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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtcaactcatctctctctctcatttattgctttctattgattccaaattcctggcaaatgtgctgttccctgtagcactacaaagtttatgataatttggtgctttgctttctgtgatccagGAATCTTCTCTCGCTCAAGTAACTCCAGCTGAGACACCAAACTCAGCCACTGATCATCGGCAGCATGGGCATATGGAATCTCCTGGGTTTGGCTTGAGGC

Basic information

species Oryza sativa
transcript LOC_Os05g45420.3
intron # 8
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|40488690|gb|BX899031.1|BX899031
EST:     GGCTGCGCACAACCAGTGGCTACCTTGGAGCTGAGTTCCATGAATCTATG                         GAATCTTCTCTCGCTCAAGTAACTCCAGCTGAGACACCAAACTCAGGCACT
genomic: GGCTGCGCACAACCAGTGGCTACCTTGGAGCTGAGTTCCATGAATCTATGgtatgtcaac ... tgtgatccagGAATCTTCTCTCGCTCAAGTAACTCCAGCTGAGACACCAAACTCAGCCACT
EST: gi|58675138|gb|CK063825.1|CK063825
EST:     GGCTGCGCACAACCAGTGGCTACCTTGGAGCTGAGTTCCATGAATCTATG                         GAATCTTCTCTCGCTCAAGTAACTCCAGCTGAGACACCAAACTCAGCCACT
genomic: GGCTGCGCACAACCAGTGGCTACCTTGGAGCTGAGTTCCATGAATCTATGgtatgtcaac ... tgtgatccagGAATCTTCTCTCGCTCAAGTAACTCCAGCTGAGACACCAAACTCAGCCACT
EST: gi|29680934|gb|CB677209.1|CB677209
EST:     GGCTGCGCACAACCAGTGGCTACCTTGGAGCTGAGTTCCATGAATCTATG                         GAATCTTCTCTCGCTCAAGTAACTCCAGCTGAGACACCAAACTCAGCCACT
genomic: GGCTGCGCACAACCAGTGGCTACCTTGGAGCTGAGTTCCATGAATCTATGgtatgtcaac ... tgtgatccagGAATCTTCTCTCGCTCAAGTAACTCCAGCTGAGACACCAAACTCAGCCACT
EST: gi|13420630|gb|AU174720.1|AU174720
EST:     GGCTGCGCACAACCAGTGGCTACCTTGGAGCTGAGTTCCATGAATCTATG                         GAATCTTCTCTCGCTCAAGTAACTCCAGCTGAGACACCAAACTCAGCCACT
genomic: GGCTGCGCACAACCAGTGGCTACCTTGGAGCTGAGTTCCATGAATCTATGgtatgtcaac ... tgtgatccagGAATCTTCTCTCGCTCAAGTAACTCCAGCTGAGACACCAAACTCAGCCACT
EST: gi|38481090|gb|CF965179.1|CF965179
EST:     GGCTGCGCACAACCAGTGGCTACCTTGGAGCTGAGTTCCATGAATCTATG                         GAATCTTCTCTCGCTCAAGTAACTCCAGCTGAGACACCAAACTCAGCCACT
genomic: GGCTGCGCACAACCAGTGGCTACCTTGGAGCTGAGTTCCATGAATCTATGgtatgtcaac ... tgtgatccagGAATCTTCTCTCGCTCAAGTAACTCCAGCTGAGACACCAAACTCAGCCACT

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: 74 (upstream exon), 71 (downstream exon)
Score: 31

GCGACAGTTGCCTACTATTTACTATTGGACAATAGGCTGCGCACAACCAGTGGCTACCTTGGAGCTGAGTTCCATGAATCTATGgtatgtcaac ... tgtgatccagGAATCTTCTCTCGCTCAAGTAACTCCAGCTGAGACACCAAACTCAGCCACTGATCATCGGCAGCATGGGCATATGGAATCTCCTGGGTTTGGCTTGAGGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccctgtagcactacaaagtttatgataatttggtgctttgctttctgtgatccagGAATCTTCTCTCGCTCAAGTAACTCCAGCTGAGACACCAAACTCAGCCACTGATCATCGGCAGCATGGGCATATGGAATCTCCTGGGTTTGGCTTGAGGC
                                   ctttgctttct  CT-rich tract
              aaagtttatgataatt  TA-rich tract