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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGCCACTAAATACCCAACCAATGCGCTTGTCCATCGTCCTGTACTCATTGACTATATTGTGTCAACGAAGgtatgctcactacctttttcattatgtgttattcttcttgagagtgcacagtacaaaagaaggggtatctttcttctctgccaccaccatcatagttctgtgaacctaaagtattccttgctatgccacttttcag

Basic information

species Oryza sativa
transcript LOC_Os01g09000.1
intron # 3
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|7332447|gb|AU085793.1|AU085793
EST:     ATGCGCTTGTCCATCGTCCTGTACTCATTGACNATATTGTGTCAACGAAG                         ATAAAGAATCCCTNCACAACTAGATGCTGCTCTGTCATTCCTTACTAATAC
genomic: ATGCGCTTGTCCATCGTCCTGTACTCATTGACTATATTGTGTCAACGAAGgtatgctcac ... cacttttcagATAAAGAAT-CCTGCACAACTAGATGCTGCTCTGTCATTCCTTACTAATAC
EST: gi|89161518|gb|CI099490.1|CI099490
EST:     ATGCGCTTGTCCATCGTCCTGTACTCATTGACTATATTGTGTCAACGAAG                         ATAAAGAATCCTGCACAACTAGATGCTGCTCTGTCATTCCTTACTAATACT
genomic: ATGCGCTTGTCCATCGTCCTGTACTCATTGACTATATTGTGTCAACGAAGgtatgctcac ... cacttttcagATAAAGAATCCTGCACAACTAGATGCTGCTCTGTCATTCCTTACTAATACT
EST: gi|88994745|gb|CI036326.1|CI036326
EST:     ATGCGCTTGTCCATCGTCCTGTACTCATTGACTATATTGTGTCAACGAAG                         ATAAAGAATCCTGCACAACTAGATGCTGCTCTGTCATTCCTTACTAATACT
genomic: ATGCGCTTGTCCATCGTCCTGTACTCATTGACTATATTGTGTCAACGAAGgtatgctcac ... cacttttcagATAAAGAATCCTGCACAACTAGATGCTGCTCTGTCATTCCTTACTAATACT
EST: gi|58672280|gb|CK060966.1|CK060966
EST:     ATGCGCTTGTCCATCGTCCTGTACTCATTGACTATATTGTGTCAACGAAG                         ATAAAGAATCCTGCACAACTAGATGCTGCTCTGTCATTCCTTACTAATACT
genomic: ATGCGCTTGTCCATCGTCCTGTACTCATTGACTATATTGTGTCAACGAAGgtatgctcac ... cacttttcagATAAAGAATCCTGCACAACTAGATGCTGCTCTGTCATTCCTTACTAATACT
EST: gi|15846919|gb|BI795195.1|BI795195
EST:     TTGTCCATCGTCCTGTACTCATTGACGTATATTGTGTCAGACGAAG                         ATAAAGAATCCTGCACAACTAGATGCTGCTCGTGTCATTCCTTACTAATA
genomic: TTGTCCATCGTCCTGTACTCATTGAC-TATATTGTGTCA-ACGAAGgtatgctcac ... cacttttcagATAAAGAATCCTGCACAACTAGATGCTGCTC-TGTCATTCCTTACTAATA
EST: gi|88311944|gb|CI577550.1|CI577550
EST:     ATGCGCTTGTCCATCGTCCTGTACTCATTGACTATATTGTGTCAACGAAG                         ATAAAGAATCCTG
genomic: ATGCGCTTGTCCATCGTCCTGTACTCATTGACTATATTGTGTCAACGAAGgtatgctcac ... cacttttcagATAAAGAATCCTG
EST: gi|88351919|gb|CI625919.1|CI625919
EST:     ATGCGCTTGTCCATCGTCCTGTACTCATTGACTATATTGTGTCAACGGAG                         ATAAAGAATCCTGCACAACTAGATGCTGCTCTGTCATTCCTTACTAATACT
genomic: ATGCGCTTGTCCATCGTCCTGTACTCATTGACTATATTGTGTCAACGAAGgtatgctcac ... cacttttcagATAAAGAATCCTGCACAACTAGATGCTGCTCTGTCATTCCTTACTAATACT
EST: gi|86826937|gb|CI268818.1|CI268818
EST:     ATGCGCTTGTCCATCGTCCTGTACTCATTGACTATATTGTGTCAACGAAG                         ATAAAGAATCCTGCACAACTAGATGCTGCTCTGTCATTCCTTACTAATACT
genomic: ATGCGCTTGTCCATCGTCCTGTACTCATTGACTATATTGTGTCAACGAAGgtatgctcac ... cacttttcagATAAAGAATCCTGCACAACTAGATGCTGCTCTGTCATTCCTTACTAATACT
EST: gi|88454226|gb|CI567831.1|CI567831
EST:     ATGCGCTTGTCCATCGTC-TGTA-TCATTGACTATATTGTGTCAAGGAAG                         ATAAAGAATCCTGCACAACTAGATGCTGCTCTGTAATTCCTTACTAATACT
genomic: ATGCGCTTGTCCATCGTCCTGTACTCATTGACTATATTGTGTCAACGAAGgtatgctcac ... cacttttcagATAAAGAATCCTGCACAACTAGATGCTGCTCTGTCATTCCTTACTAATACT
EST: gi|88294826|gb|CI604698.1|CI604698
EST:     ATGCGCTTGTCCATCGTCCTGTACTCATTGACTATATTGTGTCAACGAAG                         ATAAAGAATCCTGCACAACT
genomic: ATGCGCTTGTCCATCGTCCTGTACTCATTGACTATATTGTGTCAACGAAGgtatgctcac ... cacttttcagATAAAGAATCCTGCACAACT
EST: gi|58663041|gb|CK051727.1|CK051727
EST:     ATGCGCTTGTCCATCGTCCTGTACTCATTGACTATATTGTGTCAACGAAG                         ATAAAGAATCCTGCACAACTAGATGCTGCTCTGTCATTCCTTACTAATACT
genomic: ATGCGCTTGTCCATCGTCCTGTACTCATTGACTATATTGTGTCAACGAAGgtatgctcac ... cacttttcagATAAAGAATCCTGCACAACTAGATGCTGCTCTGTCATTCCTTACTAATACT
EST: gi|58691015|gb|CK079702.1|CK079702
EST:     ATGCGCTTGTCCATCGTCCTGTACTCATTGACTATATTGTGTCAACGAAG                         ATAAAGAATCCTGCACAACTAGATGCTGCTCTGTCATTCCTTACTAATACT
genomic: ATGCGCTTGTCCATCGTCCTGTACTCATTGACTATATTGTGTCAACGAAGgtatgctcac ... cacttttcagATAAAGAATCCTGCACAACTAGATGCTGCTCTGTCATTCCTTACTAATACT
EST: gi|88903715|gb|CI089253.1|CI089253
EST:     ATGCGCTTGTCTATCGTCCTGTACTCATTGACTATATTGTGTCAACGAAG                         ATAAAGAATCCTGCACAACTAGATGCTGCTCTGTCATTCCTTACTAATACT
genomic: ATGCGCTTGTCCATCGTCCTGTACTCATTGACTATATTGTGTCAACGAAGgtatgctcac ... cacttttcagATAAAGAATCCTGCACAACTAGATGCTGCTCTGTCATTCCTTACTAATACT
EST: gi|66921782|gb|CX108630.1|CX108630
EST:     ATGCGCTTGTCCATCGTCCTGTACTCATTGACTATATTGTGTCAACGAAG                         ATAAAGAATCCTGCACAACTAGATGCTGCTCTGTCATTCCTTACTAATACT
genomic: ATGCGCTTGTCCATCGTCCTGTACTCATTGACTATATTGTGTCAACGAAGgtatgctcac ... cacttttcagATAAAGAATCCTGCACAACTAGATGCTGCTCTGTCATTCCTTACTAATACT
EST: gi|58671495|gb|CK060181.1|CK060181
EST:     ATGCGCTTGTCCATCGTCCTGTACTCATTGACTATATTGTGTCAACGAAG                         ATAAAGAATCCTGCACAACTAGATGCTGCTCTGTCATTCCTTACTAATACT
genomic: ATGCGCTTGTCCATCGTCCTGTACTCATTGACTATATTGTGTCAACGAAGgtatgctcac ... cacttttcagATAAAGAATCCTGCACAACTAGATGCTGCTCTGTCATTCCTTACTAATACT

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: 70 (upstream exon), 71 (downstream exon)
Score: 14

GTTGCCACTAAATACCCAACCAATGCGCTTGTCCATCGTCCTGTACTCATTGACTATATTGTGTCAACGAAGgtatgctcac ... cacttttcagATAAAGAATCCTGCACAACTAGATGCTGCTCTGTCATTCCTTACTAATACTGGCCCTGACTCTTTAGATACTGGGAAGTTTGAAGAAGCCTGTGGTGTAG




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