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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagaataccatgcacattagacctaaagaagttatagagctaattaaagtcctatttgcttagccatgaagctttcctttttgtagGTTGACTCTTTAAAAAGAGTTTTGAAAAGGTTCTATGGGGAGGATCCTTTGCAATCAGAAGACTTGTCCCGTATTGTGAATTCTAACCATTTCCGTAGAT

Basic information

species Oryza sativa
transcript LOC_Os11g08300.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g08300.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G060800_T02 (Zea mays), 3'ss of exon 5
gtaaagaataccatgcacattagacctaaagaagttatagagctaattaaagtcctatttgcttagccatgaagctttcctttttgtagGTTGACTCTTTAAAAAGAGTTTTGAAAAGGTTCTATGGGGAGGATCCTTTGCAATCAGAAGACTTGTCCCGTATTGTGAATTCTAACCATTTCCGTAGAT
||| |||  |||| | |  ||       |  ||   | | |   || |    |  | | | |   |   | ||  |      || | |||| | |||||| |||||||||||| ||||||||||||||||||||||| || |||||| ||||||||| |||||||||||||| || || |||   ||||
gtatagataaccaaggatttt--cttgcacaaaacgagacactgaacttgcattttctgttccatgaagtaaatgtaaatccttggcagGTGGCCTCTTTCAAAAGAGTTTTGGAAAGGTTCTATGGGGAGGATCCTCTGGAATCAGCAGACTTGTCTCGTATTGTGAATTCGAAGCAGTTCAAAAGAT

upper sequence: LOC_Os11g08300.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G118800_T01 (Zea mays), 3'ss of exon 6
----------------------gtaaagaataccatgcacatt-agacctaaagaagttatagagctaatt---aaagtcctatttgcttagccatgaagcttt----cctttttgtagGTTGACTCTTTAAAAAGAGTTTTGAAAAGGTTCTATGGGGAGGATCCTTTGCAATCAGAAGACTTGTCCCGTATTGTGAATTCTAACCATTTCCGTAGAT
                            | |  | ||| ||   ||| | ||| ||   | | |    |||   ||  ||  |   |   ||  |  ||  | |    |||||| | |||| | ||| || ||||| |||||| ||||||| || |||||||||||| |||| ||||  ||| |||| ||||| |||||||| || || ||| | ||| 
gtatagatagataaccacgaacactgtaactttcttgcgcaaggagaaccaaaaaaaaaaaaaactggattttcaatttctgacccgtgaagtaaaaaaaatgtaaatccttttggcagGTGGCCTCCTTGAAAAGGGTTTTGGAAAGGTTTTACGGGGAGGATCCTCTGCAGTCAGCGGACCTGTCTCGTATCGTGAATTCGAAGCACTTCAGGAGAC
















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|29680879|gb|CB677154.1|CB677154
EST:     GCATTGCTCCAGACTACGTTATAACAACAAAATCATTTGCTCCAGAGCTG                         GTTGACTCTTTAAAAAGAGTTTTGAAAAGGTTCTATGGGGAGGATCCTTTG
genomic: GCATTGCTCCAGACTACGTTATAACAACAAAATCATTTGCTCCAGAGCTGgtaaagaata ... ctttttgtagGTTGACTCTTTAAAAAGAGTTTTGAAAAGGTTCTATGGGGAGGATCCTTTG
EST: gi|29660175|gb|CB656450.1|CB656450
EST:     GCATTGCTCCAGACTACGTTATAACAACAAAATCATTTGCTCCAGAGCTG                         GTTGACTCTTTAAAAAGAGTTTTG
genomic: GCATTGCTCCAGACTACGTTATAACAACAAAATCATTTGCTCCAGAGCTGgtaaagaata ... ctttttgtagGTTGACTCTTTAAAAAGAGTTTTG
EST: gi|29660180|gb|CB656455.1|CB656455
EST:     GCATTGCTCCAGACTACGTTATAACAACAAAATCATTTGCTCCAGAGCTG                         GTTGACTCTTTAAAAAGAGTTTTGAAAAGGTTCTATGGGGAGGATCCTTTG
genomic: GCATTGCTCCAGACTACGTTATAACAACAAAATCATTTGCTCCAGAGCTGgtaaagaata ... ctttttgtagGTTGACTCTTTAAAAAGAGTTTTGAAAAGGTTCTATGGGGAGGATCCTTTG
EST: gi|29645892|gb|CB650899.1|CB650899
EST:     GCATTGCTCCAGACTACGTTATAACAACAAAATCATTTGCTCCAGAGCTG                         GTTGACTCTTTAAAAAGAGTTTTGAAAAGGTTCTATGGGGAGGATCCTTTG
genomic: GCATTGCTCCAGACTACGTTATAACAACAAAATCATTTGCTCCAGAGCTGgtaaagaata ... ctttttgtagGTTGACTCTTTAAAAAGAGTTTTGAAAAGGTTCTATGGGGAGGATCCTTTG
EST: gi|29643971|gb|CB648978.1|CB648978
EST:     GCATTGCTCCAGACTACGTTATAACAACAAAATCATTTGCTCCAGAGCTG                         GTTGACTCTTTAAAAAGAGTTTTGAAAAGGTTCTATGGGGAGGATCCTTTG
genomic: GCATTGCTCCAGACTACGTTATAACAACAAAATCATTTGCTCCAGAGCTGgtaaagaata ... ctttttgtagGTTGACTCTTTAAAAAGAGTTTTGAAAAGGTTCTATGGGGAGGATCCTTTG
EST: gi|58689115|gb|CK077802.1|CK077802
EST:     GCATTGCTCCAGACTACGTTATAACAACAAAATCATTTGCTCCAGAGCTG                         GTTGACTCTTTAAAAAGAGTTT
genomic: GCATTGCTCCAGACTACGTTATAACAACAAAATCATTTGCTCCAGAGCTGgtaaagaata ... ctttttgtagGTTGACTCTTTAAAAAGAGTTT
EST: gi|29666336|gb|CB662611.1|CB662611
EST:     GCATTGCTCCAGACTACGTTATAACAACAAAATCATTTGCTCCAGAGCTG                         GTTGACTCTTTAAAAAGAGTTTTGAAAAGGTTCTATGGGGAGGATCCTTTG
genomic: GCATTGCTCCAGACTACGTTATAACAACAAAATCATTTGCTCCAGAGCTGgtaaagaata ... ctttttgtagGTTGACTCTTTAAAAAGAGTTTTGAAAAGGTTCTATGGGGAGGATCCTTTG
EST: gi|29665740|gb|CB662015.1|CB662015
EST:     GCATTGCTCCAGACTACGTTATAACAACAAAATCATTTGCTCCAGAGCTG                         GTTGACTCTTTAAAAAGAGTTTTGAAAAGGTTCTATGGGGAGGATCCTTTG
genomic: GCATTGCTCCAGACTACGTTATAACAACAAAATCATTTGCTCCAGAGCTGgtaaagaata ... ctttttgtagGTTGACTCTTTAAAAAGAGTTTTGAAAAGGTTCTATGGGGAGGATCCTTTG
EST: gi|58691193|gb|CK079880.1|CK079880
EST:     GCATTGCTCCAGACTACGTTATAACAACAAAATCATTTGCTCCAGAGCTG                         GTTGACTCTTTAAAAAGAGTTTTGAAAAGGTTCTATGGGGAGGATCCTTTG
genomic: GCATTGCTCCAGACTACGTTATAACAACAAAATCATTTGCTCCAGAGCTGgtaaagaata ... ctttttgtagGTTGACTCTTTAAAAAGAGTTTTGAAAAGGTTCTATGGGGAGGATCCTTTG
EST: gi|58691525|gb|CK080212.1|CK080212
EST:     GCATTGCTCCAGACTACGTTATAACAACAAAATCATTTGCTCCAGAGCTG                         GTTGACTCTTTAAAAAGAGTCTTGAAAAGGTTCTATGGGGAGGATCCTTTG
genomic: GCATTGCTCCAGACTACGTTATAACAACAAAATCATTTGCTCCAGAGCTGgtaaagaata ... ctttttgtagGTTGACTCTTTAAAAAGAGTTTTGAAAAGGTTCTATGGGGAGGATCCTTTG
EST: gi|29630144|gb|CB635153.1|CB635153
EST:     GCATTGCTCCAGACTACGTTATAACAACAAAATCATTTGCTCCAGAGCTG                         GTTGACTCTTTAAAAAGAGTTTTGAAAAGGTTCTATGGGGAGGATCCTTTG
genomic: GCATTGCTCCAGACTACGTTATAACAACAAAATCATTTGCTCCAGAGCTGgtaaagaata ... ctttttgtagGTTGACTCTTTAAAAAGAGTTTTGAAAAGGTTCTATGGGGAGGATCCTTTG
EST: gi|29681705|gb|CB677980.1|CB677980
EST:     GCATTGCTCCAGACTACGTTATAACAACAAAATCATTTGCTCCAGAGCTG                         GTTGACTCTTTAAAA
genomic: GCATTGCTCCAGACTACGTTATAACAACAAAATCATTTGCTCCAGAGCTGgtaaagaata ... ctttttgtagGTTGACTCTTTAAAA
EST: gi|33675797|gb|CF304036.1|CF304036
EST:     GCATTGCTCCAGACTACGTTATAACAACAAAATCATTTGCTCCAGAGCTG                         GTTGACTCTTTAAAAAGAGTTTTGAAAAGGTTCTATAGGGGAGGATCCTTT
genomic: GCATTGCTCCAGACTACGTTATAACAACAAAATCATTTGCTCCAGAGCTGgtaaagaata ... ctttttgtagGTTGACTCTTTAAAAAGAGTTTTGAAAAGGTTCTAT-GGGGAGGATCCTTT
EST: gi|58694731|gb|CK083418.1|CK083418
EST:     GCATTGCTCCAGACTACGTTATAACAACAAAATCATTTGCTCCAGAGCTG                         GTTGACTCTTTAA
genomic: GCATTGCTCCAGACTACGTTATAACAACAAAATCATTTGCTCCAGAGCTGgtaaagaata ... ctttttgtagGTTGACTCTTTAA
EST: gi|88199260|gb|CI199110.1|CI199110
EST:     GCATTGCTCCAGACTACGTTATAACAACAAAATCATTTGCTCCAGAGCTG                         GTTGACTCTTTAAAAAGAGTTTTGAAAAGGTTCTATGGGGAGGATCCTTTG
genomic: GCATTGCTCCAGACTACGTTATAACAACAAAATCATTTGCTCCAGAGCTGgtaaagaata ... ctttttgtagGTTGACTCTTTAAAAAGAGTTTTGAAAAGGTTCTATGGGGAGGATCCTTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatagagctaattaaagtcctatttgcttagccatgaagctttcctttttgtagGTTGACTCTTTAAAAAGAGTTTTGAAAAGGTTCTATGGGGAGGATCCTTTGCAATCAGAAGACTTGTCCCGTATTGTGAATTCTAACCATTTCCGTAGAT
      agctaat  putative branch site (score: 3)
                                        ctttcctttttgt  putative PPT
         taattaaagt  TA-rich tract