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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcaaaggacttcatttgatttgtttgcgaaaagcagaaatgcattatatatcttgcttcatctcatggtaggactttccgttatctaaagaaaaatcttccgtctaacgataattctgctttacatgcactagATTCCCAAAACTTTTGGTCGATGGACCGTATGGTGCACCGGCACAAGATTACCGTGAATACGATGTGCTACTTCTCATCGGGCTGGGCATCGGAGCCACC

Basic information

species Oryza sativa
transcript LOC_Os01g25820.1
intron # 11
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|29686947|gb|CB683222.1|CB683222
EST:     GGACTACTTAGAGCTGACCTTTCCAAGGGAATAACGGACGAAAAAGCAAG                         ATTCCCAAAACTTTTGGTCGATGGACCGTATGGTGCACCGGCACAAGATTA
genomic: GGACTACTTAGAGCTGACCTTTCCAAGGGAATAACGGACGAAAAAGCAAGgtgcaaagga ... catgcactagATTCCCAAAACTTTTGGTCGATGGACCGTATGGTGCACCGGCACAAGATTA
EST: gi|27577180|gb|CA999874.1|CA999874
EST:     GGACTACTTAGAGCTGACCTTTCCAAGGGAATAACGGACGAAAACGCAAG                         ATTCCCAAAACTTTTGGTCGATGGACCGTATGGTGCACCGGCACAAGATTA
genomic: GGACTACTTAGAGCTGACCTTTCCAAGGGAATAACGGACGAAAAAGCAAGgtgcaaagga ... catgcactagATTCCCAAAACTTTTGGTCGATGGACCGTATGGTGCACCGGCACAAGATTA
EST: gi|58665614|gb|CK054300.1|CK054300
EST:     GGACTACTTAGAGCTGACCTTTCCAAGGGAATAACGGACGAAAACGCAAG                         ATTCCCAAAACTTTTGGTCGATGGACCGTATGGTGCACCGGCACAAGATTA
genomic: GGACTACTTAGAGCTGACCTTTCCAAGGGAATAACGGACGAAAAAGCAAGgtgcaaagga ... catgcactagATTCCCAAAACTTTTGGTCGATGGACCGTATGGTGCACCGGCACAAGATTA
EST: gi|29679760|gb|CB676035.1|CB676035
EST:     GGACTACTTAGAGCTGACCTTTCCAAGGGAATAACGGACGAAAAAGCAAG                         ATTCCCAAAACTTTTGGTCGATGGACCGTATGGTGCACCGGCACAAGATTA
genomic: GGACTACTTAGAGCTGACCTTTCCAAGGGAATAACGGACGAAAAAGCAAGgtgcaaagga ... catgcactagATTCCCAAAACTTTTGGTCGATGGACCGTATGGTGCACCGGCACAAGATTA
EST: gi|27577154|gb|CA999848.1|CA999848
EST:     GGACTACTTAGAGCTGACCTTTCCAAGGGAATAACGGACGAAAACGCAAG                         ATTCCCAAAACTTTTGGTCGATGGACCGTATGGTGCACCGGCACAAGATTA
genomic: GGACTACTTAGAGCTGACCTTTCCAAGGGAATAACGGACGAAAAAGCAAGgtgcaaagga ... catgcactagATTCCCAAAACTTTTGGTCGATGGACCGTATGGTGCACCGGCACAAGATTA
EST: gi|29663215|gb|CB659490.1|CB659490
EST:     GGACTACTTAGAGCTGACCTTTCCAAGGGAATAACGGACGAAAAAGCAAG                         ATTCCCAAAACTTTTGGTCGATGGACCGTATGGTGCACCGGCACAAGATTA
genomic: GGACTACTTAGAGCTGACCTTTCCAAGGGAATAACGGACGAAAAAGCAAGgtgcaaagga ... catgcactagATTCCCAAAACTTTTGGTCGATGGACCGTATGGTGCACCGGCACAAGATTA
EST: gi|58670791|gb|CK059477.1|CK059477
EST:     GGACTACTTAGAGCTGACCTTTCCAAGGGAATAACGGACGAAAACGCAAG                         ATTCCCAAAACTTTTGGTCGATGGACCGTATGGTGCACCGGCACAAGATTA
genomic: GGACTACTTAGAGCTGACCTTTCCAAGGGAATAACGGACGAAAAAGCAAGgtgcaaagga ... catgcactagATTCCCAAAACTTTTGGTCGATGGACCGTATGGTGCACCGGCACAAGATTA
EST: gi|27554471|gb|CA998371.1|CA998371
EST:     GGACTACTTAGAGCTGACCTTTCCAAGGGAATAACGGACGAAAACGCAAG                         ATTCCCAAAACTTTTGGTCGATGGACCGTATGGTGCACCGGCACAAGATTA
genomic: GGACTACTTAGAGCTGACCTTTCCAAGGGAATAACGGACGAAAAAGCAAGgtgcaaagga ... catgcactagATTCCCAAAACTTTTGGTCGATGGACCGTATGGTGCACCGGCACAAGATTA
EST: gi|163925582|gb|EG715403.1|EG715403
EST:     GGACTACTTAGAGCTGACCTTTCCAAGGGAATAACGTACGAAAAAGCAAG                         ATTCCCAAAACTTTTGGTCGATGGACCGTATGGTGCACCGGCACAAGATTA
genomic: GGACTACTTAGAGCTGACCTTTCCAAGGGAATAACGGACGAAAAAGCAAGgtgcaaagga ... catgcactagATTCCCAAAACTTTTGGTCGATGGACCGTATGGTGCACCGGCACAAGATTA
EST: gi|3763131|gb|AU029883.1|AU029883
EST:     GGACGAAAAAGCAAG                         ATTCCCAAAACTTTTGGTCGATGGACCGTATGGTGCACCGGCACAAGATTA
genomic: GGACGAAAAAGCAAGgtgcaaagga ... catgcactagATTCCCAAAACTTTTGGTCGATGGACCGTATGGTGCACCGGCACAAGATTA
EST: gi|27576530|gb|CA999224.1|CA999224
EST:     GGACTACTTAGAGCTGACCTTTCCAAGGGAATAACGGACGAAAACGCAAG                         ATTCCCAAAACTTTTGGTCGATGGACCGTATGGTGCACCGGCACAAGATTA
genomic: GGACTACTTAGAGCTGACCTTTCCAAGGGAATAACGGACGAAAAAGCAAGgtgcaaagga ... catgcactagATTCCCAAAACTTTTGGTCGATGGACCGTATGGTGCACCGGCACAAGATTA

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), 75 (downstream exon)
Score: 31

GCATGCCGACCCCCCACTGAGGGAGAAAGTGGACTACTTAGAGCTGACCTTTCCAAGGGAATAACGGACGAAAAAGCAAGgtgcaaagga ... catgcactagATTCCCAAAACTTTTGGTCGATGGACCGTATGGTGCACCGGCACAAGATTACCGTGAATACGATGTGCTACTTCTCATCGGGCTGGGCATCGGAGCCACC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgttatctaaagaaaaatcttccgtctaacgataattctgctttacatgcactagATTCCCAAAACTTTTGGTCGATGGACCGTATGGTGCACCGGCACAAGATTACCGTGAATACGATGTGCTACTTCTCATCGGGCTGGGCATCGGAGCCACC
                       gtctaac  putative branch site (score: 31)
       taaagaaaaatctt  TA-rich tract