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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtaacttgcttttaatcctaattgttgtttcatctttctgcaaagcaatttttttttgcaatatgccatgtaacactgattgctaccttattcagGAGGAACAAGGCCTTGATAAAGGACCTGAGCCAACCAGCCCCCGATTCAAGTGACCTGTATTTCCCTACCCAATATTCTCAGTCTTCTTTAACACAATGC

Basic information

species Oryza sativa
transcript LOC_Os01g42380.1
intron # 17
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|33796585|gb|CF324160.1|CF324160
EST:     CACTTGGTGTTGATTTTAGTGATATATACCAAGAAGTCTGAACTTTACCA                         GAGGAACAAGGCCTTGATAAAGGACCTGAGCCAACCAGCCCCCGATTCAAG
genomic: CACTTGGTGTTGATTTTAGTGATATATA-CAAGAAGTCTGAACTTTACCAgtgagtaact ... ccttattcagGAGGAACAAGGCCTTGATAAAGGACCTGAGCCAACCAGCCCCCGATTCAAG
EST: gi|33678228|gb|CF306467.1|CF306467
EST:     GCACTTGGTGTTGATTTTAGTGATATATACAAGAAGTCTGAACTTTACCA                         GAGGAACAAGGCCTTGATAAAGGACCTGAGCCAACCAGCCCCCGATTCAAG
genomic: GCACTTGGTGTTGATTTTAGTGATATATACAAGAAGTCTGAACTTTACCAgtgagtaact ... ccttattcagGAGGAACAAGGCCTTGATAAAGGACCTGAGCCAACCAGCCCCCGATTCAAG
EST: gi|38469656|gb|CF953787.1|CF953787
EST:     GCACTTGGTGTTGATTTTAGTGATATATACAAGAAGTCTGAACTTTACCA                         GAGGAACAAGGCCTTGATAAAGGACCTGAGCCAACCAGCCCCCGATTCAAG
genomic: GCACTTGGTGTTGATTTTAGTGATATATACAAGAAGTCTGAACTTTACCAgtgagtaact ... ccttattcagGAGGAACAAGGCCTTGATAAAGGACCTGAGCCAACCAGCCCCCGATTCAAG
EST: gi|33677918|gb|CF306157.1|CF306157
EST:     GCACTTGGTGTTGATTTTAGTGATATATTCTTTATTTCTGAACTTTACCA                         GAGGAACAAGGCCTTGATAAAGGACCTGAGCCAACCAGCCCCCGATTCAAG
genomic: GCACTTGGTGTTGATTTTAGTGATATATACAAGAAGTCTGAACTTTACCAgtgagtaact ... ccttattcagGAGGAACAAGGCCTTGATAAAGGACCTGAGCCAACCAGCCCCCGATTCAAG
EST: gi|86876761|gb|CI309645.1|CI309645
EST:     GCACTTGGTGTTGATTTTAGTGATATATACAAGAAGTCTGAACTTTACCA                         GAGGAACAAGGCCTTGATAAAGGACCTGAGC
genomic: GCACTTGGTGTTGATTTTAGTGATATATACAAGAAGTCTGAACTTTACCAgtgagtaact ... ccttattcagGAGGAACAAGGCCTTGATAAAGGACCTGAGC
EST: gi|29614736|gb|CB619749.1|CB619749
EST:     GCACTTGGTGTTGATTTTAGTGATATATACAAGAAGTCTGAACTTTACCA                         GAGGAACAAGGCCTTGATAAAGGACCTGAGCCAACCAGCCCCCGATTCAAG
genomic: GCACTTGGTGTTGATTTTAGTGATATATACAAGAAGTCTGAACTTTACCAgtgagtaact ... ccttattcagGAGGAACAAGGCCTTGATAAAGGACCTGAGCCAACCAGCCCCCGATTCAAG

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), 40 (downstream exon)
Score: 4

ATAACCCAGCAACATGGATGTTGGAGGTGACAACAATTGGTCAAGAGCAGGCACTTGGTGTTGATTTTAGTGATATATACAAGAAGTCTGAACTTTACCAgtgagtaact ... ccttattcagGAGGAACAAGGCCTTGATAAAGGACCTGAGCCAACCAGCCCCCGATTCAAGTGACCTGTATTTCCCTACCCAATATTCTCAGTCTTCTTTAACACAATGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaagcaatttttttttgcaatatgccatgtaacactgattgctaccttattcagGAGGAACAAGGCCTTGATAAAGGACCTGAGCCAACCAGCCCCCGATTCAAGTGACCTGTATTTCCCTACCCAATATTCTCAGTCTTCTTTAACACAATGC
                                 cactgat  putative branch site (score: 4)
                                             ccttattc  putative PPT
      aatttttttttgcaat  TA-rich tract