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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGCAGTTAAAAAAATGAAGAGGAAGTTTTTCCAATGGGAAGAGTGCATTAGTCTGCGAGAGGTGAAGgtaatatatctcatgtgttatcaaatgaatacaaatttgttttcaaatctgtgtgcttaaaaggagaaccatccttctgcag

Basic information

species Oryza sativa
transcript LOC_Os03g63020.1
intron # 4
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|58694135|gb|CK082822.1|CK082822
EST:     AGAGGAAGTTTTTCCAATGGGAAGAGTGCATTAGTCTGCGAGAGGTGAAG                         GCACTTCAAAAACTGAATCATCCCAACATTGTGAAGTTAAAGGAGGTGACT
genomic: AGAGGAAGTTTTTCCAATGGGAAGAGTGCATTAGTCTGCGAGAGGTGAAGgtaatatatc ... ccttctgcagGCACTTCAAAAACTGAATCATCCCAACATTGTGAAGTTAAAGGAGGTGACT
EST: gi|58656490|gb|CK045170.1|CK045170
EST:     AGAGGAAGTTTTTCCAATGGGAAGAGTGCATTAGTCTGCGAGAGGTGAAG                         GCACTTCAAAAACTGAATCATCCCAACATTGTGAAGTTAAAGGAGGTGACT
genomic: AGAGGAAGTTTTTCCAATGGGAAGAGTGCATTAGTCTGCGAGAGGTGAAGgtaatatatc ... ccttctgcagGCACTTCAAAAACTGAATCATCCCAACATTGTGAAGTTAAAGGAGGTGACT
EST: gi|88324687|gb|CI587656.1|CI587656
EST:     AGAGGAAGTTTTTCCAATGGGAAGAGTGCATTAGTCTGCGAGAGGTGAAG                         GCACTTCAAAAACTGAATCATCCCAACATTGTGAAGTTAAAGGAGGTGACT
genomic: AGAGGAAGTTTTTCCAATGGGAAGAGTGCATTAGTCTGCGAGAGGTGAAGgtaatatatc ... ccttctgcagGCACTTCAAAAACTGAATCATCCCAACATTGTGAAGTTAAAGGAGGTGACT
EST: gi|29628840|gb|CB633851.1|CB633851
EST:     AGAGGAAGTTTTTCCAATGGGAAGAGTGCATTAGTCTGCGAGAGGTGAAG                         GCACTTCAAAAACTGAATCATCCCAACATTGTGAAGTTAAAGGAGGTGACT
genomic: AGAGGAAGTTTTTCCAATGGGAAGAGTGCATTAGTCTGCGAGAGGTGAAGgtaatatatc ... ccttctgcagGCACTTCAAAAACTGAATCATCCCAACATTGTGAAGTTAAAGGAGGTGACT
EST: gi|58692426|gb|CK081113.1|CK081113
EST:     AGAGGAAGTTTTTCCAATGGGAAGAGTGCATTAGTCTGCGAGAGGTGAAG                         GCACTTCAAAAACTGAATCATCCCAACATTGTGAAGTTAAAGGAGGTGACT
genomic: AGAGGAAGTTTTTCCAATGGGAAGAGTGCATTAGTCTGCGAGAGGTGAAGgtaatatatc ... ccttctgcagGCACTTCAAAAACTGAATCATCCCAACATTGTGAAGTTAAAGGAGGTGACT
EST: gi|29644978|gb|CB649985.1|CB649985
EST:     AGAGGAAGTTTTTCCAATGGGAAGAGTGCATTAGTCTGCGAGAGGTGAAG                         GCACTTCAAAAACTGAATCATCCCAACATTGTGAAGTTAAAGGAGGTGACT
genomic: AGAGGAAGTTTTTCCAATGGGAAGAGTGCATTAGTCTGCGAGAGGTGAAGgtaatatatc ... ccttctgcagGCACTTCAAAAACTGAATCATCCCAACATTGTGAAGTTAAAGGAGGTGACT
EST: gi|117226423|gb|CT848659.1|CT848659
EST:     AGAGGAAGTTTTTCCAATGGGAAGAGTGCATTAGTCTGCGAGAGGTGAAG                         GCACTTCAAAAACTGAATCATCCCAACATTGTGAAGTTAAAGGAGGTGACT
genomic: AGAGGAAGTTTTTCCAATGGGAAGAGTGCATTAGTCTGCGAGAGGTGAAGgtaatatatc ... ccttctgcagGCACTTCAAAAACTGAATCATCCCAACATTGTGAAGTTAAAGGAGGTGACT
EST: gi|29613394|gb|CB618407.1|CB618407
EST:     AGAGGAAGTTTTTCCAATGGGAAGAGTGCATTACTCTGCGAGAGGTGAAG                         GCACTTCAAAAACTGAATCATCCCAACATTGTGAAGTTAAAGGAGGTGACT
genomic: AGAGGAAGTTTTTCCAATGGGAAGAGTGCATTAGTCTGCGAGAGGTGAAGgtaatatatc ... ccttctgcagGCACTTCAAAAACTGAATCATCCCAACATTGTGAAGTTAAAGGAGGTGACT
EST: gi|29656191|gb|CB652466.1|CB652466
EST:     AGAGGAAGTTTTTCCAATGGGAAGAGTGCATTAGTCTGCGAGAGGTGAAG                         GCACTTCAAAAACTGAATCATCCCAACATTGTGAAGTTAAAGGAGGTGACT
genomic: AGAGGAAGTTTTTCCAATGGGAAGAGTGCATTAGTCTGCGAGAGGTGAAGgtaatatatc ... ccttctgcagGCACTTCAAAAACTGAATCATCCCAACATTGTGAAGTTAAAGGAGGTGACT
EST: gi|29613119|gb|CB618132.1|CB618132
EST:     AGAGGAAGTTTTTCCAATGGGAAGAGTGCATTAGTCTGCGAGAGGTGAAG                         GCACTTCAAAAACTGAATCATCCCAACATTGTGAAGTTAAAGGAGGTGACT
genomic: AGAGGAAGTTTTTCCAATGGGAAGAGTGCATTAGTCTGCGAGAGGTGAAGgtaatatatc ... ccttctgcagGCACTTCAAAAACTGAATCATCCCAACATTGTGAAGTTAAAGGAGGTGACT
EST: gi|29663526|gb|CB659801.1|CB659801
EST:     AGAGGAAGTTTTTCCAATGGGAAGAGTGCATTAGTCTGCGAGAGGTGAAG                         GCACTTCAAAAACTGAATCATCCCAACATTGTGAAGTTAAAGGAGGTGACT
genomic: AGAGGAAGTTTTTCCAATGGGAAGAGTGCATTAGTCTGCGAGAGGTGAAGgtaatatatc ... ccttctgcagGCACTTCAAAAACTGAATCATCCCAACATTGTGAAGTTAAAGGAGGTGACT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGCAGTTAAAAAAATGAAGAGGAAGTTTTTCCAATGGGAAGAGTGCATTAGTCTGCGAGAGGTGAAGgtaatatatctcatgtgttatcaaatgaatacaaatttgttttcaaatctgtgtgcttaaaaggagaaccatccttctgcag

- - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG