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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGACATCCTGCTTTTACCTGTTGGTGCTTACAGACTTTATCTTTTCAGGTGAACGTTAGTGAACTTGGTCTGGTAACCCCTGCTGGAAAAGTTGTTTGGGgtaaggcatctgttgaatgttctgcttattttgctttttaacttctccctggaacttgttccataaaacagcgttcttgtcgtgcag

Basic information

species Oryza sativa
transcript LOC_Os07g47580.2
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g47580.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G009876_T01 (Zea mays), 5'ss of exon 8
AGACATCCTGCTTTTACCTGTTGGTGCTTACAGACTTTATCTTTTCAGGTGAACGTTAGTGAACTTGGTCTGGTAACCCCTGCTGGAAAAGTTGTTTGGGgtaaggcatctgttgaatgttctgcttattttgctttttaacttctccctggaacttgttccataaaacagcgttcttgtcgtgcag
                                                || || || ||||| |||||||||||||| || ||||||||||||||||||||| ||  |||||   | | ||||| |  | ||  |    |||  || ||| || | ||||| || ||      |||||||  |||||
------------------------------------------------GTAAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGGgtgagaaatctgccaactcttctg-tgctctttttacccaac--ctaccttgaccctgttcaattaacagaatttcttgtgttgcag

upper sequence: LOC_Os07g47580.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G174204_T01 (Zea mays), 5'ss of exon 8
AGACATCCTGCTTTTACCTGTTGGTGCTTACAGACTTTATCTTTTCAGGTGAACGTTAGTGAACTTGGTCTGGTAACCCCTGCTGGAAAAGTTGTTTGGGgtaaggcatctgttgaatgttctgcttattttgctttttaacttctccctggaacttgttccataaaacagcgttcttgtcgtgcag
                                                || || || ||||| |||||||||||||| || ||||||||||||||||||||| ||  || ||   |   |||| ||  | ||||   | ||| |  || ||   | | ||| ||||| ||   | |||||  |||||
------------------------------------------------GTAAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGGgtgagaaatttgcc-agctttcttctcttcttgc---tcaaccta-ccttgagtccttttcaataaaccaaattgcttgtgttgcag

upper sequence: LOC_Os07g47580.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA10G00490.1 (Glycine max), 5'ss of exon 8
AGACATCCTGCTTTTACCTGTTGGTGCTTACAGACTTTATCTTTTCAGGTGAACGTTAGTGAACTTGGTCTGGTAACCCCTGCTGGAAAAGTTGTTTGGGgtaaggc-atctgttga--atgttctgcttattttgctttttaacttctccctggaacttgttccataaaacagcgttc-ttgtcg-tgcag
                                                ||||| || |||||||||||||| || || |||||||| |||||||| |||||||||   || | ||     |||| ||||||   |     | || || |  ||| || |  |    |  ||    |||    || | |||||
------------------------------------------------GTGAATGTCAGTGAACTTGGTCTTGTCACACCTGCTGGGAAAGTTGTGTGGGgtaagattattttttccttgtgttttgcttaccat-tgactgaaattttaactgaaattgatgtgttggaattttgtttgccgtggatgcag

upper sequence: LOC_Os07g47580.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA02G35500.1 (Glycine max), 5'ss of exon 8
AGACATCCTGCTTTTACCTGTTGGTGCTTACAGACTTTATCTTTTCAGGTGAACGTTAGTGAACTTGGTCTGGTAACCCCTGCTGGAAAAGTTGTTTGGGgtaaggc-atctgttga--atgttctgcttattttgctt--tttaacttctccctggaacttgttccataaaacagcgtt--cttgtcgtgcag
                                                ||||| || |||||||||||||| || || || ||||| |||||||| |||||||||   || ||||     |||| ||||| ||    ||   | || |  |  ||| || |  |    |  ||    |||  |  |   |||||
------------------------------------------------GTGAATGTCAGTGAACTTGGTCTTGTCACGCCGGCTGGGAAAGTTGTGTGGGgtaagattatttgttccttgtgttttgcttgttaccattgactcaaatcttaactgaaattgatgtgttggaattttgtttgccgggaatgcag

upper sequence: LOC_Os07g47580.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA10G10000.1 (Glycine max), 5'ss of exon 8
AGACATCCTGCTTTTACCTGTTGGTGCTTACAGACTTTATCTTTTCAGGTGAACGTTAGTGAACTTGGTCTGGTAACCCCTGCTGGAAAAGTTGTTTGGGgtaaggc-atctgttgaatgt--tctgcttattttgctttttaacttctccctggaacttgttccataaaacagcgttcttgtcgtgcag----
                                                ||||| || |||||||||||||| || || |||||||| |||||||| |||||||||   || ||||  ||||  | | ||||   |    |  || ||    ||| || |  |    |  ||    |||  || |||| |     
------------------------------------------------GTGAATGTCAGTGAACTTGGTCTTGTCACACCTGCTGGGAAAGTTGTGTGGGgtaagattatttgttccatgtgttttacttaccattgactgaaatttt---ctgaaattgatgtgttggaattttgtt--tgccgtgaatgcag

upper sequence: LOC_Os07g47580.2 (Oryza sativa), 5'ss of exon 7
lower sequence: EFJ37687 (Selaginella moellendorffii), 5'ss of exon 8
AGACATCCTGCTTTTACCTGTTGGTGCTTACAGACTTTATCTTTTCAGGTGAACGTTAGTGAACTTGGTCTGGTAACCCCTGCTGGAAAAGTTGTTTGGGgtaaggcatctgttgaatgttctgcttattttgctttttaacttctccctggaacttgttccataaaacagcgttcttgtcgtgcag
                                                || || ||||| || || || || ||||| ||||||||||||||||| |||||||||   | ||  ||      ||   |  ||  ||  ||||||  | |   | ||||   |  |                      
------------------------------------------------GTAAATGTTAGCGAGCTCGGACTCGTAACTCCTGCTGGAAAAGTTGTATGGGgtaagat-tttggcgatccgattgaaaacgtt--ttgctaactttactc---atcttgcctctcag---------------------

upper sequence: LOC_Os07g47580.2 (Oryza sativa), 5'ss of exon 7
lower sequence: EFJ15002 (Selaginella moellendorffii), 5'ss of exon 8
AGACATCCTGCTTTTACCTGTTGGTGCTTACAGACTTTATCTTTTCAGGTGAACGTTAGTGAACTTGGTCTGGTAACCCCTGCTGGAAAAGTTGTTTGGGgtaaggcatctgttgaatgttctgcttattttgctttttaacttctccctggaacttgttccataaaacagcgttcttgtcgtgcag
                                                || || ||||| || || || || ||||| ||||||||||||||||| |||||||||   |  |    | | | ||   |  ||  ||  ||||||  | |   | ||||   |  |                      
------------------------------------------------GTAAATGTTAGCGAGCTCGGACTCGTAACTCCTGCTGGAAAAGTTGTATGGGgtaagattttggcgatacgat-tgaaaacgtt--ttgctaactttactc---atcttgcctctcag---------------------

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|58691701|gb|CK080388.1|CK080388
EST:     GAACGTTAGTGAACTTGGTCTGGTAACCCCTGCTGGAAAAGTTGTTTGGG                         GTAAATATGCACAAGTTACAAACAACCCAGAGAATGATGGCTGTATCAATG
genomic: GAACGTTAGTGAACTTGGTCTGGTAACCCCTGCTGGAAAAGTTGTTTGGGgtaaggcatc ... tgtcgtgcagGTAAATATGCACAAGTTACAAACAACCCAGAGAATGATGGCTGTATCAATG
EST: gi|88841817|gb|CI081073.1|CI081073
EST:     GAACGTTAGTGAACTTGGTCTGGTAACCCCTGCTGGAAAAGTTGTTTGGG                         GTAAATATGCACAAGTTACAAACAACCCAGAGAATGATGGCTGTATCAATG
genomic: GAACGTTAGTGAACTTGGTCTGGTAACCCCTGCTGGAAAAGTTGTTTGGGgtaaggcatc ... tgtcgtgcagGTAAATATGCACAAGTTACAAACAACCCAGAGAATGATGGCTGTATCAATG
EST: gi|88906732|gb|CI375804.1|CI375804
EST:     GAACGTTAGTGAACTTGGTCTGGTAACCCCTGCTGGAAAAGTTGTTTGGG                         GTAAATATGCACAAGTTACAAACAACCCAGAGAATGATGGCTGTATCAATG
genomic: GAACGTTAGTGAACTTGGTCTGGTAACCCCTGCTGGAAAAGTTGTTTGGGgtaaggcatc ... tgtcgtgcagGTAAATATGCACAAGTTACAAACAACCCAGAGAATGATGGCTGTATCAATG
EST: gi|89180335|gb|CI044614.1|CI044614
EST:     GAACGTTAGTGAACTTGGTCTGGTAACCCCTGCTGGAAAAGTTGTTTGGG                         GTAAATATGCACAAGTTACAAACAACCCAGAGAATGATGGCTGTATCAATG
genomic: GAACGTTAGTGAACTTGGTCTGGTAACCCCTGCTGGAAAAGTTGTTTGGGgtaaggcatc ... tgtcgtgcagGTAAATATGCACAAGTTACAAACAACCCAGAGAATGATGGCTGTATCAATG
EST: gi|33658151|gb|CF280765.1|CF280765
EST:     GAACGTTAGTGAACTTGGTCTGGTAACCCCTGCTGGAAAAGTTGTTTGGG                         GTAAATATGCACAAGTTTCAAACAACCCAGAGAATGATGGCTGTATCAATG
genomic: GAACGTTAGTGAACTTGGTCTGGTAACCCCTGCTGGAAAAGTTGTTTGGGgtaaggcatc ... tgtcgtgcagGTAAATATGCACAAGTTACAAACAACCCAGAGAATGATGGCTGTATCAATG
EST: gi|86412923|gb|CI067328.1|CI067328
EST:     GAACGTTAGTGAACTTGGTCTGGTAACCCCTGCTGGAAAAGTTGTTTGGG                         GTAAATATGCACAAGTTACAAACAACCCAGAGAATGATGGCTGTATCAATG
genomic: GAACGTTAGTGAACTTGGTCTGGTAACCCCTGCTGGAAAAGTTGTTTGGGgtaaggcatc ... tgtcgtgcagGTAAATATGCACAAGTTACAAACAACCCAGAGAATGATGGCTGTATCAATG
EST: gi|88466867|gb|CI539663.1|CI539663
EST:     GAACGTTAGTGAACTTGGTCTGGTAACCCCTGCTGGAAAAGTTGTTTGGG                         GTAAATATGCACAAGTTACAAACAACCCAGAGAATGATGGCTGTATCAATG
genomic: GAACGTTAGTGAACTTGGTCTGGTAACCCCTGCTGGAAAAGTTGTTTGGGgtaaggcatc ... tgtcgtgcagGTAAATATGCACAAGTTACAAACAACCCAGAGAATGATGGCTGTATCAATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGACATCCTGCTTTTACCTGTTGGTGCTTACAGACTTTATCTTTTCAGGTGAACGTTAGTGAACTTGGTCTGGTAACCCCTGCTGGAAAAGTTGTTTGGGgtaaggcatctgttgaatgttctgcttattttgctttttaacttctccctggaacttgttccataaaacagcgttcttgtcgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA