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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGTTCCTAAGGAACCCAGAAAGATATATTCGTCTTGGTGCGCGACCTCCACGAGGTGTCTTGTTGgtcagttctgcagtcatttaagtaatgatgaatgttgctggactagagtttttgtactatgatgtaattcattatttacag

Basic information

species Oryza sativa
transcript LOC_Os02g43350.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g43350.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G072865_T04 (Zea mays), 5'ss of exon 3
---------------------------------------------------------------------GAGTTCCTAAGGAACCCAGAAAGATATATTCGTCTTGGTGCGCGACCTCCACGAGGTGTCTTGTTGgtcagttctgcagtcatttaagtaatgatgaatgttgctggactagagtttttgtactatgatgtaattcattatttacag------------------------------
                                                                     |||  |  ||| |   |   |||| ||  | || | |  |   |    | ||        |||   ||      |||||  ||  ||  |  ||   | | || |  |      |||||     | ||  |  |     |   | |                               
AATTCCGGCGGAGCAAAAGTTTCTGAAAGTTCGGATATAGTTACATTTGCTGATGTGGCTGGAGTAGATGAGG-CAAAAGAAGAGCTTGAAGAAATTGTGGtatggtcgtatggatcctacag-----tttgacagtagcacttgcagcaatcaaataagggaaataagctggtccatacatattttttgttcaggagttcttaaggaacccagaaagatatattcgtctcggtgctcgccctcct

upper sequence: LOC_Os02g43350.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G072865_T01 (Zea mays), 5'ss of exon 4
GAGTTCCTAAGGAACCCAGAAAGATATATTCGTCTTGGTGCGCGACCTCCACGAGGTGTCTTGTTGgtcagttctgcagtca-tttaagtaatgatgaatgttgctggactagagtttttgt-actatgatgtaattcattatttacag
|||||| |||||||||||||||||||||||||||| ||||| || ||||| || |||||||| |||||  ||||||||     ||| |||||||   | |  |||| ||| |  || ||||| || || ||||||||| || | |||||
GAGTTCTTAAGGAACCCAGAAAGATATATTCGTCTCGGTGCTCGCCCTCCTCGTGGTGTCTTATTGgttggttctgcaaatgcttttagtaatggaaactactgcttgacaattgtgtttgttaccataatgtaattctttctctacag

upper sequence: LOC_Os02g43350.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G072865_T05 (Zea mays), 5'ss of exon 4
GAGTTCCTAAGGAACCCAGAAAGATATATTCGTCTTGGTGCGCGACCTCCACGAGGTGTCTTGTTGgtcagttctgcagtca-tttaagtaatgatgaatgttgctggactagagtttttgt-actatgatgtaattcattatttacag-------------------------------------------------------------
|||||| |||||||||||||||||||||||||||| ||||| || ||||| || |||||||| |||||  ||||||||     ||| |||||||   | |  |||| ||| |  || ||||| || || ||||||||| || | |||||                                                             
GAGTTCTTAAGGAACCCAGAAAGATATAttcgtctcggtgctcgccctcctcgtggtgtcttattggttggttctgcaaatgcttttagtaatggaaactactgcttgacaattgtgtttgttaccataatgtaattctttctctacaggtgggtcttccagggactggaaagacacttcttgcaaaagccgtagcaggagaagcagaag

upper sequence: LOC_Os02g43350.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G163193_T02 (Zea mays), 5'ss of exon 4
GAGTTCCTAAGGAACCCAGAAAGATATATTCGTCTTGGTGCGCGACCTCCACGAGGTGTCTTGTTGgtcagttctgcagtcatt-taagtaatgatgaatgttgctggactagagtttttgt-actatgatgtaattcattatttacag
|||||| |||||||||||||||||||| ||||||||||||| || ||||| || |||||||| |||||  ||| ||||     | | |||||||   | |  |||| ||| |  || ||||| || ||  ||| |||| |||| |||||
GAGTTCTTAAGGAACCCAGAAAGATATGTTCGTCTTGGTGCTCGCCCTCCTCGTGGTGTCTTATTGgttggttttgcaaatgctatcagtaatggcaattactgcttgacaattgtgtttgttaccatattgttattctttatctacag

upper sequence: LOC_Os02g43350.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G072865_T03 (Zea mays), 5'ss of exon 3
--------------------------------------------------------------------GAGTTCCTAAGGAACCCAGAAAGATATATTCGTCTTGGTGCGCGACCTCCACGAGGTGTCTTGTTGgtcagttctgcagtcatttaagtaatgatgaatgttgctggactagagtttttgtactatgatgtaattcattatttacag------------------------------
                                                                    |||  |  ||| |   |   |||| ||  | || | |  |   |    | ||        |||   ||      |||||  ||  ||  |  ||   | | || |  |      |||||     | ||  |  |     |   | |                               
ATTCCGGCGGAGCAAAAGTTTCTGAAAGTTCGGATATAGTTACATTTGCTGATGTGGCTGGAGTAGATGAGG-CAAAAGAAGAGCTTGAAGAAATTGTGGTatggtcgtatggatcctacag-----tttgacagtagcacttgcagcaatcaaataagggaaataagctggtccatacatattttttgttcaggagttcttaaggaacccagaaagatatattcgtctcggtgctcgccctcct

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|29630188|gb|CB635197.1|CB635197
EST:     CAGAAAGATATATTCGTCTTGGTGCGCGACCTCCACGAGGTGTCTTGTTG                         GTGGGCCTTCCAGGAACTGGAAAGACGCTTCTTGCAAAAGCTGTCGCAGGG
genomic: CAGAAAGATATATTCGTCTTGGTGCGCGACCTCCACGAGGTGTCTTGTTGgtcagttctg ... ttatttacagGTGGGCCTTCCAGGAACTGGAAAGACGCTTCTTGCAAAAGCTGTCGCAGGG
EST: gi|29630418|gb|CB635427.1|CB635427
EST:     CAGAAAGATATATTCGTCTTGGTGCGCGACCTCCACGAGGTGTCTTGTTG                         GTGGGCCTTCCAGGAACTGGAAAGACGCTTCTTGCAAAAGCTGTCGCAGGG
genomic: CAGAAAGATATATTCGTCTTGGTGCGCGACCTCCACGAGGTGTCTTGTTGgtcagttctg ... ttatttacagGTGGGCCTTCCAGGAACTGGAAAGACGCTTCTTGCAAAAGCTGTCGCAGGG
EST: gi|29630416|gb|CB635425.1|CB635425
EST:     CAGAAAGATATATTCGTCTTGGTGCGCGACCTCCACGAGGTGTCTTGTTG                         GTGGGCCTTCCAGGAACTGGAAAGACGCTTCTTGCAAAAGCTGTCGCAGGG
genomic: CAGAAAGATATATTCGTCTTGGTGCGCGACCTCCACGAGGTGTCTTGTTGgtcagttctg ... ttatttacagGTGGGCCTTCCAGGAACTGGAAAGACGCTTCTTGCAAAAGCTGTCGCAGGG

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: 66 (upstream exon), 62 (downstream exon)
Score: 19

GAGTTCCTAAGGAACCCAGAAAGATATATTCGTCTTGGTGCGCGACCTCCACGAGGTGTCTTGTTGgtcagttctg ... ttatttacagGTGGGCCTTCCAGGAACTGGAAAGACGCTTCTTGCAAAAGCTGTCGCAGGGGAAGCTGAAGTCCCATTCATAAGTTGCTCTGCAAGTGAATTTGTGGAGT




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