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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagggatgcctgtgttctctcctggtttgctcttagtttagcaatactcatctgatcactttgctagttcaagcaggacaatttgatcgaaccgcggaactattttgggttgtattaaacatcctccatgactgatgtgtgcctaatgttatttctgaacctccctgtttacccataatttttgacagCTTCCAAGGTGGGCTTTAGGTTTGCTTTGCTTGTCAAAGAGGGTTCACTCCATCTTTGTGCTCCGCCTTTTCAACGATTGTTTCGCTATGACGTTTCTCC

Basic information

species Oryza sativa
transcript LOC_Os01g07720.4
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g07720.4 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G066362_T01 (Zea mays), 3'ss of exon 4
gtagggatgcctgtgttctctcctggtttgctcttagtttagcaatactcatctgatcactttgctagttcaagcaggacaatttgatcgaaccgcggaactattttgggttgtattaaacatcctccatgactgatgtgtgcctaatgttatttctgaa-cctccctgtttacccataatttttgacagCTTCCAAGGTGGGCTTTAGGTTTGCTTTGCTTGTCAAAGAGGGTTCACTCCATCTTTGTGCTCCGCCTTTTCAACGATTGTTTCGCTATGACGTTTCTCC
                                                                                  | ||  | |    ||     ||| |   ||||  |        |   |  |       | |||| | || |||||||  ||| ||| | |  | ||||   | ||||||||||| |||||||||||||||||||||| ||||| ||||||||||||||||||||||| ||||| |||||||| || || ||||| ||||| || ||||
----------------------------------------------------------------------------------tgtggccaagtttcgattacattct---ttgttctttgttgtttttgtatcca---catacctatt-ttgtttctgattccttcctatctctcaataacaat-gacagCTTCCATGGTGGGCTTTAGGTTTGCTTTGTTTGTCCAAGAGGGTTCACTCCATCTTTGTTCTCCGTCTTTTCAATGACTGCTTCGCCATGACATTGCTCC
















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|88576279|gb|CI670424.1|CI670424
EST:     ACATTGTGAACCTTAGCCTTGTTCTGCTGATGTACGTCAAGACTGAAGTG                         CTTCCAAGGTGGGCTTTAGGTTTGCTTTGCTTGTCAAA
genomic: ACATTGTGAACCTTAGCCTTGTTCTGCTGATGTACGTCAAGACTGAAGTGgtagggatgc ... tttttgacagCTTCCAAGGTGGGCTTTAGGTTTGCTTTGCTTGTCAAA
EST: gi|38472084|gb|CF956215.1|CF956215
EST:     ACATTGTGAACCTTAGCCTTGTTCTGCTGATGTACGTCAAGACTGAAGTG                         CTTCCATGGTGGGCTTTAGGTTTGCTTTGCTTGTCAAAGAGGGTTCACTCC
genomic: ACATTGTGAACCTTAGCCTTGTTCTGCTGATGTACGTCAAGACTGAAGTGgtagggatgc ... tttttgacagCTTCCAAGGTGGGCTTTAGGTTTGCTTTGCTTGTCAAAGAGGGTTCACTCC
EST: gi|88368729|gb|CI645151.1|CI645151
EST:     ACATTGTGAACCTTAGCCTTGTTCTGCTGATGTACGTCAAGACTGAAGTG                         CTTCCA-GGTGG
genomic: ACATTGTGAACCTTAGCCTTGTTCTGCTGATGTACGTCAAGACTGAAGTGgtagggatgc ... tttttgacagCTTCCAAGGTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgtgtgcctaatgttatttctgaacctccctgtttacccataatttttgacagCTTCCAAGGTGGGCTTTAGGTTTGCTTTGCTTGTCAAAGAGGGTTCACTCCATCTTTGTGCTCCGCCTTTTCAACGATTGTTTCGCTATGACGTTTCTCC
       gcctaat  putative branch site (score: 3)
                                             ttttt  putative PPT
          taatgttattt  TA-rich tract