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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaccaaaccaaaccaaaaccaaccgccaaaaactccgatcgcctcattgtctcattcatcatggcatctgggacttgtgtgtgcagGCAGATCATCTCCGGCAGCAGACGCTGCAGGAGATGCACAGGATCCTGACGACGCGGCAGGCGGCGAGGGGGCTCCTCGCGCTGGGGGACTACTTCCAGC

Basic information

species Oryza sativa
transcript LOC_Os04g54474.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g54474.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G131961_T02 (Zea mays), 3'ss of exon 9
-------------------------------------------gtaaccaaaccaaaccaaa---accaaccgccaaaaactccgatcgcctcattgtctcattcatcatggcatctgg--gact----tgtg-tgtgcagGCAGATCATCTCCGGCAGCAGACGCTGCAGGAGATGCACAGGATCCTGACGACGCGGCAGGCGGCGAGGGGGCTCCTCGCGCTGGGGGACTACTTCCAGC
                                           |   |    |   | |  |    ||           ||       | | |  || ||||  | |   ||  ||||   | ||    |||| ||||||||| || |||||||||| |  |||||||||  ||||||||| |||||||||||||||||||||||| ||||| || || ||||| || |||||||||||||
gtaaccgtccatccatctcctccatggatggaacgcaaacgcagggcctggtctggaacgcacgcgccgtgtcgtgtggacgtgtggtgtccctgtggctcacccgtgcgggtctctgctcggctatgctgtgctgtgcagGCGGACCATCTCCGGCTGATGACGCTGCAACAGATGCACAAGATCCTGACGACGCGGCAGGCGGCCAGGGGCCTGCTGGCGCTCGGCGACTACTTCCAGC

upper sequence: LOC_Os04g54474.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G445575_T01 (Zea mays), 3'ss of exon 10
----------------------------------------------------------------------gtaaccaaaccaaaccaaaaccaaccgccaaaaactccgatcgcctcattgt-ctcattcat-catg-----gcatctg-----------ggacttgtgtgtgcagGCAGATCATCTCCGGCAGCAGACGCTGCAGGAGATGCACAGGATCCTGACGACGCGGCAGGCGGCGAGGGGGCTCCTCGCGCTGGGGGACTACTTCCAGC
                                                                       |  ||   |||   | ||  |   || |           |  ||   |||  ||||  | | | ||     || ||||           ||   ||  ||||||||| || |||||||||| |  |||||||||| ||||||||| |||||||||| ||||||||||||| ||||| ||||| ||||| || |||||||||||||
gtaaaccggaccggtcgccaaagagccatccatcattccatctccatgcggatgcaatgcaaggcctggcctggcctggccagctcgaacgcgcgcggcgtgtgtgtgtgtgtccctgttgcgctcacccgtacgtgcccgcgcctctgctcggcgcgctggctgtgcctgtgcagGCGGACCATCTCCGGCTGACGACGCTGCAGCAGATGCACAAGATCCTGACGCCGCGGCAGGCGGCCAGGGGCCTCCTGGCGCTCGGCGACTACTTCCAGC

upper sequence: LOC_Os04g54474.2 (Oryza sativa), 3'ss of exon 9
lower sequence: EFJ18699 (Selaginella moellendorffii), 3'ss of exon 2
gtaaccaaaccaaaccaaaaccaaccgccaaaaactccgatcgcctcattgtctcattcatcatggcatctgggacttgtgtgtgcagGCAGATCATCTCCGGCAGCAGACGCTGCAGGAGATGCACAGGATCCTGACGACGCGGCAGGCGGCGAGGGGGCTCCTCGCGCTGGGGGACTACTTCCAGC
                                     ||   ||| |  | | || |||    ||  |      | |  |  | |||||||||| ||||||| ||||| ||||||||| | ||||||||||| || || ||| | || || ||  |||||||||| ||| ||||||||||||||  | 
---------------------------------gtaacgcgagccgcgatctttctttctcgctgata------attctttggcgcagGCAGATAATCTCCGCCAGCAAACGCTGCAGCAAATGCACAGGATTCTAACCACGAGACAAGCCGCTCGGGGGCTCCTTGCGATGGGGGACTACTTCGCGA

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|87035053|gb|CI189677.1|CI189677
EST:     TGGCCAACGCCGTGGAGCAGCTCAGATCCCTCGTCCAGTTCGTTACCCAG                         GCAGATCATCTCCGGCAGCAGACGCTGCAGGAGATGCACAGGATCCTGACG
genomic: TGGCCAACGCCGTGGAGCAGCTCAGATCCCTCGTCCAGTTCGTTACCCAGgtaaccaaac ... gtgtgtgcagGCAGATCATCTCCGGCAGCAGACGCTGCAGGAGATGCACAGGATCCTGACG
EST: gi|325494159|gb|JG458683.1|JG458683
EST:     TGGGCAACGCCGTGGAGCAGCTCAGATCCCTCGTCCAGTTCGTTACCCAG                         GCAGATCATCTCCGGCAGCAGACGCTGCAGGAGATGCACAGGATCCTGACG
genomic: TGGCCAACGCCGTGGAGCAGCTCAGATCCCTCGTCCAGTTCGTTACCCAGgtaaccaaac ... gtgtgtgcagGCAGATCATCTCCGGCAGCAGACGCTGCAGGAGATGCACAGGATCCTGACG
EST: gi|29659309|gb|CB655584.1|CB655584
EST:     TGGCCAACGCCGTGGAGCAGCTCAGATCCCTCGTCCAGTTCGTTACCCAG                         GCAGATCATCTCCGGCAGCAGACGCTGCAGGAGATGCACAGGATCCTGACG
genomic: TGGCCAACGCCGTGGAGCAGCTCAGATCCCTCGTCCAGTTCGTTACCCAGgtaaccaaac ... gtgtgtgcagGCAGATCATCTCCGGCAGCAGACGCTGCAGGAGATGCACAGGATCCTGACG
EST: gi|29642526|gb|CB647533.1|CB647533
EST:     TGGCCAACGCCGTGGAGCAGCTCAGATCCCTCGTCCAGTTTGTTACCCAG                         GCAGATCATCTCCGGCAGCAGACGCTGCAGGAGATGCACAGGATCCTGACG
genomic: TGGCCAACGCCGTGGAGCAGCTCAGATCCCTCGTCCAGTTCGTTACCCAGgtaaccaaac ... gtgtgtgcagGCAGATCATCTCCGGCAGCAGACGCTGCAGGAGATGCACAGGATCCTGACG
EST: gi|29640854|gb|CB645861.1|CB645861
EST:     TGGCCAACGCCGTGGAGCAGCTCAGATCCCTCGTCCAGTTTGTTACCCAG                         GCAGATCATCTCCGGCAGCAGACGCTGCAGGAGATGCACAGGATCCTGACG
genomic: TGGCCAACGCCGTGGAGCAGCTCAGATCCCTCGTCCAGTTCGTTACCCAGgtaaccaaac ... gtgtgtgcagGCAGATCATCTCCGGCAGCAGACGCTGCAGGAGATGCACAGGATCCTGACG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaccaaaccaaaccaaaaccaaccgccaaaaactccgatcgcctcattgtctcattcatcatggcatctgggacttgtgtgtgcagGCAGATCATCTCCGGCAGCAGACGCTGCAGGAGATGCACAGGATCCTGACGACGCGGCAGGCGGCGAGGGGGCTCCTCGCGCTGGGGGACTACTTCCAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC