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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggggcctctggaaaaaggagtatttttgtccaattcctcaaacaaataatattccaaattatgaccaggtggtgtttctatacacctagagaaggattacatattaatttatcctcgcagGTCGCATATCCTTACTGCTCTGCATGTTTTGGCCGATGCTACCCCAATGGAGCAATATTGATCACAGAGCGACGAAGCACATTCGACGCAGTCAGCCAGC

Basic information

species Oryza sativa
transcript LOC_Os12g35290.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g35290.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G006781_T02 (Zea mays), 3'ss of exon 10
------------------------------------------------------------gtaaggggcctctggaaaaagg---agtatttttgtccaattcctcaaacaaataatattccaaattatgaccaggtggtgtttctatacacctagagaaggattacatattaatttatcctcgcagGTCGCATATCCTTACTGCTCTGCATGTTTTGGCCGATGCTACCCCAATGGAGCAATATTGATCACAGAGCGACGAAGCACATTCGACGCAGTCAGCCAGC
                                                             ||     |   || ||  |     | |   |  |||  |  | | || |     | |||  |||| |  |  |     | | ||| || || ||| ||  | | |||| ||  |||  | |  ||||| ||||||||||| ||  | ||||||||||||||||||||||| || || |||| ||||||| ||||||| | | ||||||| ||||| ||| | ||||
gtttgtttagttttccatgatagaccagtggttttgaatctgataagagaacataacttgctacaacacacatgaaatgaaaccaaatgactcagtcttacccgtaaagc---ctaaattgtaaataaacagtaaacatt-tgtctttagacgtagggagagttcacatcttggttttccatatcagGTTGCATATCCTTATTGTGCCGCATGTTTTGGCCGATGCTACCCAAACGGGGCAACATTGATCTCAGAGCGTCAAGGCACATTTGACGCTGTCCGTCAGC

upper sequence: LOC_Os12g35290.1 (Oryza sativa), 3'ss of exon 11
lower sequence: AC235544.1_FGT004 (Zea mays), 3'ss of exon 11
---------------------------------------------------gtaaggggcctctggaaaaa-ggagtatttttgtccaattcctcaa-acaaataatattccaaattatgaccaggtggtgtttctatacacctagagaaggattacatattaatttatcctcgcagGTCGCATATCCTTACTGCTCTGCATGTTTTGGCCGATGCTACCCCAATGGAGCAATATTGATCACAGAGCGACGAAGCACATTCGACGCAGTCAGCCAGC
                                                    |||   ||  |   | | | | | |     ||    | || ||   ||| |||| |  | ||| | | | ||     | | ||| || |  ||| ||  | | |||| ||  |||  | |  ||||| | | ||||||| ||  | ||||||||||| ||||||||||| ||||| |||| ||||||| ||||| | | | ||||| | ||||| ||| | ||||
gtttgtttagttttccatgatagaccagtggttttcagtctacaagcgaacataacttgctacaacacacatgaaatgaaactgaatgactcatccttacacataa-agcctaaactgtaaaca-----tttatctttagaggtagggagagttcacatcttggttttccataccagGTTGTACATCCTTATTGTGCCGCATGTTTTGGTCGATGCTACCCGAATGGGGCAACATTGATCTCAGAGTGTCAAGGCACACTGGACGCTGTCCGTCAGC
















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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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caggtggtgtttctatacacctagagaaggattacatattaatttatcctcgcagGTCGCATATCCTTACTGCTCTGCATGTTTTGGCCGATGCTACCCCAATGGAGCAATATTGATCACAGAGCGACGAAGCACATTCGACGCAGTCAGCCAGC
                                    tattaat  putative branch site (score: 10)
                                          tttatcctc  CT-rich tract
                          aaggattacatattaa  TA-rich tract