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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagagctcgccccgactcatctcgtcgtgggaagttcgcgtggttgcggcttctccgcccgcgcttggtctcgctgtgtttttttttttgttcggtggatttaattttgttttgctttttttttttctctggtgttgcagATCTGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGCTT

Basic information

species Oryza sativa
transcript LOC_Os06g37440.1
intron # 1
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|58693057|gb|CK081744.1|CK081744
EST:     ACGATCTCGTCTCGCACCGCCTCTCTCTCGGT                         ATCTGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGC
genomic: ACGATCTCGTCTCGCACCGCCTCTCTCTCGGTgtaagagctc ... ggtgttgcagATCTGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGC
EST: gi|88300178|gb|CI582412.1|CI582412
EST:     ACGATCTCGTCTCGCACCGCCTCTCTCTCGGT                         ATCTGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGC
genomic: ACGATCTCGTCTCGCACCGCCTCTCTCTCGGTgtaagagctc ... ggtgttgcagATCTGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGC
EST: gi|58692670|gb|CK081357.1|CK081357
EST:     GCCGCGCGCCGCCG-CGACGATCTCGTCTCGCACCGCCTCTCTCTCGGT                         ATCTGAGATNTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGC
genomic: GCCGC-CGCCGCCGCCGACGATCTCGTCTCGCACCGCCTCTCTCTCGGTgtaagagctc ... ggtgttgcagATCTGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGC
EST: gi|88393909|gb|CI684174.1|CI684174
EST:     ACGATCTCGTCTCGCACCGCCTCTCTCTCGGT                         ATCTGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGC
genomic: ACGATCTCGTCTCGCACCGCCTCTCTCTCGGTgtaagagctc ... ggtgttgcagATCTGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGC
EST: gi|29642157|gb|CB647164.1|CB647164
EST:     ACGATCTCGTCTCGCACCGCCTCTCTCTCGGT                         ATCTGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGC
genomic: ACGATCTCGTCTCGCACCGCCTCTCTCTCGGTgtaagagctc ... ggtgttgcagATCTGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGC
EST: gi|88299640|gb|CI574753.1|CI574753
EST:     ACGATCTCGTCTCGCACCGCCTCTCTCTCGGT                         ATCTGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGC
genomic: ACGATCTCGTCTCGCACCGCCTCTCTCTCGGTgtaagagctc ... ggtgttgcagATCTGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGC
EST: gi|33797048|gb|CF324390.1|CF324390
EST:     CTCGTCTCGCACCGCCTCTCTCTCGGT                         ATCTGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGC
genomic: CTCGTCTCGCACCGCCTCTCTCTCGGTgtaagagctc ... ggtgttgcagATCTGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGC
EST: gi|66917477|gb|CX104325.1|CX104325
EST:     GCCGACGCCGACGATCTCGTCTCGCACCGCCTCTCTCTCGGT                         ATCTGACATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGC
genomic: GCCGCCGCCGACGATCTCGTCTCGCACCGCCTCTCTCTCGGTgtaagagctc ... ggtgttgcagATCTGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGC
EST: gi|88340432|gb|CI659638.1|CI659638
EST:     ACGATCTCGTCTCGCACCGCCTCTCTCTCGGT                         ATCTGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGC
genomic: ACGATCTCGTCTCGCACCGCCTCTCTCTCGGTgtaagagctc ... ggtgttgcagATCTGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGC
EST: gi|88325683|gb|CI648126.1|CI648126
EST:     ACGATCTCGTCTCGCACCGCCTCTCTCTCGGT                         ATCTGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGC
genomic: ACGATCTCGTCTCGCACCGCCTCTCTCTCGGTgtaagagctc ... ggtgttgcagATCTGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGC
EST: gi|88392537|gb|CI625359.1|CI625359
EST:     GATCTCGTCTCGCACCGCCTCTCTCTCGGT                         ATCTGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGAATGGCGC
genomic: GATCTCGTCTCGCACCGCCTCTCTCTCGGTgtaagagctc ... ggtgttgcagATCTGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGC
EST: gi|88402181|gb|CI615024.1|CI615024
EST:     ACGATCTCGTCTCGCACCGCCTCTCTCTCGGT                         ATCTGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGC
genomic: ACGATCTCGTCTCGCACCGCCTCTCTCTCGGTgtaagagctc ... ggtgttgcagATCTGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGC
EST: gi|58677886|gb|CK066573.1|CK066573
EST:     CTCGCACCGCCTCTCTCTCGGT                         ATCTGAGATTTGGATCGGGCGCGAGGCCGGCGGCGCCAGTCGGCATGGCGC
genomic: CTCGCACCGCCTCTCTCTCGGTgtaagagctc ... ggtgttgcagATCTGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGC
EST: gi|88403316|gb|CI573039.1|CI573039
EST:     ACGATCTCGTCTCGCACCGCCTCTCTCTCGGT                         ATCTGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGC
genomic: ACGATCTCGTCTCGCACCGCCTCTCTCTCGGTgtaagagctc ... ggtgttgcagATCTGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGC
EST: gi|88421445|gb|CI618569.1|CI618569
EST:     ACGATCTCGTCTCGCACCGCCTCTCTCTCGGT                         ATCTGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGC
genomic: ACGATCTCGTCTCGCACCGCCTCTCTCTCGGTgtaagagctc ... ggtgttgcagATCTGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGC
EST: gi|88432577|gb|CI567616.1|CI567616
EST:     ACGATCTCGTCTCGCACCGCCTCTCTCTCGGT                         ATCTGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGC
genomic: ACGATCTCGTCTCGCACCGCCTCTCTCTCGGTgtaagagctc ... ggtgttgcagATCTGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGC
EST: gi|33658387|gb|CF281000.1|CF281000
EST:     ACGATCTCGTCTCGCACCGCCTCTCTCTCGGT                         ATCTGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGC
genomic: ACGATCTCGTCTCGCACCGCCTCTCTCTCGGTgtaagagctc ... ggtgttgcagATCTGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGC
EST: gi|33794630|gb|CF323201.1|CF323201
EST:     GCCGCCGCCGCCGCCGACGATCTCGTCTCGCACCGCCTCTCTCTCGGT                         ATCTGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGC
genomic: GCCGCCGCCGCCGCCGACGATCTCGTCTCGCACCGCCTCTCTCTCGGTgtaagagctc ... ggtgttgcagATCTGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGC

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: 75 (upstream exon), 75 (downstream exon)
Score: 99

CTCGTCTCCCGTACCAACTAAACCCCCTTCTCTCTCCGCTGGGGTTCTCGCCGCCGCCGCCGCCGCCGACGATCTCGTCTCGCACCGCCTCTCTCTCGGTgtaagagctc ... ggtgttgcagATCTGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGCTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgttcggtggatttaattttgttttgctttttttttttctctggtgttgcagATCTGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGCTT
             atttaat  putative branch site (score: 99)
                   ttttgttttgcttttt  CT-rich tract
             atttaattttgttttg  TA-rich tract