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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCAGAAGACGCGCTGTCCAAGTGTCTAGACAGAAGCATGTACATGGCCACTACTTCAGGAACTCATGAAGATTGTGAGAGAAAATGCAGCATATGCCAGgcaagttcatttgcatgagtagattgcgcatgacactgtttgcagagttggattgtactgactactatgtacgaaatctttctgtgtgcattcttcag

Basic information

species Oryza sativa
transcript LOC_Os04g51400.3
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g51400.3 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G140924_T02 (Zea mays), 5'ss of exon 4
TTCAGAAGACGCGCTGTCCAAGTGTCTAGACAGAAGCATGTACATGGCCACTACTTCAGGAACTCATGAAGATTGTGAGAGAAAATGCAGCATATGCCAGgcaagttcatttgcatgag--tagattgcgc------atgacactgtttgcagagttggattgtactgactactatgtacgaaatctttctgtgtgcattcttcag
|||||| || || |||||| ||| ||| | || ||| | |||||| |||| || |||| |||||||||||||||| | |||||||||||||||||||||||||||||||| | | |||||| | | || | | ||||| | | | | | | || || || ||||| |
TTCAGACGATGCATTGTCCACGTGCCTAAATAGGAGCCTCTACATGCCCACAGCTCCAGGGTCTCATGAAGATTGTGAAACAAAATGCAGCATATGCCAGgcaagttcatttgtactatatcagattgttctgtatcaggatattagttgcaacctctaaattttttttttctgttgcgtgagatgtttctcag------------

upper sequence: LOC_Os04g51400.3 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G053909_T01 (Zea mays), 5'ss of exon 5
TTCAGAAGACGCGCTGTCCAAGTGTCTAGACAGAAGCATGTACATGGCCACTACTTCAGGAACTCATGAAGATTGTGAGAGAAAATGCAGCATATGCCAGgcaagttcatttgcatgagtagattgcgcatgacactgtttgcagagttggattgtactgactactat-gtacgaaatctttctgtgtgcattcttcag
|||||| |||||| | ||| ||| || |||| || | |||||| |||| ||||||| |||||||||||||||| |||||||||||| ||||||||||||||||||||| || | | | | | || | | | | || | || | | ||||| |||| |
TTCAGACGACGCGTTATCCGCGTGCCTGAACAGGAGGCTCTACATGCCCACAGCTTCAGGTTCTCATGAAGATTGTGAAAGAAAATGCAGCGTATGCCAGgcaagttcatttgtatcggattgctctgtagtaggatgat-aagatgcaacctctaaatgttttctgttgcgtgaaatgtttcag--------------
















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|29676639|gb|CB672914.1|CB672914
EST:     CTACTTCAGGAACTCATGAAGATTGTGAGAGAAAATGCAGCATATGCCAG                         GAGGAATATTCAGATGGTGAGGAGGTGGGCAAGATGGTCTGCAAACATTAC
genomic: CTACTTCAGGAACTCATGAAGATTGTGAGAGAAAATGCAGCATATGCCAGgcaagttcat ... cattcttcagGAGGAATATTCAGATGGTGAGGAGGTGGGCAAGATGGTCTGCAAACATTAC
EST: gi|33675698|gb|CF303937.1|CF303937
EST:     CTACTTCAGGAACTCATGAAGATTGTGAGAGAAAATGCAGCATATGCCAG                         GAGGAATATTCAGATGGTGAGGAGGTGGGCAAGATGGTCTGCAAACATTAC
genomic: CTACTTCAGGAACTCATGAAGATTGTGAGAGAAAATGCAGCATATGCCAGgcaagttcat ... cattcttcagGAGGAATATTCAGATGGTGAGGAGGTGGGCAAGATGGTCTGCAAACATTAC
EST: gi|58691609|gb|CK080296.1|CK080296
EST:     CTACTTCAGGAACTCATGAAGATTGTGAGAGAAAATGCAGCATATGCCAG                         GAGGAATATTCAGATGGTGAGGAGGTGGGCAAGATGGTCTGCAAACATTAC
genomic: CTACTTCAGGAACTCATGAAGATTGTGAGAGAAAATGCAGCATATGCCAGgcaagttcat ... cattcttcagGAGGAATATTCAGATGGTGAGGAGGTGGGCAAGATGGTCTGCAAACATTAC
EST: gi|89196993|gb|CI021833.1|CI021833
EST:     CTACTTCAGGAACTCATGAAGATTGTGAGAGAAAATGCAGCATATGCCAG                         GAGGAATATTCAGATGGTGAGGAGGTGGGCAAGATGGTCTGCAAACATTAC
genomic: CTACTTCAGGAACTCATGAAGATTGTGAGAGAAAATGCAGCATATGCCAGgcaagttcat ... cattcttcagGAGGAATATTCAGATGGTGAGGAGGTGGGCAAGATGGTCTGCAAACATTAC
EST: gi|12622915|gb|AU173128.1|AU173128
EST:     CTACTTCAGGAACTCATGAAGATTGTGAGAGAAAATGCAGCATATGCCAG                         GAGGAATATTCAGATGGTGAGGAGGTGGGCAAGATGGTCTGCAAACATTAC
genomic: CTACTTCAGGAACTCATGAAGATTGTGAGAGAAAATGCAGCATATGCCAGgcaagttcat ... cattcttcagGAGGAATATTCAGATGGTGAGGAGGTGGGCAAGATGGTCTGCAAACATTAC
EST: gi|29666124|gb|CB662399.1|CB662399
EST:     CTACTTCAGGAACTCATGAAGATTGTGAGAGAAAATGCAGCATATGCCAG                         GAGGAATATTCAGATGGTGAGGAGGTGGGCAAGATGGTCTGCAAACATTAC
genomic: CTACTTCAGGAACTCATGAAGATTGTGAGAGAAAATGCAGCATATGCCAGgcaagttcat ... cattcttcagGAGGAATATTCAGATGGTGAGGAGGTGGGCAAGATGGTCTGCAAACATTAC
EST: gi|11173166|gb|AU164645.1|AU164645
EST:     CTACTTCAGGAACTCATGAAGATTGTGAGAGAAAATGCAGCATATGCCAG                         GAGGAATATTCAGATGGTGAGGAGGTGGGCAAGATGGTCTGCAAACATNAC
genomic: CTACTTCAGGAACTCATGAAGATTGTGAGAGAAAATGCAGCATATGCCAGgcaagttcat ... cattcttcagGAGGAATATTCAGATGGTGAGGAGGTGGGCAAGATGGTCTGCAAACATTAC
EST: gi|29671277|gb|CB667552.1|CB667552
EST:     CTACTTCAGGAACTCATGAAGATTGTGAGAGAAAATGCAGCATATGCCAG                         GAGGAATATTCAGATGGTGAGGAGGTGGGCAAGATGGTCTGCAAACATTAC
genomic: CTACTTCAGGAACTCATGAAGATTGTGAGAGAAAATGCAGCATATGCCAGgcaagttcat ... cattcttcagGAGGAATATTCAGATGGTGAGGAGGTGGGCAAGATGGTCTGCAAACATTAC
EST: gi|18386506|gb|BM419704.1|BM419704
EST:     CTACTTCAGGAACTCATGAAGATTGTGAGAGAAAATGCAGCATATGCCAG                         GAGGAATATTCAGATGGTGAGGAGGTGGGCAAGATGGTCTGCAAACATTAC
genomic: CTACTTCAGGAACTCATGAAGATTGTGAGAGAAAATGCAGCATATGCCAGgcaagttcat ... cattcttcagGAGGAATATTCAGATGGTGAGGAGGTGGGCAAGATGGTCTGCAAACATTAC
EST: gi|29666123|gb|CB662398.1|CB662398
EST:     CTACTTCAGGAACTCATGAAGATTGTGAGAGAAAATGCAGCATATGCCAG                         GAGGAATATTCAGATGGTGAGGAGGTGGGCAAGATGGTCTGCAAACATTAC
genomic: CTACTTCAGGAACTCATGAAGATTGTGAGAGAAAATGCAGCATATGCCAGgcaagttcat ... cattcttcagGAGGAATATTCAGATGGTGAGGAGGTGGGCAAGATGGTCTGCAAACATTAC
EST: gi|29676637|gb|CB672912.1|CB672912
EST:     CTACTTCAGGAACTCATGAAGATTGTGAGAGAAAATGCAGCATATGCCAG                         GAGGAATATTCAGATGGTGAGGAGGTGGGCAAGATGGTCTGCAAACATTAC
genomic: CTACTTCAGGAACTCATGAAGATTGTGAGAGAAAATGCAGCATATGCCAGgcaagttcat ... cattcttcagGAGGAATATTCAGATGGTGAGGAGGTGGGCAAGATGGTCTGCAAACATTAC
EST: gi|86841641|gb|CI337348.1|CI337348
EST:     CTACTTCAGGAACTCATGAAGATTGTGAGAGAAAATGCAGCATATGCCAG                         GAGGAATATTCAGATGGTGAGGAGGTGGGCAAGATGGTCTGCAAACATTAC
genomic: CTACTTCAGGAACTCATGAAGATTGTGAGAGAAAATGCAGCATATGCCAGgcaagttcat ... cattcttcagGAGGAATATTCAGATGGTGAGGAGGTGGGCAAGATGGTCTGCAAACATTAC
EST: gi|9865894|gb|AU101644.1|AU101644
EST:     CTACTTCAGGAACTCATGAAGATTGTGAGAGAAAATGCAGCATATGCCAG                         GAGGAATATTCAGATGGTGAGGAGGTGGGCAAGATGGTCTGCAAACATTAC
genomic: CTACTTCAGGAACTCATGAAGATTGTGAGAGAAAATGCAGCATATGCCAGgcaagttcat ... cattcttcagGAGGAATATTCAGATGGTGAGGAGGTGGGCAAGATGGTCTGCAAACATTAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCAGAAGACGCGCTGTCCAAGTGTCTAGACAGAAGCATGTACATGGCCACTACTTCAGGAACTCATGAAGATTGTGAGAGAAAATGCAGCATATGCCAGgcaagttcatttgcatgagtagattgcgcatgacactgtttgcagagttggattgtactgactactatgtacgaaatctttctgtgtgcattcttcag

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