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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcctgtgtgacatctatttttcactaggaaataccttaaagctgcacaaatgtcttatgcttttaatttgtttttctctgttatgtccattttaaatttgtcattatgtggtgcagcttttgtgaattctaacatctggatttgtaaacttaacaagtactagATATACCACGGCCATTGATATGTGGTCATTTGGCTGTATAGTCGCTGAACTATATATAGGATTGCCTTTATTTCCTGGAGCGTCAGAATACGATGTCCTA

Basic information

species Oryza sativa
transcript LOC_Os02g47410.3
intron # 8
splice site 3'
intron type U12 (go to U12 genes for details)

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|58607868|gb|CK035901.1|CK035901
EST:     AGTGGGTATTACAGATCTCCGGAAGTACTTCTTGGTTACCC                         ATATACCACGGCCATTGATATGTGGTCATTTGGCTGTATAGTCGCTGAACT
genomic: AGTCGGTATTACAGATCTCCGGAAGTACTTCTTGGTTACCCgtatcctgtg ... caagtactagATATACCACGGCCATTGATATGTGGTCATTTGGCTGTATAGTCGCTGAACT
EST: gi|29638402|gb|CB643411.1|CB643411
EST:     AGTCGGTATTACAGATCTCCGGAAGTACTTCTTGGTTACCC                         ATATACCACGGCCATTGATATGTGGTCATTTGGCTGTATAGTCGCTGAACT
genomic: AGTCGGTATTACAGATCTCCGGAAGTACTTCTTGGTTACCCgtatcctgtg ... caagtactagATATACCACGGCCATTGATATGTGGTCATTTGGCTGTATAGTCGCTGAACT
EST: gi|58658947|gb|CK047627.1|CK047627
EST:     ATTACAGATCTCCGGAAGTACTTCTTGGTTACCC                         ATATACCACGGCCATTGATATGTGGTCATTTGGCTGTATAGTCGCTGAACT
genomic: ATTACAGATCTCCGGAAGTACTTCTTGGTTACCCgtatcctgtg ... caagtactagATATACCACGGCCATTGATATGTGGTCATTTGGCTGTATAGTCGCTGAACT
EST: gi|58673354|gb|CK062040.1|CK062040
EST:     AGTCGGTATTACAGATCTCCGGAAGTACTTCTTGGTTACCC                         ATATAACACGGCCATTGATATGTGGTCATTTGGCTGTATAGTCGCTGAACT
genomic: AGTCGGTATTACAGATCTCCGGAAGTACTTCTTGGTTACCCgtatcctgtg ... caagtactagATATACCACGGCCATTGATATGTGGTCATTTGGCTGTATAGTCGCTGAACT
EST: gi|58610888|gb|CK038600.1|CK038600
EST:     AGTCGGTATTACAGATCTCCGGAAGTACTTCTTGGTTACCC                         ATATACCACGGCCATTGATATGTGGTCATTTGGCTGTATAGTCGCTGAACT
genomic: AGTCGGTATTACAGATCTCCGGAAGTACTTCTTGGTTACCCgtatcctgtg ... caagtactagATATACCACGGCCATTGATATGTGGTCATTTGGCTGTATAGTCGCTGAACT

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: 67 (upstream exon), 75 (downstream exon)
Score: 40

AGTCGGTATTACAGATCTCCGGAAGTACTTCTTGGTTACCCgtatcctgtg ... caagtactagATATACCACGGCCATTGATATGTGGTCATTTGGCTGTATAGTCGCTGAACTATATATAGGATTGCCTTTATTTCCTGGAGCGTCAGAATACGATGTCCTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtgcagcttttgtgaattctaacatctggatttgtaaacttaacaagtactagATATACCACGGCCATTGATATGTGGTCATTTGGCTGTATAGTCGCTGAACTATATATAGGATTGCCTTTATTTCCTGGAGCGTCAGAATACGATGTCCTA
 aaacttaac  putative branch site 
                               atttgtaaacttaa  TA-rich tract