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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATGAAGAGGCTAGCTGTTGGCAAGTGGGGATGTAACAACGGGCAGGCATGCATTGCTCCAGACTACGTTATAACAACAAAATCATTTGCTCCAGAGCTGgtaaagaataccatgcacattagacctaaagaagttatagagctaattaaagtcctatttgcttagccatgaagctttcctttttgtag

Basic information

species Oryza sativa
transcript LOC_Os11g08300.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g08300.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G060800_T02 (Zea mays), 5'ss of exon 5
CATGAAGAGGCTAGCTGTTGGCAAGTGGGGATGTAACAACGGGCAGGCATGCATTGCTCCAGACTACGTTATAACAACAAAATCATTTGCTCCAGAGCTGgtaaagaataccatgcacattagacctaaagaagttatagagctaattaaagtcctatttgcttagccatgaagctttcctttttgtag
    |||||| | | ||||||||| |||||||| |||||||| || ||||||||||||||||| ||| | ||||| |||||||||||||| || ||||||||| |||  |||| | |  ||       |  ||   | | |   || |    |  | | | |   |   | ||  |      || | ||
TGCTAAGAGGATTGTTGTTGGCAAATGGGGATGCAACAACGGCCAAGCATGCATTGCTCCAGATTACATCATAACGACAAAATCATTTGCACCGGAGCTGgtatagataaccaaggatttt--cttgcacaaaacgagacactgaacttgcattttctgttccatgaagtaaatgtaaatccttggcag

upper sequence: LOC_Os11g08300.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G118800_T01 (Zea mays), 5'ss of exon 6
CATGAAGAGGCTAGCTGTTGGCAAGTGGGGATGTAACAACGGGCAGGCATGCATTGCTCCAGACTACGTTATAACAACAAAATCATTTGCTCCAGAGCTGgtaaaga---ata-ccatgcacattagacct---------aaagaagtt-----atagagctaattaaagtcctatttgcttagccatgaagctt------------tcctttttgtag
| | |||||| | | ||||||||| |||||||| |||||||| || ||||||||||| ||||||||| | ||||| |||||||||||||| |||||||||||| |||   ||| ||| | ||| |  | ||         || ||         | | |   || |  | |   | || || | || |||||               ||||||| | ||
CGTCAAGAGGATCGTTGTTGGCAAATGGGGATGCAACAACGGCCAAGCATGCATTGCCCCAGACTACATCATAACGACAAAATCATTTGCGCCAGAGCTGgtatagatagataaccacgaacactgtaactttcttgcgcaaggagaaccaaaaaaaaaaaaaactggattttcaatttctgacccgtgaagtaaaaaaaatgtaaatccttttggcag
















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

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATGAAGAGGCTAGCTGTTGGCAAGTGGGGATGTAACAACGGGCAGGCATGCATTGCTCCAGACTACGTTATAACAACAAAATCATTTGCTCCAGAGCTGgtaaagaataccatgcacattagacctaaagaagttatagagctaattaaagtcctatttgcttagccatgaagctttcctttttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT