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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgtatacctcaatttaattcttcattgatggtgacaaatatgatatgcttgcactttgaattggaacaacaagcaatgaactaatctccttgataacagtcagttacattccctaaaaataaaaatgtaatatccatgttccatcgcctgtcatagGAAGAAATGCCCAATGAGGATGCAGCAGAGGAAGATGAAGAATCAGAGATTGGCATGTGGGAGTCCATAGCATGGCTCGCGATGTTGACATTATGGGTGT

Basic information

species Oryza sativa
transcript LOC_Os04g55940.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g55940.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G040017_T02 (Zea mays), 3'ss of exon 6
gtaagtgtatacctcaatttaattcttcattgatggtgacaaatatgatatgcttgcactttgaattggaacaacaagcaatgaactaatctccttgataacagtcagttacattccctaaaaataaaaatgtaatatccatgttccatcgcctgtcatagGAAGAAATGCCCAATGAGGATGCAGCAGAGGAAGATGAAGAATCAGAGATTGGCATGTGGGAGTCCATAGCATGGCTCGCGATGTTGACATTATGGGTGT
                                                 |  ||||   |   ||  |   |    |  | || | |||| |  |  | ||  ||    |||||        |||| |  |||  |  |||| |||       | | |||||||||   ||| | |||||||   |||||||||||||||||| | |||||||||||||||||| |  || ||||||| ||| | || ||| | |||||||
------------------------------------------------caatcttgtgat--aaagagtttcttgcaatattgcattaatttagtatagaatggtgcaatacatc-------aataca--tgttttcaccatattcag--aaatattatagGAAGAGGCGCCTATTGAGGATATTGCAGAGGAAGATGAAGAAGCTGAGATTGGCATGTGGGAGGCAGTAACATGGCTTGCGGTTTTAACACTCTGGGTGT

upper sequence: LOC_Os04g55940.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G143356_T01 (Zea mays), 3'ss of exon 7
gtaagtgtatacctcaatttaattcttcattgatggtgacaaatatgatatgcttgcactttgaattggaacaacaagcaatgaactaatctccttgataacagtcagttacattccctaaaaataaaaatgtaatatccatgttccatcgcctgtcatagGAAGAAATGCCCAATGAGGATGCAGCAGAGGAAGATGAAGAATCAGAGATTGGCATGTGGGAGTCCATAGCATGGCTCGCGATGTTGACATTATGGGTGT
                                            |  |  | ||||   |   ||  |   |    |  | || |||||| |  |  | ||  ||    |||||    | |                 |||| |||       | |  ||||||||   ||| |  ||||||    | || |||||||||||| | |||||||||||||||||| |  || ||||||| ||| |||| ||||| |||||||
----------------------------------------gcgaaccacgtccttgtgat--aaagagtttcttgcaatactgcactaatttagtatagaatggtgcaatacatgttttca-----------------ccatattcagaaa--tattgtagGAAGAGGCGCCTAGCGAGGATAACCCGGAAGAAGATGAAGAAGCTGAGATTGGCATGTGGGAGGCAGTAACATGGCTTGCGGTGTTAACATTCTGGGTGT
















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|286840|gb|D15647.1|D15647
EST:     GACGGAATAATGCTTATAGTCCAATTGGCAGT                         GAAGAAATGCCCAATGAGGATGCAGCAGAGGAAGATGAAGAATCAGAGATT
genomic: GACGGAATAATGCTTATAGTCCAATTGGCAGTgtaagtgtat ... cctgtcatagGAAGAAATGCCCAATGAGGATGCAGCAGAGGAAGATGAAGAATCAGAGATT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttacattccctaaaaataaaaatgtaatatccatgttccatcgcctgtcatagGAAGAAATGCCCAATGAGGATGCAGCAGAGGAAGATGAAGAATCAGAGATTGGCATGTGGGAGTCCATAGCATGGCTCGCGATGTTGACATTATGGGTGT
         ccctaaa  putative branch site (score: 3)
            taaaaataaaaatgta  TA-rich tract