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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCGCTCCGGCGTGGTGGCCATGGACGCCGCCGGCGCCGATGCAGACCAAGCCCGGCTGCACCAGCTGGGCTACAGGCAAGAGCTCAAGCGTGGCCTCTCgtatgtgcttcttcttcccttcttttaccacacttcattgcgatcatttttcaccaaattaagcttgtgagtgttaatttggcatatattgcaatcctttgttag

Basic information

species Oryza sativa
transcript LOC_Os01g71740.1
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|88569388|gb|CI660563.1|CI660563
EST:     GCCCGGCTGCACCAGCTGGGCTACAGGCAAGAGCTCAAGCGTGGCCTCTC                         CCTTGTTTCCAACTTCGCCTTCTCCTTCTCCATCATCTCCGTGCTGACGGG
genomic: GCCCGGCTGCACCAGCTGGGCTACAGGCAAGAGCTCAAGCGTGGCCTCTCgtatgtgctt ... cctttgttagCCTTGTTTCCAACTTCGCCTTCTCCTTCTCCATCATCTCCGTGCTGACGGG
EST: gi|88696500|gb|CI740075.1|CI740075
EST:     GCCCGGCTGCACCAGCTGGGCTACAGGCAAGAGCTCAAGCGTGGCCTCTC                         CCTTGTTTCCAACTTCGCCTTCTCCTTCTCCATCATCTCCGTGCTGACGGG
genomic: GCCCGGCTGCACCAGCTGGGCTACAGGCAAGAGCTCAAGCGTGGCCTCTCgtatgtgctt ... cctttgttagCCTTGTTTCCAACTTCGCCTTCTCCTTCTCCATCATCTCCGTGCTGACGGG
EST: gi|88290383|gb|CI665172.1|CI665172
EST:     GCCCGGCTGCACCAGCTGGGCTACAGGCAAGAGCTCAAGCGTGGCCTCTC                         CCTTGTTTCCAACTTCGCCTTCTCCTTCTCCATCATCTCCGTGCTGACGGG
genomic: GCCCGGCTGCACCAGCTGGGCTACAGGCAAGAGCTCAAGCGTGGCCTCTCgtatgtgctt ... cctttgttagCCTTGTTTCCAACTTCGCCTTCTCCTTCTCCATCATCTCCGTGCTGACGGG
EST: gi|88720209|gb|CI743508.1|CI743508
EST:     GCCCGGCTGCACCAGCTGGGCTACAGGCAAGAGCTCAAGCGTGGCCTCTC                         CCTTGTTTCCAACTTCGCCTTCTCCTTCTCCATCATCTCCGTGCTGACGGG
genomic: GCCCGGCTGCACCAGCTGGGCTACAGGCAAGAGCTCAAGCGTGGCCTCTCgtatgtgctt ... cctttgttagCCTTGTTTCCAACTTCGCCTTCTCCTTCTCCATCATCTCCGTGCTGACGGG
EST: gi|88719257|gb|CI742767.1|CI742767
EST:     GCCCGGCTGCACCAGCTGGGCTACAGGCAAGAGCTCAAGCGTGGCCTCTC                         CCTTGTTTCCAACTTCGCCTTCTCCTTCTCCATCATCTCCGTGCTGACGGG
genomic: GCCCGGCTGCACCAGCTGGGCTACAGGCAAGAGCTCAAGCGTGGCCTCTCgtatgtgctt ... cctttgttagCCTTGTTTCCAACTTCGCCTTCTCCTTCTCCATCATCTCCGTGCTGACGGG
EST: gi|88720346|gb|CI743645.1|CI743645
EST:     GCCCGGNTGCACCAGCTGGGCTACAGGCAAGAGCTCAAGCGTGGCCTCTC                         CCTTGTTTCCAACTTCGCCTTCTCCTTCTCCATCATCTCCGTGCTGACGGG
genomic: GCCCGGCTGCACCAGCTGGGCTACAGGCAAGAGCTCAAGCGTGGCCTCTCgtatgtgctt ... cctttgttagCCTTGTTTCCAACTTCGCCTTCTCCTTCTCCATCATCTCCGTGCTGACGGG
EST: gi|88296231|gb|CI667621.1|CI667621
EST:     GCCCGGCTGCACCAGCTGGGCTACAGGCAAGAGCTCAAGCGTGGCCTCTC                         CCTTGTTTCCAACTTCGCCTTCTCCTTCTCCATCATCTCCGTGCTGACGGG
genomic: GCCCGGCTGCACCAGCTGGGCTACAGGCAAGAGCTCAAGCGTGGCCTCTCgtatgtgctt ... cctttgttagCCTTGTTTCCAACTTCGCCTTCTCCTTCTCCATCATCTCCGTGCTGACGGG
EST: gi|86821680|gb|CI309186.1|CI309186
EST:     GCCCGGCTGCACCAGCTGGGCTACAGGCAAGAGCTCAAGCGTGGCCTCTC                         CCTTGTTTCCAACTTCGCCTTCTCCTTCTCCATCATCTCCGTGCTGACGGG
genomic: GCCCGGCTGCACCAGCTGGGCTACAGGCAAGAGCTCAAGCGTGGCCTCTCgtatgtgctt ... cctttgttagCCTTGTTTCCAACTTCGCCTTCTCCTTCTCCATCATCTCCGTGCTGACGGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCGCTCCGGCGTGGTGGCCATGGACGCCGCCGGCGCCGATGCAGACCAAGCCCGGCTGCACCAGCTGGGCTACAGGCAAGAGCTCAAGCGTGGCCTCTCgtatgtgcttcttcttcccttcttttaccacacttcattgcgatcatttttcaccaaattaagcttgtgagtgttaatttggcatatattgcaatcctttgttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA