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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTCCTACGAGGTTGTACTTATGGGATTCGCTTCCTCGGAATGCCATGGGAAAGgtgcgggctgaaaattttttcttctttgcagttgtgttgagtttgttacttacctattgcttttatcag

Basic information

species Oryza sativa
transcript LOC_Os01g55590.1
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g55590.1 (Oryza sativa), 5'ss of exon 16
lower sequence: GRMZM2G460078_T01 (Zea mays), 5'ss of exon 16
ATTCCTACGAGGTTGTACTTATGGGATTCGCTTCCTCGGAATGCCATGGGAAAGgtgcgggctgaaaattttttcttctttgcagttgtgttgagtttgttacttacct------attgcttttatcag
||||| || ||  | ||||| |||||||| ||||||||||||||||||||||||||| || |  |  || |  |      | |  | || | | | | || ||| || |       |||||| | ||||
ATTCCAACAAGACTATACTTGTGGGATTCTCTTCCTCGGAATGCCATGGGAAAGgtggggac--atgatgtccttgaaaataccctcgtatcgtgctcgtaactgacttttagccgttgcttatttcag
















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|88323534|gb|CI556165.1|CI556165
EST:     CTACGAGGTTGTACTTATGGGATTCGCTTCCTCGGAATGCCATGGGAAAG                         GTCAACAAGAAGGAGCTGAAGAAATTATTAGGAGCTTAGCTGTGGTTCCAG
genomic: CTACGAGGTTGTACTTATGGGATTCGCTTCCTCGGAATGCCATGGGAAAGgtgcgggctg ... cttttatcagGTCAACAAGAAGGAGCTGAAGAAATTATTAGGAGCTTAGCTGTGGTTCCAG
EST: gi|86863465|gb|CI345208.1|CI345208
EST:     CTACGAGGTTGTACTTATGGGATTCGCTTCCTCGGAATGCCATGGGAAAG                         GTCAACAAGAAGGAGCTGAAGAAATTATTAGGAGCTTAGCTGTGGTTCCAG
genomic: CTACGAGGTTGTACTTATGGGATTCGCTTCCTCGGAATGCCATGGGAAAGgtgcgggctg ... cttttatcagGTCAACAAGAAGGAGCTGAAGAAATTATTAGGAGCTTAGCTGTGGTTCCAG
EST: gi|88487395|gb|CI424666.1|CI424666
EST:     CTAGGAGGTTGTACTTATGGGATTCGCTTCCTCGGAATGCCATGGGAAAG                         GTCAACAAGAAGGGAGCTGAAGAAATTATTAGGAGCTTAGCTGTGGTTCCA
genomic: CTACGAGGTTGTACTTATGGGATTCGCTTCCTCGGAATGCCATGGGAAAGgtgcgggctg ... cttttatcagGTCAACAAGAA-GGAGCTGAAGAAATTATTAGGAGCTTAGCTGTGGTTCCA
EST: gi|88830050|gb|CI074722.1|CI074722
EST:     CTACGAGGTTGTACTTATGGGATTCGCTTCCTCGGAATGCCATGGGAAAG                         GTCAACAAGAAGGAGCTGAAGAAATTATTAGGAGCTTAGCTGTGGTTCCAG
genomic: CTACGAGGTTGTACTTATGGGATTCGCTTCCTCGGAATGCCATGGGAAAGgtgcgggctg ... cttttatcagGTCAACAAGAAGGAGCTGAAGAAATTATTAGGAGCTTAGCTGTGGTTCCAG
EST: gi|10852848|gb|AT003358.1|AT003358
EST:     CTACGAGGTTGTACTTATGGGATTCGCTTCCTCGGAATGCCATGGGAAAG                         GTCAACAAGAAGGAGCTGAAGAAATTATTAGGAGCTTAGCTGTGGTTCCAG
genomic: CTACGAGGTTGTACTTATGGGATTCGCTTCCTCGGAATGCCATGGGAAAGgtgcgggctg ... cttttatcagGTCAACAAGAAGGAGCTGAAGAAATTATTAGGAGCTTAGCTGTGGTTCCAG
EST: gi|89185889|gb|CI047758.1|CI047758
EST:     CTACGAGGTTGTACTTATGGGATTCGCTTCCTCGGAATGCCATGGGAAAG                         GTCAACAAGAAGGAGCTGAAGAAATTATTAGGAGCTTAGCTGTGGTTCCAG
genomic: CTACGAGGTTGTACTTATGGGATTCGCTTCCTCGGAATGCCATGGGAAAGgtgcgggctg ... cttttatcagGTCAACAAGAAGGAGCTGAAGAAATTATTAGGAGCTTAGCTGTGGTTCCAG
EST: gi|88828610|gb|CI073480.1|CI073480
EST:     CTACGAGGTTGTACTTATGGGATTCGCTTCCTCGGAATGCCATGGGAAAG                         GTCAACAAGAAGGAGCTGAAGAAATTATTAGGAGCTTAGCTGTGGTTCCAG
genomic: CTACGAGGTTGTACTTATGGGATTCGCTTCCTCGGAATGCCATGGGAAAGgtgcgggctg ... cttttatcagGTCAACAAGAAGGAGCTGAAGAAATTATTAGGAGCTTAGCTGTGGTTCCAG
EST: gi|88326141|gb|CI651196.1|CI651196
EST:     CTACGAGGTTGTACTTATGGGATTCGCTTCCTCGGAATGCCATGGGAAAG                         GTCAACAAGAAGGAGCTGAAGAAATTATTAGGAGCTTAGCTGTGGTTCCAG
genomic: CTACGAGGTTGTACTTATGGGATTCGCTTCCTCGGAATGCCATGGGAAAGgtgcgggctg ... cttttatcagGTCAACAAGAAGGAGCTGAAGAAATTATTAGGAGCTTAGCTGTGGTTCCAG
EST: gi|88427585|gb|CI548838.1|CI548838
EST:     CTACGAGGTTGTACTTATGGGATTCGCTTCCTCGGAATGCCATGGGAAAG                         GTCAACAAGAAGGAGCTGAAGAAATTATTAGGAGCTTAGCTGTGGTTCCAG
genomic: CTACGAGGTTGTACTTATGGGATTCGCTTCCTCGGAATGCCATGGGAAAGgtgcgggctg ... cttttatcagGTCAACAAGAAGGAGCTGAAGAAATTATTAGGAGCTTAGCTGTGGTTCCAG
EST: gi|44678307|gb|CR291741.1|CR291741
EST:     CTACGAGGTTGTACTTATGGGATTCGCTTCCTCGGAATGCCATGGGAAAG                         GTCAACAAGAAGGAGCTGAAGAAATTATTAGGAGCTTAGCTGTGGTTCCAG
genomic: CTACGAGGTTGTACTTATGGGATTCGCTTCCTCGGAATGCCATGGGAAAGgtgcgggctg ... cttttatcagGTCAACAAGAAGGAGCTGAAGAAATTATTAGGAGCTTAGCTGTGGTTCCAG
EST: gi|29689640|gb|CB685915.1|CB685915
EST:     CTACGAGGTTGTACTTATGGGATTCCCTTCCTCGGAATGCCATGGGAAAG                         GTCAACAAGAAGGAGCTGAAGAAATTATTAGGAGCTTAGCTGTGGTTCCAG
genomic: CTACGAGGTTGTACTTATGGGATTCGCTTCCTCGGAATGCCATGGGAAAGgtgcgggctg ... cttttatcagGTCAACAAGAAGGAGCTGAAGAAATTATTAGGAGCTTAGCTGTGGTTCCAG
EST: gi|24208242|gb|AU225269.1|AU225269
EST:     GAGGTTGTACTTATGGGATTCGCTTCCTCGGAATGCCATGGGAAAG                         GTCAACAAGAAGGAGCTGAAGAAATTATTAGGAGCTTAGCTGTGGTTCCAG
genomic: GAGGTTGTACTTATGGGATTCGCTTCCTCGGAATGCCATGGGAAAGgtgcgggctg ... cttttatcagGTCAACAAGAAGGAGCTGAAGAAATTATTAGGAGCTTAGCTGTGGTTCCAG
EST: gi|86603012|gb|CI357376.1|CI357376
EST:     CTACGAGGTTGTACTTATGGGATTCGCTTCCTCGGAATGCCATGGGAAAG                         GTCAACAAGAAGGAGCTGAAGAAATTATTAGGAGCTTAGCTGTGGTTCCAG
genomic: CTACGAGGTTGTACTTATGGGATTCGCTTCCTCGGAATGCCATGGGAAAGgtgcgggctg ... cttttatcagGTCAACAAGAAGGAGCTGAAGAAATTATTAGGAGCTTAGCTGTGGTTCCAG
EST: gi|88558329|gb|CI488809.1|CI488809
EST:     CTACGAGGTTGTACTTATGGGATTCGCTTCCTCGGAATGCCATGGGAAAG                         GTCAACAAGAAGGAGCTGAAGAAATTATTAGGAGCTTAGCTGTGGTTCCAG
genomic: CTACGAGGTTGTACTTATGGGATTCGCTTCCTCGGAATGCCATGGGAAAGgtgcgggctg ... cttttatcagGTCAACAAGAAGGAGCTGAAGAAATTATTAGGAGCTTAGCTGTGGTTCCAG
EST: gi|87016222|gb|CI271633.1|CI271633
EST:     CTACGAGGTTGTACTTATGGGATTCGCTTCCTCGGAATGCCATGGGAAAG                         GTCAACAAGAAGGAGCTGAAGAAATTATTAGGAGCTTAGCTGTGGTTCCAG
genomic: CTACGAGGTTGTACTTATGGGATTCGCTTCCTCGGAATGCCATGGGAAAGgtgcgggctg ... cttttatcagGTCAACAAGAAGGAGCTGAAGAAATTATTAGGAGCTTAGCTGTGGTTCCAG
EST: gi|88557745|gb|CI488179.1|CI488179
EST:     CTACGAGGTTGTACTTATGGGATTCGCTTCCTCGGAATGCCATGGGAAAG                         GTCAACAAGAAGGAGCTGAAGAAATTATTAGGAGCTTAGCTGTGGTTCCAG
genomic: CTACGAGGTTGTACTTATGGGATTCGCTTCCTCGGAATGCCATGGGAAAGgtgcgggctg ... cttttatcagGTCAACAAGAAGGAGCTGAAGAAATTATTAGGAGCTTAGCTGTGGTTCCAG
EST: gi|88383395|gb|CI540808.1|CI540808
EST:     CTACGAGGTTGTACTTATGGGATTCGCTTCCTCGGAATGCCATGGGAAAG                         GTCAACAAGAAGGAGCTGAAGAAATTATTAGGAGCTTAGCTGTGGTTCCAG
genomic: CTACGAGGTTGTACTTATGGGATTCGCTTCCTCGGAATGCCATGGGAAAGgtgcgggctg ... cttttatcagGTCAACAAGAAGGAGCTGAAGAAATTATTAGGAGCTTAGCTGTGGTTCCAG

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: 54 (upstream exon), 75 (downstream exon)
Score: 49

ATTCCTACGAGGTTGTACTTATGGGATTCGCTTCCTCGGAATGCCATGGGAAAGgtgcgggctg ... cttttatcagGTCAACAAGAAGGAGCTGAAGAAATTATTAGGAGCTTAGCTGTGGTTCCAGGAAGGCAGACATTGTAATGGTTAGCTAATAAATATTTTTCGCATTGATA




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