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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttatcctttgcactttgatacacatagtaacatcaagctctgtggactgtacttacaacaaataggttggattttgatatttttatttcgctggttacctttagactctggcattgacatactgttcctcctttttttttgtatgttcaaatgttgtagTTGGTGTTCTCATCATCAGCTGCAGTTTATGGATCACCGAAGAACTCACCCTGCACAGAAGAGTTTCCTCTCACTCCAAACAATCCATATGGCAAAACAA

Basic information

species Oryza sativa
transcript LOC_Os08g28730.1
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|58661081|gb|CK049761.1|CK049761
EST:     ATGGAACAGTAAATCTTCTGGAAGTTATGTCTGCCCATGGATGTAAGAAG                         TTGGTGTTCTCATCATCAGCTGCAGTTTATGGATCACCGAAGAACTCACCC
genomic: ATGGAACAGTAAATCTTCTGGAAGTTATGTCTGCCCATGGATGTAAGAAGgtatttatcc ... aatgttgtagTTGGTGTTCTCATCATCAGCTGCAGTTTATGGATCACCGAAGAACTCACCC
EST: gi|163928869|gb|EG709747.1|EG709747
EST:     ATGGAACAGTAAATCTTCTGGAAGTTATGTCTGCCCATGGATGTAAGAAG                         TTGGTGTTCTCATCATCAGCTGCAGTTTATGGATCACCGAAGAACTCACCC
genomic: ATGGAACAGTAAATCTTCTGGAAGTTATGTCTGCCCATGGATGTAAGAAGgtatttatcc ... aatgttgtagTTGGTGTTCTCATCATCAGCTGCAGTTTATGGATCACCGAAGAACTCACCC
EST: gi|58662148|gb|CK050828.1|CK050828
EST:     ATGGAACAGTAAATCTTCTGGAAGTTATGTCTGCCCATGGATGTAAGAAG                         TTGGTGTTCTCATCATCAGCTGCAGTTTATGGATCACCGAAGAACTCACCC
genomic: ATGGAACAGTAAATCTTCTGGAAGTTATGTCTGCCCATGGATGTAAGAAGgtatttatcc ... aatgttgtagTTGGTGTTCTCATCATCAGCTGCAGTTTATGGATCACCGAAGAACTCACCC

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: 73 (upstream exon), 72 (downstream exon)
Score: 37

TGTGGGCGAAAGTGTGCAGAAGCCATTGCTTTATTACGACAACAATGTTAATGGAACAGTAAATCTTCTGGAAGTTATGTCTGCCCATGGATGTAAGAAGgtatttatcc ... aatgttgtagTTGGTGTTCTCATCATCAGCTGCAGTTTATGGATCACCGAAGAACTCACCCTGCACAGAAGAGTTTCCTCTCACTCCAAACAATCCATATGGCAAAACAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actctggcattgacatactgttcctcctttttttttgtatgttcaaatgttgtagTTGGTGTTCTCATCATCAGCTGCAGTTTATGGATCACCGAAGAACTCACCCTGCACAGAAGAGTTTCCTCTCACTCCAAACAATCCATATGGCAAAACAA
       cattgac  putative branch site (score: 37)
                           tttttttttgtatgtt  TA-rich tract