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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcataattgagatatttgatactagatatattgtaaacggcaaagtagcataatgctttgttgatggattaaggtctccatcacatataaaaccttggccaattgaacagGTTGGATTGCTAAATGTTGACGGTTACTACGATCCACTGCTCGCGTTGTTCGACAAAGGCGAGGCGGAGGGCTTCATCAACTCTGATTGTAGACAAATAT

Basic information

species Oryza sativa
transcript LOC_Os05g46360.1
intron # 5
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|86435016|gb|CI106249.1|CI106249
EST:     TTAGAGATGATAACATGGTGCCAACTTGGAATTCATGACAAGCCA                         GTTGGATTGCTAAATGTTGACGGTTACTACGATCCACTGCTCGCGTTGTTC
genomic: TTAGAGATGATAACATGGTGCCAACTTGGAATTCATGACAAGCCAgtaagcataa ... aattgaacagGTTGGATTGCTAAATGTTGACGGTTACTACGATCCACTGCTCGCGTTGTTC
EST: gi|38468858|gb|CF952989.1|CF952989
EST:     AGCTGTTAGAGATGATAACATGGTGCCAACTTGGAATTCATGACAAGCCA                         GTTGGATTGCTAAATGTTGACGGTTACTACGATCCACTGCTCGCGTTGTTC
genomic: AGCTGTTAGAGATGATAACATGGTGCCAACTTGGAATTCATGACAAGCCAgtaagcataa ... aattgaacagGTTGGATTGCTAAATGTTGACGGTTACTACGATCCACTGCTCGCGTTGTTC
EST: gi|88515323|gb|CI442977.1|CI442977
EST:     AGCTGTTAGAGATGATAACATGGTGCCAACTTGGAATTCATGACAAGCCA                         GTTGGATTGCTAAATGTTGACGGTTACTACGATCCACTGCTCGCGTTGTTC
genomic: AGCTGTTAGAGATGATAACATGGTGCCAACTTGGAATTCATGACAAGCCAgtaagcataa ... aattgaacagGTTGGATTGCTAAATGTTGACGGTTACTACGATCCACTGCTCGCGTTGTTC
EST: gi|86866134|gb|CI336840.1|CI336840
EST:     AGCTGTTAGAGATGATAACAT-GTGCCAACTTGGAATTCAT-ACAAGCCA                         GTTGGATTGCTAAATGTTGACGGTTAGTACGATCCACTGCTCGCGTTGTTC
genomic: AGCTGTTAGAGATGATAACATGGTGCCAACTTGGAATTCATGACAAGCCAgtaagcataa ... aattgaacagGTTGGATTGCTAAATGTTGACGGTTACTACGATCCACTGCTCGCGTTGTTC
EST: gi|58592728|gb|CF991036.1|CF991036
EST:     AGCTGTTAGAGATGATAACATGGTGCCAACTTGGAATTCATGACAAGCCA                         GTTGGATTGCTAAATG
genomic: AGCTGTTAGAGATGATAACATGGTGCCAACTTGGAATTCATGACAAGCCAgtaagcataa ... aattgaacagGTTGGATTGCTAAATG

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: 71 (upstream exon), 75 (downstream exon)
Score: 17

GGGGCTATGGAACAATGGAGGAGCTGTTAGAGATGATAACATGGTGCCAACTTGGAATTCATGACAAGCCAgtaagcataa ... aattgaacagGTTGGATTGCTAAATGTTGACGGTTACTACGATCCACTGCTCGCGTTGTTCGACAAAGGCGAGGCGGAGGGCTTCATCAACTCTGATTGTAGACAAATAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttgttgatggattaaggtctccatcacatataaaaccttggccaattgaacagGTTGGATTGCTAAATGTTGACGGTTACTACGATCCACTGCTCGCGTTGTTCGACAAAGGCGAGGCGGAGGGCTTCATCAACTCTGATTGTAGACAAATAT
   tgttgat  putative branch site (score: 17)
                           acatataaaa  TA-rich tract