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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCCCAGTTGGCAGTCATGTTGTGGGTGCCTTCATAATGCCCTGTGGGAATTGCTTCTACTGTGTTAAGgtaagtaaataataatagtaccttctccttcatgccattctttccaagagaaaaaaaaaagaagaagagaggttgctttgctttcttgattgcacacatgtacatcaacttgatatag

Basic information

species Oryza sativa
transcript LOC_Os08g01760.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g01760.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G024303_T01 (Zea mays), 5'ss of exon 3
GTTCCCAGTTGGCAGTCATGTTGTGGGTGCCTTCATAATGCCCTGTGGGAATTGCTTCTACTGTGTTAAGgtaagtaaataataatagtaccttctccttcatgccattctttccaagagaaaaaaaaaagaagaagagaggttgctttgctttcttgattgcacacatgtacatcaacttgatatag
||||||||| || ||||| || || || |||||||||||||| |||||||| ||||||||||| |||||||||          |  ||    |  |   | | | |||   || |                            |||||| ||| |||| || | | ||||  |||  | || ||| ||
GTTCCCAGTCGGAAGTCACGTCGTCGGCGCCTTCATAATGCCATGTGGGAACTGCTTCTACTGCGTTAAGgtag---------agcagc-tttgttgaattacggcatatgtttctg--------------------------tgcttttcttgcttg-ttacgctcatgcccattgatttaatacag

upper sequence: LOC_Os08g01760.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G135526_T01 (Zea mays), 5'ss of exon 3
GTTCCCAGTTGGCAGTCATGTTGTGGGTGCCTTCATAATGCCCTGTGGGAATTGCTTCTACTGTGTTAAGgta-agtaaataataatagtaccttctccttcatgccattctttccaagagaaaaaaaaaagaagaagagaggttgctttgctttcttgattgcacacatgtacatcaacttgatatag
||||||||| || || || || || || || ||||||||||| |||||||| ||||||||||| ||||||||| ||    |  |  | | |  |  |     ||   || | || ||              |          | |  |     ||  ||| |   | ||||| |||  |     || ||
GTTCCCAGTAGGAAGCCACGTCGTCGGCGCGTTCATAATGCCATGTGGGAACTGCTTCTACTGCGTTAAGgtagagcttctcttggtcgaatgtcatggcatatat-atccctttcattttcctctcctgtgttctgc----gcttttcattcttgctgactatgctcatgtgcattgat---gtacag
















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|2312625|gb|C28780.1|C28780
EST:     TTGTGGGTGCCTTCATAATGCCCTGT-GGAATTGCTTCTACTGTGTTAAG                         GGCCAAGAAGATCTGTGTGAGTCTTTCTTTGCATACAACCGTGCTAAAGGA
genomic: TTGTGGGTGCCTTCATAATGCCCTGTGGGAATTGCTTCTACTGTGTTAAGgtaagtaaat ... cttgatatagGGCCAAGAAGATCTGTGTGAGTCTTTCTTTGCATACAACCGTGCTAAAGGA
EST: gi|44674419|gb|CR287853.1|CR287853
EST:     TTGTGGGTGCCTTCATAATGCCCTGTGGGAATTGCTTCTACTGTGTTAAG                         GGCCAAGAAGATCTGTGTGAGTCTTTCTTTGCATACAACCGTGCTAAAGGA
genomic: TTGTGGGTGCCTTCATAATGCCCTGTGGGAATTGCTTCTACTGTGTTAAGgtaagtaaat ... cttgatatagGGCCAAGAAGATCTGTGTGAGTCTTTCTTTGCATACAACCGTGCTAAAGGA
EST: gi|7593811|gb|AU065734.2|AU065734
EST:     TTGTGGGTGCCTTCATAATGCCCTGTGGGAATTGCTTCTACTGTGTTAAG                         GGCCAAGAAGATCTGTGTGAGTCTTTCTTTGCATACAACCGTGCTAAAGGA
genomic: TTGTGGGTGCCTTCATAATGCCCTGTGGGAATTGCTTCTACTGTGTTAAGgtaagtaaat ... cttgatatagGGCCAAGAAGATCTGTGTGAGTCTTTCTTTGCATACAACCGTGCTAAAGGA
EST: gi|11863309|gb|AU065733.2|AU065733
EST:     TTGTGGGTGCCTTCATAATGCCCTGTGGGAATTGCTTCTACTGTGTTAAG                         GGNCAAGAAGATCTGTGTGAGTCTTTCTTTGCATACAACCGTGCTAAAGGA
genomic: TTGTGGGTGCCTTCATAATGCCCTGTGGGAATTGCTTCTACTGTGTTAAGgtaagtaaat ... cttgatatagGGCCAAGAAGATCTGTGTGAGTCTTTCTTTGCATACAACCGTGCTAAAGGA
EST: gi|66916958|gb|CX103806.1|CX103806
EST:     GCTTCTACTGTGTTAAG                         GGCCAAGAAGATCTGTGTGAGTCTTTCTTTGCATACAACCGTGCTAAAGGA
genomic: GCTTCTACTGTGTTAAGgtaagtaaat ... cttgatatagGGCCAAGAAGATCTGTGTGAGTCTTTCTTTGCATACAACCGTGCTAAAGGA

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

GTTCCCAGTTGGCAGTCATGTTGTGGGTGCCTTCATAATGCCCTGTGGGAATTGCTTCTACTGTGTTAAGgtaagtaaat ... cttgatatagGGCCAAGAAGATCTGTGTGAGTCTTTCTTTGCATACAACCGTGCTAAAGGAACGCTATACGATGGTCAAACCCGATTATTCCTTCGTAGCAATG




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