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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAAAAGGGAACACTGGGTGATGCTTCTGCACTCAAGCCAACACTGATGACCGCTGTACCTGCTATACTTGATCGTGTTCGTGATGGTGTGAGAAAGAAGgtactgcactttaagctgtttcgtccaatgttcttcatctctttcttaatttactgattgttatttttcatattgggatggctttag

Basic information

species Oryza sativa
transcript LOC_Os12g07110.2
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g07110.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G118286_T01 (Zea mays), 5'ss of exon 6
AAAAAAGGGAACACTGGGTGATGCTTCTGCACTCAAGCCAACACTGATGACCGCTGTACCTGCTATACTTGATCGTGTTCGTGATGGTGTGAGAAAGAAGgtactgcactttaagctgtttcg-tccaatgttcttcatctctttcttaatttactgattgttatttttcatattgggatggctttag
|||||||||||| || ||||||||||||||||| ||||||||| ||||||| |||||||||||||||||||||||| ||||||||||||| || || |||||| ||  ||| |   ||||  | |||| ||| |       ||| || |  ||| |||  | ||  |||  | ||| |||| ||| ||
AAAAAAGGGAACTCTAGGTGATGCTTCTGCACTAAAGCCAACATTGATGACTGCTGTACCTGCTATACTTGATCGTATTCGTGATGGTGTCAGGAAAAAGgtaatgtccttcacattgttctggtccagtgtac-------cttgctga--ttattgacagctaccttttgtgttgagatgtcttcag

upper sequence: LOC_Os12g07110.2 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv18s0001g02810.t01 (Vitis vinifera), 5'ss of exon 7
AAAAAAGGGAACACTGGGTGATGCTTCTGCACTCAAGCCAACACTGATGACCGCTGTACCTGCTATACTTGATCGTGTTCGTGATGGTGTGAGAAAGAAGgtac-tgcactttaagctgttt-----cgtcca-atgt-----tcttcatctctttcttaatttactg--attgttatttttcatattgggatggctttag-----------------------------------------------------------------
|||||  ||||||  ||| ||||| ||||| ||    |||||| ||||||| ||||| || || || |||||||||||||| ||||||||| | ||||||||   || | |||    ||  |       | || |||      | ||||| |||      ||  |  |  ||| ||||| |  || ||||  ||  |||                                                                   
AAAAAGAGGAACAAAGGGGGATGCCTCTGCTCTGGTACCAACAGTGATGACGGCTGTCCCAGCCATTCTTGATCGTGTTCGAGATGGTGTGCGCAAGAAGgtttgtgaattttggcatgcataagaatatacatatgcatacatattcatatctgcaagcatgcatagttattattattatatattttggtgtgtatttgagaatgttgaatttgatgtctgatacaaggtgattacataaataatgaattttgttaacacttcag

upper sequence: LOC_Os12g07110.2 (Oryza sativa), 5'ss of exon 5
lower sequence: EFJ35799 (Selaginella moellendorffii), 5'ss of exon 5
AAAAAAGGGAACACTGGGTGATGCTTCTGCACTCAAGCCAACACTGATGACCGCTGTACCTGCTATACTTGATCGTGTTCGTGATGGTGTGAGAAAGAAGgtactgcactttaagctgtttcgtccaatgttcttcatctctttcttaatttactgattgttatttttcatattgggatggctttag
||||||||| ||    ||||| | |   |  || ||||| ||  ||||||| ||||| || |||||||||||||| ||||| |||||||||||||  | ||||       |||  | | || |     ||    | |    |   | |   | ||||                              
AAAAAAGGGGACCAAAGGTGACGTTGGAGAGCTAAAGCCGACTTTGATGACTGCTGTTCCGGCTATACTTGATCGCGTTCGAGATGGTGTGAGAAGAACGgtaagcttgcttataccggtttgctttttgaagctaaaagttcgatgatgatgctgaag----------------------------

upper sequence: LOC_Os12g07110.2 (Oryza sativa), 5'ss of exon 5
lower sequence: EFJ36404 (Selaginella moellendorffii), 5'ss of exon 5
AAAAAAGGGAACACTGGGTGATGCTTCTGCACTCAAGCCAACACTGATGACCGCTGTACCTGCTATACTTGATCGTGTTCGTGATGGTGTGAGAAAGAAGgtactgcactttaagctgtttcgtccaatgttcttcatctctttcttaatttactgattgttatttttcatattgggatggctttag
||||||||| ||    ||||||| |   |  || ||||| ||  ||||||| ||||| || |||||||||||||| ||||| |||||||||||||  | ||||       |||  | | || ||    ||    | |    |   | |   | ||||                              
AAAAAAGGGGACCAAAGGTGATGTTGGAGAGCTAAAGCCGACTTTGATGACTGCTGTTCCGGCTATACTTGATCGCGTTCGAGATGGTGTGAGAAGAACGgtaagcttgcttataccggtttgttttttgaagctaaaagttcgatgatgatgctgaag----------------------------

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|29669841|gb|CB666116.1|CB666116
EST:     CCGCTGTACCTGCTATACTTGATCGTGTTCGTGATGGTGTGAGAAAGAAG                         GTGGATACAAAGGGTGGTGTAGCAAAGCAGTTATTTGATGTTGCCTATAAT
genomic: CCGCTGTACCTGCTATACTTGATCGTGTTCGTGATGGTGTGAGAAAGAAGgtactgcact ... atggctttagGTGGATACAAAGGGTGGTGTAGCAAAGCAGTTATTTGATGTTGCCTATAAT
EST: gi|29614988|gb|CB620001.1|CB620001
EST:     CCGCTGTACCTGCTATACTTGATCGTGTTCGTGATGGTGTGAGAAAGAAG                         GTGGATACAAAGGGTGGTGTAGCAAAGCAGTTATTTGATGTTGCCTATAAT
genomic: CCGCTGTACCTGCTATACTTGATCGTGTTCGTGATGGTGTGAGAAAGAAGgtactgcact ... atggctttagGTGGATACAAAGGGTGGTGTAGCAAAGCAGTTATTTGATGTTGCCTATAAT
EST: gi|29675500|gb|CB671775.1|CB671775
EST:     CCGCTGTACCTGCTATACTTGATCGTGTTCGTGATGGTGTGAGAAAGAAG                         GTGGATACAAAGGGTGGTGTAGCAAAGCAGTTATTTGATGTTGCCTATAAT
genomic: CCGCTGTACCTGCTATACTTGATCGTGTTCGTGATGGTGTGAGAAAGAAGgtactgcact ... atggctttagGTGGATACAAAGGGTGGTGTAGCAAAGCAGTTATTTGATGTTGCCTATAAT
EST: gi|86829547|gb|CI286740.1|CI286740
EST:     CCGCTGTACCTGCTATACTTGATCGTGTTCGTGATGGTGTGAGAAAGAAG                         GTGGATACAAAGGGTGGTGTAGCAAAGCAGTTATTTGATGTTGCCTATAAT
genomic: CCGCTGTACCTGCTATACTTGATCGTGTTCGTGATGGTGTGAGAAAGAAGgtactgcact ... atggctttagGTGGATACAAAGGGTGGTGTAGCAAAGCAGTTATTTGATGTTGCCTATAAT
EST: gi|58030548|gb|CX728091.1|CX728091
EST:     CCGCTGTACCTGCTATACTTGATCGTGTTCGTGATGGTGTGAGAAAGAAG                         GTGGATACAAAGGGTGGTGTAGCAAAGCAGTTATTTGATGTTGCCTATAAT
genomic: CCGCTGTACCTGCTATACTTGATCGTGTTCGTGATGGTGTGAGAAAGAAGgtactgcact ... atggctttagGTGGATACAAAGGGTGGTGTAGCAAAGCAGTTATTTGATGTTGCCTATAAT
EST: gi|29672201|gb|CB668476.1|CB668476
EST:     CCGCTGTACCTGCTATACTTGATCGTGTTCGTGATGGTGTGAGAAAGAAG                         GTGGATACAAAGGGTGGTGTAGCAAAGCAGTTATTTGATGTTGCCTATAAT
genomic: CCGCTGTACCTGCTATACTTGATCGTGTTCGTGATGGTGTGAGAAAGAAGgtactgcact ... atggctttagGTGGATACAAAGGGTGGTGTAGCAAAGCAGTTATTTGATGTTGCCTATAAT
EST: gi|29614945|gb|CB619958.1|CB619958
EST:     CCGCTGTACCTGCTATACTTGATCGTGTTCGTGATGGTGTGAGAAAGAAG                         GTGGATACAAAGGGTGGTGTAGCAAAGCAGTTATTTGATGTTGCCTATAAT
genomic: CCGCTGTACCTGCTATACTTGATCGTGTTCGTGATGGTGTGAGAAAGAAGgtactgcact ... atggctttagGTGGATACAAAGGGTGGTGTAGCAAAGCAGTTATTTGATGTTGCCTATAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAAAAGGGAACACTGGGTGATGCTTCTGCACTCAAGCCAACACTGATGACCGCTGTACCTGCTATACTTGATCGTGTTCGTGATGGTGTGAGAAAGAAGgtactgcactttaagctgtttcgtccaatgttcttcatctctttcttaatttactgattgttatttttcatattgggatggctttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG