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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaactatttgtggtccagaaattttgttttggtctttggttatcaaaacacatgcaccacaagaaaaagaattactagaagtgtgtcaccaaatacacgctaatttatttgctcttttgcagATACTCATCAAAACAAATATTGCAAGTTGTGGAGTTCTGGATTTTGCAGCTTGATCCTGTGAAGTACTGTTAACAAAATGCCCCCGATCATATGCTTCCA

Basic information

species Oryza sativa
transcript LOC_Os04g35920.2
intron # 12
splice site 3'
intron type U2

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|218503496|gb|FG966805.1|FG966805
EST:     AAGTGTGGGTTCAAAAATCAAGCTCGGCGACGTGATCTTGTCCAATGATG                         ATACTCATCAAAACAAATATTGCAAGTTGTGGAGTTCTGGATTTTGCAGCT
genomic: AAGTGTGGGTTCAAAAATCAAGCTCGGCGACGTGATCTTGTCCAATGATGgtaaactatt ... tcttttgcagATACTCATCAAAACAAATATTGCAAGTTGTGGAGTTCTGGATTTTGCAGCT
EST: gi|33684829|gb|CF313068.1|CF313068
EST:     AAGTGTGGGTTCAAAAATCAAGCTCGGCGACGTGATCTTGTCCAATGATG                         ATACTCATCAAAACAAATATTGCAAGTTGTGGAGTTCTGGATTTTGCAGCT
genomic: AAGTGTGGGTTCAAAAATCAAGCTCGGCGACGTGATCTTGTCCAATGATGgtaaactatt ... tcttttgcagATACTCATCAAAACAAATATTGCAAGTTGTGGAGTTCTGGATTTTGCAGCT
EST: gi|29671972|gb|CB668247.1|CB668247
EST:     AAGTGTGGGTTCAAAAATCAAGCTCGGCGACGTGATCTTGTCCCATGATG                         ATACTCATCAAAACAAATATTGCAAGTTGTGGAGTTCTGGATTTTGCAGCT
genomic: AAGTGTGGGTTCAAAAATCAAGCTCGGCGACGTGATCTTGTCCAATGATGgtaaactatt ... tcttttgcagATACTCATCAAAACAAATATTGCAAGTTGTGGAGTTCTGGATTTTGCAGCT
EST: gi|29626480|gb|CB631491.1|CB631491
EST:     AAGTGTGGGTTCAAAAATCAAGCTCGGCGACGTGATCTTGTCCAATGATG                         ATACTCATCAAAACAAATATTGCAAGTTGTGGAGTTCTGGATTTTGCAGCT
genomic: AAGTGTGGGTTCAAAAATCAAGCTCGGCGACGTGATCTTGTCCAATGATGgtaaactatt ... tcttttgcagATACTCATCAAAACAAATATTGCAAGTTGTGGAGTTCTGGATTTTGCAGCT
EST: gi|58606714|gb|CK034747.1|CK034747
EST:     AAGTGTGGGTTCAAAAGTCAAGCTCGGCGACGTGATCTTGTCCAATGATG                         ATACTCATCAAAACAAATATTGCAAGTTGTGGAGTTCTGGATTTTGCAGCT
genomic: AAGTGTGGGTTCAAAAATCAAGCTCGGCGACGTGATCTTGTCCAATGATGgtaaactatt ... tcttttgcagATACTCATCAAAACAAATATTGCAAGTTGTGGAGTTCTGGATTTTGCAGCT
EST: gi|89175126|gb|CI111645.1|CI111645
EST:     AAGTGTGGGTTCAAAAATCAAGCTCGGCGACGTGATCTTGTCCAATGATG                         ATACTCATCGAGACGAATATTGCAAGTTGTGGAGTTCTGGATTTTGCAGCT
genomic: AAGTGTGGGTTCAAAAATCAAGCTCGGCGACGTGATCTTGTCCAATGATGgtaaactatt ... tcttttgcagATACTCATCAAAACAAATATTGCAAGTTGTGGAGTTCTGGATTTTGCAGCT

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: 70 (upstream exon), 52 (downstream exon)
Score: 12

AGGCAAGTGTGGGTTCAAAAATCAAGCTCGGCGACGTGATCTTGTCCAATGATGgtaaactatt ... tcttttgcagATACTCATCAAAACAAATATTGCAAGTTGTGGAGTTCTGGATTTTGCAGCTTGATCCTGTGAAGTACTGTTAACAAAATGCCCCCGATCATATGCTTCCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaattactagaagtgtgtcaccaaatacacgctaatttatttgctcttttgcagATACTCATCAAAACAAATATTGCAAGTTGTGGAGTTCTGGATTTTGCAGCTTGATCCTGTGAAGTACTGTTAACAAAATGCCCCCGATCATATGCTTCCA
                              cgctaat  putative branch site (score: 12)
                                    tttatttgctctttt  CT-rich tract
                                 taatttattt  TA-rich tract