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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gataaatcaattcagctcaataattatggcttgatagtccccacacaaagatggaattggcagttaacagttcctaatgcttttgtcctatgttctgcagGCGTTTTGGTACATGGCCAGTAGCAATACATGTTGGGACAAAGTACAGAGTGGTTCTAGAAGGCCCCGTTTGTAAGGGTAATCAAGTCACTGGATGGCAT

Basic information

species Oryza sativa
transcript LOC_Os01g48440.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g48440.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G037469_T01 (Zea mays), 3'ss of exon 2
-gataaatcaattcagctcaataattatggcttgatagtccccacacaaagatggaattggcagttaaca--gttcctaatgcttttgtcctatgttctgcagGCGTTTTGGTACATGGCCAGTAGCAATACATGTTGGGACAAAGTACAGAGTGGTTCTAGAAGGCCCCGTTTGTAAGGGTAATCAAGTCACTGGATGGCAT
   ||   || |     |||   || |     |  ||    |  | |     |  || || ||||| | |  |||||| ||| ||||  |  |||| ||||||||| |||||||| ||||||||||| | |||||||||  | | |||||  |||||| | ||||| || || |||| |||||||||||||||||||||||||
ttgtagcacagtaatattcaccgat-acaatcttctatgagcacctctcgtctcaaagtgacagttgagaatgttcctcatgatttt--ctgatgtcctgcagGCGCTTTGGTACGTGGCCAGTAGCGACACATGTTGGAGCCAGGTACAAGGTGGTTTTGGAAGGGCCTGTCTGTAGGGGTAATCAAGTCACTGGATGGCAT
















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|218479027|gb|FG957912.1|FG957912
EST:     GAAGAGAGAGCATACTCAGCTGACCTGTTTGAAGAAATGCGGAAAATAAG                         GCGTATTGGTACATGGCCAGTAGCAATACATGTTGGGACAAAGTACAGAGT
genomic: GAAGAGAGAGCATACTCAGCTGACCTGTTTGAAGAAATGCGGAAAATAAGgtgacaaccc ... tgttctgcagGCGTTTTGGTACATGGCCAGTAGCAATACATGTTGGGACAAAGTACAGAGT
EST: gi|33676774|gb|CF305013.1|CF305013
EST:     GAAGAGAGAGCATACTCAGCTGACCTGTTTGAAGAAATGCGGAAAATAAG                         GGCGTTTTGGTACATGGCCAGTAGCAATACATGTTGGGAC
genomic: GAAGAGAGAGCATACTCAGCTGACCTGTTTGAAGAAATGCGGAAAATAAGgtgacaaccc ... tgttctgcagG-CGTTTTGGTACATGGCCAGTAGCAATACATGTTGGGAC
EST: gi|29614630|gb|CB619643.1|CB619643
EST:     GAAGAGAGAGCATACTCAGCTGACCTGTTTGAAGAAATGCGGAAAATAAG                         GCGTTTTGGTACATGGCCAGTAGCAATACATGTTGGGACAAAGTACAGAGT
genomic: GAAGAGAGAGCATACTCAGCTGACCTGTTTGAAGAAATGCGGAAAATAAGgtgacaaccc ... tgttctgcagGCGTTTTGGTACATGGCCAGTAGCAATACATGTTGGGACAAAGTACAGAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaagatggaattggcagttaacagttcctaatgcttttgtcctatgttctgcagGCGTTTTGGTACATGGCCAGTAGCAATACATGTTGGGACAAAGTACAGAGTGGTTCTAGAAGGCCCCGTTTGTAAGGGTAATCAAGTCACTGGATGGCAT
                          tcctaat  putative branch site (score: 2)