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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atattgtacattttttagcatcgtcatagatgagtctattcttccttcgattttctgttctatgtttgatctttatgctatctttttttctgaactgtagGAGCCATGAGTGGTGGATAATCAAATTTCAGAAGGTCCTGCAAGATTCTACCTCAGTGTCCCTTTTTTGTCGAGGTTCCTGCTCTGTGAACTGCTGATAT

Basic information

species Oryza sativa
transcript LOC_Os01g46040.1
intron # 1
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|16754364|gb|BM038743.1|BM038743
EST:     TGGTC-CGGAGCAC-GGGCCGCCCTCGCCGGCGTGGTTAAGGTGAAGCAG                         GAGCCATGAGTGGTGGATAATCAAATTTCAGAAGGTCCTGCAAGATTCTAC
genomic: TGGTCGCGGAGCACGGGGCCGCCCTCGCCGGCGTGGTTAAGGTGAAGCAGgtaacatctg ... tgaactgtagGAGCCATGAGTGGTGGATAATCAAATTTCAGAAGGTCCTGCAAGATTCTAC
EST: gi|88243873|gb|CI242995.1|CI242995
EST:     TGGCCGCGGAGCACGGGGCCGCCCTCGCCGGCGTGGTTAAGGTGAAGCAG                         GAGCCATGAGTGGTGGATAATCAAATTTCAGAAGGTCCTGCAAGATTCTAC
genomic: TGGTCGCGGAGCACGGGGCCGCCCTCGCCGGCGTGGTTAAGGTGAAGCAGgtaacatctg ... tgaactgtagGAGCCATGAGTGGTGGATAATCAAATTTCAGAAGGTCCTGCAAGATTCTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcgattttctgttctatgtttgatctttatgctatctttttttctgaactgtagGAGCCATGAGTGGTGGATAATCAAATTTCAGAAGGTCCTGCAAGATTCTACCTCAGTGTCCCTTTTTTGTCGAGGTTCCTGCTCTGTGAACTGCTGATAT
                  gtttgat  putative branch site (score: 5)
 tctttatgctatcttt  CT-rich tract
 tatcttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atattgtacattttttagcatcgtcatagatgagtctattcttccttcgattttctgttctatgtttgatctttatgctatctttttttctgaactgtagGAGCCATGAGTGGTGGATAATCAAATTTCAGAAGGTCCTGCAAGATTCTACCTCAGTGTCCCTTTTTTGTCGAGGTTCCTGCTCTGTGAACTGCTGATAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttatgct