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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagaaaacaatgatttacatccttcaatttacctttatatttttttacaattctgttgtgattttcacacagatataaacttctgttgatcatttaacagGTCCTGAGCAATTGAAGCAGAAGCAGGTTAATTCTGATTCATCTGACAAAAAAGATTCACCACTGCAAACTCTGGAACCGTCCACCCTCCAAGCACTTTA

Basic information

species Oryza sativa
transcript LOC_Os01g56640.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g56640.3 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G079468_T01 (Zea mays), 3'ss of exon 11
aagaaaacaatgatttacatccttcaatttacctttatatttttttacaattctgttgtgattttcacacagatataaacttctgttgatcatttaacagGTCCTGAGCAATTGAAGCAGA---AGCAGGTTAATTCTGATTCATCTGACAAAAAAGATTCACCACTGCAAACTCTGGAACCGTCCACCCTCCAAGCACTTTA---------------------------
                            | ||   || |||| | |    || | || || || |        |||   ||| || ||| ||   ||||  |  | |     | |   |     | ||||||       |||||  |  |||||| ||||||||||| | |||||||||||| ||||| || |||||||| ||                           
----------------------------taacggctacatttgtatttgtttttattatgtttctttgtatcctattcccttttgatga-cagcaaacaatttatcaatttataatttatgtttatcagGTTTCCAGCTATTCAATTTGCAAAAA-GATTCACCACTACGAACTCTGGAACCCTCCACTCTGCAAGCACTCTATGAACTCATCTCACTGGTCCATGATGG
















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|4715475|gb|AU056592.1|AU056592
EST:     TTGTTCAAAAGGTACAACTGTTTGTCAGCCTACAGATGAAGAATCAGGAG                         GTCCTGAGCAATTGAAGCAGAAGCAGGTTAATTCTGATTCATCTGACAAAA
genomic: TTGTTCAAAAGGTACAACTGTTTGTCAGCCTACAGATGAAGAATCAGGAGgtcaatattt ... catttaacagGTCCTGAGCAATTGAAGCAGAAGCAGGTTAATTCTGATTCATCTGACAAAA
EST: gi|4715422|gb|AU056539.1|AU056539
EST:     TTGTTCAAAAGGTACAACTGTTTGTCAGCCTACAGATGAAGAATCAGGAG                         GTCCTGAGCAATTGAAGCAGAAGCAGGTTAATTCTGATTCATCTGACAAAA
genomic: TTGTTCAAAAGGTACAACTGTTTGTCAGCCTACAGATGAAGAATCAGGAGgtcaatattt ... catttaacagGTCCTGAGCAATTGAAGCAGAAGCAGGTTAATTCTGATTCATCTGACAAAA
EST: gi|33680312|gb|CF308551.1|CF308551
EST:     TTGTTCAAAAGGTACAACTGTTTGTCAGCCTACAGATGAAGAATCAGGAG                         GTCCTGAGCAATTGAAGCAGAAGCAGGTTAATTCTGATTCATCTGACAAAA
genomic: TTGTTCAAAAGGTACAACTGTTTGTCAGCCTACAGATGAAGAATCAGGAGgtcaatattt ... catttaacagGTCCTGAGCAATTGAAGCAGAAGCAGGTTAATTCTGATTCATCTGACAAAA
EST: gi|5803388|gb|AI978336.1|AI978336
EST:     TTGTTCAAAAGGTACAACTGTTTGTCAGCCTACAGATGAAGAATCAGGAG                         GTCCTGAGCAATTGAAGCAGAAGCAGGTTAATTCTGATTCATCTGACAAAA
genomic: TTGTTCAAAAGGTACAACTGTTTGTCAGCCTACAGATGAAGAATCAGGAGgtcaatattt ... catttaacagGTCCTGAGCAATTGAAGCAGAAGCAGGTTAATTCTGATTCATCTGACAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacaattctgttgtgattttcacacagatataaacttctgttgatcatttaacagGTCCTGAGCAATTGAAGCAGAAGCAGGTTAATTCTGATTCATCTGACAAAAAAGATTCACCACTGCAAACTCTGGAACCGTCCACCCTCCAAGCACTTTA
                                      tgttgat  putative branch site (score: 4)
                           atataaactt  TA-rich tract