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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgcctcaagaaataaactgatctcccttgtgaagtttaatgttgcatttataatgaccacctgaattttaactataatggtagtccttgatcaatgttgtgacattgcaataactgaatgtttcagATGGATACTTTGCTTTCCCCAAGCTCCAAGAGCTATTACGCCTGTGTAGGGGAGAGTACTCATGCATTTCAGAGCCCCTCCAAGGACCTTAAGGTTATAA

Basic information

species Oryza sativa
transcript LOC_Os08g42600.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g42600.2 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G033828_T02 (Zea mays), 3'ss of exon 17
gtacgcctcaagaaataaactgatctcccttgtgaagtttaatgttgcatttataatgaccacctgaatt--ttaactataatgg-tagtccttgatcaa-tgt-tgtgacat-tgcaataactgaatgtttcagATGGATACTTTGCTTTCCCCAAGCTCCAAGAGCTATTACGCCTGTGTAGGGGAGAGTACTCATGCATTTCAGAGCCCCTCCAAGGACCTTAAGGTTATAA
            || |||| |      |  | |    |  | |||||   ||  |     ||||||| |    ||  | |  |||  | ||||| ||||| ||  |||||||      |||||||||   | |||||||| ||| | || ||||| |||||||||||||| ||||| || || || ||||| ||  | || || |||||||||||||||||||| |||| ||| |
----------gtaagtaaaatagctgtcaattttttttgcagtgttgtggtttcaggtttcacctgactgagctattttttttgggcaatccttcatcaaatgcctgtgacaaactttataactgaactctccagATGGACACTCTTCTGTCCCCGAGCTCCAAGAGCTACTACGCGTGCGTCGGCGAGAGCACCTACGCGTTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCA

upper sequence: LOC_Os08g42600.2 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G016997_T01 (Zea mays), 3'ss of exon 16
gtacgcctcaagaaataaactgatctcccttgtgaagtttaatgttgcatttataatgaccacctgaattttaactataatggtagtccttgatcaatgttgtgacattgcaataactgaatgtttcagATGGATACTTTGCTTTCCCCAAGCTCCAAGAGCTATTACGCCTGTGTAGGGGAGAGTACTCATGCATTTCAGAGCCCCTCCAAGGACCTTAAGGTTATAA
                                                     |||     ||||||   | || |||  |  || | ||  ||||||| ||||||| |    ||||    |  | |||||||||||||| || || |||||| | ||||||||||| || ||||| || ||||||||  |||| || || ||||||||||||||||| |||| ||| |
----------------------------------------------------gtaaga--tacctga--ctgaaatattttcataattctccatcaatgctgtgacaattttgtaac----tactccagATGGATACTTTACTCTCACCAAGCCCAAAGAGCTATTATGCATGTGTCGGCGAGAGTACCTATGCGTTCCAAAGCCCCTCCAAGGACCTGAAGGCTATCA
















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|58675166|gb|CK063853.1|CK063853
EST:     AAGTTTCTGCTGCTCATAACGTATATGTTTCACCCTTGCGCACATCAAAG                         ATGGATACTTTGCTTTCCCCAAGCTCCAAGAGCTATTACGCCTGTGTAGGG
genomic: AAGTTTCTGCTGCTCATAACGTATATGTTTCACCCTTGCGCACATCAAAGgtacgcctca ... aatgtttcagATGGATACTTTGCTTTCCCCAAGCTCCAAGAGCTATTACGCCTGTGTAGGG
EST: gi|58602114|gb|CK012642.1|CK012642
EST:     AAGTTTCTGCTGCTCATAACGTATATGTTTCACCCTTGCGCACATCAAAG                         ATGGATACTTTGCTTTCCCCAAGCTCCAAGAGCTATTACGCCTGTGTAGGG
genomic: AAGTTTCTGCTGCTCATAACGTATATGTTTCACCCTTGCGCACATCAAAGgtacgcctca ... aatgtttcagATGGATACTTTGCTTTCCCCAAGCTCCAAGAGCTATTACGCCTGTGTAGGG
EST: gi|218484308|gb|FG956791.1|FG956791
EST:     AAGTTTCTGCTGCTCATAACGTATATGTTTCACCCTTGCGCACATCAAAG                         ATGGATACTTTGCTTTCCCCAAGCTCCAAGAGCTATTACGCCTGTGTAGGG
genomic: AAGTTTCTGCTGCTCATAACGTATATGTTTCACCCTTGCGCACATCAAAGgtacgcctca ... aatgtttcagATGGATACTTTGCTTTCCCCAAGCTCCAAGAGCTATTACGCCTGTGTAGGG
EST: gi|33805335|gb|CF328545.1|CF328545
EST:     AAGTTTCTGCTGCTCATAACGTATATGTTTCACCCTTGCGCACATCAAAG                         ATGGATACTTTGCTTTCCCCAAGCTCCATGAGCTATTACGCCTGTGTAGGG
genomic: AAGTTTCTGCTGCTCATAACGTATATGTTTCACCCTTGCGCACATCAAAGgtacgcctca ... aatgtttcagATGGATACTTTGCTTTCCCCAAGCTCCAAGAGCTATTACGCCTGTGTAGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctataatggtagtccttgatcaatgttgtgacattgcaataactgaatgtttcagATGGATACTTTGCTTTCCCCAAGCTCCAAGAGCTATTACGCCTGTGTAGGGGAGAGTACTCATGCATTTCAGAGCCCCTCCAAGGACCTTAAGGTTATAA
                                    caataac  putative branch site (score: 2)
                                     aataact  TA-rich tract