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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttatgcacttacacttgtatgttgtttgccctgtgagattttatattttttgggttgatcattcagtggattcatgacacctaatctgtacttttatagGGACATCCAGAAATAGTTGTCCAACTCGTTGACCTGATTGGCATCACATCAATAATGGAG

Basic information

species Oryza sativa
transcript LOC_Os01g40340.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g40340.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM5G806347_T01 (Zea mays), 3'ss of exon 6
gttatgcacttacacttgtatgttgtttgccctgtgagatttta-tattttttgggttgatcattcag-tggattcatgacaccta-atctgtac-ttttatagGGACATCCAGAAATAGTTGTCCAACTCGTTGACCTGATTGGCATCACATCAATAATGGAG
    |   |  |   | |  |    |||   ||   || |  || | | |||||   | | ||||||  | |||| |||  || |  ||   | | |||||||||| |||||| | ||||||||||| || ||||||||||||||||||||||| |||||||||
----taagcaaaatttggggtacccttttgtctacaagctaatagtttcttttgaactcaacattcaaatagatttatgggacttttattattgcattttatagGGGCATCCAAAGATAGTTGTCCAGCTTGTTGACCTGATTGGCATCACATCGATAATGGAG

upper sequence: LOC_Os01g40340.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G470292_T02 (Zea mays), 3'ss of exon 5
gttatgcacttacacttgtatgttgtttgccctgtgagattttatattttttgggttgatcattcagtggattc----atgacacctaatctgtacttttatagGGACATCCAGAAATAGTTGTCCAACTCGTTGACCTGATTGGCATCACATCAATAATGGAG
 ||||  |  |  | |  |   |         ||||  |   |   ||   || ||  |  |   | | | |||    |  ||   || | |    |||||||||| |||||||| ||||||||||| || ||||||||||||||||||||||| |||||||||
cttatctatatgaaatc-tgcttaagcaaaattgtggtaccct---ttcactgtgtctacaagctaatagtttctgtaactacctttattattgctttttatagGGGCATCCAGAGATAGTTGTCCAGCTTGTTGACCTGATTGGCATCACATCGATAATGGAG
















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|88695505|gb|CI737543.1|CI737543
EST:     TAATATGTTTGATGCTGCGGAAGACTGCTCCTCTTATGGCTTATGTTCAG                         GGACATCCAGAAATAGTTGTCCAACTCGTTGACCTGATTGGCATCACATCA
genomic: TAATATGTTTGATGCTGCGGAAGACTGCTCCTCTTATGGCTTATGTTCAGgtattccttg ... acttttatagGGACATCCAGAAATAGTTGTCCAACTCGTTGACCTGATTGGCATCACATCA
EST: gi|58605044|gb|CK033077.1|CK033077
EST:     TAATATGTTTGATGCTGCGGAAGACTGCTCCTCTTATGGCTTATGTTCAG                         GGACATCCAGAAATAGTTGTCCAACTCGTTGACCTGATTGGCATCACATCA
genomic: TAATATGTTTGATGCTGCGGAAGACTGCTCCTCTTATGGCTTATGTTCAGgtattccttg ... acttttatagGGACATCCAGAAATAGTTGTCCAACTCGTTGACCTGATTGGCATCACATCA
EST: gi|29669991|gb|CB666266.1|CB666266
EST:     TAATATGTTTGATGCTGCGGAAGACTGCTCCTCTTATGGCTTATGTTCAG                         GGACATCCAGAAATAGTTGTCCAACTCGTTGACCTGATTGGCATCACATCA
genomic: TAATATGTTTGATGCTGCGGAAGACTGCTCCTCTTATGGCTTATGTTCAGgtattccttg ... acttttatagGGACATCCAGAAATAGTTGTCCAACTCGTTGACCTGATTGGCATCACATCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttttgggttgatcattcagtggattcatgacacctaatctgtacttttatagGGACATCCAGAAATAGTTGTCCAACTCGTTGACCTGATTGGCATCACATCAATAATGGAG
                                  acctaat  putative branch site (score: 3)
                                            tactttt  putative PPT
                                            tacttttata  TA-rich tract