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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcaaattcaatcaatttctttcctacaaattttaaacataggaaactctttaatcacagggtgtttgcattaatgttgagctgtgacatgttggtttggaaaggtgaacatgtttttgttacactgtagGTGCCAGCCTTCTTGTATATCAACTTTTTATCTACCGTTGGGTTGATAAAATTCTTGGACCTATCAACTCAACCCGCATTGCGTCG

Basic information

species Oryza sativa
transcript LOC_Os11g04030.1
intron # 11
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|29678071|gb|CB674346.1|CB674346
EST:     TGGACTCAGCTTTTCATCTAAAGATGTTGGGCAAGTTCTTGCAGTGGCAG                         GTGCCAGCCTTCTTGTATATCAACTTTTTATCTACCGTTGGGTTGATAAAA
genomic: TGGACTCAGCTTTTCATCTAAAGATGTTGGGCAAGTTCTTGCAGTGGCAGgtaagtcaaa ... tacactgtagGTGCCAGCCTTCTTGTATATCAACTTTTTATCTACCGTTGGGTTGATAAAA
EST: gi|29680055|gb|CB676330.1|CB676330
EST:     TGGACTCAGCTTTTCATCTAAAGATGTTGGGCAAGTTCTTGCAGTGGCAG                         GTGCCAGCCTTCTTGTATATCAACTTTTTATCTACCGTTGGGTTGATAAAA
genomic: TGGACTCAGCTTTTCATCTAAAGATGTTGGGCAAGTTCTTGCAGTGGCAGgtaagtcaaa ... tacactgtagGTGCCAGCCTTCTTGTATATCAACTTTTTATCTACCGTTGGGTTGATAAAA
EST: gi|87006928|gb|CI275236.1|CI275236
EST:     TGGACTCA-CTTTT-ATCT-AAGATGTTGGCCGA-TTCTTGCAGTGGCA-                         GTGCCAACCTTCTTGTATATCAACTTTTTATCTACCGTTGGGTTGATAAAA
genomic: TGGACTCAGCTTTTCATCTAAAGATGTTGGGCAAGTTCTTGCAGTGGCAGgtaagtcaaa ... tacactgtagGTGCCAGCCTTCTTGTATATCAACTTTTTATCTACCGTTGGGTTGATAAAA
EST: gi|29644402|gb|CB649409.1|CB649409
EST:     TGGACTCAGCTTTTCATCTAAAGATGTTGGGCAAGTTCTTGCAGTGGCAG                         GTGCCAGCCTTCTTGTATATCAACTTTTTATCTACCGTTGGGTTGATAAAA
genomic: TGGACTCAGCTTTTCATCTAAAGATGTTGGGCAAGTTCTTGCAGTGGCAGgtaagtcaaa ... tacactgtagGTGCCAGCCTTCTTGTATATCAACTTTTTATCTACCGTTGGGTTGATAAAA
EST: gi|29679866|gb|CB676141.1|CB676141
EST:     CAAGTTCTTGCAGTGGCAG                         GTGCCAGCCTTCTTGTATATCAACTTTTTATCTACCGTTGGGTTGATAAAA
genomic: CAAGTTCTTGCAGTGGCAGgtaagtcaaa ... tacactgtagGTGCCAGCCTTCTTGTATATCAACTTTTTATCTACCGTTGGGTTGATAAAA

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: 63 (upstream exon), 54 (downstream exon)
Score: 21

ATATTTTCTCTGTGGACTGTAAGTGATAGAAAATATGGTGGACTCAGCTTTTCATCTAAAGATGTTGGGCAAGTTCTTGCAGTGGCAGgtaagtcaaa ... tacactgtagGTGCCAGCCTTCTTGTATATCAACTTTTTATCTACCGTTGGGTTGATAAAATTCTTGGACCTATCAACTCAACCCGCATTGCGTCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgagctgtgacatgttggtttggaaaggtgaacatgtttttgttacactgtagGTGCCAGCCTTCTTGTATATCAACTTTTTATCTACCGTTGGGTTGATAAAATTCTTGGACCTATCAACTCAACCCGCATTGCGTCG
                                      tttttgtt  CT-rich tract
                                      tttttgtta  TA-rich tract