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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattggtttctcctactatttgtgagtatcttttgtttaacagcatcctcctgaatgattgcagcacttgttggctgtttgttttttctgttcattcatgtgtttttctcagagacattacaagtgcaaaaatgcttactattgtttcattttccagAACCATTTGATGAAGGTTCTACACCTGCATGCTTTAGAGCCAAAGCG

Basic information

species Oryza sativa
transcript LOC_Os05g27870.1
intron # 16
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|427959|gb|D24104.1|D24104
EST:     TCAGGCACGCCCTTGGTGGACACCAACAACAAGTGTTAATTTTCTGTCAG                         AACCATTTGATGAAGGTTCTACACCTGCATGCTTTAGAGCCAAAGCG
genomic: TCAGGCACGCCCTTGGTGGACACCAACAACAAGTGTTAATTTTCTGTCAGgtaattggtt ... cattttccagAACCATTTGATGAAGGTTCTACACCTGCATGCTTTAGAGCCAAAGCG
EST: gi|29677067|gb|CB673342.1|CB673342
EST:     TCAGGCACGCCCTTGGTGGACACCAACAACAAGTGTTAATTTTCTGTCAG                         AACCATTTGATGAAGGTTCTACACCTGCATGCTTTAGAGCCAAAGCG
genomic: TCAGGCACGCCCTTGGTGGACACCAACAACAAGTGTTAATTTTCTGTCAGgtaattggtt ... cattttccagAACCATTTGATGAAGGTTCTACACCTGCATGCTTTAGAGCCAAAGCG
EST: gi|11025806|gb|AU162407.1|AU162407
EST:     CCCTTGGTGGACCCCCCACCACCAAGTGTNAATTTCCTGTCAG                         AACCATTTGATGAAGGTTCTACACCTGCATGCTTTAGAGCCAAAGCCG
genomic: CCCTTGGTGGA--CACCAACAACAAGTGTTAATTTTCTGTCAGgtaattggtt ... cattttccagAACCATTTGATGAAGGTTCTACACCTGCATGCTTTAGAGCCAAAG-CG

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: 72 (upstream exon), 71 (downstream exon)
Score: 19

GAACTATCAAACGAAGACAACGTGAAACGCTTTACTTTTAACGAAGATCTTCAGGCACGCCCTTGGTGGACACCAACAACAAGTGTTAATTTTCTGTCAGgtaattggtt ... cattttccagAACCATTTGATGAAGGTTCTACACCTGCATGCTTTAGAGCCAAAGCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttctcagagacattacaagtgcaaaaatgcttactattgtttcattttccagAACCATTTGATGAAGGTTCTACACCTGCATGCTTTAGAGCCAAAGCG
                              tgcttac  putative branch site (score: 19)
                                       ttgtttcattttcc  putative PPT
                                     tattgtttcatttt  TA-rich tract