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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcatgttcttggtactattttttttaaaaaaatgaattaaaatgtttccgtgttcttggtactaattaacagcgcactatgatgtttattgtgcaacagATGTGGATCTCCAAGGCTGAATATGACGAATCAGGCCCAGCGATTGTCCACCGGAAGTGCTTCTAAGTTCTTGGTCTTATTTATTCTCAAGTTCTTGCCG

Basic information

species Oryza sativa
transcript LOC_Os12g06660.1
intron # 4
splice site 3'
intron type U2

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|88249243|gb|CI249092.1|CI249092
EST:     GTGTCTGGATTGGTGGATCCATCCTTGCCTCCCTTAGCACCTTCCAACAG                         ATGTAGATCTCCAAGGCTGAATATGACGAATCAGGCCCAGCGATTGTCCAC
genomic: GTGTCTGGATTGGTGGATCCATCCTTGCCTCCCTTAGCACCTTCCAACAGgtaaaatttt ... tgtgcaacagATGTGGATCTCCAAGGCTGAATATGACGAATCAGGCCCAGCGATTGTCCAC
EST: gi|86419021|gb|CI053822.1|CI053822
EST:     GTGTCTGGATTGGTGGATCCATCCTTGCCTCCCTTAGCACCTTCCAACAG                         ATGTGGATCTCCAAGGCTGAATATGACGAATCAGGCCCAGCGATTGTCCAC
genomic: GTGTCTGGATTGGTGGATCCATCCTTGCCTCCCTTAGCACCTTCCAACAGgtaaaatttt ... tgtgcaacagATGTGGATCTCCAAGGCTGAATATGACGAATCAGGCCCAGCGATTGTCCAC
EST: gi|86433123|gb|CI093466.1|CI093466
EST:     GTGTCTGGATTGGTGGATCCATCCTTGCCTCCCTTAGCACCTTCCAACAG                         ATGTGGATCTCCAAGGCTGAATATGACGAATCAGGCCCAGCGATTGTCCAC
genomic: GTGTCTGGATTGGTGGATCCATCCTTGCCTCCCTTAGCACCTTCCAACAGgtaaaatttt ... tgtgcaacagATGTGGATCTCCAAGGCTGAATATGACGAATCAGGCCCAGCGATTGTCCAC
EST: gi|88483157|gb|CI420428.1|CI420428
EST:     GTGTCTGGATTGGTGGATCCATCCTTGCCTCCCTTAGCACCTTCCAACAG                         ATGTGGATCTCCAAGGCTGAATATGACGAATCAGGCCCAGCGATTGTCCAC
genomic: GTGTCTGGATTGGTGGATCCATCCTTGCCTCCCTTAGCACCTTCCAACAGgtaaaatttt ... tgtgcaacagATGTGGATCTCCAAGGCTGAATATGACGAATCAGGCCCAGCGATTGTCCAC
EST: gi|88521702|gb|CI448369.1|CI448369
EST:     GTGTCTGGATTGGTGGATCCATCCTTGCCTCCCTTAACACCTTCCAACAG                         ATGTGGATCTCCAAGGCTGAATATGACGAATCAGGCCCAGCGATTGTCCAC
genomic: GTGTCTGGATTGGTGGATCCATCCTTGCCTCCCTTAGCACCTTCCAACAGgtaaaatttt ... tgtgcaacagATGTGGATCTCCAAGGCTGAATATGACGAATCAGGCCCAGCGATTGTCCAC
EST: gi|86253292|gb|CI058217.1|CI058217
EST:     GTGTCTGGATTGGTGGATCCATCCTTGCCTCCCTTAGCACCTTCCAACAG                         ATGTGGATCTCCAAGGCTGAATATGACGAATCAGGCCCAGCGATTGTCCAC
genomic: GTGTCTGGATTGGTGGATCCATCCTTGCCTCCCTTAGCACCTTCCAACAGgtaaaatttt ... tgtgcaacagATGTGGATCTCCAAGGCTGAATATGACGAATCAGGCCCAGCGATTGTCCAC
EST: gi|86594000|gb|CI260229.1|CI260229
EST:     GTGTCTGGATTGGTGGATCCATCCTTGCCTCCCTTAGCACCTTCCAACAG                         ATGTGGATCTCCAAGGCTGAATATGACGAATCAGGCCCAGCGATTGTCCAC
genomic: GTGTCTGGATTGGTGGATCCATCCTTGCCTCCCTTAGCACCTTCCAACAGgtaaaatttt ... tgtgcaacagATGTGGATCTCCAAGGCTGAATATGACGAATCAGGCCCAGCGATTGTCCAC
EST: gi|88503607|gb|CI431113.1|CI431113
EST:     TGGATCCATCCTTGCCTCCCTTAGCACCTTCCAACAG                         ATGTGGATCTCCAAGGCTGAATATGACGAATCAGGCCCAGCGATTGTCCAC
genomic: TGGATCCATCCTTGCCTCCCTTAGCACCTTCCAACAGgtaaaatttt ... tgtgcaacagATGTGGATCTCCAAGGCTGAATATGACGAATCAGGCCCAGCGATTGTCCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttccgtgttcttggtactaattaacagcgcactatgatgtttattgtgcaacagATGTGGATCTCCAAGGCTGAATATGACGAATCAGGCCCAGCGATTGTCCACCGGAAGTGCTTCTAAGTTCTTGGTCTTATTTATTCTCAAGTTCTTGCCG
               tactaattaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcatgttcttggtactattttttttaaaaaaatgaattaaaatgtttccgtgttcttggtactaattaacagcgcactatgatgtttattgtgcaacagATGTGGATCTCCAAGGCTGAATATGACGAATCAGGCCCAGCGATTGTCCACCGGAAGTGCTTCTAAGTTCTTGGTCTTATTTATTCTCAAGTTCTTGCCG

- catgttc
- - - - - tggtact
- - - - - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgatgt