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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gagtatatgagattgtcttctatatgcaatttacttcatatcgacatttttctgcagaattgcaaaactgacgccttgttttccatctggaattgtgcagGGGAGCAAAATGCTCAAACCGGAAAAATGGCACACATGTTTTGATAATGATGGAAAGGTCATAGGTTTCCGTAAAGCCCTAAAATTCATTGTCTTAGGG

Basic information

species Oryza sativa
transcript LOC_Os01g01010.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g01010.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G031043_T01 (Zea mays), 3'ss of exon 3
--gagtatatgagattgtcttctatatgcaatttacttcatatcgacatttttctgcagaattgcaaaactgacgcc-ttgttttccatctggaattgtgcagGGGAGCAAAATGCTCAAACCGGAAAAATGGCACACATGTTTTGATAATGATGGAAAGGTCATAGGTTTCCGTAAAGCCCTAAAATTCATTGTCTTAGGG
  ||||| |||| | | |   | |    |||   |  ||| |||   ||||  || |     | ||  | ||||    || | ||| ||| | ||  |||||||| | || |||||| ||||| |||| ||||||| | |||||||| | ||| || ||||  ||| |||||||||||||||| || |||||||||||||| 
aggagtacatgaaactattagcaagtatcaacacatgtcacatc---atttaacttctctccttcactattgacaatgttttcttctatccgcaaccgtgcagGGAAACAGAATGCTGAAACCAGAAAGATGGCACGCGTGTTTTGACAGTGACGGGAAGGCTATATGTTTCCGTAAAGCCCTTAAGTTCATTGTCTTAGGA
















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|29635202|gb|CB640211.1|CB640211
EST:     CCCTCGTCCGTGACATTGGCGACCCCTGCCTCAACCCATCCCCCGTTAAG                         GGGAGCAAAATGCTCAAACCGGAAAAATGGCACACATGTTT
genomic: CCCTCGTCCGTGACATTGGCGACCCCTGCCTCAACCCATCCCCCGTTAAGgttcgcctac ... aattgtgcagGGGAGCAAAATGCTCAAACCGGAAAAATGGCACACATGTTT
EST: gi|29675456|gb|CB671731.1|CB671731
EST:     CCCTCGTCCGTGACATTGGCGACCCCTGCCTCAACCCATCCCCCGTTAAG                         GGGAGCAAAATGCTCAAACCGGAAAAATGGCACACATGTTTTGATAATGAT
genomic: CCCTCGTCCGTGACATTGGCGACCCCTGCCTCAACCCATCCCCCGTTAAGgttcgcctac ... aattgtgcagGGGAGCAAAATGCTCAAACCGGAAAAATGGCACACATGTTTTGATAATGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttttctgcagaattgcaaaactgacgccttgttttccatctggaattgtgcagGGGAGCAAAATGCTCAAACCGGAAAAATGGCACACATGTTTTGATAATGATGGAAAGGTCATAGGTTTCCGTAAAGCCCTAAAATTCATTGTCTTAGGG
                    aactgac  putative branch site (score: 2)
                              ttgtttt  TA-rich tract