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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaccaatcattatgtgcttctcactgtatttcagagagagacttgaaaagccaagtactgctcaggatgtatttgatttgacctttttggccctatcaacagGACAAATTGCTGGCATCGCAATTGCTATTCTGATTGTCCTCTTCCTTGTTCAGCGTTTTGGCACGGACAAAGTTGGTTACTCATTTGGCCCTATAATCTT

Basic information

species Oryza sativa
transcript LOC_Os01g70490.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g70490.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G084779_T02 (Zea mays), 3'ss of exon 4
-----gtaaaccaatcattatgtgcttctcactgtatttcagagagagacttgaaaagccaag-------tactgctcaggatgt--atttgatttgacctttttggccctatcaacagGACAAATTGCTGGCATCGCAATTGCTATTCTGATTGTCCTCTTCCTTGTTCAGCGTTTTGGCACGGACAAAGTTGGTTACTCATTTGGCCCTATAATCTT
       |  | |  ||||      ||   | | ||| |   | ||    |  || ||   |        ||||| | ||| ||   | || || ||||||| ||   |  ||||||||||||||||| ||||||| |||| || ||| |||| |||||||| ||||||||| | |||||||| ||||||||||||||| ||||||  |||||||||||
gtacaacaggctatgcattg-aaattttgaaatatatattcaacaggagttacaacagtttaaataactttactgtttaggttgggaacttaatctgaccttcttaatcg-atcaacagGACAAATTGTTGGCATCTCAATAGCCATTTTGATCGTCCTCTTTCTTGTTCAGTGCTTTGGCACAGACAAAGTTGGTTACACATTTGCACCTATAATCTT
















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|29625228|gb|CB630239.1|CB630239
EST:     GCTTAGCGCTGTTGGGGGGATCAAGGAATCAGCAAAGTCCCTGACTCAAG                         GACAAATTGCTGGCATCGCAATTGCTATTCTGATTGTCCTCTTCCTTGTTC
genomic: GCTTAGCGCTGTTGGGGGGATCAAGGAATCAGCAAAGTCCCTGACTCAAGgtaaaccaat ... ctatcaacagGACAAATTGCTGGCATCGCAATTGCTATTCTGATTGTCCTCTTCCTTGTTC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagccaagtactgctcaggatgtatttgatttgacctttttggccctatcaacagGACAAATTGCTGGCATCGCAATTGCTATTCTGATTGTCCTCTTCCTTGTTCAGCGTTTTGGCACGGACAAAGTTGGTTACTCATTTGGCCCTATAATCTT
                            atttgac  putative branch site (score: 4)
                                           ccctatc  putative PPT
                      tatttgattt  TA-rich tract