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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTAGATCGCTTCCGGAGACATCCAACCGCGGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGGgtgagtcccctttggatctgttatgtttatttaggggaccagttttcactgttttgtaagcatggaattcgaaaagagcggtgtttgattcctcccgtca...

Basic information

species Oryza sativa
transcript LOC_Os01g03070.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g03070.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G093050_T04 (Zea mays), 5'ss of exon 2
------GTGTAGATCGCTTCCGGAGACATCCAACCGCGGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGGgtgagtccc-----ctttggatctgttatgtttatttagggg-accagttttcactgttttgtaagcatggaattcgaaaagagcggtgtttgattcctcccgtca
      | ||||||||    |  |||     | || ||   |||||||| ||||||||||||||||||||||| |||||||| || |||||||  |     ||| |||||  ||   ||||| |  |||    |||| |   || | ||   ||         ||   |   |    |||     |  |    
GAGAAGGAGTAGATCGTCGACCCAGA-----ACCCTCGCTGATGGCGACTTTCGCGAAACCTGAGAACGCGCTGAAGAGAGCCGAAGgtgagttgctgggacttgggatcgatt---tttatctgcgggtggtagttgttgatgctatgcctgctgcatgcgggatttgtcagacccttgcgaattagca---
















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|88370850|gb|CI592616.1|CI592616
EST:     GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGG                         AGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
genomic: GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGGgtgagtcccc ... tctacttcagAGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
EST: gi|88726955|gb|CI750610.1|CI750610
EST:     GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGG                         AGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
genomic: GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGGgtgagtcccc ... tctacttcagAGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
EST: gi|88310182|gb|CI657606.1|CI657606
EST:     GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGG                         AGTTGATACATGTGGGGCAGAAGCAGGCAGCGCTACAGGCGTAACATGATC
genomic: GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGGgtgagtcccc ... tctacttcagAGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
EST: gi|88364312|gb|CI612261.1|CI612261
EST:     GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGG                         AGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
genomic: GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGGgtgagtcccc ... tctacttcagAGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
EST: gi|88347801|gb|CI655154.1|CI655154
EST:     GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGG                         AGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
genomic: GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGGgtgagtcccc ... tctacttcagAGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
EST: gi|88352152|gb|CI613803.1|CI613803
EST:     GGCCATGGCGACCTTCGCGAAAACTGAGAAAGCGCTCAAGAGAGCGGAGG                         AGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
genomic: GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGGgtgagtcccc ... tctacttcagAGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
EST: gi|88730926|gb|CI754539.1|CI754539
EST:     GGCCATGGCGACCTTCGCGAAACCTGAGAACGCACTCAAGAGAGCGGAGG                         AGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
genomic: GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGGgtgagtcccc ... tctacttcagAGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
EST: gi|88314718|gb|CI608177.1|CI608177
EST:     GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGG                         AGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
genomic: GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGGgtgagtcccc ... tctacttcagAGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
EST: gi|88390540|gb|CI609165.1|CI609165
EST:     GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGG                         AGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
genomic: GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGGgtgagtcccc ... tctacttcagAGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
EST: gi|88316752|gb|CI624194.1|CI624194
EST:     GGGCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGG                         AGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
genomic: GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGGgtgagtcccc ... tctacttcagAGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
EST: gi|88736241|gb|CI759749.1|CI759749
EST:     GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGG                         AGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
genomic: GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGGgtgagtcccc ... tctacttcagAGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
EST: gi|88719635|gb|CI743145.1|CI743145
EST:     GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGG                         AGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
genomic: GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGGgtgagtcccc ... tctacttcagAGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
EST: gi|88423421|gb|CI576546.1|CI576546
EST:     GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGG                         AGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
genomic: GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGGgtgagtcccc ... tctacttcagAGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
EST: gi|88312839|gb|CI589935.1|CI589935
EST:     GGCCATGGCGACCTTAGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGG                         AGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
genomic: GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGGgtgagtcccc ... tctacttcagAGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
EST: gi|29626201|gb|CB631212.1|CB631212
EST:     GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGG                         AGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
genomic: GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGGgtgagtcccc ... tctacttcagAGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
EST: gi|88421421|gb|CI569861.1|CI569861
EST:     GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGG                         AGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
genomic: GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGGgtgagtcccc ... tctacttcagAGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
EST: gi|88403718|gb|CI611373.1|CI611373
EST:     GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGG                         AGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
genomic: GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGGgtgagtcccc ... tctacttcagAGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
EST: gi|88731382|gb|CI754995.1|CI754995
EST:     GGCCATGGCGACCTTCGCGAAAACTGAGAACGCGCTCAAGAGAGCGGAGG                         AGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
genomic: GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGGgtgagtcccc ... tctacttcagAGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
EST: gi|88352132|gb|CI613783.1|CI613783
EST:     GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGG                         AGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
genomic: GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGGgtgagtcccc ... tctacttcagAGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
EST: gi|88316017|gb|CI618893.1|CI618893
EST:     GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGG                         AGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
genomic: GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGGgtgagtcccc ... tctacttcagAGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
EST: gi|88311895|gb|CI577501.1|CI577501
EST:     GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGG                         AGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
genomic: GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGGgtgagtcccc ... tctacttcagAGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
EST: gi|88389001|gb|CI595235.1|CI595235
EST:     GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGG                         AGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
genomic: GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGGgtgagtcccc ... tctacttcagAGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
EST: gi|88367768|gb|CI570507.1|CI570507
EST:     GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGG                         AGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
genomic: GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGGgtgagtcccc ... tctacttcagAGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGTAGATCGCTTCCGGAGACATCCAACCGCGGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGGgtgagtcccctttggatctgttatgtttatttaggggaccagttttcactgttttgtaagcatggaattcgaaaagagcggtgtttgattcctcccgtca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA