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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtgttctacattttctgagtctcgcttatgagtccatctcgtgatcagcttcaccatatataaccttgaatgcgcagGCCGCCGGAGCAACGTCGGAGGAGGACACGGGCGCGCTGCTGCTCCCGGGCTCGACGGGGTCGAACCAGTGCGTGTACACGCTCTACGTGGAGACGGGCT

Basic information

species Oryza sativa
transcript LOC_Os04g38360.1
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|38479282|gb|CF963415.1|CF963415
EST:     TGGCGCATAAGCTCCGCTGCTTTGCGGCACTCATTTCCATGGCGGCTTTG                         GCCGCCGGAGCAACGTCGGAGGAGGACACGGGCGCGCTGCTGCTCCCGGGC
genomic: TGGCGCATAAGCTCCTCTGCTTTGCGGCACTCATTTCCATGGCGGCTTTGgtacgtgttc ... gaatgcgcagGCCGCCGGAGCAACGTCGGAGGAGGACACGGGCGCGCTGCTGCTCCCGGGC
EST: gi|112785432|gb|EE590676.1|EE590676
EST:     TGGCGCATAAGCTCCTCTGCTTTGCGGCACTCATTTCCATGGCGGCTTTG                         GCCGCCGGAGCAACGTCGGAGGAGGACACGGGCGCGCTGCTGCTCCCGGGC
genomic: TGGCGCATAAGCTCCTCTGCTTTGCGGCACTCATTTCCATGGCGGCTTTGgtacgtgttc ... gaatgcgcagGCCGCCGGAGCAACGTCGGAGGAGGACACGGGCGCGCTGCTGCTCCCGGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgcttatgagtccatctcgtgatcagcttcaccatatataaccttgaatgcgcagGCCGCCGGAGCAACGTCGGAGGAGGACACGGGCGCGCTGCTGCTCCCGGGCTCGACGGGGTCGAACCAGTGCGTGTACACGCTCTACGTGGAGACGGGCT
                                   atataac  putative branch site (score: 3)
                                 atatataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtgttctacattttctgagtctcgcttatgagtccatctcgtgatcagcttcaccatatataaccttgaatgcgcagGCCGCCGGAGCAACGTCGGAGGAGGACACGGGCGCGCTGCTGCTCCCGGGCTCGACGGGGTCGAACCAGTGCGTGTACACGCTCTACGTGGAGACGGGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA