGTTGATCACAGCCATCAAAAC
EST: gi|349823336|gb|FQ402535.1|FQ402535
EST:     GTAATTCCTAATTTCCATCTCCCAATGCGTAGTTTTGAAGTTAAAAATAG                         GACATCAGTAGATGATATCAAGTCTCTTAGGTTGATCACAGCCATCAAAAC
genomic: GTAATTCCTAATTTCCATCTCCCAATGCGTAGTTTTGAAGTTAAAAATAGgtaagctatt ... atgcttgcagGACATCAGTAGATGATATCAAGTCTCTTAGGTTGATCACAGCCATCAAAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattaaaaagaaaggggaaatggattataacctactgttcctctcatgcttgcagGACATCAGTAGATGATATCAAGTCTCTTAGGTTGATCACAGCCATCAAAACTCCATATCTTCCGGATGGCAGGTTTGATCTGGAAGCATATGATGCTTTG
                        ttataac  putative branch site (score: 2)
                                     ttcctctcatgctt  putative PPT
                       attataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctggagttgaaaattgataaccaaaggaggttgaatactcgcttttattaaaaagaaaggggaaatggattataacctactgttcctctcatgcttgcagGACATCAGTAGATGATATCAAGTCTCTTAGGTTGATCACAGCCATCAAAACTCCATATCTTCCGGATGGCAGGTTTGATCTGGAAGCATATGATGCTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - gaaaatt
- - - - - - - - -taaccaa
- - - - - - - - - - - - - - - - - - - - - - - - - -aaagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaatgga