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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattctgtcattccgaaattagcatttttgatattctgtatatgttggcattataataatgatgtcttgttccccctacagCTGGAGAAGATCAAGGCTGAAATAGCTGAAGTTTCTGATAATCCTCAAGGTTTACTTCTAGAGGCACTCCATTCTGCTGGCTATTCTGGGGCACTGGCGA

Basic information

species Oryza sativa
transcript LOC_Os01g53700.1
intron # 3
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|117222072|gb|CT852607.1|CT852607
EST:     TTGATAGTGTGAGGAACCCAGCCTTTTTTAACTGGGAGATTAAAGAGCAG                         CTGGAGAAGATCAAGGCTGAAATAGCTGAAGTTTCTGATAATCCTCAAGGT
genomic: TTGATAGTGTGAGGAACCCAGCCTTTTTTAACTGGGAGATTAAAGAGCAGgtattctgtc ... ccccctacagCTGGAGAAGATCAAGGCTGAAATAGCTGAAGTTTCTGATAATCCTCAAGGT
EST: gi|33678525|gb|CF306764.1|CF306764
EST:     TTGATAGTGTGAGGAACCCAGCCTTTTTTAACTGGGAGATTAAAGAGCAG                         CTGGAGAAGATCAAGGCTGAAATAGCTGAAGTTTCTGATAATCCTCAAGGT
genomic: TTGATAGTGTGAGGAACCCAGCCTTTTTTAACTGGGAGATTAAAGAGCAGgtattctgtc ... ccccctacagCTGGAGAAGATCAAGGCTGAAATAGCTGAAGTTTCTGATAATCCTCAAGGT
EST: gi|33795923|gb|CF323829.1|CF323829
EST:     TTGATAGTGTGAGGAACCCAGCCTTTTTTAACTGGGAGATTAAAGAGCAG                         CTGGAGAAGATCAAGGCTGAAATAGCTGAAGTTTCTGATAATCCTCAAGGT
genomic: TTGATAGTGTGAGGAACCCAGCCTTTTTTAACTGGGAGATTAAAGAGCAGgtattctgtc ... ccccctacagCTGGAGAAGATCAAGGCTGAAATAGCTGAAGTTTCTGATAATCCTCAAGGT
EST: gi|33677885|gb|CF306124.1|CF306124
EST:     TTGATAGTGTGAGGAACCCAGCCTTTTTTAACTGGGAGATTAAAGAGCAG                         CTGGAGAAGATCAAGGCTGAAATAGCTGAAGTTTCTGATAATTCTCAAGGT
genomic: TTGATAGTGTGAGGAACCCAGCCTTTTTTAACTGGGAGATTAAAGAGCAGgtattctgtc ... ccccctacagCTGGAGAAGATCAAGGCTGAAATAGCTGAAGTTTCTGATAATCCTCAAGGT

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: 50 (upstream exon), 73 (downstream exon)
Score: 67

TACCTATGATGCATTCAAGGCCTATGTACCTGAGATGGTTGAAGTGCTTATTGATAGTGTGAGGAACCCAGCCTTTTTTAACTGGGAGATTAAAGAGCAGgtattctgtc ... ccccctacagCTGGAGAAGATCAAGGCTGAAATAGCTGAAGTTTCTGATAATCCTCAAGGTTTACTTCTAGAGGCACTCCATTCTGCTGGCTATTCTGGGGCACTGGCGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgatattctgtatatgttggcattataataatgatgtcttgttccccctacagCTGGAGAAGATCAAGGCTGAAATAGCTGAAGTTTCTGATAATCCTCAAGGTTTACTTCTAGAGGCACTCCATTCTGCTGGCTATTCTGGGGCACTGGCGA
 ttttgat  putative branch site (score: 67)
                                    tgtcttgttccccct  putative PPT
                       attataataatgatgt  TA-rich tract