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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGATGAGTCCTTGTACAATAGAGTGGCATCCCTCCTTGATGTTATGGGCAAGgttaacttcttttatctacaatcagtactccatttaggccctcatattgagccaggaaatgcacttacgctgtccttactctgaaatcag

Basic information

species Oryza sativa
transcript LOC_Os01g39270.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g39270.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM5G848696_T01 (Zea mays), 5'ss of exon 8
GTGATGAGTCCTTGTACAATAGAGTGGCATCCCTCCTTGATGTTATGGGCAAGgttaacttcttttatctacaatcagtactccatttaggccctcatattgagcc-aggaaatgcacttacgctgtc---cttactctgaaatcag
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GTGATGAGTCCTTGTACAAGAGAGTGGCGCCCCTCCTTGATGTCATGGGGAAGgttaa--tctcctatctgcaa--agtaccgtttccttgatcacattctgtaccgagaaaatgcgctaattttttctgccttattctgaaaccag
















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|89182128|gb|CI012062.1|CI012062
EST:     ATGAGTCCTTGTACAATAGAGTGGCATCCCTCCTTGATGTTATGGGCAAG                         TCAAGATTTTTCCTCGGTGACGTTGGCAAAGGTGCAGACATGAAGCTCGTT
genomic: ATGAGTCCTTGTACAATAGAGTGGCATCCCTCCTTGATGTTATGGGCAAGgttaacttct ... ctgaaatcagTCAAGATTTTTCCTCGGTGACGTTGGCAAAGGTGCAGACATGAAGCTCGTT
EST: gi|16576901|gb|BI804197.1|BI804197
EST:     GATGTTAT-GGCAAG                         TCAAAGA-TTTTCCTC-GTGACGTT-GCAAA-GTGCAAGACATGAAGCTCG
genomic: GATGTTATGGGCAAGgttaacttct ... ctgaaatcagTC-AAGATTTTTCCTCGGTGACGTTGGCAAAGGTGC-AGACATGAAGCTCG
EST: gi|38472714|gb|CF956846.1|CF956846
EST:     ATGAGTCCTTGTACAATAGAGTGGCATCCCTCCTTGATGTTATGGGCAAG                         TCAAGATTTTTCCTCGGTGACGTTGGCAAAGGTGCAGACATGAAGCTCGTT
genomic: ATGAGTCCTTGTACAATAGAGTGGCATCCCTCCTTGATGTTATGGGCAAGgttaacttct ... ctgaaatcagTCAAGATTTTTCCTCGGTGACGTTGGCAAAGGTGCAGACATGAAGCTCGTT
EST: gi|88971438|gb|CI017752.1|CI017752
EST:     GTTATGGGCAAG                         TCAAGATTTTTCCTCGGTGACGTTGGCAAAGGTGCAGACATGAAGCTCGTT
genomic: GTTATGGGCAAGgttaacttct ... ctgaaatcagTCAAGATTTTTCCTCGGTGACGTTGGCAAAGGTGCAGACATGAAGCTCGTT
EST: gi|38471057|gb|CF955188.1|CF955188
EST:     ATGAGTCCTTGTACAATAGAGTGGCATCCCTCCTTGATGTTATGGGCAAG                         TCAAGATTTTTCCTCGGTGACGTTGGCAAAGGTGCAGACATGAAGCTCGTT
genomic: ATGAGTCCTTGTACAATAGAGTGGCATCCCTCCTTGATGTTATGGGCAAGgttaacttct ... ctgaaatcagTCAAGATTTTTCCTCGGTGACGTTGGCAAAGGTGCAGACATGAAGCTCGTT

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: 60 (upstream exon), 58 (downstream exon)
Score: 10

GTGATGAGTCCTTGTACAATAGAGTGGCATCCCTCCTTGATGTTATGGGCAAGgttaacttct ... ctgaaatcagTCAAGATTTTTCCTCGGTGACGTTGGCAAAGGTGCAGACATGAAGCTCGTTGTTAATATGGTCATGGGGAG




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