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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgccattattatgcccctgagttagtatttgttagatcatttttcataattgtttgacaaattgtgatgcaaatgaccacagTGGGGACATAATCTTCCTTTGCTGTATGACCGTGTTCTGAAGTACCCCGAGCGTGTACAAAATTTGTACTTCACTTACCTGTTTGTTCTTCGGGCTGTGA

Basic information

species Oryza sativa
transcript LOC_Os03g52340.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g52340.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G521844_T01 (Zea mays), 3'ss of exon 5
gtatgtgccattattatgcccctgagttagtatttgttagatcatttttcataattgttt-gacaaattgtgatgcaaatgaccacagTGGGGACATAATCTTCCTTTGCTGTATGACCGTGTTCTGAAGTACCCCGAGCGTGTACAAAATTTGTACTTCACTTACCTGTTTGTTCTTCGGGCTGTGA
||||||| |   ||||| | |||   ||| | ||| ||    ||  |||| ||||| ||| ||| | || | ||| |||||  ||||||||||||| |||||| ||||||||||||||||||| ||||||||||| || ||||| || ||| | |||||||| ||||||||||||||||| || ||||
gtatgtgaccgaattatcctccttcattattttttattgtgccaagtttcgtaattattttgaccacttctaatgtaaatggtcacagTGGGGACAAAATCTTTCTTTGCTGTATGACCGTGTCCTGAAGTACCCAGAACGTGTCCAGAATCTATACTTCACCTACCTGTTTGTTCTTCGAGCCGTGA

upper sequence: LOC_Os03g52340.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G108115_T01 (Zea mays), 3'ss of exon 5
gtatgtgccattattatgcccctgag-ttagtatttgttagatcatttttcataattgttt-gacaaattgtgatgcaaa--tgaccacagTGGGGACATAATCTTCCTTTGCTGTATGACCGTGTTCTGAAGTACCCCGAGCGTGTACAAAATTTGTACTTCACTTACCTGTTTGTTCTTCGGGCTGTGA
||||||| |   ||||| | |||  | ||| | ||| ||    ||   | ||||||||||| ||| | || | ||| |||  ||  ||||||||||||| |||||||||||| |||||||||| || ||||||||||| || ||||| || ||| |||||||||| |||||||||||||||||||| ||||
gtatgtgaccagattatcctcctttgcttattgtttattgtgccaagatgcataattgttttgaccacttctaatgtaaaaatggtcacagTGGGGACAAAATCTTCCTTTGTTGTATGACCGCGTCCTGAAGTACCCAGAACGTGTCCAGAATCTGTACTTCACCTACCTGTTTGTTCTTCGGGCCGTGA
















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|58657197|gb|CK045877.1|CK045877
EST:     TTTCAGTACACATTGCTTATGATTATCTTCTAGATGAATCTGCCAACTTG                         TGGGGACATAATCTTCCTTTGCTGTATGACCGTGTTCTGAAGTACCCCGAG
genomic: TTTCAGTACACATTGCTTATGATTATCTTCTAGATGAATCTGCCAACTTGgtatgtgcca ... atgaccacagTGGGGACATAATCTTCCTTTGCTGTATGACCGTGTTCTGAAGTACCCCGAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgttagatcatttttcataattgtttgacaaattgtgatgcaaatgaccacagTGGGGACATAATCTTCCTTTGCTGTATGACCGTGTTCTGAAGTACCCCGAGCGTGTACAAAATTTGTACTTCACTTACCTGTTTGTTCTTCGGGCTGTGA
                        gtttgac  putative branch site (score: 4)
           atttttcataattgtt  TA-rich tract