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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATCACAATTCGTGAAATTCGAGAGCATCAGTGGTTTCAGATTCGCCTTCCTCGTTACTTAGCAGTGCCTCCACCAGACACAGCACAGCAAGCCAAAATGgtacttcctttgtgtcacattcttaacgagttgttcatttatgtatcaaattttatctactaatgtaattttcttgagatatacttatagagtataataa...

Basic information

species Oryza sativa
transcript LOC_Os03g17980.2
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g17980.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G107867_T02 (Zea mays), 5'ss of exon 6
AATCACAATTCGTGAAATTCGAGAGCATCAGTGGTTTCAGATTCGCCTTCCTCGTTACTTAGCAGTGCCTCCACCAGACACAGCACAGCAAGCCAAAATGgtacttcctttgtgtcaca--ttcttaacgagttgtt-catttatgtat-caaattttatctactaatgtaattttcttgagatatacttata-gagtataataa
|||||||||| | |||||||| |||||||| ||||| |||||||||||||| |||||||| ||||||||||||||||| ||  |||| |||||||||||||||  |||| |  || | |  |   ||    | | || |||   ||| | |||| ||| |    |  |  | |  | |  ||  | |  || | | ||||     
AATCACAATTAGGGAAATTCGGGAGCATCAATGGTTCCAGATTCGCCTTCCACGTTACTTGGCAGTGCCTCCACCAGATACGACACAACAAGCCAAAATGgtatgtcctctcagttataagtggctatactgctattgcatgcttgtgttcaaagtttctaattttgtccactaatatgtaggaaaaagtagatgtgtat-----
















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|58667418|gb|CK056104.1|CK056104
EST:     CTCGTTACTTAGCAGTGCCTCCACCAGACACAGCACAGCAAGCCAAAATG                         ATTGATGAAGATACCCTTCAAGATGTCGTAAACTTGGGTTATGGAAAGGAC
genomic: CTCGTTACTTAGCAGTGCCTCCACCAGACACAGCACAGCAAGCCAAAATGgtacttcctt ... ttttttgaagATTGATGAAGATACCCTTCAAGATGTCGTAAACTTGGGTTATGGAAAGGAC
EST: gi|58666104|gb|CK054790.1|CK054790
EST:     CTCGTTACTTAGCAGTGCCTCCACCAGACACAGCACAGCAAGCCAAAATG                         ATTGATGAAGATACCCTTCAAGATGTCGTAAACTTGGGTTATGGAAAGGAC
genomic: CTCGTTACTTAGCAGTGCCTCCACCAGACACAGCACAGCAAGCCAAAATGgtacttcctt ... ttttttgaagATTGATGAAGATACCCTTCAAGATGTCGTAAACTTGGGTTATGGAAAGGAC
EST: gi|58674982|gb|CK063669.1|CK063669
EST:     TCGTTTACTTAGCAGTGCCTCCACCAGACACAGCACAGCAAGCCAAAATG                         ATTGATGAAGATACCCTTCAAGATGTCGTAAACTTGGGTTATGGAAAGGAC
genomic: TCGTT-ACTTAGCAGTGCCTCCACCAGACACAGCACAGCAAGCCAAAATGgtacttcctt ... ttttttgaagATTGATGAAGATACCCTTCAAGATGTCGTAAACTTGGGTTATGGAAAGGAC
EST: gi|218478287|gb|FG959067.1|FG959067
EST:     CTCGTTACTTAGCAGTGCCTCCACCAGACACAGCACAGCAAGCCAAAATG                         ATTGATGAAGATACCCTTCAAGATGTCGTAAACTTGGGTTATGGAAAGGAC
genomic: CTCGTTACTTAGCAGTGCCTCCACCAGACACAGCACAGCAAGCCAAAATGgtacttcctt ... ttttttgaagATTGATGAAGATACCCTTCAAGATGTCGTAAACTTGGGTTATGGAAAGGAC
EST: gi|218482816|gb|FG952976.1|FG952976
EST:     CTCGTTACTTAGCAGTGCCTCCACCAGACACAGCACAGCAAGCCAAAATG                         ATGGATGAAGATACCCTTCAAGATGTCGTAAACTTGGGTTATGGAAAGGAC
genomic: CTCGTTACTTAGCAGTGCCTCCACCAGACACAGCACAGCAAGCCAAAATGgtacttcctt ... ttttttgaagATTGATGAAGATACCCTTCAAGATGTCGTAAACTTGGGTTATGGAAAGGAC
EST: gi|218482252|gb|FG960526.1|FG960526
EST:     CTCGTTACTTAGCAGTGCCTCCACCAGACACAGCACAGCAAGCCAAAATG                         ATTGATGAAGATACCCTTCAAGATGTCGTAAACTTGGGTTATGGAAAGGAC
genomic: CTCGTTACTTAGCAGTGCCTCCACCAGACACAGCACAGCAAGCCAAAATGgtacttcctt ... ttttttgaagATTGATGAAGATACCCTTCAAGATGTCGTAAACTTGGGTTATGGAAAGGAC
EST: gi|218502900|gb|FG954558.1|FG954558
EST:     CTCGTTACTTAGCAGTGACTCCACCAGACACAGAACAGAAAGCCAAAATG                         ATTGATGAAGATCCCCTTCA
genomic: CTCGTTACTTAGCAGTGCCTCCACCAGACACAGCACAGCAAGCCAAAATGgtacttcctt ... ttttttgaagATTGATGAAGATACCCTTCA
EST: gi|2317303|gb|C22357.1|C22357
EST:     CTCGTTACTTAGCAGTGCCTCCACCAGACACAGCACAGCAAGCCAAAATG                         ATTGATGAAGATACCCTTCAAGATGTCGTAAACTTGGGTTATGGAAAGGAC
genomic: CTCGTTACTTAGCAGTGCCTCCACCAGACACAGCACAGCAAGCCAAAATGgtacttcctt ... ttttttgaagATTGATGAAGATACCCTTCAAGATGTCGTAAACTTGGGTTATGGAAAGGAC
EST: gi|218484843|gb|FG952392.1|FG952392
EST:     CTCGTTACTTAGCAGTGCCTCCACCAGACACAGCACAGCAAGCCAAAATG                         ATTGATGAAGATACCCTTCAAGATGTCGTAAACTTGGGTTATGGAAAGGAC
genomic: CTCGTTACTTAGCAGTGCCTCCACCAGACACAGCACAGCAAGCCAAAATGgtacttcctt ... ttttttgaagATTGATGAAGATACCCTTCAAGATGTCGTAAACTTGGGTTATGGAAAGGAC
EST: gi|29614995|gb|CB620008.1|CB620008
EST:     CTCGTTACTTAGCAGTGCCTCCACCAGACACAGCACAGCAAGCCAAAATG                         ATTGATGAAGATACCCTTCAAGATGTCGTANACTTGGGTTATGGAAAGGAC
genomic: CTCGTTACTTAGCAGTGCCTCCACCAGACACAGCACAGCAAGCCAAAATGgtacttcctt ... ttttttgaagATTGATGAAGATACCCTTCAAGATGTCGTAAACTTGGGTTATGGAAAGGAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATCACAATTCGTGAAATTCGAGAGCATCAGTGGTTTCAGATTCGCCTTCCTCGTTACTTAGCAGTGCCTCCACCAGACACAGCACAGCAAGCCAAAATGgtacttcctttgtgtcacattcttaacgagttgttcatttatgtatcaaattttatctactaatgtaattttcttgagatatacttatagagtataataa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG