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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCAAGAATCTTCCGCATAAACCCTGGGAGGACCCGTCATTCTTTAGGTGGAGAAAGCGGGAGGCTCATGTGCCGTTGCGCTCACATGACACACCTGAAGgtagagattgcagcactgaacccagaaccactatgtaggtagatagaagatttggttgtacagtgattttcggattgatttgttttctcttgtcaatag

Basic information

species Oryza sativa
transcript LOC_Os01g72340.1
intron # 2
splice site 5'
intron type U2

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|88329338|gb|CI653252.1|CI653252
EST:     GAGAAAGCGGGAGGCTCATGTGCCGTTGCGCTCACATGACACACCTGAAG                         GAGCCCTCAAGTATTGGCATGAACGGAGGAATGTGAACTATCTTAATTCTG
genomic: GAGAAAGCGGGAGGCTCATGTGCCGTTGCGCTCACATGACACACCTGAAGgtagagattg ... ttgtcaatagGAGCCCTCAAGTATTGGCATGAACGGAGGAATGTGAACTATCTTAATTCTG
EST: gi|88576463|gb|CI670608.1|CI670608
EST:     GAGAAAGCGGGAGGCTCATGTGCCGTTGCGCTCACATGACACACCTGAAG                         GAGCCCTCAAGTATTGGCATGAACGGAGGAATGTGAACTATCTTAATTCTG
genomic: GAGAAAGCGGGAGGCTCATGTGCCGTTGCGCTCACATGACACACCTGAAGgtagagattg ... ttgtcaatagGAGCCCTCAAGTATTGGCATGAACGGAGGAATGTGAACTATCTTAATTCTG
EST: gi|88432766|gb|CI690614.1|CI690614
EST:     GAGAAAGCGGGAGGCTCATGTGCCGTTGCGCTCACATGACACACCTGAAG                         GAGCCCTCAAGTATTGGCATGAACGGAGGAATGTGAACTATCTTAATTCTG
genomic: GAGAAAGCGGGAGGCTCATGTGCCGTTGCGCTCACATGACACACCTGAAGgtagagattg ... ttgtcaatagGAGCCCTCAAGTATTGGCATGAACGGAGGAATGTGAACTATCTTAATTCTG
EST: gi|88422474|gb|CI571456.1|CI571456
EST:     GAGAAAGCGGGAGGCTCATGTGCCGTTGCGCTCACATGACACACCTGAAG                         GAGCCCTCAAGTATTGGCATGAACGGAGGAATGTGAACTATCTTAATTCTG
genomic: GAGAAAGCGGGAGGCTCATGTGCCGTTGCGCTCACATGACACACCTGAAGgtagagattg ... ttgtcaatagGAGCCCTCAAGTATTGGCATGAACGGAGGAATGTGAACTATCTTAATTCTG
EST: gi|88401622|gb|CI588563.1|CI588563
EST:     GAGAAAGCGGGAGGCTCATGTGCCGTTGCGCTAACATGACACACCTGAAG                         GAGCCCTCAAGTATTGGCATGAACGGAGGAATGTGAACTATCTTAATTCTG
genomic: GAGAAAGCGGGAGGCTCATGTGCCGTTGCGCTCACATGACACACCTGAAGgtagagattg ... ttgtcaatagGAGCCCTCAAGTATTGGCATGAACGGAGGAATGTGAACTATCTTAATTCTG
EST: gi|88365009|gb|CI616428.1|CI616428
EST:     GAGAAAGCGGGAGGCTCATGTGCCGTTGCGCTCACATGACACACCTGAAG                         GAGCCCTCAAGTATTGGCATGAACGGAGGAATGTGAACTATCTTAATTCTG
genomic: GAGAAAGCGGGAGGCTCATGTGCCGTTGCGCTCACATGACACACCTGAAGgtagagattg ... ttgtcaatagGAGCCCTCAAGTATTGGCATGAACGGAGGAATGTGAACTATCTTAATTCTG
EST: gi|88363573|gb|CI618134.1|CI618134
EST:     GAGAAAGCGGGAGGCTCATGTGCCGTTGCGCTCACATGACACACCTGAAG                         GAGCCCTCAAGTATTGGCATGAACGGAGGAATGTGAACTATCTTAATTCTG
genomic: GAGAAAGCGGGAGGCTCATGTGCCGTTGCGCTCACATGACACACCTGAAGgtagagattg ... ttgtcaatagGAGCCCTCAAGTATTGGCATGAACGGAGGAATGTGAACTATCTTAATTCTG
EST: gi|88370937|gb|CI595049.1|CI595049
EST:     GAGAAAGCGGGAGGCTCATGTGCCGTTGCGCTCACATGACACACCTGAAG                         GAGCCCTCAAGTATTGGCATGAACGGAGGAATGTGAACTATCTTAATTCTG
genomic: GAGAAAGCGGGAGGCTCATGTGCCGTTGCGCTCACATGACACACCTGAAGgtagagattg ... ttgtcaatagGAGCCCTCAAGTATTGGCATGAACGGAGGAATGTGAACTATCTTAATTCTG
EST: gi|29621652|gb|CB626663.1|CB626663
EST:     CTCACATGACACACCTGAAG                         GAGCCCTCAAGTATTGGCATGAACGGAGGAATGTGAACTATCTTAATTCTG
genomic: CTCACATGACACACCTGAAGgtagagattg ... ttgtcaatagGAGCCCTCAAGTATTGGCATGAACGGAGGAATGTGAACTATCTTAATTCTG
EST: gi|88393970|gb|CI684238.1|CI684238
EST:     GAGAAAGCGGGAGGCTCATGTGCCGTTGCGCTCACATGACACACCTGAAG                         GAGCCCTCAAGTATTGGCATGAACGGAGGAATGTGAACTATCTTAATTCTG
genomic: GAGAAAGCGGGAGGCTCATGTGCCGTTGCGCTCACATGACACACCTGAAGgtagagattg ... ttgtcaatagGAGCCCTCAAGTATTGGCATGAACGGAGGAATGTGAACTATCTTAATTCTG
EST: gi|58690363|gb|CK079050.1|CK079050
EST:     GAGAAAGCGGGAGGCTCATGTGCCGTTGCGCTCACATGACACACCTGAAG                         GAGCCCTCAAGTATTGGCATGAACGGAGGAATGTGAACTATCTTAATTCTG
genomic: GAGAAAGCGGGAGGCTCATGTGCCGTTGCGCTCACATGACACACCTGAAGgtagagattg ... ttgtcaatagGAGCCCTCAAGTATTGGCATGAACGGAGGAATGTGAACTATCTTAATTCTG
EST: gi|58668740|gb|CK057426.1|CK057426
EST:     GAGAAAGCGGGAGGCTCATGTGCCGTTGCGCTCACATGACACACCTGAAG                         GAGCCCTCAAGTATTGGCATGAACGGAGGAATGTGAACTATCTTAATTCTG
genomic: GAGAAAGCGGGAGGCTCATGTGCCGTTGCGCTCACATGACACACCTGAAGgtagagattg ... ttgtcaatagGAGCCCTCAAGTATTGGCATGAACGGAGGAATGTGAACTATCTTAATTCTG
EST: gi|88370912|gb|CI595024.1|CI595024
EST:     GAGAAAGCGGGAGGCTCATGTGCCGTTGCGCTCACATGACACACCTGAAG                         GAGCCCTCAAGTATT
genomic: GAGAAAGCGGGAGGCTCATGTGCCGTTGCGCTCACATGACACACCTGAAGgtagagattg ... ttgtcaatagGAGCCCTCAAGTATT
EST: gi|2428458|gb|C72921.1|C72921
EST:     GAGAAAGCGGGAGGCTCATGTGCCGTTGCGCTCACATGACACACCTGAAG                         GAGCCCTCAAGTATTGGCATGAACGGAGGAATGTGAACTATCTTAATTCTG
genomic: GAGAAAGCGGGAGGCTCATGTGCCGTTGCGCTCACATGACACACCTGAAGgtagagattg ... ttgtcaatagGAGCCCTCAAGTATTGGCATGAACGGAGGAATGTGAACTATCTTAATTCTG
EST: gi|88575002|gb|CI666771.1|CI666771
EST:     GAGAAAGCGGGAGGCTCATGTGCCGTTGCGCTCACATGACACACCTGAAG                         GAGCCCTCAAGTATTGGCATGAACGGAGGAATGTGAACTATCTTAATTCTG
genomic: GAGAAAGCGGGAGGCTCATGTGCCGTTGCGCTCACATGACACACCTGAAGgtagagattg ... ttgtcaatagGAGCCCTCAAGTATTGGCATGAACGGAGGAATGTGAACTATCTTAATTCTG
EST: gi|88361282|gb|CI626386.1|CI626386
EST:     AGAAAGCGGGAGGCTCATGTGCCGTTGCGCCTCACATGACACACCTGAAG                         GAGCCCTCAAGTATTGGCATGAACGGAGGAATGTGAACTATCTTAATTCTG
genomic: AGAAAGCGGGAGGCTCATGTGCCGTTGCGC-TCACATGACACACCTGAAGgtagagattg ... ttgtcaatagGAGCCCTCAAGTATTGGCATGAACGGAGGAATGTGAACTATCTTAATTCTG
EST: gi|88333029|gb|CI639877.1|CI639877
EST:     GAGAAAGCGGGAGGCTCATGTGCCGTTGCGCTCACATGACACACCTGAAG                         GAGCCCTCAAGTATTGGCATGAACGGAGGAATGTGAACTATCTTAATTCTG
genomic: GAGAAAGCGGGAGGCTCATGTGCCGTTGCGCTCACATGACACACCTGAAGgtagagattg ... ttgtcaatagGAGCCCTCAAGTATTGGCATGAACGGAGGAATGTGAACTATCTTAATTCTG
EST: gi|88390016|gb|CI590529.1|CI590529
EST:     GAGAAAGCGGGAGGCTCATGTGCCGTTGCGCTCACATGACACACCTGAAG                         GAGCCCTCAAGTATTGGCATGAAAGGAGGAATGTGAACTATCTTAATTCTG
genomic: GAGAAAGCGGGAGGCTCATGTGCCGTTGCGCTCACATGACACACCTGAAGgtagagattg ... ttgtcaatagGAGCCCTCAAGTATTGGCATGAACGGAGGAATGTGAACTATCTTAATTCTG
EST: gi|88393415|gb|CI618303.1|CI618303
EST:     GAGAAAGCGGGAGGCTCATGTGCCGTTGCGCTCACATGACACAACTGAAG                         GAGCCCTCAAGTATTGGCATGAACGGAGGAATGTGAACTATCTTAATTCTG
genomic: GAGAAAGCGGGAGGCTCATGTGCCGTTGCGCTCACATGACACACCTGAAGgtagagattg ... ttgtcaatagGAGCCCTCAAGTATTGGCATGAACGGAGGAATGTGAACTATCTTAATTCTG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 75 (upstream exon), 75 (downstream exon)
Score: 17

GCCAAGAATCTTCCGCATAAACCCTGGGAGGACCCGTCATTCTTTAGGTGGAGAAAGCGGGAGGCTCATGTGCCGTTGCGCTCACATGACACACCTGAAGgtagagattg ... ttgtcaatagGAGCCCTCAAGTATTGGCATGAACGGAGGAATGTGAACTATCTTAATTCTGACTCTGCTGTTTGGAATGATGACGCGGTTCGTGGTGCCCTGGAAAGTGC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCAAGAATCTTCCGCATAAACCCTGGGAGGACCCGTCATTCTTTAGGTGGAGAAAGCGGGAGGCTCATGTGCCGTTGCGCTCACATGACACACCTGAAGgtagagattgcagcactgaacccagaaccactatgtaggtagatagaagatttggttgtacagtgattttcggattgatttgttttctcttgtcaatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG