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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_Os03g24220.1
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


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttttttttttcttgcctattcaaatttgttaggatctaaatttgcctttgtagGAATTCATTGCTACTCAAAATAGGCCAAAGACAACAAGAGTAACCCGAGTGATTCAAGGGTACGAGAATCATACATTCAAGTCTAAGTTTGAATCATGGC
                                   atctaaa  putative branch site (score: 3)
                                          tttgccttt  CT-rich tract
                  tattcaaatttgtta  TA-rich tract