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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggcacttctcttcttacagcgtgcagtctcacacttacataaaactcaatgatcactaatgttgttgcacttctgccagGAATTTACCCACCTTTTCACCCAATGATTGGATTACAGTTCTATACTTGCGGAAAGCTTGAATG

Basic information

species Oryza sativa
transcript LOC_Os03g49730.2
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g49730.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G457881_T03 (Zea mays), 3'ss of exon 12
---------gtaaggcacttctct---tcttacagcgtgcagtctcacacttac-----ataaaactcaatgatcactaatgttgttgcacttctgccagGAATTTACCCACCTTTTCACCCAATGATTGGATTACAGTTCTATACTTGCGGAAAGCTTGAATG------------------------------------
         ||| ||| ||  | |   || |      | ||  ||     ||||     | ||| ||||||| ||||||||||| ||     ||    |||| |||| ||||||||||| || |||||||||||||| ||||||||||| ||||||||||||||                                    
tcacatttggtagggctctgttttagatcctgtttttttcacactttttgttacttccaacaaagctcaatgctcactaatgtttttatctatccattagGAGTTTATCCACCTTTTCATCCGATGATTGGATTACAATTCTATACTTGTGGAAAGCTTGAATGGTATGGACTATTAGCCCTTACCTATTTACCTCACAC

upper sequence: LOC_Os03g49730.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G457881_T01 (Zea mays), 3'ss of exon 14
---------gtaaggcacttctct---tcttacagcgtgcagtctcacacttac-----ataaaactcaatgatcactaatgttgttgcacttctgccagGAATTTACCCACCTTTTCACCCAATGATTGGATTACAGTTCTATACTTGCGGAAAGCTTGAATG
         ||| ||| ||  | |   || |      | ||  ||     ||||     | ||| ||||||| ||||||||||| ||     ||    |||| |||| ||||||||||| || |||||||||||||| ||||||||||| ||||||||||||||
tcacatttggtagggctctgttttagatcctgtttttttcacactttttgttacttccaacaaagctcaatgctcactaatgtttttatctatccattagGAGTTTATCCACCTTTTCATCCGATGATTGGATTACAATTCTATACTTGTGGAAAGCTTGAATG
















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|87029842|gb|CI274523.1|CI274523
EST:     TTGGCAGACTGCATTGATGTATTGCAGATTGACAATTCCAGTTTATGAAA                         GAATTTACCCACCTTTTCACCCAATGATTGGATTACAGTTCTATACTTGCG
genomic: TTGGCAGACTGCATTGATGTATTGCAGATTGACAATTCCAGTTTATGAAAgtaaggcact ... cttctgccagGAATTTACCCACCTTTTCACCCAATGATTGGATTACAGTTCTATACTTGCG
EST: gi|58684796|gb|CK073483.1|CK073483
EST:     TTGGCAGACTGCATTGATGTATTGCAGATTGACAATTCCAGTTTATGAAA                         GAATTTACCCACCTTTTCACCCAATGATTGGATTACAGTTCTATACTTGCG
genomic: TTGGCAGACTGCATTGATGTATTGCAGATTGACAATTCCAGTTTATGAAAgtaaggcact ... cttctgccagGAATTTACCCACCTTTTCACCCAATGATTGGATTACAGTTCTATACTTGCG
EST: gi|86426152|gb|CI071249.1|CI071249
EST:     CAGTTTATGAAA                         GAATTTACCCACCTTTTCACCCAATGATTGGATTACAGTTCTATACTTGCG
genomic: CAGTTTATGAAAgtaaggcact ... cttctgccagGAATTTACCCACCTTTTCACCCAATGATTGGATTACAGTTCTATACTTGCG
EST: gi|88908158|gb|CI090754.1|CI090754
EST:     TGGCAGACTGCATTGATGTATTGCAGATTGACAATTCCAGTTTATGAAA                         GAATTTACCCACCTTTTCACCCAATGATTGGATTACAGTTCTATACTTGCG
genomic: TGGCAGACTGCATTGATGTATTGCAGATTGACAATTCCAGTTTATGAAAgtaaggcact ... cttctgccagGAATTTACCCACCTTTTCACCCAATGATTGGATTACAGTTCTATACTTGCG
EST: gi|87029746|gb|CI274427.1|CI274427
EST:     TTGGCAGACTGCATTGATGTATTGCAGATTGACAATTCCAGTTTATGAAA                         GAATTTACCCACCTTTTCACCCAATGATTGGATTACAGTTCTATACTTGCG
genomic: TTGGCAGACTGCATTGATGTATTGCAGATTGACAATTCCAGTTTATGAAAgtaaggcact ... cttctgccagGAATTTACCCACCTTTTCACCCAATGATTGGATTACAGTTCTATACTTGCG
EST: gi|86259978|gb|CI065851.1|CI065851
EST:     AATTCCAGTTTATGAAA                         GAATTTACCCACCTTTTCACCCAATGATTGGATTACAGTTCTATACTTGCG
genomic: AATTCCAGTTTATGAAAgtaaggcact ... cttctgccagGAATTTACCCACCTTTTCACCCAATGATTGGATTACAGTTCTATACTTGCG
EST: gi|7332557|gb|AU085903.1|AU085903
EST:     TTGGCAGACTGCATTGATGTATTGCAGATTGACAATTCCAGTTTATGAAA                         GAATTTACCCACCTTTTCACCCAATGATTGGATTACAGTTCTATACTTGCG
genomic: TTGGCAGACTGCATTGATGTATTGCAGATTGACAATTCCAGTTTATGAAAgtaaggcact ... cttctgccagGAATTTACCCACCTTTTCACCCAATGATTGGATTACAGTTCTATACTTGCG

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: 43 (upstream exon), 72 (downstream exon)
Score: 8

ATATATATGGAGTTACAAGATTGGCAGACTGCATTGATGTATTGCAGATTGACAATTCCAGTTTATGAAAgtaaggcact ... cttctgccagGAATTTACCCACCTTTTCACCCAATGATTGGATTACAGTTCTATACTTGCGGAAAGCTTGAATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtctcacacttacataaaactcaatgatcactaatgttgttgcacttctgccagGAATTTACCCACCTTTTCACCCAATGATTGGATTACAGTTCTATACTTGCGGAAAGCTTGAATG
                             cactaat  putative branch site (score: 8)
                                             cttctgcc  putative PPT
          ttacataaaa  TA-rich tract