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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcatgcttcgagcgcttcgtccgttctgattttttttttagcccgactgtttgagaatcgtctgactgacctgataaagcctaattttactgccattttagCTCCCCAAGCGCCGTGAATTGGTAGGACTTTTGTGGGAGGCGCTGGTTTCTGCTCTACTCACAGCAAGTTTCTAAA

Basic information

species Oryza sativa
transcript LOC_Os03g17570.1
intron # 2
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|29665633|gb|CB661908.1|CB661908
EST:     CGACCCGNCTTTTTTCTTAGCGATTTTCTTTCCTCTTCTCTCAGGCTGAG                         CTCCCCAAGCGCCGTGAATTGGTAGGACTTTTGTGGGAGGCGCTGGTTTCT
genomic: CGACCCG-CTTTTTTCTTAGCGATTTTCTTTCCTCTTCTCTCAGGCTGAGgcatgcttcg ... gccattttagCTCCCCAAGCGCCGTGAATTGGTAGGACTTTTGTGGGAGGCGCTGGTTTCT
EST: gi|88330650|gb|CI635280.1|CI635280
EST:     GCGACCCGCTTTTTTCTTAGCGATTTTCTTTCCTCTTCTCTCAGGCTGAG                         CTCCCCAAGCGCCGTGAATTGGTAGGACTTTTGTGGGAGGCGCTGGTTTCT
genomic: GCGACCCGCTTTTTTCTTAGCGATTTTCTTTCCTCTTCTCTCAGGCTGAGgcatgcttcg ... gccattttagCTCCCCAAGCGCCGTGAATTGGTAGGACTTTTGTGGGAGGCGCTGGTTTCT
EST: gi|88573494|gb|CI665065.1|CI665065
EST:     GCGACCCGCTTTTTTCTTAGCGATTTTCTTTCCTCTTCTCTCAGGCTGAG                         CTCCCCAAGCGCCGTGAATTGGTAGGACTTTTGTGGGAGGCGCTGGTTTCT
genomic: GCGACCCGCTTTTTTCTTAGCGATTTTCTTTCCTCTTCTCTCAGGCTGAGgcatgcttcg ... gccattttagCTCCCCAAGCGCCGTGAATTGGTAGGACTTTTGTGGGAGGCGCTGGTTTCT
EST: gi|88695536|gb|CI737574.1|CI737574
EST:     GCGACCCGCTTTTTTCTTAGCGATTTTCTTTCCTCTTCTCTCAGGCTGAG                         CTCCCCAAGCGCCGTGAATTGGTAGGACTTTTGTGGGAGGCGCTGGTTTCT
genomic: GCGACCCGCTTTTTTCTTAGCGATTTTCTTTCCTCTTCTCTCAGGCTGAGgcatgcttcg ... gccattttagCTCCCCAAGCGCCGTGAATTGGTAGGACTTTTGTGGGAGGCGCTGGTTTCT
EST: gi|29661058|gb|CB657333.1|CB657333
EST:     GCGACCCGCTTTTTTCTTAGCGATTTTCTTTCCTCTTCTCTCAGGCTGAG                         CTCCCCAAGCGCCGTGAATTGGTAGGACTTTTGTGGGAGGCGCTGGTTTCT
genomic: GCGACCCGCTTTTTTCTTAGCGATTTTCTTTCCTCTTCTCTCAGGCTGAGgcatgcttcg ... gccattttagCTCCCCAAGCGCCGTGAATTGGTAGGACTTTTGTGGGAGGCGCTGGTTTCT
EST: gi|88359680|gb|CI622370.1|CI622370
EST:     CGACCCGCCTTTTTTCTTAGCGATTTTCCTTCCTCTTCTCTCAGGCTGAG                         CTCCCCAAGCGCCGTGAATTGGTAGGACTTTTGTGGGAGGCGCTGGTTTCT
genomic: CGACCCGC-TTTTTTCTTAGCGATTTTCTTTCCTCTTCTCTCAGGCTGAGgcatgcttcg ... gccattttagCTCCCCAAGCGCCGTGAATTGGTAGGACTTTTGTGGGAGGCGCTGGTTTCT
EST: gi|88391633|gb|CI600822.1|CI600822
EST:     GCGACCCGCTTTTTTCTTAGCGATTTTCTTTCCTCTTCTCTCAGGCTGAG                         CTCCCCAAGCGCCGTGAATTGGTAGGACTTTTGTGGGAGGCGCTGGTTTCT
genomic: GCGACCCGCTTTTTTCTTAGCGATTTTCTTTCCTCTTCTCTCAGGCTGAGgcatgcttcg ... gccattttagCTCCCCAAGCGCCGTGAATTGGTAGGACTTTTGTGGGAGGCGCTGGTTTCT
EST: gi|88288553|gb|CI663342.1|CI663342
EST:     GCGACCCGCTTTTTTCTTAGCGATTTTCTTTCCTCTTCTCTCAGGCTGAG                         CTCCCCAAGCGCCGTGAATTGGTAGGACTTTTGTGGGAGGCGCTGGTTTCT
genomic: GCGACCCGCTTTTTTCTTAGCGATTTTCTTTCCTCTTCTCTCAGGCTGAGgcatgcttcg ... gccattttagCTCCCCAAGCGCCGTGAATTGGTAGGACTTTTGTGGGAGGCGCTGGTTTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtttgagaatcgtctgactgacctgataaagcctaattttactgccattttagCTCCCCAAGCGCCGTGAATTGGTAGGACTTTTGTGGGAGGCGCTGGTTTCTGCTCTACTCACAGCAAGTTTCTAAA
                                              ccatttt  CT-rich tract
                                   taattttact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcatgcttcgagcgcttcgtccgttctgattttttttttagcccgactgtttgagaatcgtctgactgacctgataaagcctaattttactgccattttagCTCCCCAAGCGCCGTGAATTGGTAGGACTTTTGTGGGAGGCGCTGGTTTCTGCTCTACTCACAGCAAGTTTCTAAA

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