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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGGAACTGGATCACGCACGCAGCAATATGGGGCAGTATAGTCGCAACGCTGATTTGTGTCATGGTCATAGACTCCATACCGATATTGCCTGGTTTCTGgtatgcactcatttgaactattttggttgcttttttttccccggataaatgtatacctggttgctgactctgcatttgtatgacag

Basic information

species Oryza sativa
transcript LOC_Os03g20949.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g20949.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G407825_T01 (Zea mays), 5'ss of exon 6
GATGGAACTGGATCACGCACGCAGCAATATGGGGCAGTATAGTCGCAACGCTGATTTGTGTCATGGTCATAGACTCCATACCGATATTGCCTGGTTTCTGgtatgcactcatttgaactattttggttgcttttttttccccggataaatgtatacctggttgctgactctgcatttgtatgacag
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GATGGAACTGGATTACGCATGCGGCAATATGGGGTAGCATTGCTGCGACATGGATTTGTGTCATGATCATAGATTCCATACCAATCATGCCTGGTTTTTGgtaagcacgcattccag-tattt--gttttctacacttaaacgaa-aagtatgttcacaattactgattcggtaactgtatgacag
















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|88234807|gb|CI232658.1|CI232658
EST:     CTGATTTGTGTCATGGTCATAGACTCCATACCGATATTGCCTGGTTTCTG                         GGCAATATACAAGGTGATGGGAACTGGACTGTTTTGGGCATTGCTGCTCGC
genomic: CTGATTTGTGTCATGGTCATAGACTCCATACCGATATTGCCTGGTTTCTGgtatgcactc ... tgtatgacagGGCAATATACAAGGTGATGGGAACTGGACTGTTTTGGGCATTGCTGCTCGC
EST: gi|88234304|gb|CI234153.1|CI234153
EST:     CTGATTTGTGTCATGGTCATAGACTCCATACCGATATTGCCTGGTTTCTG                         GGCAATATACAAGGTGATGGGAACTGGACTGTTTTGGGCATTGCTGCTCGC
genomic: CTGATTTGTGTCATGGTCATAGACTCCATACCGATATTGCCTGGTTTCTGgtatgcactc ... tgtatgacagGGCAATATACAAGGTGATGGGAACTGGACTGTTTTGGGCATTGCTGCTCGC
EST: gi|29624673|gb|CB629684.1|CB629684
EST:     CTGATTTGTGTCATGGTCATAGACTCCATACCGATATTGCCTGGTTTCTG                         GGCAATATACAAGGTGATGGGAACTGGACTGTTTTGGGCATTGCTGCTCGC
genomic: CTGATTTGTGTCATGGTCATAGACTCCATACCGATATTGCCTGGTTTCTGgtatgcactc ... tgtatgacagGGCAATATACAAGGTGATGGGAACTGGACTGTTTTGGGCATTGCTGCTCGC
EST: gi|58693462|gb|CK082149.1|CK082149
EST:     CTGATTTGTGTCATGGTCATAGACTCCATACCGATATTGCCTGGTTTCTG                         GGCAATATACAAGGTGATGGGAACTGGACTGTTTTGGGCATTGCTGCTCGC
genomic: CTGATTTGTGTCATGGTCATAGACTCCATACCGATATTGCCTGGTTTCTGgtatgcactc ... tgtatgacagGGCAATATACAAGGTGATGGGAACTGGACTGTTTTGGGCATTGCTGCTCGC
EST: gi|88233517|gb|CI233366.1|CI233366
EST:     CTGATTTGTGTCATGGTCATAGACTCCATACCGATATTGCCTGGTTTCTG                         GGCAATATACAAGGTGATGGGAACTGGACTGTTTTGGGCATTGCTGCTCGC
genomic: CTGATTTGTGTCATGGTCATAGACTCCATACCGATATTGCCTGGTTTCTGgtatgcactc ... tgtatgacagGGCAATATACAAGGTGATGGGAACTGGACTGTTTTGGGCATTGCTGCTCGC
EST: gi|88844603|gb|CI020450.1|CI020450
EST:     CTGATTTGTGTCATGGTCATAGACTCCATACCGATATTGCCTGGTTTCTG                         GGCAATATACAAGGTGATGGGAACTGGACTGTTTTGGGCATTGCTGCTCGC
genomic: CTGATTTGTGTCATGGTCATAGACTCCATACCGATATTGCCTGGTTTCTGgtatgcactc ... tgtatgacagGGCAATATACAAGGTGATGGGAACTGGACTGTTTTGGGCATTGCTGCTCGC
EST: gi|29682137|gb|CB678412.1|CB678412
EST:     CTGATTTGTGTCATGGTCATAGACTCCATACCGATATTGCCTGGTTTCTG                         GGCAATATACAAGGTGATGGGAACTGGACTGTTTTGGGCATTGCTGCTCGC
genomic: CTGATTTGTGTCATGGTCATAGACTCCATACCGATATTGCCTGGTTTCTGgtatgcactc ... tgtatgacagGGCAATATACAAGGTGATGGGAACTGGACTGTTTTGGGCATTGCTGCTCGC
EST: gi|87014064|gb|CI273254.1|CI273254
EST:     CTGATTTGTGTCATGGTCATAGACTCCATACCGATATTGCCTGGTTTCTG                         GGCAATATACAAGGTGATGGGAACTGGACTGTTTTGGGCATTGCTGCTCGC
genomic: CTGATTTGTGTCATGGTCATAGACTCCATACCGATATTGCCTGGTTTCTGgtatgcactc ... tgtatgacagGGCAATATACAAGGTGATGGGAACTGGACTGTTTTGGGCATTGCTGCTCGC
EST: gi|29644800|gb|CB649807.1|CB649807
EST:     CTGATTTGTGTCATGGTCATAGACTCCATACCGATATTGCCTGGTTTCTG                         GGCAATATACAAGGTGATGGGAACTGGACTGTTTTGGGCATTGCTGCTCGC
genomic: CTGATTTGTGTCATGGTCATAGACTCCATACCGATATTGCCTGGTTTCTGgtatgcactc ... tgtatgacagGGCAATATACAAGGTGATGGGAACTGGACTGTTTTGGGCATTGCTGCTCGC
EST: gi|88273852|gb|CI394258.1|CI394258
EST:     TGCCTGGTTTCTG                         GGCAATATACAAGGTGATGGGAACTGGACTGTTTTGGGCAGTTGCTGCTCG
genomic: TGCCTGGTTTCTGgtatgcactc ... tgtatgacagGGCAATATACAAGGTGATGGGAACTGGACTGTTTTGGGCA-TTGCTGCTCG
EST: gi|86436954|gb|CI118676.1|CI118676
EST:     CTGATTTGTGTCATGGTCATAGACTCCATACCGATATTGCCTGGTTTCTG                         GGCAATATACAAGGTGATGGGAACTGGACTGTTTTGGGCATTGCTGCTCGC
genomic: CTGATTTGTGTCATGGTCATAGACTCCATACCGATATTGCCTGGTTTCTGgtatgcactc ... tgtatgacagGGCAATATACAAGGTGATGGGAACTGGACTGTTTTGGGCATTGCTGCTCGC
EST: gi|88200902|gb|CI198754.1|CI198754
EST:     CTGATTTGTGTCATGGTCATAGACTCCATACCGATATTGCCTGGTTTCTG                         GGCAATATACAAGGTGATGGGAACTGGACTGTTTTGGGCATTGCTGCTCGC
genomic: CTGATTTGTGTCATGGTCATAGACTCCATACCGATATTGCCTGGTTTCTGgtatgcactc ... tgtatgacagGGCAATATACAAGGTGATGGGAACTGGACTGTTTTGGGCATTGCTGCTCGC
EST: gi|86858248|gb|CI271131.1|CI271131
EST:     CTGATTTGTGTCATGGTCATAGACTCCATACCGATATTGCCTGGTTTCTG                         GGCAATATACAAGGTGATGGGAACTGGACTGTTTTGGGCATTGCTGCTCGC
genomic: CTGATTTGTGTCATGGTCATAGACTCCATACCGATATTGCCTGGTTTCTGgtatgcactc ... tgtatgacagGGCAATATACAAGGTGATGGGAACTGGACTGTTTTGGGCATTGCTGCTCGC

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: 49 (upstream exon), 27 (downstream exon)
Score: 1

GATGGAACTGGATCACGCACGCAGCAATATGGGGCAGTATAGTCGCAACGCTGATTTGTGTCATGGTCATAGACTCCATACCGATATTGCCTGGTTTCTGgtatgcactc ... tgtatgacagGGCAATATACAAGGTGATGGGAACTGGACTGTTTTGGGCATTGCTGCTCGCGGTAATTGTGGTTGGAATGATTCCTCATTTTGTCGCTAAGGCCATAAGG




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