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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAGCAACATCGCCGCCGCCACCGCCAGCCGCAACAGCACCGACGACGAGGACGAGCTGAGAATACGAGGCGATGCCGAAATCCAAGCGCAACCGCCCTGgtaactgcatctaatccctatactccgcggcgattcgttgctcatccatctatctgactgattctattcttacctcgctcatatcctatcttttgcaatt...

Basic information

species Oryza sativa
transcript LOC_Os12g01430.1
intron # 1
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|33798312|gb|CF325013.1|CF325013
EST:     GAGGAGCTGAGAATACGAGGCGATGCCGAAATCCAAGCGCAACCGCCCTG                         TAACCTTATCCAAGACCAAGAAGAAGCCTGGATTAGAGCGCAAGGGCAAAG
genomic: GACGAGCTGAGAATACGAGGCGATGCCGAAATCCAAGCGCAACCGCCCTGgtaactgcat ... tcgagcgcagTAACCTTATCCAAGACCAAGAAGAAGCCTGGATTAGAGCGCAAGGGCAAAG
EST: gi|33822729|gb|CF337172.1|CF337172
EST:     GAGGAGCTGAGAATACGAGGCGATGCCGAAATCCAAGCGCAACCGCCCTG                         TAACCTTATCCAAGACCAAGAAGAAGCCTGGATTAGAGCGCAAGGGCAAAG
genomic: GACGAGCTGAGAATACGAGGCGATGCCGAAATCCAAGCGCAACCGCCCTGgtaactgcat ... tcgagcgcagTAACCTTATCCAAGACCAAGAAGAAGCCTGGATTAGAGCGCAAGGGCAAAG
EST: gi|88728599|gb|CI752109.1|CI752109
EST:     GACGAGCTGAGAATACGAGGCGATGCCGAAATCCAAGCGCAACCGCCCTG                         TAACCTTATCCAAGACCAAGAAGAAGCCTGGATTAGAGCGCAAGGGCAAAG
genomic: GACGAGCTGAGAATACGAGGCGATGCCGAAATCCAAGCGCAACCGCCCTGgtaactgcat ... tcgagcgcagTAACCTTATCCAAGACCAAGAAGAAGCCTGGATTAGAGCGCAAGGGCAAAG
EST: gi|88296130|gb|CI667520.1|CI667520
EST:     GACGAGCTGAGAATACGAGGCGATGCCGAAATCCAAGCGCAACCGCCCTG                         TAACCTTATCCAAGACCAAGAAGAAGCCTGGATTAGAGCGCAAGGGCAAAG
genomic: GACGAGCTGAGAATACGAGGCGATGCCGAAATCCAAGCGCAACCGCCCTGgtaactgcat ... tcgagcgcagTAACCTTATCCAAGACCAAGAAGAAGCCTGGATTAGAGCGCAAGGGCAAAG
EST: gi|33686639|gb|CF314878.1|CF314878
EST:     GACGAGCTGAGAATACGAGGCGATGCCGAAATCCAAGCGCAACCGCCCTG                         TAACCTTATCCAAGACCAAGAAGAAGCCTGGATTAGAGCGCAAGGGCAAAG
genomic: GACGAGCTGAGAATACGAGGCGATGCCGAAATCCAAGCGCAACCGCCCTGgtaactgcat ... tcgagcgcagTAACCTTATCCAAGACCAAGAAGAAGCCTGGATTAGAGCGCAAGGGCAAAG
EST: gi|163918505|gb|EG711435.1|EG711435
EST:     AGAATACGAGGCGATGCCGAAATCCAAGCGCAACCGCCCTG                         TAACCTTATCCAAGACCAAGAAGAAGCCTGGATTAGAGCGCAAGGGCAAAG
genomic: AGAATACGAGGCGATGCCGAAATCCAAGCGCAACCGCCCTGgtaactgcat ... tcgagcgcagTAACCTTATCCAAGACCAAGAAGAAGCCTGGATTAGAGCGCAAGGGCAAAG
EST: gi|33798269|gb|CF324991.1|CF324991
EST:     GAGGAGCTGAGAATACGAGGCGATGCCGAAATCCAAGCGCAACCGCCCTG                         TAACCTTATCCAAGACCAAGAAGAAGCCTGGATTAGAGCGCAAGGGCAAAG
genomic: GACGAGCTGAGAATACGAGGCGATGCCGAAATCCAAGCGCAACCGCCCTGgtaactgcat ... tcgagcgcagTAACCTTATCCAAGACCAAGAAGAAGCCTGGATTAGAGCGCAAGGGCAAAG
EST: gi|88342605|gb|CI656127.1|CI656127
EST:     GAGGAGCTGAGAATACGAGGCGATGCCGAAATCCAAGCGCAACCGCCCTG                         TAACCTTATCCAAGACCAAGAAGAAGCCTGGATTAGAGCGCAAGGGCAAAG
genomic: GACGAGCTGAGAATACGAGGCGATGCCGAAATCCAAGCGCAACCGCCCTGgtaactgcat ... tcgagcgcagTAACCTTATCCAAGACCAAGAAGAAGCCTGGATTAGAGCGCAAGGGCAAAG
EST: gi|55440809|gb|CV733716.1|CV733716
EST:     GAGGAGCTGAGAATACGAGGCGATGCCGAAATCCAAGCGCAACCGCCCTG                         TAACCTTATCCAAGACCAAGAAGAAGCCTGGATTAGAGCGCAAGGGCAAAG
genomic: GACGAGCTGAGAATACGAGGCGATGCCGAAATCCAAGCGCAACCGCCCTGgtaactgcat ... tcgagcgcagTAACCTTATCCAAGACCAAGAAGAAGCCTGGATTAGAGCGCAAGGGCAAAG
EST: gi|88454180|gb|CI694474.1|CI694474
EST:     GAGGAGCTGAGAATACGAGGCGATGCCGAAATCCAAGCGCAACCGCCCTG                         TAACCTTATCCAAGACCAAGAAGAAGCCTGGATTAGAGCGCAAGGGCAAAG
genomic: GACGAGCTGAGAATACGAGGCGATGCCGAAATCCAAGCGCAACCGCCCTGgtaactgcat ... tcgagcgcagTAACCTTATCCAAGACCAAGAAGAAGCCTGGATTAGAGCGCAAGGGCAAAG
EST: gi|88722956|gb|CI746466.1|CI746466
EST:     GAGGAGCTGAGAATACGAGGCGATGCCGAAATCCAAGCGCAACCGCCCTG                         TAACCTTATCCAAGACCAAGAAGAAGCCTGGATTAGAGCGCAAGGGCAAAG
genomic: GACGAGCTGAGAATACGAGGCGATGCCGAAATCCAAGCGCAACCGCCCTGgtaactgcat ... tcgagcgcagTAACCTTATCCAAGACCAAGAAGAAGCCTGGATTAGAGCGCAAGGGCAAAG
EST: gi|88347469|gb|CI637409.1|CI637409
EST:     GACGAGCTGAGAATACGAGGCGATGCCGAAATCCAAGCGCAACCGCCCTG                         TAACCTTATCCAAGACCAAGAAGAAGCCTGGATTAGAGCGCAAGGGCAAAG
genomic: GACGAGCTGAGAATACGAGGCGATGCCGAAATCCAAGCGCAACCGCCCTGgtaactgcat ... tcgagcgcagTAACCTTATCCAAGACCAAGAAGAAGCCTGGATTAGAGCGCAAGGGCAAAG
EST: gi|218490970|gb|FG950243.1|FG950243
EST:     GACGAGCTGAGAATACGAGGCGATGCCGAAATCCAAGCGCAACCGCCCTG                         TAACCTTATCCAAGACCAAGAAGAAGCCTGGATTAGAGCGCAAGGGCAAAG
genomic: GACGAGCTGAGAATACGAGGCGATGCCGAAATCCAAGCGCAACCGCCCTGgtaactgcat ... tcgagcgcagTAACCTTATCCAAGACCAAGAAGAAGCCTGGATTAGAGCGCAAGGGCAAAG
EST: gi|163925538|gb|EG713379.1|EG713379
EST:     CAACCGCCCTG                         TAACCTTATCCAAGACCAAGAAGAAGCCTGGATTAGAGCGCAAGGGCAAAG
genomic: CAACCGCCCTGgtaactgcat ... tcgagcgcagTAACCTTATCCAAGACCAAGAAGAAGCCTGGATTAGAGCGCAAGGGCAAAG
EST: gi|88302253|gb|CI668099.1|CI668099
EST:     GACGAGCTGAGAATACGAGGCGATGCCGAAATCCAAGCGCAACCGCCCTG                         TAACCTTATCCAAGACCAAGAAGAAGCCTGGATTAGAGCGCAAGGGCAAAG
genomic: GACGAGCTGAGAATACGAGGCGATGCCGAAATCCAAGCGCAACCGCCCTGgtaactgcat ... tcgagcgcagTAACCTTATCCAAGACCAAGAAGAAGCCTGGATTAGAGCGCAAGGGCAAAG
EST: gi|88302497|gb|CI668343.1|CI668343
EST:     GACGAGCTGAGAATACGAGGCGATGCCGAAATCCAAGCGCAACCGCCCTG                         TAACCTTATCCAAGACCAAGAAGAAGCCTGGATTAGAGCGCAAGGGCAAAG
genomic: GACGAGCTGAGAATACGAGGCGATGCCGAAATCCAAGCGCAACCGCCCTGgtaactgcat ... tcgagcgcagTAACCTTATCCAAGACCAAGAAGAAGCCTGGATTAGAGCGCAAGGGCAAAG
EST: gi|88294157|gb|CI667131.1|CI667131
EST:     GACGAGCTGAGAATACGAGGCGATGCCGAAATCCAAGCGCAACCGCCCTG                         TAACCTTATCCAAGACCAAGAAGAAGCCTGGATTAGAGCGCAAGGGCAAAG
genomic: GACGAGCTGAGAATACGAGGCGATGCCGAAATCCAAGCGCAACCGCCCTGgtaactgcat ... tcgagcgcagTAACCTTATCCAAGACCAAGAAGAAGCCTGGATTAGAGCGCAAGGGCAAAG
EST: gi|218498120|gb|FG965520.1|FG965520
EST:     ACGAGCTGAGAATACGA-GCGAGTGCCGAAATCCAAGCGCAACCGCCCTG                         TAACCTTATCCAAGACCAAGAAGAAGCCTGGATTA-AGCGCAAGGGC-AAG
genomic: ACGAGCTGAGAATACGAGGCGA-TGCCGAAATCCAAGCGCAACCGCCCTGgtaactgcat ... tcgagcgcagTAACCTTATCCAAGACCAAGAAGAAGCCTGGATTAGAGCGCAAGGGCAAAG
EST: gi|88301855|gb|CI667701.1|CI667701
EST:     GACGAGCTGAGAATACGAGGCGATGCCGAAATCCAAGCGCAACCGCCCTG                         TAACCTTATCCAAGACCAAGAAGAAGCCTGGATTAGAGCGCAAGGGCAAAG
genomic: GACGAGCTGAGAATACGAGGCGATGCCGAAATCCAAGCGCAACCGCCCTGgtaactgcat ... tcgagcgcagTAACCTTATCCAAGACCAAGAAGAAGCCTGGATTAGAGCGCAAGGGCAAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAGCAACATCGCCGCCGCCACCGCCAGCCGCAACAGCACCGACGACGAGGACGAGCTGAGAATACGAGGCGATGCCGAAATCCAAGCGCAACCGCCCTGgtaactgcatctaatccctatactccgcggcgattcgttgctcatccatctatctgactgattctattcttacctcgctcatatcctatcttttgcaatt

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