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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACAAGCCGTTTCTGACTCCCTAGTCAGATACAATGCCATGCGGATGCTGCGTGGAAATGAGTCCTCTCTTTTCCTTTCACTTTGCCAGGCATTTATTGAGgtaaggggcctctggaaaaaggagtatttttgtccaattcctcaaacaaataatattccaaattatgaccaggtggtgtttctatacacctagagaaggattacatattaatttatcctcgcag

Basic information

species Oryza sativa
transcript LOC_Os12g35290.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g35290.1 (Oryza sativa), 5'ss of exon 11
lower sequence: AC235544.1_FGT004 (Zea mays), 5'ss of exon 11
ACAAGCCGTTTCTGACTCCCTAGTCAGATACAATGCCATGCGGATGCTGCGTGGAAATGAGTCCTCTCTTTTCCTTTCACTTTGCCAGGCATTTATTGAGgtaag---gggcctctg-gaaaaaggagtattttt--gtccaattcctcaaacaa------ataatattc-caaattatgaccaggtggtgtttctatacacctagagaaggattacatattaatttatcctcgcag-----------------------------------
||| || || |||||||||||||| |||||||| || ||||||||||| ||||||||||||||| |||||||||| ||||| |||||||||||||| |||||  |    |   ||   || | |  |||  ||||  ||| |    |  | | ||      | || |  |   || |   ||    ||     ||  ||||| || ||    |     ||   ||||||| |   ||                                   
ACATGCAGTCTCTGACTCCCTAGTAAGATACAAAGCTATGCGGATGCTTCGTGGAAATGAGTCCGCTCTTTTCCTGTCACTCTGCCAGGCATTTATCGAGgtttgtttagttttccatgatagaccagtggttttcagtctacaagcgaacataacttgctacaacacacatgaaatgaaactgaatgactcatccttacacataaagcctaaac-tgtaaacatttatctttagaggtagggagagttcacatcttggttttccataccag

upper sequence: LOC_Os12g35290.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G006781_T02 (Zea mays), 5'ss of exon 10
ACAAGCCGTTTCTGACTCCCTAGTCAGATACAATGCCATGCGGATGCTGCGTGGAAATGAGTCCTCTCTTTTCCTTTCACTTTGCCAGGCATTTATTGAGgtaag---gggcctctg-gaaaaaggagtatttttg--tccaat--------------tcctcaaacaaataatattccaaatta--tgaccaggtggtgtttctatacacctagagaaggattacatattaa---tttatcctcgcag-----------------------------------
||| || || |||||||||||||| |||||||| || ||||||||||| ||||||||||||||| | |||||||||||||| ||||||||||| || |||||  |    |   ||   || | |  |||  |||||  ||  ||              | ||  |||| | |  |    |||  |  ||||   ||  |     || |  |||| |     | || | | |||   ||| || |   |                                    
ACATGCAGTCTCTGACTCCCTAGTAAGATACAAAGCTATGCGGATGCTTCGTGGAAATGAGTCCGCCCTTTTCCTTTCACTATGCCAGGCATTCATCGAGgtttgtttagttttccatgatagaccagtggttttgaatctgataagagaacataacttgctacaacacacatgaaatgaaaccaaatgactcagtcttacccgta-aagcctaaattgtaaataaacagtaaacatttgtctttagacgtagggagagttcacatcttggttttccatatcag
















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|27576399|gb|CA999093.1|CA999093
EST:     GTGGAAATGAGTCCTCTCTTTTCCTTTCACTTTGCCAGGCATTTATTGAG                         GTCGCATATCCTTACTGCTCTGCATGTTTTGGCCGATGCTACCCCAATGGA
genomic: GTGGAAATGAGTCCTCTCTTTTCCTTTCACTTTGCCAGGCATTTATTGAGgtaaggggcc ... atcctcgcagGTCGCATATCCTTACTGCTCTGCATGTTTTGGCCGATGCTACCCCAATGGA
EST: gi|66917594|gb|CX104442.1|CX104442
EST:     GTGGAAATGAGTCCTCTCTTTTCCTTTCACTTTGCCAGGCATTTATTGAG                         GTCGCATATCCTTACTGCTCTGCATGTTTTGGCCGATGCTACCCCAATGGA
genomic: GTGGAAATGAGTCCTCTCTTTTCCTTTCACTTTGCCAGGCATTTATTGAGgtaaggggcc ... atcctcgcagGTCGCATATCCTTACTGCTCTGCATGTTTTGGCCGATGCTACCCCAATGGA
EST: gi|29660604|gb|CB656879.1|CB656879
EST:     GTGGAAATGAGTCCTCTCTTTTCCTTTCACTTTGCCAGGCATTTATTGAG                         GTCGCATATCCTTACTGCTCTGCATGTTTTGGCCGATGCTACCCCAATGGA
genomic: GTGGAAATGAGTCCTCTCTTTTCCTTTCACTTTGCCAGGCATTTATTGAGgtaaggggcc ... atcctcgcagGTCGCATATCCTTACTGCTCTGCATGTTTTGGCCGATGCTACCCCAATGGA
EST: gi|27577987|gb|CB000682.1|CB000682
EST:     GTGGAAATGAGTCCTCTCTTTTCCTTTCACTTTGCCAGGCATTTATTGAG                         GTCGCATATCCTTACTGCTCTGCATGTTTTGGCCGATGCTACCCCAATGGA
genomic: GTGGAAATGAGTCCTCTCTTTTCCTTTCACTTTGCCAGGCATTTATTGAGgtaaggggcc ... atcctcgcagGTCGCATATCCTTACTGCTCTGCATGTTTTGGCCGATGCTACCCCAATGGA
EST: gi|29660544|gb|CB656819.1|CB656819
EST:     GTGGAAATGAGTCCTCTCTTTTCCTTTCACTTTGCCAGGCATTTATTGAG                         GTCGCATATCCTTACTGCTCTGCATGTTTTGGCCGATGCTACCCCAATGGA
genomic: GTGGAAATGAGTCCTCTCTTTTCCTTTCACTTTGCCAGGCATTTATTGAGgtaaggggcc ... atcctcgcagGTCGCATATCCTTACTGCTCTGCATGTTTTGGCCGATGCTACCCCAATGGA
EST: gi|163928149|gb|EG714313.1|EG714313
EST:     GTGGAAATGAGTCCTCTCTTTTCCTTTCACTTTGCCAGGCGTTTATTGAG                         GTCGCATATCCTTACTGCTCTGCATGTTTTGGCCGATGCTACCCCAATGGA
genomic: GTGGAAATGAGTCCTCTCTTTTCCTTTCACTTTGCCAGGCATTTATTGAGgtaaggggcc ... atcctcgcagGTCGCATATCCTTACTGCTCTGCATGTTTTGGCCGATGCTACCCCAATGGA

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: 60 (upstream exon), 72 (downstream exon)
Score: 10

ACAAGCCGTTTCTGACTCCCTAGTCAGATACAATGCCATGCGGATGCTGCGTGGAAATGAGTCCTCTCTTTTCCTTTCACTTTGCCAGGCATTTATTGAGgtaaggggcc ... atcctcgcagGTCGCATATCCTTACTGCTCTGCATGTTTTGGCCGATGCTACCCCAATGGAGCAATATTGATCACAGAGCGACGAAGCACATTCGACGCAGTCAGCCAGC




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