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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTATATGCGAATTATGCTATTGGAAAGGATGTCCAGGCAATGAAAGCTGTGGTCGGAGAGGAAGCACTCTCTTCTGAGGATCTGgtatctctctttctctctcctcctttctgtagaaactatgtgtttgttttttcacatctttctctagcaataatttctcatagattaaaatcacaaagtattaacctggggttgggttgtctaaaattcag

Basic information

species Vitis vinifera
transcript Vv18s0001g01020.t01
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g01020.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 5'ss of exon 14
CTATATGCGAATTATGCTATTGGAAAGGATGTCCAGGCAATGAAAGCTGTGGTCGGAGAGGAAGCACTCTCTTCTGAGGATCTGgtatctctctttctctctcctcctttctgtagaaactatgtgtttgt---tttttcacatctttctctagcaataatttctcatagattaaaatcacaaagtattaacctggggttgggttgtctaaaattcag
|| ||||| || ||||| ||||| |||||||||||||| |||||||| || || |||||||| || ||||||||||||||||||||        || || ||  |   |  || |  ||     || |  |   | ||| | |  |   | ||  | |   |  | ||                                                  
CTTTATGCCAACTATGCAATTGGGAAGGATGTCCAGGCCATGAAAGCCGTTGTGGGAGAGGAGGCGCTCTCTTCTGAGGATCTGgt--------ttgtcactaataactattgaaataatcccatgctgatgtctcttttagaagtaaatttaatattctatctttatctgcag--------------------------------------------

upper sequence: Vv18s0001g01020.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: GRMZM2G094497_T02 (Zea mays), 5'ss of exon 13
CTATATGCGAATTATGCTATTGGAAAGGATGTCCAGGCAATGAAAGCTGTGGTCGGAGAGGAAGCACTCTCTTCTGAGGATCTGgtatctctctttctctctcctcctttctgtagaaactatgtgtttgttttttcacatctttctctagcaataatttctcatagattaaaatcacaaagtattaacctggggttgggttgtctaaaattcag
|| ||||| || |||||||||||||||||||| ||||| ||||| ||||| || |||||||| |||||||| ||||||||||||||            || |      |    || ||    |  ||| ||| |||  ||     |   | |  |||| |    |   |||   |  || ||                                 
CTTTATGCCAACTATGCTATTGGAAAGGATGTTCAGGCCATGAAGGCTGTCGTTGGAGAGGAGGCACTCTCGTCTGAGGATCTGgt------------ctgttgcgagtgaaata-aattcgtaagttagttctttttcagacccccaaaact-taatgttctgttcctta---ttgcacag---------------------------------

upper sequence: Vv18s0001g01020.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: PP1S85_75V6.1 (Physcomitrella patens), 5'ss of exon 13
CTATATGCGAATTATGCTATTGGAAAGGATGTCCAGGCAATGAAAGCTGTGGTCGGAGAGGAAGCACTCTCTTCTGAGGATCTGgtatctctctttctctctcctcctttctgtagaaactatgtgtttgttttttcacatctttctctagcaataatttctcatagattaaaatcacaaagtattaacctggggttgggttgtctaaaattcag
 | || || ||||||||||| || |||||||| || || ||||| |||||||| |||||||||||  | ||||| || ||||||||| || | |   ||     | || | | |   |  |     |||| |  |     |  | || |||   | | ||  |  ||    |  |  |   ||  |||  ||   |    |||| ||     |||
TTGTACGCAAATTATGCTATCGGGAAGGATGTGCAAGCCATGAAGGCTGTGGTGGGAGAGGAAGCCTTGTCTTCAGAAGATCTGgtacctgt-tgcttcatattttctgtttatgatatttcatcatttgatgctctctgttatcctgtagagcttagtttactgagtcagatctgtctgcgtgataa--tgacttcaaattgt-tacttgacag

upper sequence: Vv18s0001g01020.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: PP1S425_12V6.1 (Physcomitrella patens), 5'ss of exon 13
CTATATGCGAATTATGCTATTGGAAAGGATGTCCAGGCAATGAAAGCTGTGGTCGGAGAGGAAGCACTCTCTTCTGAGGATCTGgtatc--tctctttctctctcctcctttct--gtagaaactatgtgtttgttttttcacatcttt----ctctagcaataatttctcatagattaa----aatcacaaagtattaacctggggttgggttgtctaa--aattcag-----
 | || || || ||||| |||||||||||||| || || ||||| |||||||| ||||| |||||  | ||||| ||||||||||||||  |||| |||| | | | | || |   || || |   |    |    | | || || ||      | |    || || |||  ||  |||       ||  ||  | || ||       ||        ||     ||       
TTGTACGCAAACTATGCGATTGGAAAGGATGTACAAGCCATGAAGGCTGTGGTGGGAGAAGAAGCCTTGTCTTCAGAGGATCTGgtatccatctcattctatttgcccgttacgcagtggacatcctacaatgaaatctccatatgttgatggttttgaacattatctctagtacgttatctctggtctgaagcttttcactccctaatgacactctcaaccggctctatgcag

upper sequence: Vv18s0001g01020.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: PP1S100_117V6.1 (Physcomitrella patens), 5'ss of exon 14
CTATATGCGAATTATGCTATTGGAAAGGATGTCCAGGCAATGAAAGCTGTGGTCGGAGAGGAAGCACTCTCTTCTGAGGATCTGgtatctctctt--tctctctcctcctttctgtagaaactatgtgtttgttttttcacatctttctctagcaataatttct-catagattaaaatcacaaagtattaacctggggttgggttgtctaaaattcag--------
 | ||||| |||||||| |||||||||||||| || |||||||| ||||| || |||||||||||  | ||||| || ||||||||| |    |   |    ||    ||    | ||||   |  |  ||   |||| |  |   ||  |  |  | |||||     | | |    |     |    ||      | ||   |  ||     ||  |        
TTGTATGCTAATTATGCCATTGGAAAGGATGTTCAAGCAATGAAGGCTGTCGTTGGAGAGGAAGCTTTGTCTTCAGAAGATCTGgtaccctcgtgaatactcctgtgactgcaagcagaactcaatttgttcaatttttat-ttaatccatgccgctcatttccgtgcatactccgctatgtcaactctatttgttgcttacatcctcacttgttttgttttccag

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|110421686|gb|EC987986.1|EC987986
EST:     AGGCAATGAAAGCTGTGGTCGGAGAGGAAGCACTCTCTTCTGAGGATCTG                         CTTTATCTGGAGTTCCTAGACAAATTCGAGAGGAAATTTGTGGCTCAAGGG
genomic: AGGCAATGAAAGCTGTGGTCGGAGAGGAAGCACTCTCTTCTGAGGATCTGgtatctctct ... taaaattcagCTTTATCTGGAGTTCCTAGACAAATTCGAGAGGAAATTTGTGGCTCAAGGG
EST: gi|37184152|gb|CF603506.1|CF603506
EST:     AGGCAATGAAAGCTGTGGTCGGAGAAGAAGCACTCTCTTCTGAGGATCTG                         CTTTATCTGGAGTTCCTAGACAAATTCGAGAGGAAAT
genomic: AGGCAATGAAAGCTGTGGTCGGAGAGGAAGCACTCTCTTCTGAGGATCTGgtatctctct ... taaaattcagCTTTATCTGGAGTTCCTAGACAAATTCGAGAGGAAAT
EST: gi|30128132|gb|CB913471.1|CB913471
EST:     AGGCAATGAAAGCTGTGGTCGGAGAAGAAGCACTCTCTTCTGAGGATCTG                         CTTTATCTGGAGTTCCTAGACAAATTCGAGAGGAAATTTGTGGCTCAAGGG
genomic: AGGCAATGAAAGCTGTGGTCGGAGAGGAAGCACTCTCTTCTGAGGATCTGgtatctctct ... taaaattcagCTTTATCTGGAGTTCCTAGACAAATTCGAGAGGAAATTTGTGGCTCAAGGG
EST: gi|110421897|gb|EC988201.1|EC988201
EST:     AGGCAATGAAAGCTGTGGTCGGAGAAGAAGCACTCTCTTCTGAGGATCTG                         CTTTATCTGGAGTTCCTAGACAAATTCGAGAGGAAATTTGTGGCTCAAGGG
genomic: AGGCAATGAAAGCTGTGGTCGGAGAGGAAGCACTCTCTTCTGAGGATCTGgtatctctct ... taaaattcagCTTTATCTGGAGTTCCTAGACAAATTCGAGAGGAAATTTGTGGCTCAAGGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTATATGCGAATTATGCTATTGGAAAGGATGTCCAGGCAATGAAAGCTGTGGTCGGAGAGGAAGCACTCTCTTCTGAGGATCTGgtatctctctttctctctcctcctttctgtagaaactatgtgtttgttttttcacatctttctctagcaataatttctcatagattaaaatcacaaagtattaacctggggttgggttgtctaaaattcag

- - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT