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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtggcctttttttttttttttacaaatggaaagtacttcatttttgttgcctttccccttattatcttgtacctgactacataatatccctgacagCAAGCACGGATACTCGATGATAAATATATGTTGGAAAGGCGCATTGCTCAAATGCGGATG

Basic information

species Oryza sativa
transcript LOC_Os01g01800.1
intron # 5
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|29674957|gb|CB671232.1|CB671232
EST:     AGGAAGAGATTGCGCAATTAAGAAAACATCTTGCTGACTACTCATTGAAG                         CAAGCACGGATACTCGATGATAAATATATGTTGGAAAAGCGCATTGCTCAA
genomic: AGGAAGAGATTGCGCAATTAAGAAAACATCTTGCTGACTACTCATTGAAGgtggcctttt ... tccctgacagCAAGCACGGATACTCGATGATAAATATATGTTGGAAAGGCGCATTGCTCAA
EST: gi|32947856|gb|BP184428.1|BP184428
EST:     AGGAAGAGATTGCGCAATTAAGAAAACATCTTGCTGACTACTCATTGAAG                         CAAGCACGGATACTCGATGATAAATATATGTTGGAAAGGCGCATTGCTCAA
genomic: AGGAAGAGATTGCGCAATTAAGAAAACATCTTGCTGACTACTCATTGAAGgtggcctttt ... tccctgacagCAAGCACGGATACTCGATGATAAATATATGTTGGAAAGGCGCATTGCTCAA
EST: gi|58673928|gb|CK062614.1|CK062614
EST:     AGGAAGAGATTGCGCAATTAAGAAAACATCTTGCTGACTACTCATTGAAG                         CAAGCACGGATACTCGATGATAAATATATGTTGGAAAGGCGCATTGCTCAA
genomic: AGGAAGAGATTGCGCAATTAAGAAAACATCTTGCTGACTACTCATTGAAGgtggcctttt ... tccctgacagCAAGCACGGATACTCGATGATAAATATATGTTGGAAAGGCGCATTGCTCAA
EST: gi|29628865|gb|CB633876.1|CB633876
EST:     AGGAAGAGATTGCGCAATTAAGAAAACATCTTGCTGACTACTCATTGAAG                         CAAGCACGGATACTCGATGATATATATATGTTGGAGAGGCGCATTGCTCAA
genomic: AGGAAGAGATTGCGCAATTAAGAAAACATCTTGCTGACTACTCATTGAAGgtggcctttt ... tccctgacagCAAGCACGGATACTCGATGATAAATATATGTTGGAAAGGCGCATTGCTCAA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 72 (upstream exon), 57 (downstream exon)
Score: 11

GATCTTACTGCTAAGATCAAAGAAAATGAGGAAGAGATTGCGCAATTAAGAAAACATCTTGCTGACTACTCATTGAAGgtggcctttt ... tccctgacagCAAGCACGGATACTCGATGATAAATATATGTTGGAAAGGCGCATTGCTCAAATGCGGATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgttgcctttccccttattatcttgtacctgactacataatatccctgacagCAAGCACGGATACTCGATGATAAATATATGTTGGAAAGGCGCATTGCTCAAATGCGGATG
                             acctgac  putative branch site (score: 11)
                                           tatccct  putative PPT
                 ttattatctt  TA-rich tract