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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gagcaatgatgttgtcctcttggttattttttatttgccatagtattgtgtgcctcagtcttctagtttaagaaagtaacaagtagttctcttatttcagATATGACAAATATTACCAAACCCCACGTGTCTGGCTTACCGGATATGATGAG

Basic information

species Oryza sativa
transcript LOC_Os01g10290.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g10290.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM5G818887_T02 (Zea mays), 3'ss of exon 5
gagcaatgatgttgtcctcttggttattttttatttgccatagtattgtgtgcctcagtcttctagtttaagaaagtaacaagtagttc----tcttatttcagATATGACAAATATTACCAAACCCCACGTGTCTGGCTTACCGGATATGATGAG
     || |  || ||   ||  | || || | |       |||  |   | | |  | |    | || ||  | | |||| |||  |     || |||| ||| |||||||| || |||||||| |||||||||||||| || |||||||| |||
---ggataagattatctaattaat-atcttgtgtggaaagcagttcttacttcttgtgacccacacttgaattaggaaacatgtaactaatgatcctattgcagGTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAG

upper sequence: LOC_Os01g10290.2 (Oryza sativa), 3'ss of exon 5
lower sequence: AT5G61500.1 (Arabidopsis thaliana), 3'ss of exon 5
--gagcaatgatgttgtcctcttggt----tattttttatttgccat--agtattgtgtgcctcagtcttctagtttaagaaagtaacaagtagttctc---ttatttcagATATGACAAATATTACCAAACCCCACGTGTCTGGCTTACCGGATATGATGAG
   ||||     | | || ||   ||    || |   | ||  |  |    ||| |  | | |   | |  |    ||  ||   |||   || |||||   ||  ||||| ||||| || ||||||||||| || ||||| ||||| ||||| |||||||||
gtaagcatcccgggtttcttcaaagtgtagtactgcgttttgacttttagatatagctttcttacatttggtccagtagtaagcaaacttataattctcactttggttcagGTATGATAAGTATTACCAAACTCCTCGTGTTTGGCTGACCGGTTATGATGAG
















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|29638207|gb|CB643216.1|CB643216
EST:     CCTGAAGATGACAACATCCTTCGTACTAGGACATATGACGTTAGCATCAC                         ATATGACAAATATTGCCAAACCCCCCGTGTCTGGCTTACCGGATATGATGA
genomic: CCTGAAGATGACAACATCCTTCGTACTAGGACATATGACGTTAGCATCACgtaagctctt ... cttatttcagATATGACAAATATTACCAAACCCCACGTGTCTGGCTTACCGGATATGATGA
EST: gi|55440203|gb|CV733411.1|CV733411
EST:     CCTGAAGATGACAACATCCTTCGTACTAGGACATATGACGTTAGCATCAC                         ATATGACAAATATTACCAAACCCCACGTGTCTGGCTTACCGGATATGATGA
genomic: CCTGAAGATGACAACATCCTTCGTACTAGGACATATGACGTTAGCATCACgtaagctctt ... cttatttcagATATGACAAATATTACCAAACCCCACGTGTCTGGCTTACCGGATATGATGA
EST: gi|86497450|gb|CI140083.1|CI140083
EST:     CCTGAAGATGACAACATCCTTCGTACTAGGACATATGACGTTAGCATCAC                         ATATGACAAATATTACCAAACCCCACGTGTCTGGCTTACCGGATATGATGA
genomic: CCTGAAGATGACAACATCCTTCGTACTAGGACATATGACGTTAGCATCACgtaagctctt ... cttatttcagATATGACAAATATTACCAAACCCCACGTGTCTGGCTTACCGGATATGATGA
EST: gi|29686213|gb|CB682488.1|CB682488
EST:     CCTGAAGATGACAACATCCTTCGTACTAGGACATATGACGTTAGCATCAC                         ATATGACAAATATTACCAAACCCCACGTGTCTGGCTTACCGGATATGATGA
genomic: CCTGAAGATGACAACATCCTTCGTACTAGGACATATGACGTTAGCATCACgtaagctctt ... cttatttcagATATGACAAATATTACCAAACCCCACGTGTCTGGCTTACCGGATATGATGA
EST: gi|87015628|gb|CI277586.1|CI277586
EST:     CCTGAAGATGACAACATCCTTCGTACTAGGACATATGACGTTAGCATCAC                         ATATGACAAATATTACCAAACCCCACGTGTCTGGCTTACCGGATATGATGA
genomic: CCTGAAGATGACAACATCCTTCGTACTAGGACATATGACGTTAGCATCACgtaagctctt ... cttatttcagATATGACAAATATTACCAAACCCCACGTGTCTGGCTTACCGGATATGATGA

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: 52 (upstream exon), 71 (downstream exon)
Score: 53

GCTACCGCTCAACCTTCATATTTTGTCGCAGAAGAGCCTGAAGATGACAACATCCTTCGTACTAGGACATATGACGTTAGCATCACgtaagctctt ... cttatttcagATATGACAAATATTACCAAACCCCACGTGTCTGGCTTACCGGATATGATGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtgtgcctcagtcttctagtttaagaaagtaacaagtagttctcttatttcagATATGACAAATATTACCAAACCCCACGTGTCTGGCTTACCGGATATGATGAG
                            aagtaac  putative branch site (score: 53)
                                         ttctcttatttc  putative PPT
                     tttaagaaa  TA-rich tract