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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atatcttcaatgtactgaatgtttttattttccttaccagaaaatgtttgaatttgccatgattcttctgtgattaacttcctcatattgtttgtattagCTATCTGCAATAACCACCATTGGATTTGTCAAAGGCGCCCCAGAAATTGATGTACAAGGCTTTAATGTGTACCACAAGAATCGTTTAATAGCG

Basic information

species Oryza sativa
transcript LOC_Os01g36840.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g36840.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G030596_T02 (Zea mays), 3'ss of exon 11
atatcttcaatgtactgaatgtttttattttccttaccagaaaatgtttgaatttgccatgattcttctgtgattaacttcctcatattgtttgtatt----agCTATCTGCAATAACCACCATTGGATTTGTCAAAGGCGCCCCAGAAATTGATGTACAAGGCTTTAATGTGTACCACAAGAATCGTTTAATAGCG
          ||||    |||||||  ||||  |||    |  |  |   |||||    |   |  | |  ||  | ||  || ||     |  | ||    ||  ||| | ||| || |||||||| ||||| ||||| || ||||| || ||||||||||| |||||||| || ||||| || ||| |||||  |
----tgcgggtgtagcctatgttttattttttattatactatcaaatcaaaattttgattttcttgttttagaaaatctctctgattggcctcatgttttgcagTCATCGGTAATCACAACCATTGGGTTTGTTAAAGGTGCACCAGATATAGATGTACAAGGGTTTAATGTATATCACAAAAACCGTCTAATATTG
















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|86905480|gb|CI285443.1|CI285443
EST:     TGTATCCTGAATGCGTGTTGTATAAACCACAAATTGCTGGGCTTGCAGAG                         CTATCTGCAATAACCACCATTGGATTTGTCAAAGGCGCCCCAGAAATTGAT
genomic: TGTATCCTGAATGCGTGTTGTATAAACCACAAATTGCTGGGCTTGCAGAGgtacgtgcaa ... tttgtattagCTATCTGCAATAACCACCATTGGATTTGTCAAAGGCGCCCCAGAAATTGAT
EST: gi|88570562|gb|CI661935.1|CI661935
EST:     TGTATCCTGAATGCGTGTTGTATAAACCACAAATTGCTGGGCTTGCAGAG                         CTATCTGCAATAACCACCATTGGATTTGTCAAAGGCGCCCCAGAAA
genomic: TGTATCCTGAATGCGTGTTGTATAAACCACAAATTGCTGGGCTTGCAGAGgtacgtgcaa ... tttgtattagCTATCTGCAATAACCACCATTGGATTTGTCAAAGGCGCCCCAGAAA
EST: gi|11171117|gb|AU163632.1|AU163632
EST:     AATTGCTGGGCTTGCAGAG                         CTATCTGCAATAACCACCATTGGATTTGTCAAAGGCGCCCCAGAAATTGAT
genomic: AATTGCTGGGCTTGCAGAGgtacgtgcaa ... tttgtattagCTATCTGCAATAACCACCATTGGATTTGTCAAAGGCGCCCCAGAAATTGAT
EST: gi|87023564|gb|CI286315.1|CI286315
EST:     TGTATCCTGAATGCGTGTTGTATAAACCACAAATTGCTGGGCTTGCAGAG                         CTATCTGCAATAACCACCATTGGATTTGTCAAAGGCGCCCCAGAAATTGAT
genomic: TGTATCCTGAATGCGTGTTGTATAAACCACAAATTGCTGGGCTTGCAGAGgtacgtgcaa ... tttgtattagCTATCTGCAATAACCACCATTGGATTTGTCAAAGGCGCCCCAGAAATTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttgaatttgccatgattcttctgtgattaacttcctcatattgtttgtattagCTATCTGCAATAACCACCATTGGATTTGTCAAAGGCGCCCCAGAAATTGATGTACAAGGCTTTAATGTGTACCACAAGAATCGTTTAATAGCG
                          gattaac  putative branch site (score: 2)
                                       atattgtttgtatta  TA-rich tract