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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttccatcagttaacgttgaagctttaagctacttagtcatctagtaatatatcttaccctgcagGTAGGGAAGGCATGTGGCGAGAAATGGAATACAATGACATTTGAG

Basic information

species Oryza sativa
transcript LOC_Os01g47600.1
intron # 2
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|87027058|gb|CI261505.1|CI261505
EST:     TTCGGAAAACTTACAAGGAAGAAAATCCAAGTGTAAAATCAATGCAAGAA                         GTAGGGAAGGCATGTGGCGAGAAATGGAATACAATGACATTTGAG
genomic: TTCGGAAAACTTACAAGGAAGAAAATCCAAGTGTAAAATCAATGCAAGAAgtaagtttcc ... taccctgcagGTAGGGAAGGCATGTGGCGAGAAATGGAATACAATGACATTTGAG
EST: gi|86532522|gb|CI172728.1|CI172728
EST:     TTCGGAAAACTTACAAGGAAGAAAATCCAAGTGTAAAATCAATGCAAGAA                         GTAGGGAAGGCATGTGGCGAGAAATGGAATACAATGACATTTGAG
genomic: TTCGGAAAACTTACAAGGAAGAAAATCCAAGTGTAAAATCAATGCAAGAAgtaagtttcc ... taccctgcagGTAGGGAAGGCATGTGGCGAGAAATGGAATACAATGACATTTGAG
EST: gi|86526333|gb|CI166539.1|CI166539
EST:     TTCGGAAAACTTACAAGGAAGAAAATCCAAGTGTAAAATCAATGCAAGAA                         GTAGGGAAGGCATGTGGCGAGAAATGGAATACAATGACATTTGAG
genomic: TTCGGAAAACTTACAAGGAAGAAAATCCAAGTGTAAAATCAATGCAAGAAgtaagtttcc ... taccctgcagGTAGGGAAGGCATGTGGCGAGAAATGGAATACAATGACATTTGAG
EST: gi|88513571|gb|CI441077.1|CI441077
EST:     ATCAATGCAAGAA                         GTAGGGAAGGCATGTGGCGAGAAATGGAATACAATGACATTTGAG
genomic: ATCAATGCAAGAAgtaagtttcc ... taccctgcagGTAGGGAAGGCATGTGGCGAGAAATGGAATACAATGACATTTGAG
EST: gi|88956119|gb|CI092407.1|CI092407
EST:     TTCGGAAAACTTACAAGGAAGAAAATCCAAGTGTAAAATCAATGCAAGAA                         GTAGGGAAGGCATGTGGCGAGAAATGGAATACAATGACATTTGAG
genomic: TTCGGAAAACTTACAAGGAAGAAAATCCAAGTGTAAAATCAATGCAAGAAgtaagtttcc ... taccctgcagGTAGGGAAGGCATGTGGCGAGAAATGGAATACAATGACATTTGAG
EST: gi|88519234|gb|CI446888.1|CI446888
EST:     CAAGGAAGAAAATCCAAGTGTAAAATCAATGCAAGAA                         GTAGGGAAGGCATGTGGCGAGAAATGGAATACAATGACATTTGAG
genomic: CAAGGAAGAAAATCCAAGTGTAAAATCAATGCAAGAAgtaagtttcc ... taccctgcagGTAGGGAAGGCATGTGGCGAGAAATGGAATACAATGACATTTGAG
EST: gi|87010545|gb|CI283620.1|CI283620
EST:     TTCGGAAAACTTACAAGGAAGAAAATCCAAGTGTAAAATCAATGCAAGAA                         GTAGGGAAGGCATGTGGCGAGAAATGGAATACAATGACATTTGAG
genomic: TTCGGAAAACTTACAAGGAAGAAAATCCAAGTGTAAAATCAATGCAAGAAgtaagtttcc ... taccctgcagGTAGGGAAGGCATGTGGCGAGAAATGGAATACAATGACATTTGAG

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: 58 (upstream exon), 45 (downstream exon)
Score: 16

GGAGGATTTTCGGAAAACTTACAAGGAAGAAAATCCAAGTGTAAAATCAATGCAAGAAgtaagtttcc ... taccctgcagGTAGGGAAGGCATGTGGCGAGAAATGGAATACAATGACATTTGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaacgttgaagctttaagctacttagtcatctagtaatatatcttaccctgcagGTAGGGAAGGCATGTGGCGAGAAATGGAATACAATGACATTTGAG
                                         atcttac  putative branch site (score: 16)
                                          tcttaccct  CT-rich tract
                                tagtaatatatctta  TA-rich tract