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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCTCTGATATTATATCGAAAGAGTTCGCTGGTCATCCTAAGATCTATATTTGGGATGGGGAAGgtagatgaaatataacactaagttattcatgatgtaatatatttattatgcatgttgttacatttgtaagttgtaacaagttgattttatttttgcag

Basic information

species Oryza sativa
transcript LOC_Os02g33230.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g33230.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G026900_T02 (Zea mays), 5'ss of exon 7
GTCTCTGATATTATATCGAAAGAGTTCGCTGGTCATCCTAAGATCTATATTTGGGATGGGGAAGgtaga---tgaaatataacactaagttattcatgatgtaatatatttattatgcatgttgttacatttgtaagttgtaacaagttgattttatttttgcag
||  |||||| |||||  ||||| || ||||| ||||| ||| ||||||||||| |||| |||||||||   ||||   || | ||||||| ||||          ||||||||  || | ||| |  | ||||      || |||     ||||| || | |||
GTTGCTGATACTATATTTAAAGAATTTGCTGGACATCCCAAGGTCTATATTTGGAATGGTGAAGgtagaatctgaagactagctctaagttgttca---------gtatttatt--gctttttgctcaacttgttgaac-tagcaa-ccatttttacttctacag
















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|29660003|gb|CB656278.1|CB656278
EST:     ATCGAAAGAGTTCGCTGGTCATCCTAAGATCTATATTTGGGATGGGGAAG                         AACCTAACCCGCACATGGGGCATCTTGCATGGGCTGATGCTTTTGTTGTAA
genomic: ATCGAAAGAGTTCGCTGGTCATCCTAAGATCTATATTTGGGATGGGGAAGgtagatgaaa ... atttttgcagAACCTAACCCGCACATGGGGCATCTTGCATGGGCTGATGCTTTTGTTGTAA
EST: gi|58694686|gb|CK083373.1|CK083373
EST:     ATCGAAAGAGTTCGCTGGTCATCCTAAGATCTATATTTGGGATGGGGAAG                         AACCTAACCCGCACATGGGGCATCTTGCATGGGCTGATGCTTTTGTTGTAA
genomic: ATCGAAAGAGTTCGCTGGTCATCCTAAGATCTATATTTGGGATGGGGAAGgtagatgaaa ... atttttgcagAACCTAACCCGCACATGGGGCATCTTGCATGGGCTGATGCTTTTGTTGTAA
EST: gi|29660002|gb|CB656277.1|CB656277
EST:     ATCGAAAGAGTTCGCTGGTCATCCTAAGATCTATATTTGGGATGGGGAAG                         AACCTAACCCGCACATGGGGCATCTTGCATGGGCTGATGCTTTTGTTGTAA
genomic: ATCGAAAGAGTTCGCTGGTCATCCTAAGATCTATATTTGGGATGGGGAAGgtagatgaaa ... atttttgcagAACCTAACCCGCACATGGGGCATCTTGCATGGGCTGATGCTTTTGTTGTAA
EST: gi|86501379|gb|CI144012.1|CI144012
EST:     ATCGAAAGAGTTCGCTGGTCATCCTAAGATCTATATTTGGGATGGGGAAG                         AACCTAACCCGCACATGGGGCATCTTGCATGGGCTGATGCTTTTGTTGTAA
genomic: ATCGAAAGAGTTCGCTGGTCATCCTAAGATCTATATTTGGGATGGGGAAGgtagatgaaa ... atttttgcagAACCTAACCCGCACATGGGGCATCTTGCATGGGCTGATGCTTTTGTTGTAA
EST: gi|38472562|gb|CF956694.1|CF956694
EST:     ATCGAAAGAGTTCGCTGGTCATCCTAAGATCTATATTTGGGATGGGGAAG                         AACCTAACCCGCACATGGGGCATCTTGCATGGGCTGATGCTTTTGTTGTAA
genomic: ATCGAAAGAGTTCGCTGGTCATCCTAAGATCTATATTTGGGATGGGGAAGgtagatgaaa ... atttttgcagAACCTAACCCGCACATGGGGCATCTTGCATGGGCTGATGCTTTTGTTGTAA
EST: gi|40486326|gb|BX897909.1|BX897909
EST:     ATCGAAAGAGTTCGCTGGTCATCCTAAGATCTATATTTGGGATGGGGAAG                         AAACTAAACCGGACATGGGGCATCTTGCATGGGCTGATGCTTTTGTTGTAA
genomic: ATCGAAAGAGTTCGCTGGTCATCCTAAGATCTATATTTGGGATGGGGAAGgtagatgaaa ... atttttgcagAACCTAACCCGCACATGGGGCATCTTGCATGGGCTGATGCTTTTGTTGTAA
EST: gi|29677033|gb|CB673308.1|CB673308
EST:     ATCGAAAGAGTTCGCTGGTCATCCTAAGATCTATATTTGGGATGGGGAAG                         AACCTAACCCGCACATGGGGCATCTTGCATGGGCTGATGCTTTTGTCGTAA
genomic: ATCGAAAGAGTTCGCTGGTCATCCTAAGATCTATATTTGGGATGGGGAAGgtagatgaaa ... atttttgcagAACCTAACCCGCACATGGGGCATCTTGCATGGGCTGATGCTTTTGTTGTAA

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: 64 (upstream exon), 74 (downstream exon)
Score: 30

GTCTCTGATATTATATCGAAAGAGTTCGCTGGTCATCCTAAGATCTATATTTGGGATGGGGAAGgtagatgaaa ... atttttgcagAACCTAACCCGCACATGGGGCATCTTGCATGGGCTGATGCTTTTGTTGTAACAGCTGATTCTATAAGTATGTTAAGTGAGGCTTGTAGCACAGG




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