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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgcaatttcaataatataacaattatatgcaagaggtcctagcactatctaaaaggaaaaaaaaaatccacaaccatttcttgattctggcatttctcctgttgcagGTCTTACAGTCGCATCATTTTGTTATCTGCAATTCTTCCCATATCCTTATGACGCAGACG

Basic information

species Oryza sativa
transcript LOC_Os09g13870.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g13870.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G024615_T05 (Zea mays), 3'ss of exon 7
gtttgcaatttcaataatataacaattatatgc--aagaggtcctagcactatctaaaag----gaaaaaaaaaatccacaaccatttcttgattctggcatttctcctgttgcagGTCTTACAGTCGCATCATTTTGTTATCTGCAATTCTTCCCATATCCTTATGACGCAGACG
        |||  | ||| | | || ||| | |  |||||| |  ||   | |||| | |    ||| | | | |         ||||||||     | || ||   || |||||||||||||||| || |||||||| ||||| || || || |||||||||| ||| |  || |
-------gtttgtaaaatttgataaatattttctaaagaggacgcagatttttctagatgttctgaatacacataattgatcatatttcttgccatggccactt--gcttttgcagGTCTTACAGTTGCTTCATTTTGCTATCTACAGTTTTTTCCATATCCTTTTGATGGCGATG
















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|88220376|gb|CI219936.1|CI219936
EST:     GGATGACTACTGGCATCACTGGCAGGATGTATTTGCAGGCTCTCTGATAG                         GTCTTACAGTCGCATCATTTTGTTATCTGCAATTCTTCCCATATCCTTATG
genomic: GGATGACTACTGGCATCACTGGCAGGATGTATTTGCAGGCTCTCTGATAGgtttgcaatt ... cctgttgcagGTCTTACAGTCGCATCATTTTGTTATCTGCAATTCTTCCCATATCCTTATG
EST: gi|33666578|gb|CF297545.1|CF297545
EST:     GGATGACTACTGGCATCACTGGCAGGATGTATTTGCAGGCTCTCTGATAG                         GTCTTACAGTCGCATCATTTTGTTATCTGCAATTCTTCCCATATCCTTATG
genomic: GGATGACTACTGGCATCACTGGCAGGATGTATTTGCAGGCTCTCTGATAGgtttgcaatt ... cctgttgcagGTCTTACAGTCGCATCATTTTGTTATCTGCAATTCTTCCCATATCCTTATG
EST: gi|29642304|gb|CB647311.1|CB647311
EST:     GGATGACTACTGGCATCACTGGCAGGATGTATTTGCAGGCTCTCTGATAG                         GTCTTACAGTCGCATCATTTTGTTATCTGCAATTCTTCCCATATCCTTATG
genomic: GGATGACTACTGGCATCACTGGCAGGATGTATTTGCAGGCTCTCTGATAGgtttgcaatt ... cctgttgcagGTCTTACAGTCGCATCATTTTGTTATCTGCAATTCTTCCCATATCCTTATG
EST: gi|29640277|gb|CB645286.1|CB645286
EST:     GGATGACTACTGGCATCACTGGCAGGATGTATTTGCAGGCTCTCTGATAG                         GTCTTACAGTCGCATCATTTTGTTATCTGCAATTCTTCCCATATCCTTATG
genomic: GGATGACTACTGGCATCACTGGCAGGATGTATTTGCAGGCTCTCTGATAGgtttgcaatt ... cctgttgcagGTCTTACAGTCGCATCATTTTGTTATCTGCAATTCTTCCCATATCCTTATG
EST: gi|29641223|gb|CB646230.1|CB646230
EST:     GGATGACTACTGGCATCACTGGCAGGATGTATTTGCAGGCTCTCTGATAG                         GTCTTACAGTCGCATCATTTTGTTATCTGCAATTCTTCCCATATCCTTATG
genomic: GGATGACTACTGGCATCACTGGCAGGATGTATTTGCAGGCTCTCTGATAGgtttgcaatt ... cctgttgcagGTCTTACAGTCGCATCATTTTGTTATCTGCAATTCTTCCCATATCCTTATG
EST: gi|29642639|gb|CB647646.1|CB647646
EST:     GGATGACTACTGGCATCACTGGCAGGATGTATTTGCAGGCTCTCTGATAG                         GTCTTACAGTCGCATCATTTTGTTATCTGCAATTCTTCCCATATCCTTATG
genomic: GGATGACTACTGGCATCACTGGCAGGATGTATTTGCAGGCTCTCTGATAGgtttgcaatt ... cctgttgcagGTCTTACAGTCGCATCATTTTGTTATCTGCAATTCTTCCCATATCCTTATG
EST: gi|29671234|gb|CB667509.1|CB667509
EST:     GGATGACTACTGGCATCACTGGCAGGATGTATTTGCAGGCTCTCTGATAG                         GTCTTACAGTCGCATCATTTTGTTATCTGCAATTCTTCCCATATCCTTATG
genomic: GGATGACTACTGGCATCACTGGCAGGATGTATTTGCAGGCTCTCTGATAGgtttgcaatt ... cctgttgcagGTCTTACAGTCGCATCATTTTGTTATCTGCAATTCTTCCCATATCCTTATG
EST: gi|88984260|gb|CI020176.1|CI020176
EST:     TGCAGGCTCTCTGATAG                         GTCTTACAGTCGCATCATTTTGTTATCTGCAATTCTTCCCATATCCTTATG
genomic: TGCAGGCTCTCTGATAGgtttgcaatt ... cctgttgcagGTCTTACAGTCGCATCATTTTGTTATCTGCAATTCTTCCCATATCCTTATG
EST: gi|8858798|gb|AU096116.1|AU096116
EST:     GGATGACTACTGGCATCACTGGCAGGATGTATTTGCAGGCTCTCTGATAG                         GTCTTACAGTCGCATCATTTTGTTATCTGCAATTCTTCCCATATCCTTATG
genomic: GGATGACTACTGGCATCACTGGCAGGATGTATTTGCAGGCTCTCTGATAGgtttgcaatt ... cctgttgcagGTCTTACAGTCGCATCATTTTGTTATCTGCAATTCTTCCCATATCCTTATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaggaaaaaaaaaatccacaaccatttcttgattctggcatttctcctgttgcagGTCTTACAGTCGCATCATTTTGTTATCTGCAATTCTTCCCATATCCTTATGACGCAGACG
                          tcttgat  putative branch site (score: 4)
                                        tttctcctgtt  putative PPT
     aaaaaaaaat  TA-rich tract