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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGTTATACTGGATCCCTTGCTCGCTTTCAGGAATGAACTGAAAGgtgtgctatttatcttctttaatttgatatatgaagattggttagctaacctgaaaaggtttttttttctttctcatgctttctaatatttcag

Basic information

species Oryza sativa
transcript LOC_Os06g30460.4
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g30460.4 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G082664_T01 (Zea mays), 5'ss of exon 12
ATGTTATACTGGATCCCTTGCTCGCTTTCAGGAATGAACTGAAAGgtgtgctatttatcttctttaatttgata---tatgaagattggttagct---------------aacctgaaaa---ggtttttttttctttctcatgctttctaatatttcag
||||| | |||||||||||||||||||||||||||||||| ||||||||| ||| |||||||||| |  ||||    |      ||  |  | ||               |  | || ||   |     | ||  ||  | |||  |||    ||| |||
ATGTTGTGCTGGATCCCTTGCTCGCTTTCAGGAATGAACTAAAAGgtgtgttatatatcttcttttacctgatgattttcagtaatcagacaacttttattattttcaatagtcagataacaggaaaggtcttgtttgataatgacttcgttcattgcag
















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|58599848|gb|CK010376.1|CK010376
EST:     ATGTTATACTGGATCCTTTGCTCGCTTTCAGGAATGAACTGAAAG                         AGCAACATGGGGTTAAAGTTTCAG
genomic: ATGTTATACTGGATCCCTTGCTCGCTTTCAGGAATGAACTGAAAGgtgtgctatt ... aatatttcagAGCAACATGGGGTTAAAGTTTCAG
EST: gi|218488261|gb|FG947096.1|FG947096
EST:     ATGTTATACTGGATCCTTTGCTCGCTTTCAGGAATGAACTGAAAG                         AGCAACATGGGGTTAAAGTTTCAGTAAATGACATTGTCATAAAGGCTGTTG
genomic: ATGTTATACTGGATCCCTTGCTCGCTTTCAGGAATGAACTGAAAGgtgtgctatt ... aatatttcagAGCAACATGGGGTTAAAGTTTCAGTAAATGACATTGTCATAAAGGCTGTTG
EST: gi|117245735|gb|CT848475.1|CT848475
EST:     ATGTTATACTGGATCCTTTGCTCGCTTTCAGGAATGAACTGAAAG                         AGCAACATGGGGTTAAAGTTTCAGTAAATGACATTGTCATAAAGGCTGTTG
genomic: ATGTTATACTGGATCCCTTGCTCGCTTTCAGGAATGAACTGAAAGgtgtgctatt ... aatatttcagAGCAACATGGGGTTAAAGTTTCAGTAAATGACATTGTCATAAAGGCTGTTG
EST: gi|218481815|gb|FG945396.1|FG945396
EST:     ATGTTATACTGGATCCTTTGCTCGCTTTCAGGAATGAACTGAAAG                         AGCAACATGGGGTTAAAGTTTCAGTAAATGACATTGTCATAAAGGCTGTTG
genomic: ATGTTATACTGGATCCCTTGCTCGCTTTCAGGAATGAACTGAAAGgtgtgctatt ... aatatttcagAGCAACATGGGGTTAAAGTTTCAGTAAATGACATTGTCATAAAGGCTGTTG
EST: gi|58692196|gb|CK080883.1|CK080883
EST:     ATGTTATACTGGATCCTTTGCTCGCTTTCAGGAATGAACTGAAAG                         AGCAACATGGGGTTAAAGTTTCAGTAAATGACATTGTCATAAAGGCTGTTG
genomic: ATGTTATACTGGATCCCTTGCTCGCTTTCAGGAATGAACTGAAAGgtgtgctatt ... aatatttcagAGCAACATGGGGTTAAAGTTTCAGTAAATGACATTGTCATAAAGGCTGTTG
EST: gi|27578288|gb|CB000983.1|CB000983
EST:     ATGTTATACTGGATCCCTTGCTCGCTTTCAGGAATGAACTGAAAG                         AGCAACATGGGGTTAAAGTTTCAGTAAATGACATTGTCATAAAGGCTGTTG
genomic: ATGTTATACTGGATCCCTTGCTCGCTTTCAGGAATGAACTGAAAGgtgtgctatt ... aatatttcagAGCAACATGGGGTTAAAGTTTCAGTAAATGACATTGTCATAAAGGCTGTTG
EST: gi|27578255|gb|CB000950.1|CB000950
EST:     ATGTTATACTGGATCCCTTGCTCGCTTTCAGGAATGAACTGAAAG                         AGCAACATGGGGTTAAAGTTTCAGTAAATGACATTGTCATAAAGGCTGTTG
genomic: ATGTTATACTGGATCCCTTGCTCGCTTTCAGGAATGAACTGAAAGgtgtgctatt ... aatatttcagAGCAACATGGGGTTAAAGTTTCAGTAAATGACATTGTCATAAAGGCTGTTG
EST: gi|58678110|gb|CK066797.1|CK066797
EST:     ATGTTATACTGGATCCTTTGCTCGCTTTCAGGAATGAACTGAAAG                         AGCAACATGGGGTTAAAGTTTCAGTAAATGACATTGTCATAAAGGCTGTTG
genomic: ATGTTATACTGGATCCCTTGCTCGCTTTCAGGAATGAACTGAAAGgtgtgctatt ... aatatttcagAGCAACATGGGGTTAAAGTTTCAGTAAATGACATTGTCATAAAGGCTGTTG
EST: gi|218482631|gb|FG947596.1|FG947596
EST:     ATGTTATACTGGATCCTTTGCTCGCTTTCAGGAATGAACTGAAAG                         AGCAACATGGGGTTAAAGTTTCAGTAAATGACATTGTCATAAAGGCTGTTG
genomic: ATGTTATACTGGATCCCTTGCTCGCTTTCAGGAATGAACTGAAAGgtgtgctatt ... aatatttcagAGCAACATGGGGTTAAAGTTTCAGTAAATGACATTGTCATAAAGGCTGTTG

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: 61 (upstream exon), 75 (downstream exon)
Score: 34

ATGTTATACTGGATCCCTTGCTCGCTTTCAGGAATGAACTGAAAGgtgtgctatt ... aatatttcagAGCAACATGGGGTTAAAGTTTCAGTAAATGACATTGTCATAAAGGCTGTTGCACTTGCCTTACGGAATGTACCAGAAGCAAATG




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