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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGCACACGTGGTGTCATTTTGGGAAGTGAGCCTATTTGCCCACCTGACTGCTTTCAGTACAAGGGAACACTTGATGTATTCTTGAAAGTTGTTAGACAGgtaatgtgactttaattcctttttatagttttatgcaagtatcgatttctagagcacagagaatttaacacttttggttaattggttgttacag

Basic information

species Oryza sativa
transcript LOC_Os08g29720.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g29720.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G106703_T02 (Zea mays), 5'ss of exon 3
ATGCACACGTGGTGTCATTTTGGGAAGTGAGCCTATTTGCCCACCTGACTGCTTTCAGTACAAGGGAACACTTGATGTATTCTTGAAAGTTGTTAGACAGgtaatgtgactttaattcctttttatag------ttttatgcaagtatcgatttctagagcacagagaatttaacacttttggttaattggttgttacag
||||||||||||| || |  | |||||||||||  |||| || ||||| ||||| ||||||||||||||||||||||||||||||||||| ||||||||||||        || |||| ||||  ||       ||||| ||||||  |  | | |   | ||||| ||  | |||    || |||||||||||||  ||
ATGCACACGTGGTCTCTTACTAGGAAGTGAGCCAGTTTGTCCTCCTGATTGCTTCCAGTACAAGGGAACACTTGATGTATTCTTGAAAGTGGTTAGACAGgtagctaagtgttcattctttttggtacctcgtcttttaagcaagtggcagtatatgatggacagataaactcacagcagtgcttaattggttgttttag

upper sequence: LOC_Os08g29720.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G059018_T02 (Zea mays), 5'ss of exon 3
ATGCACACGTGGTGTCATTTTGGGAAGTGAGCCTATTTGCCCACCTGACTGCTTTCAGTACAAGGGAACACTTGATGTATTCTTGAAAGTTGTTAGACAGgtaatgtgactttaattcctttttatag-ttttatgcaagtatcgatttctagagcacagagaatttaacacttttggttaattggttgttacag
 |||||||||||| |  | || |||||||||||  |||| || ||||||||||| ||||||||||| ||||||||||||||||||||||| |||||||||||||       || |||  || |  |   ||||| ||||||  | || | |   | ||||| ||  | ||     || |||  ||||||||  ||
GTGCACACGTGGTCTTGTATTAGGAAGTGAGCCAGTTTGTCCTCCTGACTGCTTCCAGTACAAGGGGACACTTGATGTATTCTTGAAAGTGGTTAGACAGgtaactaagtgttcattttttatagtttcttttaagcaagtggcaatgtatgatggacagataaactcactacagtgttta--tggttgttttag
















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|218497482|gb|FG960434.1|FG960434
EST:     GCTTTCAGTACAAGGGAACACTTGATGTATTCTTGAAAGTTGTTAGACAG                         GAAGGATTTGGTAGATTATGGAGAGGTACAAATGCAGGCTTGGCGTTAGCA
genomic: GCTTTCAGTACAAGGGAACACTTGATGTATTCTTGAAAGTTGTTAGACAGgtaatgtgac ... gttgttacagGAAGGATTTGGTAGATTATGGAGAGGTACAAATGCAGGCTTGGCGTTAGCA
EST: gi|29661210|gb|CB657485.1|CB657485
EST:     GCTTTCAGTACAAGGGAACACTTGATGTATTCTTGAAAGTTGTTAGACAG                         GAAGGATTTGGTAGATTATGGAGAGGTACAAATGCAGGCTTGGCGTTAGCA
genomic: GCTTTCAGTACAAGGGAACACTTGATGTATTCTTGAAAGTTGTTAGACAGgtaatgtgac ... gttgttacagGAAGGATTTGGTAGATTATGGAGAGGTACAAATGCAGGCTTGGCGTTAGCA
EST: gi|7273806|gb|AU083350.1|AU083350
EST:     GCTTTCAGTACAAGGGAACACTTGATGTATTCTTGAAAGTTGTTAGACAG                         GAAGGATTTGGTAGATTATGGAGAGGTA
genomic: GCTTTCAGTACAAGGGAACACTTGATGTATTCTTGAAAGTTGTTAGACAGgtaatgtgac ... gttgttacagGAAGGATTTGGTAGATTATGGAGAGGTA
EST: gi|58693531|gb|CK082218.1|CK082218
EST:     GCTTTCAGTACAAGGGAACAC-TGATGTATTCTTGAGAGTTGTTAGACAG                         GAAGGATTTGGTAGATTATGGAGAGGTACAAATGCAGGCTTGGCGTTAGCA
genomic: GCTTTCAGTACAAGGGAACACTTGATGTATTCTTGAAAGTTGTTAGACAGgtaatgtgac ... gttgttacagGAAGGATTTGGTAGATTATGGAGAGGTACAAATGCAGGCTTGGCGTTAGCA
EST: gi|58672713|gb|CK061399.1|CK061399
EST:     GCTTTCAGTACAAGGGAACACTTGATGTATTCTTGAAAGTTGTTAGACAG                         GAAGGATTTGGTAGATTATGGAGAGGTACAAATGCAGGCTTGGCGTTAGCA
genomic: GCTTTCAGTACAAGGGAACACTTGATGTATTCTTGAAAGTTGTTAGACAGgtaatgtgac ... gttgttacagGAAGGATTTGGTAGATTATGGAGAGGTACAAATGCAGGCTTGGCGTTAGCA
EST: gi|25797756|gb|CA753717.1|CA753717
EST:     GCTTTCAGTACAAGGGAACACTTGATGTATTCTTGAAAGTTGTTAGACAG                         GAAGGATTTGGTAGATTATGGAGAGGTACAAATGCAGGCTTGGCGTTAGCA
genomic: GCTTTCAGTACAAGGGAACACTTGATGTATTCTTGAAAGTTGTTAGACAGgtaatgtgac ... gttgttacagGAAGGATTTGGTAGATTATGGAGAGGTACAAATGCAGGCTTGGCGTTAGCA
EST: gi|58607537|gb|CK035570.1|CK035570
EST:     GCTTTCAGTACAAGGGAACACTTGATGTATTCTTGAAAGTTGTTAGACAG                         GAAGGATTTGGTAGATTATGGAGAGGTACAAATGCAGGCTTGGCGTTAGCA
genomic: GCTTTCAGTACAAGGGAACACTTGATGTATTCTTGAAAGTTGTTAGACAGgtaatgtgac ... gttgttacagGAAGGATTTGGTAGATTATGGAGAGGTACAAATGCAGGCTTGGCGTTAGCA
EST: gi|7274031|gb|AU083575.1|AU083575
EST:     GCTTTCAGTACAAGGGAACACTTGATGTATTCTTGAAAGTTGTTAGACAG                         GAAGGATTTGGTAGATTATGGAGAGGTACAAATGCAGGCTTGGCGTTAN-A
genomic: GCTTTCAGTACAAGGGAACACTTGATGTATTCTTGAAAGTTGTTAGACAGgtaatgtgac ... gttgttacagGAAGGATTTGGTAGATTATGGAGAGGTACAAATGCAGGCTTGGCGTTAGCA
EST: gi|29680567|gb|CB676842.1|CB676842
EST:     GCTTTCAGTACAAGGGAACACTTGATGTATTCTTGAAAGTTGTTAGACAG                         GAAGGATTTGGTAGATTATGGAGAGGTACAAATGCAGGCTTGGCGTTAGCA
genomic: GCTTTCAGTACAAGGGAACACTTGATGTATTCTTGAAAGTTGTTAGACAGgtaatgtgac ... gttgttacagGAAGGATTTGGTAGATTATGGAGAGGTACAAATGCAGGCTTGGCGTTAGCA
EST: gi|29677504|gb|CB673779.1|CB673779
EST:     GCTTTCAGTACAAGGGAACACTTGATGTATTCTTGAAAGTTGTTAGACAG                         GAAGGATTTGGTAGATTATGGAGAGGTACAAATGCAGGCTTGGCGTTAGCA
genomic: GCTTTCAGTACAAGGGAACACTTGATGTATTCTTGAAAGTTGTTAGACAGgtaatgtgac ... gttgttacagGAAGGATTTGGTAGATTATGGAGAGGTACAAATGCAGGCTTGGCGTTAGCA

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: 71 (upstream exon), 60 (downstream exon)
Score: 72

ATGCACACGTGGTGTCATTTTGGGAAGTGAGCCTATTTGCCCACCTGACTGCTTTCAGTACAAGGGAACACTTGATGTATTCTTGAAAGTTGTTAGACAGgtaatgtgac ... gttgttacagGAAGGATTTGGTAGATTATGGAGAGGTACAAATGCAGGCTTGGCGTTAGCAGTACCAACT




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