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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtctcaagccattgttttcttcttttttttttcttgcctattcaaatttgttaggatctaaatttgcctttgtagGAATTCATTGCTACTCAAAATAGGCCAAAGACAACAAGAGTAACCCGAGTGATTCAAGGGTACGAGAATCATACATTCAAGTCTAAGTTTGAATCATGGC

Basic information

species Oryza sativa
transcript LOC_Os03g24220.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g24220.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G323479_T01 (Zea mays), 3'ss of exon 13
gtaagtctcaagccattgttttcttcttttttttttcttgcctattcaaatttgttaggatctaaatttgcctttgtagGAATTCATTGCTACTCAAAATAGGCCAAAGACAACAAGAGTAACCCGAGTGATTCAAGGGTACGAGAATCATACATTCAAGTCTAAGTTTGAATCATGGC
||||  ||  | ||   ||||  | |||| ||  ||  |  | |  || || | |||   |  || ||  |   ||||| ||||||||  ||   ||||||| ||||||||||||||| |||| | |||||||||||| |  |||||||| |||||||||||||||||||| |||||||
gtaaacctacatcccaagtttattgctttcttgctttgt-tcaaaacatatatcttatc-taaaagttacctcctgtagAAATTCATTATTAAAGAAAATAGACCAAAGACAACAAGAATAACTCAAGTGATTCAAGGTTTTGAGAATCACACATTCAAGTCTAAGTTTGAGTCATGGC

upper sequence: LOC_Os03g24220.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G081322_T01 (Zea mays), 3'ss of exon 8
gtaagtctcaagccattgttttcttcttttttttttcttgcctattcaaatttgttaggatctaaatttgcctttgtagGAATTCATTGCTACTCAAAATAGGCCAAAGACAACAAGAGTAACCCGAGTGATTCAAGGGTACGAGAATCATACATTCAAGTCTAAGTTTGAATCATGGC
||||  |   ||||    |||  | |||| ||   |  | |  | |  ||  | |    |    | ||  |   ||||| ||| ||||  ||   ||||||| ||||||||||||||| |||| | |||||| ||||| |||||||||||||| ||||||||||||||||| |||||||
gtaaacccatagcccaattttattgctttcttgccttgttcacaatataacctatctaaa----agttacctcctgtagAAATACATTATTAAAGAAAATAGACCAAAGACAACAAGAATAACTCAAGTGATCCAAGGTTACGAGAATCATACGTTCAAGTCTAAGTTTGAGTCATGGC

upper sequence: LOC_Os03g24220.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv08s0007g08690.t01 (Vitis vinifera), 3'ss of exon 7
gtaagtctcaagccattgttttcttcttttttttttcttgcctattcaaatttgttaggatcta-aatttgcctttgtagGAATTCATTGCTACTCAAAATAGGCCAAAGACAACAAGAGTAACCCGAGTGATTCAAGGGTACGAGAATCATACATTCAAGTCTAAGTTTGAATCATGGC
         |     || |  ||   || |   | |  |   |||   ||     |   ||||  ||||| | |    |||||||  || |||  |||||||| |||||| ||||  | |||||||| || ||||||||||| ||||  ||| |||||||||| || ||||| || ||||
-------gtagaagcttatcatccatttatccatgttctttatataacaacgaactctcatctccaattttcttcctcagGAATTTGTTTCTAGCCAAAATAGACCAAAGGCAACTCGTGTAACCCGGGTTATTCAAGGGTATGAGACACATTCATTCAAGTCCAACTTTGATTCTTGGC

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|58668298|gb|CK056984.1|CK056984
EST:     GTCGACTAACACAAGTGGAGGAGAGAAAAGCTGCAAGTGCAGCAGTTGAG                         GAATTCATTGCTACTCAAAATAGGCCAAAGACAACAAGAGTAACCCGAGTG
genomic: GTCGACTAACACAAGTGGAGGAGAGAAAAGCTGCAAGTGCAGCAGTTGAGgtaagtctca ... gcctttgtagGAATTCATTGCTACTCAAAATAGGCCAAAGACAACAAGAGTAACCCGAGTG
EST: gi|11442605|gb|BF430508.1|BF430508
EST:     GTCGACTAACACAAGTGGAGGAGAGAAAAGCTGCAAGTGCAGCAGTTGAG                         GAATTCATTGCTACTCAAAATA
genomic: GTCGACTAACACAAGTGGAGGAGAGAAAAGCTGCAAGTGCAGCAGTTGAGgtaagtctca ... gcctttgtagGAATTCATTGCTACTCAAAATA
EST: gi|58670145|gb|CK058831.1|CK058831
EST:     GTCGACTAACACAAGTGGAGGAGAGAAAAGCTGCAAGTGCAGCAGTTGAG                         GAATTCATTGCTACTCAAAATAGGCCAAAGACAACAAGAGTAACCCGAGTG
genomic: GTCGACTAACACAAGTGGAGGAGAGAAAAGCTGCAAGTGCAGCAGTTGAGgtaagtctca ... gcctttgtagGAATTCATTGCTACTCAAAATAGGCCAAAGACAACAAGAGTAACCCGAGTG

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: 65 (upstream exon), 70 (downstream exon)
Score: 89

CAATAAGTGCTTTTTGGTCGACTGTGGGTCTGATTTATTTATATGGGTTGGTCGACTAACACAAGTGGAGGAGAGAAAAGCTGCAAGTGCAGCAGTTGAGgtaagtctca ... gcctttgtagGAATTCATTGCTACTCAAAATAGGCCAAAGACAACAAGAGTAACCCGAGTGATTCAAGGGTACGAGAATCATACATTCAAGTCTAAGTTTGAATCATGGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttttttttttcttgcctattcaaatttgttaggatctaaatttgcctttgtagGAATTCATTGCTACTCAAAATAGGCCAAAGACAACAAGAGTAACCCGAGTGATTCAAGGGTACGAGAATCATACATTCAAGTCTAAGTTTGAATCATGGC
                                   atctaaa  putative branch site (score: 89)
                                          tttgccttt  CT-rich tract
                  tattcaaatttgtta  TA-rich tract