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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGAAAGAGAGCTCAAGAAGCAGAAAAGGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAGgtatgatgttaaattgttaacatgacattggactcgttattttcttcagaacatcatggatagtcttattgaagcaccaaaatatttgttccag

Basic information

species Oryza sativa
transcript LOC_Os02g03580.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g03580.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G153144_T01 (Zea mays), 5'ss of exon 12
GATGAAAGAGAGCTCAAGAAGCAGAAAAGGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAGgtatgatgttaaatt---gttaacatgacattggactcgttattt--tcttcagaacatcatggatagtcttattgaagcaccaaaatatttgttccag--------
|||||||| || ||||||||||| ||| |||||||||||||| | ||||| ||||| ||||||||||||||||||||||| |  ||  | | |   | ||||||    |||    |   | |   |||||  |   ||| |   | | |  |    ||          || ||| |         
GATGAAAGGGAACTCAAGAAGCAAAAACGGAAGCAGTCTAATAGAGAATCGGCACGCAGATCCCGGCTGCGCAAGCAGgtgttgtgcaacactaatgctaacatcgtcttgcttcctgaactccatcttctaagtttcaagaggattttgttcagtgctttcgtgatcttattcgattattctag

upper sequence: LOC_Os02g03580.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G019106_T01 (Zea mays), 5'ss of exon 12
GATGAAAGAGAGCTCAAGAAGCAGAAAAGGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAGgtatgatgttaaatt---gttaacatg-acattg--gactcgttattttcttc--agaacatcatggatagtcttattgaa-gcaccaaaatatttgttccag---------
|||||||| |||||||||||||||||  |||||||||| ||  | || || || || ||||||||||||||||| |||||    ||  |   |   | | |||   ||  ||    ||   | |  |||||  |||    || |   | | |  |  || ||    |    | |  | | |         
GATGAAAGGGAGCTCAAGAAGCAGAAGCGGAAGCAGTCAAACAGAGAGTCCGCTCGCAGATCCCGGCTGCGCAAACAGgtgctgtgcaaccctcgtgctgacacccaccctgctagctgaatttcatcttctaagagacccaagagaaatttcgtccaacgctttcatgggtcttgttcggttgttccag

upper sequence: LOC_Os02g03580.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GLYMA08G34280.1 (Glycine max), 5'ss of exon 11
GATGAAAGAGAGCTCAAGAAGCAGAAAAGGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAGgtatgatgttaaattgttaacatgacattggactcgttattttcttcagaacatcatgg--atagtcttattgaagcaccaaa-atatttgttccag
|| ||||||||||| || |  || |   |||||||||||||||||||||| ||||| |||||| || | || ||||||||          |  |  |  || || ||   |    |  |   | |||  ||| || |  ||| | | | |            || ||  |  |||
GACGAAAGAGAGCTTAAAAGACAAAGGCGGAAGCAGTCTAATCGGGAATCTGCACGCAGATCCAGGTTACGGAAGCAGgtg---------acagagagtataacctttttcatacttctggttgcaggtcataattgtcatattttaaatccctttttgtgcatgttgttctcag

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|89197742|gb|CI013732.1|CI013732
EST:     GGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAG                         GCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAAC
genomic: GGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAGgtatgatgtt ... tttgttccagGCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAAC
EST: gi|88903327|gb|CI088865.1|CI088865
EST:     GGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAG                         GCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAAC
genomic: GGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAGgtatgatgtt ... tttgttccagGCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAAC
EST: gi|113931076|gb|DQ883825.1|DQ883825
EST:     GGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAG                         GCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACA
genomic: GGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAGgtatgatgtt ... tttgttccagGCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACA
EST: gi|29670500|gb|CB666775.1|CB666775
EST:     GGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAG                         GCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAAC
genomic: GGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAGgtatgatgtt ... tttgttccagGCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAAC
EST: gi|86497997|gb|CI140630.1|CI140630
EST:     GGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAG                         GCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAAC
genomic: GGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAGgtatgatgtt ... tttgttccagGCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAAC
EST: gi|86505811|gb|CI148444.1|CI148444
EST:     GGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAG                         GCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAAC
genomic: GGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAGgtatgatgtt ... tttgttccagGCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAAC
EST: gi|88850496|gb|CI093177.1|CI093177
EST:     AGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAG                         GCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAAC
genomic: AGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAGgtatgatgtt ... tttgttccagGCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAAC
EST: gi|86879457|gb|CI327145.1|CI327145
EST:     GGGAATCAGCACGTAGATCCCGGCTGGGCAAGCAG                         GCTGAGTGT-AAGAGCTTTGTGTACGCGCTGACAATTTAAGGGCAGAAAAC
genomic: GGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAGgtatgatgtt ... tttgttccagGCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAAC
EST: gi|29670501|gb|CB666776.1|CB666776
EST:     GGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAG                         GCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAAC
genomic: GGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAGgtatgatgtt ... tttgttccagGCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAAC
EST: gi|88829448|gb|CI074318.1|CI074318
EST:     GGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAG                         GCTGAGTGTGAAGAGCTTTCTGCACGCGCTGACAATTTAAGGGCAGAAAAC
genomic: GGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAGgtatgatgtt ... tttgttccagGCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAAC
EST: gi|88965389|gb|CI011640.1|CI011640
EST:     GGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAG                         GCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAAC
genomic: GGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAGgtatgatgtt ... tttgttccagGCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAAC
EST: gi|29665043|gb|CB661318.1|CB661318
EST:     GGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAG                         GCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAAC
genomic: GGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAGgtatgatgtt ... tttgttccagGCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAAC
EST: gi|88517412|gb|CI445066.1|CI445066
EST:     GAATCAGCACGTAGATCCCGGCTGCGCAAGCAG                         GCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAAC
genomic: GAATCAGCACGTAGATCCCGGCTGCGCAAGCAGgtatgatgtt ... tttgttccagGCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAAC
EST: gi|32948093|gb|BP184665.1|BP184665
EST:     GGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAG                         GCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACA
genomic: GGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAGgtatgatgtt ... tttgttccagGCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACA
EST: gi|86488210|gb|CI130843.1|CI130843
EST:     GGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAG                         GCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAAC
genomic: GGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAGgtatgatgtt ... tttgttccagGCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAAC
EST: gi|86252236|gb|CI055973.1|CI055973
EST:     GGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAG                         GCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACCATTTAAGGGCAGAAAAC
genomic: GGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAGgtatgatgtt ... tttgttccagGCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAAC
EST: gi|88958454|gb|CI095970.1|CI095970
EST:     GGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAG                         GCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAAC
genomic: GGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAGgtatgatgtt ... tttgttccagGCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAAC
EST: gi|89172965|gb|CI040858.1|CI040858
EST:     GGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAG                         GCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAAC
genomic: GGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAGgtatgatgtt ... tttgttccagGCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAAC

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: 63 (upstream exon), 70 (downstream exon)
Score: 9

GATGAAAGAGAGCTCAAGAAGCAGAAAAGGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAGgtatgatgtt ... tttgttccagGCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAACTCCTCTCTTAGGGCTGAGCTTGAACGGATCAAAAAGGAGTACGAGGCAC




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