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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggttgttcgagccatgctagaaatcctatgcacagatacttggatttgttagatgatatatttggtttttgccctattatatctgctggaagaaagtactcactatgtacactgttgtgataaacatattttatttttcactaaaaaactgcagGAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCAACGTCCGAGTTCCAAC

Basic information

species Oryza sativa
transcript LOC_Os12g07060.1
intron # 16
splice site 3'
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|218480866|gb|FG958004.1|FG958004
EST:     GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGAGCAAAG                         GAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
genomic: GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAGgttggttgtt ... aaaactgcagGAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
EST: gi|218491432|gb|FG970302.1|FG970302
EST:     GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG                         GAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
genomic: GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAGgttggttgtt ... aaaactgcagGAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
EST: gi|33806065|gb|CF328912.1|CF328912
EST:     GGTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCTTCAGGGGCAAAG                         GAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
genomic: GGTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAGgttggttgtt ... aaaactgcagGAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
EST: gi|218496597|gb|FG964017.1|FG964017
EST:     GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG                         GAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
genomic: GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAGgttggttgtt ... aaaactgcagGAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
EST: gi|86478861|gb|CI121494.1|CI121494
EST:     GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG                         GAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
genomic: GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAGgttggttgtt ... aaaactgcagGAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
EST: gi|33806063|gb|CF328911.1|CF328911
EST:     GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG                         GAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
genomic: GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAGgttggttgtt ... aaaactgcagGAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
EST: gi|89175720|gb|CI042741.1|CI042741
EST:     GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG                         GAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
genomic: GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAGgttggttgtt ... aaaactgcagGAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
EST: gi|88845990|gb|CI084720.1|CI084720
EST:     GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG                         GAATAAAAGCACGGAATTCCCCAGCCTATGGGAGTCAGTATATTCACTTCA
genomic: GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAGgttggttgtt ... aaaactgcagGAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
EST: gi|88228631|gb|CI228111.1|CI228111
EST:     GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG                         GAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
genomic: GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAGgttggttgtt ... aaaactgcagGAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
EST: gi|58680289|gb|CK068976.1|CK068976
EST:     GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG                         GAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
genomic: GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAGgttggttgtt ... aaaactgcagGAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
EST: gi|86501480|gb|CI144113.1|CI144113
EST:     GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG                         GAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
genomic: GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAGgttggttgtt ... aaaactgcagGAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
EST: gi|88488210|gb|CI425481.1|CI425481
EST:     CAGGGGCAAAG                         GAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
genomic: CAGGGGCAAAGgttggttgtt ... aaaactgcagGAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
EST: gi|88228692|gb|CI228172.1|CI228172
EST:     GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG                         GAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
genomic: GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAGgttggttgtt ... aaaactgcagGAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
EST: gi|58657698|gb|CK046378.1|CK046378
EST:     GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG                         GAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
genomic: GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAGgttggttgtt ... aaaactgcagGAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
EST: gi|218487624|gb|FG950213.1|FG950213
EST:     GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG                         GAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
genomic: GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAGgttggttgtt ... aaaactgcagGAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
EST: gi|86874336|gb|CI335948.1|CI335948
EST:     GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG                         GAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
genomic: GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAGgttggttgtt ... aaaactgcagGAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
EST: gi|88243593|gb|CI243990.1|CI243990
EST:     GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG                         GAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
genomic: GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAGgttggttgtt ... aaaactgcagGAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA

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: 49 (upstream exon), 67 (downstream exon)
Score: 23

GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAGgttggttgtt ... aaaactgcagGAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCAACGTCCGAGTTCCAAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcactatgtacactgttgtgataaacatattttatttttcactaaaaaactgcagGAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCAACGTCCGAGTTCCAAC
               ttgtgataaacatatt  TA-rich tract