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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGCAACTGACAAATGCATTATGGCATTGCTTTTTCTGATTGTTTGTGGTGTGATTGCAATTATTGTTGTTAAGgtatgttcttcaggttttttctatgtacttccatctcctgaggattatgagtggattatccaatcaaacacacaactaaatttcattggtgatgaaaaat...

Basic information

species Oryza sativa
transcript LOC_Os03g25390.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g25390.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G330650_T02 (Zea mays), 5'ss of exon 8
GTTGCAACTGACAAATGCATTATGGCATTGCTTTTTCTGATTGTTTGTGGTGTGATTGCAATTATTGTTGTTAAGgtatgttcttcaggttttt--tctatgtac-------ttccatctcctgaggattatgagtggattatccaatcaaacacacaactaaatttcattggtgatgaaaaat-------------------------------------
||||| ||||||||||| || |||||||| || || ||||| ||||  ||||||||||| || |||||||| |||||||||     | |||| |  ||   || |       | || ||   | |  ||| |    |||  |  |     | | |   |    |||  |      |||  | |                                      
GTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGTGTGATTGCTATCATTGTTGTCAAGgtatgtataatatgtttgtcatcagcgtgcagaagaataccttcagttcaacattcttctaggagaactcgtgtcatctccgtatattattctacaacaaatgtgagacgaatgaaaagcctaactacatattttaattcttgcag
















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|86883289|gb|CI337947.1|CI337947
EST:     TGTGATTCCAAGTTATTGGGGTTAAG                         ATTGTCAACCCACATAACAAGAACATCCGCGACATCCCAGGACGTGCTCCG
genomic: TGTGATTGCAA-TTATTGTTGTTAAGgtatgttctt ... tttttaacagATTGTCAACCCACATAACAAGAACATCCGCGACATCCCAGGACTTGCTCCG
EST: gi|13423375|gb|AU176536.1|AU176536
EST:     CATTGCTTTTTCTGATTGTTTGTGGTGTGANTGCAATTATTGTTGTTAAG                         ATTGTCAACCCACATAACAAGAACATCCGCGACATCCCAGGACTTGCTCCG
genomic: CATTGCTTTTTCTGATTGTTTGTGGTGTGATTGCAATTATTGTTGTTAAGgtatgttctt ... tttttaacagATTGTCAACCCACATAACAAGAACATCCGCGACATCCCAGGACTTGCTCCG
EST: gi|88969737|gb|CI383240.1|CI383240
EST:     TTGCTTTTTCTGATTGTTTGTGGTGTGATTGCAATTATTGTTGTTAAG                         ATTGTCAACCCACATAACAAGAACATCCGCGACATCCCAGGACTTGCTCCG
genomic: TTGCTTTTTCTGATTGTTTGTGGTGTGATTGCAATTATTGTTGTTAAGgtatgttctt ... tttttaacagATTGTCAACCCACATAACAAGAACATCCGCGACATCCCAGGACTTGCTCCG
EST: gi|30227163|gb|CB965055.1|CB965055
EST:     CATTGCTTTTTCTGATTGTTTGTGGTGTGATTGCAATTATTGTTGTTAAG                         ATTGTCAACCCACATAACAAGAACATCCGCGACATCCCAGGACTTGCTCCG
genomic: CATTGCTTTTTCTGATTGTTTGTGGTGTGATTGCAATTATTGTTGTTAAGgtatgttctt ... tttttaacagATTGTCAACCCACATAACAAGAACATCCGCGACATCCCAGGACTTGCTCCG
EST: gi|88264485|gb|CI368259.1|CI368259
EST:     CATTGCTTTTTCTGATTGTTTGTGGTGTGATTGCAATTATTGTTGTTAAG                         ATTGTCAACCCACATAACAAGAACATCCGCGACATCCCAGGACTTGCTCCG
genomic: CATTGCTTTTTCTGATTGTTTGTGGTGTGATTGCAATTATTGTTGTTAAGgtatgttctt ... tttttaacagATTGTCAACCCACATAACAAGAACATCCGCGACATCCCAGGACTTGCTCCG
EST: gi|27921131|gb|CB096939.1|CB096939
EST:     CATTGCTTTTTCTGATTGTTTGTGGTGTGATTGCAATTATTGTTGTTAAG                         ATTGTCAACCCACATAACAAGAACATCCGCGACATCCCAGGACTTGCTCCG
genomic: CATTGCTTTTTCTGATTGTTTGTGGTGTGATTGCAATTATTGTTGTTAAGgtatgttctt ... tttttaacagATTGTCAACCCACATAACAAGAACATCCGCGACATCCCAGGACTTGCTCCG
EST: gi|30228758|gb|CB966648.1|CB966648
EST:     CATTGCTTTTTCTGATTGTTTGTGGTGTGATTGCAATTATTGTTGTTAAG                         ATTGTCAACCCACATAACAAGAACATCCGCGACATCCCAGGACTTGCTCCG
genomic: CATTGCTTTTTCTGATTGTTTGTGGTGTGATTGCAATTATTGTTGTTAAGgtatgttctt ... tttttaacagATTGTCAACCCACATAACAAGAACATCCGCGACATCCCAGGACTTGCTCCG
EST: gi|88424981|gb|CI562296.1|CI562296
EST:     GTGGTGTGATTGCAATTATTGTTGTTAAG                         ATTGTCAACCCACATAACAAGAACATCCGCGACATCCCAGGACTTGCTCCG
genomic: GTGGTGTGATTGCAATTATTGTTGTTAAGgtatgttctt ... tttttaacagATTGTCAACCCACATAACAAGAACATCCGCGACATCCCAGGACTTGCTCCG
EST: gi|88509241|gb|CI436747.1|CI436747
EST:     CATTGCTTTTTCTGATTGTTTGTGGTGTGATTGCAATTATTGTTGTTAAG                         ATTGTCAACCCACATAACAAGAACATCCGCGACATCCCAGGACTTGCTCCG
genomic: CATTGCTTTTTCTGATTGTTTGTGGTGTGATTGCAATTATTGTTGTTAAGgtatgttctt ... tttttaacagATTGTCAACCCACATAACAAGAACATCCGCGACATCCCAGGACTTGCTCCG
EST: gi|30228750|gb|CB966640.1|CB966640
EST:     CATTGCTTTTTCTGATTGTTTGTGGTGTGATTGCAATTATTGTTGTTAAG                         ATTGTCAACCCACATAACAAGAACATCCGCGACATCCCAGGACTTGCTCCG
genomic: CATTGCTTTTTCTGATTGTTTGTGGTGTGATTGCAATTATTGTTGTTAAGgtatgttctt ... tttttaacagATTGTCAACCCACATAACAAGAACATCCGCGACATCCCAGGACTTGCTCCG
EST: gi|15008275|gb|AU222663.1|AU222663
EST:     CATTGCTTTTTCTGATTGTTTGTGGTGTGATTGCAATTATTGTTGTTAAG                         ATTGTCAACCCACATAACAAGAACATCCGCGACATCCCAGGACTTGCTCCG
genomic: CATTGCTTTTTCTGATTGTTTGTGGTGTGATTGCAATTATTGTTGTTAAGgtatgttctt ... tttttaacagATTGTCAACCCACATAACAAGAACATCCGCGACATCCCAGGACTTGCTCCG
EST: gi|15855989|gb|BI808801.1|BI808801
EST:     CATTGCTTTTTCTGATTGTTTGTGGTGTGATTGCCATTATTGTTGTTAAG                         ATTGTCAACCCACATAACCAGAACATCCGCGACATCCCAGGACTTGCTCCG
genomic: CATTGCTTTTTCTGATTGTTTGTGGTGTGATTGCAATTATTGTTGTTAAGgtatgttctt ... tttttaacagATTGTCAACCCACATAACAAGAACATCCGCGACATCCCAGGACTTGCTCCG
EST: gi|88969544|gb|CI383054.1|CI383054
EST:     CATTGCTTTTTCTGATTGTTTGTGGTGTGATTGCAATTATTGTTGTTAAG                         ATTGTCAACCCACATAACAAGAACATCCGCGACATCCCAGGACTTGCTCCG
genomic: CATTGCTTTTTCTGATTGTTTGTGGTGTGATTGCAATTATTGTTGTTAAGgtatgttctt ... tttttaacagATTGTCAACCCACATAACAAGAACATCCGCGACATCCCAGGACTTGCTCCG
EST: gi|88503164|gb|CI430670.1|CI430670
EST:     TGTTTGTGGTGTGATTGCAATTATTGTTGTTAAG                         ATTGTCAACCCACATAACAAGAACATCCGCGACATCCCAGGACTTGCTCCG
genomic: TGTTTGTGGTGTGATTGCAATTATTGTTGTTAAGgtatgttctt ... tttttaacagATTGTCAACCCACATAACAAGAACATCCGCGACATCCCAGGACTTGCTCCG
EST: gi|87015371|gb|CI275561.1|CI275561
EST:     CATTGCTTTTTCTGATTGTTTGTGGTGTGATTGCAATTATTGTTGTTAAG                         ATTGTCAACCCACATAACAAGAACATCCGCGACATCCCAGGACTTGCTCCG
genomic: CATTGCTTTTTCTGATTGTTTGTGGTGTGATTGCAATTATTGTTGTTAAGgtatgttctt ... tttttaacagATTGTCAACCCACATAACAAGAACATCCGCGACATCCCAGGACTTGCTCCG
EST: gi|88520726|gb|CI446382.1|CI446382
EST:     CATTGCTTTTTCTGATTGTTTGTGGTGTGATTGCAATTATTGTTGTTAAG                         ATTGTCAACCCACATAACAAGAACATCCGCGACATCCCAGGACTTGCTCCG
genomic: CATTGCTTTTTCTGATTGTTTGTGGTGTGATTGCAATTATTGTTGTTAAGgtatgttctt ... tttttaacagATTGTCAACCCACATAACAAGAACATCCGCGACATCCCAGGACTTGCTCCG
EST: gi|89186178|gb|CI048047.1|CI048047
EST:     CATTGCTTTTTCTGATTGTTTGTGGTGTGATTGCAATTATTGTTGTTAAG                         ATTGTCAACCCACATAACAAGAACATCCGCGACATCCCAGGACTTGCTCCG
genomic: CATTGCTTTTTCTGATTGTTTGTGGTGTGATTGCAATTATTGTTGTTAAGgtatgttctt ... tttttaacagATTGTCAACCCACATAACAAGAACATCCGCGACATCCCAGGACTTGCTCCG
EST: gi|86594199|gb|CI262427.1|CI262427
EST:     CATTGCTTTTTCTGATTGTTTGTGGTGTGATTGCAATTATTGTTGTTAAG                         ATTGTCAACCCACATAACAAGAACATCCGCGACATCCCAGGACTTGCTCCG
genomic: CATTGCTTTTTCTGATTGTTTGTGGTGTGATTGCAATTATTGTTGTTAAGgtatgttctt ... tttttaacagATTGTCAACCCACATAACAAGAACATCCGCGACATCCCAGGACTTGCTCCG
EST: gi|88262856|gb|CI364434.1|CI364434
EST:     CATTGCTTTTTCTGATTGTTTGTGGTGTGATTGCAATTATTGTTGTTAAG                         ATTGTCAACCCACATAACAAGAACATCCGCGACATCCCAGGACTTGCTCCG
genomic: CATTGCTTTTTCTGATTGTTTGTGGTGTGATTGCAATTATTGTTGTTAAGgtatgttctt ... tttttaacagATTGTCAACCCACATAACAAGAACATCCGCGACATCCCAGGACTTGCTCCG
EST: gi|86864804|gb|CI344294.1|CI344294
EST:     CATTGCTTTTTCTGATTGTTTGTGGTGTGATTGCAATTATTGTTGTTAAG                         ATTGTCAACCCACATAACAAGAACATCCGCGACATCCCAGGACTTGCTCCG
genomic: CATTGCTTTTTCTGATTGTTTGTGGTGTGATTGCAATTATTGTTGTTAAGgtatgttctt ... tttttaacagATTGTCAACCCACATAACAAGAACATCCGCGACATCCCAGGACTTGCTCCG
EST: gi|88275141|gb|CI395745.1|CI395745
EST:     CATTGCTTTTTCTGATTGTTTGTGGTGTGATTGCAATTATTGTTGTTAAG                         ATTGTCAACCCACATAACAAGAACATCCGCGACATCCCAGGACTTGCTCCG
genomic: CATTGCTTTTTCTGATTGTTTGTGGTGTGATTGCAATTATTGTTGTTAAGgtatgttctt ... tttttaacagATTGTCAACCCACATAACAAGAACATCCGCGACATCCCAGGACTTGCTCCG
EST: gi|88827221|gb|CI777786.1|CI777786
EST:     CATTGCTTTTTCTGATTGTTTGTGGTGTGATTGCAATTATTGTTGTTAAG                         ATTGTCAACCCACATA
genomic: CATTGCTTTTTCTGATTGTTTGTGGTGTGATTGCAATTATTGTTGTTAAGgtatgttctt ... tttttaacagATTGTCAACCCACATA
EST: gi|14980927|gb|BI305605.1|BI305605
EST:     CATTGCTTTTTCTGATTGTTTGTGGTGTGATTGCAATTATTGTTGTTAAG                         ATTGTCAACCCACATAACAAGAACATCCGCGACATCCCAGGACTTGCTCCG
genomic: CATTGCTTTTTCTGATTGTTTGTGGTGTGATTGCAATTATTGTTGTTAAGgtatgttctt ... tttttaacagATTGTCAACCCACATAACAAGAACATCCGCGACATCCCAGGACTTGCTCCG

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: 69 (upstream exon), 70 (downstream exon)
Score: 30

GTTGCAACTGACAAATGCATTATGGCATTGCTTTTTCTGATTGTTTGTGGTGTGATTGCAATTATTGTTGTTAAGgtatgttctt ... tttttaacagATTGTCAACCCACATAACAAGAACATCCGCGACATCCCAGGACTTGCTCCGCCTGCTCAAAATTTCCAGATTAGTAACAGGAGACTGCTGTCGGTAGAAA




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