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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGATTTGAAGCTGATGGTTGACACCAACCTAGAGGCTTATAGATTATCCATCTCCTGGTCGAGGATTATTCCAAgtatgagcatttcagaagattttttattgttgtacttgtatgcaagaattttcaacattatttctaatttcttgtttttgaaactaacgtttttcag

Basic information

species Oryza sativa
transcript LOC_Os01g70520.1
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|29612788|gb|CB617801.1|CB617801
EST:     TAACCTAGAGGCTTATAGATTATCCATCTCCTGGTCGAGGATTATTCCAA                         ATGGGAGGGGTGATGTCAATCCAAAAGGGCTACAATACTACAATGACATCA
genomic: CAACCTAGAGGCTTATAGATTATCCATCTCCTGGTCGAGGATTATTCCAAgtatgagcat ... cgtttttcagATGGGAGGGGTGATGTCAATCCAAAAGGGCTACAATACTACAATGACATCA
EST: gi|29620623|gb|CB625634.1|CB625634
EST:     TAACCTAGAGGCTTATACATTATCCATCTCCTGGTCGAGGATTATTCCAA                         ATGGGAGGGGTGATGTCAATCCAAAAGGGCTACTATACTACAATGACATCA
genomic: CAACCTAGAGGCTTATAGATTATCCATCTCCTGGTCGAGGATTATTCCAAgtatgagcat ... cgtttttcagATGGGAGGGGTGATGTCAATCCAAAAGGGCTACAATACTACAATGACATCA
EST: gi|58678434|gb|CK067121.1|CK067121
EST:     CAACCTAGAGGCTTATAGATTATCCATCTCCTGGTCGAGGATTATTCCAA                         ATGGGAGGGGTGATGTCAATCCAAAAGGGCTACAATACTACAATGACATCA
genomic: CAACCTAGAGGCTTATAGATTATCCATCTCCTGGTCGAGGATTATTCCAAgtatgagcat ... cgtttttcagATGGGAGGGGTGATGTCAATCCAAAAGGGCTACAATACTACAATGACATCA
EST: gi|58587977|gb|CF986285.1|CF986285
EST:     TAACCTAGAGGCTTATAGATTATCCATCTCCTGGTCGAGGATTATTCCAA                         ATGGGAGGGGTGATGTCAATCCAAAAGGGCTACAATACTACAATGACATCA
genomic: CAACCTAGAGGCTTATAGATTATCCATCTCCTGGTCGAGGATTATTCCAAgtatgagcat ... cgtttttcagATGGGAGGGGTGATGTCAATCCAAAAGGGCTACAATACTACAATGACATCA
EST: gi|88420750|gb|CI564586.1|CI564586
EST:     AACCCTAGAGGCTTATAGATTATCCATCTCCTGGTCGAGGATTATTC-AA                         ATGGGAGGGGTGATGTCAATC-AAAAGGGCTA-AATACTACAATGACATCA
genomic: AACC-TAGAGGCTTATAGATTATCCATCTCCTGGTCGAGGATTATTCCAAgtatgagcat ... cgtttttcagATGGGAGGGGTGATGTCAATCCAAAAGGGCTACAATACTACAATGACATCA
EST: gi|88313076|gb|CI592360.1|CI592360
EST:     CAACCTAGAGGCTTATAGATTATCCATCTCCTGGTCGAGGATTATTCCAA                         ATGGGAGGGGTGATGTCAATCCAAAAGGGCTACAATACTACAATGACATCA
genomic: CAACCTAGAGGCTTATAGATTATCCATCTCCTGGTCGAGGATTATTCCAAgtatgagcat ... cgtttttcagATGGGAGGGGTGATGTCAATCCAAAAGGGCTACAATACTACAATGACATCA
EST: gi|88454325|gb|CI569897.1|CI569897
EST:     CAACCTAGAGGCTTATAGATTATCCATCTCCTGGTCGAGGATTAT-CCAA                         ATGGGAGGGGTGATGTCA-TCCAAAAGGGCTACCATACTACA
genomic: CAACCTAGAGGCTTATAGATTATCCATCTCCTGGTCGAGGATTATTCCAAgtatgagcat ... cgtttttcagATGGGAGGGGTGATGTCAATCCAAAAGGGCTACAATACTACA
EST: gi|29619009|gb|CB624021.1|CB624021
EST:     TAACCTAGAGGCTTATAGATTATCCATCTCCTGGTCGAGGATTATTCCAA                         ATGGGAGGGGTGATGTCAATCCAAAAGGGCTACAATACTACAATGACATCA
genomic: CAACCTAGAGGCTTATAGATTATCCATCTCCTGGTCGAGGATTATTCCAAgtatgagcat ... cgtttttcagATGGGAGGGGTGATGTCAATCCAAAAGGGCTACAATACTACAATGACATCA
EST: gi|58593808|gb|CF992116.1|CF992116
EST:     TAACCTAGAGGCTTATAGATTATCCATCTCCTGGTCGAGGATTATTCCAA                         ATGGGAGGGGTGATGTCAATCCAAAAGGGCTACAATACTACAATGACATCA
genomic: CAACCTAGAGGCTTATAGATTATCCATCTCCTGGTCGAGGATTATTCCAAgtatgagcat ... cgtttttcagATGGGAGGGGTGATGTCAATCCAAAAGGGCTACAATACTACAATGACATCA
EST: gi|117242417|gb|CT842994.1|CT842994
EST:     TAACCTAGAGGCTTATAGATTATCCATCTCCTGGTCGAGGATTATTCCAA                         ATGGGAGGGGTGATGTCAATCCAAAAGGGCTACAATACTACAATGACATCA
genomic: CAACCTAGAGGCTTATAGATTATCCATCTCCTGGTCGAGGATTATTCCAAgtatgagcat ... cgtttttcagATGGGAGGGGTGATGTCAATCCAAAAGGGCTACAATACTACAATGACATCA
EST: gi|29614528|gb|CB619541.1|CB619541
EST:     TAACCTAGAGGCTTATAGATTATCCATCTCCTGGTCGAGGATTATTCCAA                         ATGGGAGGGGTGATGTCAATCCAAAAGGGCTACAATACTACAATGACATCA
genomic: CAACCTAGAGGCTTATAGATTATCCATCTCCTGGTCGAGGATTATTCCAAgtatgagcat ... cgtttttcagATGGGAGGGGTGATGTCAATCCAAAAGGGCTACAATACTACAATGACATCA
EST: gi|58609911|gb|CK037944.1|CK037944
EST:     TAACCTAGAGGCTTATAGATTATCCATCTCCTGGTCGAGGATTATTCCAA                         ATGGGAGGGGTGATGTCAATCCACAAGGGCTACAATACTACAATGACATCA
genomic: CAACCTAGAGGCTTATAGATTATCCATCTCCTGGTCGAGGATTATTCCAAgtatgagcat ... cgtttttcagATGGGAGGGGTGATGTCAATCCAAAAGGGCTACAATACTACAATGACATCA
EST: gi|58689675|gb|CK078362.1|CK078362
EST:     TAACCTAGAGGCTTATAGATTATCCATCTCCTGGTCGAGGATTATTCCAA                         ATGGGAGGGGTGATGTCAATCCAAAAGGGCTACAATACTACAATGACATCA
genomic: CAACCTAGAGGCTTATAGATTATCCATCTCCTGGTCGAGGATTATTCCAAgtatgagcat ... cgtttttcagATGGGAGGGGTGATGTCAATCCAAAAGGGCTACAATACTACAATGACATCA
EST: gi|88454346|gb|CI569918.1|CI569918
EST:     CAACCTAGAGGCTTATAGATTATCCATCTCCTGGTCGAGGATTATTCCAA                         ATGGGAGGGGTGATGTCAATCCAAAAGGGCTACAATACTACAATGACATCA
genomic: CAACCTAGAGGCTTATAGATTATCCATCTCCTGGTCGAGGATTATTCCAAgtatgagcat ... cgtttttcagATGGGAGGGGTGATGTCAATCCAAAAGGGCTACAATACTACAATGACATCA

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGATTTGAAGCTGATGGTTGACACCAACCTAGAGGCTTATAGATTATCCATCTCCTGGTCGAGGATTATTCCAAgtatgagcatttcagaagattttttattgttgtacttgtatgcaagaattttcaacattatttctaatttcttgtttttgaaactaacgtttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT