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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTGGGGGTTACTCTTGGTCCAAAAGGGAGGAATGTTGTTCTGGAGAGCAAGTATGGGTCCCCGAAAATTGTTAATGATGGTGTTACTGTGGCAAGAGAGgtataaattatcattgaataatgaatatttatacttctggtggtgggccgactagagcattaaagaaaatatgggttatgataatttatttacgtatata...

Basic information

species Vitis vinifera
transcript Vv09s0002g03930.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g03930.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: LOC_Os06g02380.1 (Oryza sativa), 5'ss of exon 3
AGTGGGGGTTACTCTTGGTCCAAAAGGGAGGAATGTTGTTCTGGAGAGCAAGTATGGGTCCCCGAAAATTGTTAATGATGGTGTTACTGTGGCAAGAGAGgtata----aattatcattgaat-aatgaatatttatacttctggtggtgggccgactagagcattaaagaaaatatgggttatgataatttatttacgtatata
 || || ||||| || || ||||| || |||||||||||| |||||||||||||||||||||| |  ||||| |||||||||||||| || ||||||||||||||    | |  | ||||  | ||  |  ||| |   | ||     |  ||    | |  |  ||    | |  |        | ||  | |||   |     
TGTTGGAGTTACACTGGGACCAAAGGGAAGGAATGTTGTTTTGGAGAGCAAGTATGGGTCCCCTAGGATTGTCAATGATGGTGTTACAGTTGCAAGAGAGgtatattacagtgtttattgcgtcaaatagcattgaatttccttacaatttgcttgtttg--ctgtatgctatacttccacagaaaaaaaatgtttgttttg---

upper sequence: Vv09s0002g03930.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: LOC_Os02g01280.1 (Oryza sativa), 5'ss of exon 3
AGTGGGGGTTACTCTTGGTCCAAAAGGGAGGAATGTTGTTCTGGAGAGCAAGTATGGGTCCCCGAAAATTGTTAATGATGGTGTTACTGTGGCAAGAGAGgtataaattat-cattgaataatgaatatt-------tatacttctggtggtgggccgact-agagcattaaagaaaata--tggg---ttatgataatttatttacgtatata---------------------------------------------------------------------
 || || || || ||||||||||||||  |||||||||| || |||||||||||||| || || |||||||| |||||||||||||| || ||||  |||||||      |  | | ||   |   | ||       |  | | ||     ||     | | ||||  ||    |||||   ||     ||   ||||  | |||   |   ||                                                                     
CGTTGGAGTCACCCTTGGTCCAAAAGGACGGAATGTTGTCCTTGAGAGCAAGTATGGATCACCTAAAATTGTCAATGATGGTGTTACCGTTGCAAAGGAGgtatgccacgtatagtaaactgttcgtgttcttatgatgcaatcctatcattgcttaaattcagagttttctgaaaaatgactgaacatttggcataaactgtttgttttcttatgatgcaatcctatcatagcttaaattcagagttttctgaaaaatgagtgaacatttggcatgcaccag

upper sequence: Vv09s0002g03930.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GRMZM2G133698_T03 (Zea mays), 5'ss of exon 3
AGTGGGGGTTACTCTTGGTCCAAAAGGGAGGAATGTTGTTCTGGAGAGCAAGTATGGGTCCCCGAAAATTGTTAATGATGGTGTTACTGTGGCAAGAGAGgtataaattatcattgaataatgaatatttatacttctggtggtgggccgactagagcattaaagaaaatatgggttatgata-atttatttacgtatata----------------------------------------------
                         || |||||||||||| |||||||||||||||| || || ||||||||||| ||||||||||| || || ||||||||| |    |   ||          || ||| | ||    || | |  ||   |   ||| |      ||||   || |  |  | || ||  | || ||                                               
------------------------GGGAAGGAATGTTGTTTTGGAGAGCAAGTATGGTTCTCCTAAAATTGTTAACGATGGTGTTACAGTTGCCAGAGAGGTACAGTGCAATGTTACCATGGTTgtacttagaatttgattgctagctcgtaaattacataacgttgtatatatttttttctccaattcttgtcatacatgttttacaggtcatattcttataacccatgtaatgcatatactttag

upper sequence: Vv09s0002g03930.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GRMZM2G015989_T01 (Zea mays), 5'ss of exon 3
AGTGGGGGTTACTCTTGGTCCAAAAGGGAGGAATGTTGTTCTGGAGAGCAAGTATGGGTCCCCGAAAATTGTTAATGATGGTGTTACTGTGGCAAGAGAGgtataaattatcattgaataatgaatatt-tatacttctggtggtgggccgactagagcattaaagaaaatatgggttatgataa-tttatttacgtatata--------------------
 || |||||||||||||| ||||| ||| | ||||| || || || ||||||||||| || || |||||||| ||||||||||| ||||||||||  |||||  | ||  | | |  | | | |  ||  | |  |  || | ||    | || | | | |     ||  | | |    ||   | |||  | |  | |                       
CGTCGGGGTTACTCTTGGACCAAAGGGGCGAAATGTAGTCCTCGAAAGCAAGTATGGCTCACCTAAAATTGTCAATGATGGTGTCACTGTGGCAAAGGAGgtgcacatc-tgactacaaacttaccatcgtttgttcttgctcgtactgcaaccataccctgctctaacttcttgtggctgccgagtttcctcatatgttctgggctgtggccatgcaccag

upper sequence: Vv09s0002g03930.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GRMZM2G083716_T04 (Zea mays), 5'ss of exon 3
AGTGGGGGTTACTCTTGGTCCAAAAGGGAGGAATGTTGTTCTGGAGAGCAAGTATGGGTCCCCGAAAATTGTTAATGATGGTGTTACTGTGGCAAGAGAGgtataaattatcattgaataatgaatatttatacttctggtggtgggccgactagagcattaaagaaaatatgggttatgataatttatttacgtatata--
||| || ||||| || || || || || |||||||| ||| ||||||||||||| || || || || |||||||| ||||| ||||| || |||||||||||| |    |    |          || ||  | || || | |   || || || |  |   || |||  |  |   |          ||  |  ||  |  
AGTTGGAGTTACACTCGGACCGAAGGGAAGGAATGTCGTTTTGGAGAGCAAGTACGGCTCTCCCAAGATTGTTAACGATGGCGTTACAGTTGCAAGAGAGgtacagtgcaatgctatcatggctgtacttggaatt-tgcttgctagctga-taaattacataaaaaaggacagaccagtgctggcggttcccacatgaata

upper sequence: Vv09s0002g03930.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: PP1S14_298V6.1 (Physcomitrella patens), 5'ss of exon 2
AGTGGGGGTTACTCTTGGTCCAAAAGGGAGGAATGTTGTTCTGGAGAGCAAGTATGGGTCCCCGAAAATTGTTAATGATGGTGTTACTGTGGCAAGAGAGgtataaattatcat--------tgaataatgaatatttatact-----tctggt-------ggtgggc-cgactagagcattaaagaaaatatgggttatgataatttatttacgtatata---------------------------------------------------------------------
 || || || ||| | || || || ||  | || || || || |||||||||||||| || || |||||||| ||||| ||||| |||||||| |  |||||      |  |||        |||     || |  ||||  |       ||||       | |  || ||| |      || | |       ||  ||  ||  |    | | || |                                                                        
TGTTGGTGTCACTTTGGGGCCCAAGGGCCGAAACGTCGTGCTTGAGAGCAAGTATGGCTCACCCAAAATTGTGAATGACGGTGTCACTGTGGCCAAGGAGgttagggcttgcatcctctctatgagcccggatttattatgttgtttacttggtttttttggataagcgcgattttttttttgaggggggcggggtgtagaatcttgggataaggtttcgttctttcttgaattagatgcgcatgagtttgagcttttcaattaacgcgctgaatctcggaactcaacag

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|161710172|gb|FC061070.1|FC061070
EST:     AGTATGGGTCCCCGAAAATTGTTAATGATGGTGTTACTGTGGCAAGAGAG                         GTAGAGTTGGAGGACCCTGTTGAGAACA
genomic: AGTATGGGTCCCCGAAAATTGTTAATGATGGTGTTACTGTGGCAAGAGAGgtataaatta ... ctcttcatagGTAGAGTTGGAGGACCCTGTTGAGAACA




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTGGGGGTTACTCTTGGTCCAAAAGGGAGGAATGTTGTTCTGGAGAGCAAGTATGGGTCCCCGAAAATTGTTAATGATGGTGTTACTGTGGCAAGAGAGgtataaattatcattgaataatgaatatttatacttctggtggtgggccgactagagcattaaagaaaatatgggttatgataatttatttacgtatata

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagaaaa