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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCGGCACCAAGTTCGCACTGAAGATGACGATTATGAACAACGTATGGCTCGGCGCGTGATTGTTCTAGCAGCAGTGGAGCATCAGGGTGCACCGGCACAGgtatgatgttgacatttagtggaaaagatcttaggtgcactttcatggcggtggcttacagcatgcatcttcataattttttaaaaaaatttgtatttgc...

Basic information

species Oryza sativa
transcript LOC_Os02g09820.1
intron # 1
splice site 5'
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|218480664|gb|FG956914.1|FG956914
EST:     GGCGCGTGATTGTTCTAGCAGCAGTGGAGCATCAGGGTGCACCGGCACAG                         GGCTGTGGAGACAGCGCAACCATGGGTGCTGAAGGCGCAAGTGAATGTGTG
genomic: GGCGCGTGATTGTTCTAGCAGCAGTGGAGCATCAGGGTGCACCGGCACAGgtatgatgtt ... acattgacagGGCTGTGGAGACAGCGCAACCATGGGTGCTGAAGGCGCAAGTGAATGTGTG
EST: gi|88994217|gb|CI116181.1|CI116181
EST:     GGCGCGTGATTGTTCTAGCAGCAGTGGAGCATCAGGGTGCACCGGCACAG                         GGCTGTGGAGACAGCGCAACCATGGGTGCTGAAGGCGCAAGTGAATGTGTG
genomic: GGCGCGTGATTGTTCTAGCAGCAGTGGAGCATCAGGGTGCACCGGCACAGgtatgatgtt ... acattgacagGGCTGTGGAGACAGCGCAACCATGGGTGCTGAAGGCGCAAGTGAATGTGTG
EST: gi|86494080|gb|CI136713.1|CI136713
EST:     GGCGCGTGATTGTTCTAGCAGCAGTGGAGCATCAGGGTGCACCGGCACAG                         GGCTGTGGAGACAGCGCAACCATGGGTGCTGAAGGCGCAAGTGAATGTGTG
genomic: GGCGCGTGATTGTTCTAGCAGCAGTGGAGCATCAGGGTGCACCGGCACAGgtatgatgtt ... acattgacagGGCTGTGGAGACAGCGCAACCATGGGTGCTGAAGGCGCAAGTGAATGTGTG
EST: gi|86502763|gb|CI145396.1|CI145396
EST:     GGCGCGTGATTGTTCTAGCAGCAGTGGAGCATCAGGGTGCACCGGCACAG                         GGCTGTGGAGACAGCGCAACCATGGGTGCTGAAGGCGCAAGTGAATGTGTG
genomic: GGCGCGTGATTGTTCTAGCAGCAGTGGAGCATCAGGGTGCACCGGCACAGgtatgatgtt ... acattgacagGGCTGTGGAGACAGCGCAACCATGGGTGCTGAAGGCGCAAGTGAATGTGTG
EST: gi|86432671|gb|CI086282.1|CI086282
EST:     GGCGCGTGATTGTTCTAGCAGCAGTGGAGCATCAGGGTGCACCGGCACAG                         GGCTGTGGAGACAGCGCAACCATGGGTGCTGAAGGCGCAAGTGAATGTGTG
genomic: GGCGCGTGATTGTTCTAGCAGCAGTGGAGCATCAGGGTGCACCGGCACAGgtatgatgtt ... acattgacagGGCTGTGGAGACAGCGCAACCATGGGTGCTGAAGGCGCAAGTGAATGTGTG
EST: gi|86859422|gb|CI278840.1|CI278840
EST:     GGCGCGTGATTGTTCTAGCAGCAGTGGAGCATCAGGGTGCACCGGCACAG                         GGCTTTGGAGACAGCGCAACCATGGGTGCTGAAGGCGCAAGTGAATGTGTG
genomic: GGCGCGTGATTGTTCTAGCAGCAGTGGAGCATCAGGGTGCACCGGCACAGgtatgatgtt ... acattgacagGGCTGTGGAGACAGCGCAACCATGGGTGCTGAAGGCGCAAGTGAATGTGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCGGCACCAAGTTCGCACTGAAGATGACGATTATGAACAACGTATGGCTCGGCGCGTGATTGTTCTAGCAGCAGTGGAGCATCAGGGTGCACCGGCACAGgtatgatgttgacatttagtggaaaagatcttaggtgcactttcatggcggtggcttacagcatgcatcttcataattttttaaaaaaatttgtatttgc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggcggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaa