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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCTGACTGTGACGCAGGTGGAGCAGATGAAGGTGGAGGCGAAGGTGGGCGAAATCTACCGCGTCCTCTTCGGCAACGCGCCCAACGCCAATTCCCTCATgtaagcgaacccttcgagagcgctgtcgctatcactttgctttagttactcgcagtgtttgtgcatgtagagtgctgtggcggattgggatgcgagagat...

Basic information

species Oryza sativa
transcript LOC_Os01g53600.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g53600.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G158562_T03 (Zea mays), 5'ss of exon 1
GGCTGACTGTGACGCAGGTGGAGCAGATGAAGGTGGAGGCGAAGGTGGGCGAAATCTACCGCGTCCTCTTCGGCAACGCGCCCAACGCCAATTCCCTCATgtaagcgaacccttcgagagcgctgtcgctatcactttgctttagttactcgcagtgtttgt--gcatgtag-agtgctgtggcggattgggatgcgagagat
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GGCTCACGGTGACGTAGGTGGAGCAGATGAAGGTGGAGGCCAGGGTTGGCGACATCTACCGCTCCCTCTTCGGGGCCGCGCCCAACACGAAATCCATCATgtgagc-atccctaagcacacgctagttttctcacttctatttgagtatatcccctggctgccgacagccggcagtgct-tggcgggtctcaacgcatg-gat
















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|58674014|gb|CK062700.1|CK062700
EST:     GAAATCTACCGCGTCCTCTTCGGCAACGCGCCAAACGCCAATTCCCTCAT                         GTTAGAGCTGTGGCGTGAGCAGCATGTTGAGTATTTGACGAGAGGCCTGAA
genomic: GAAATCTACCGCGTCCTCTTCGGCAACGCGCCCAACGCCAATTCCCTCATgtaagcgaac ... actgcttcagGTTAGAGCTGTGGCGTGAGCAGCATGTTGAGTATTTGACGAGAGGGCTGAA
EST: gi|29673186|gb|CB669461.1|CB669461
EST:     GAAATCTACCGCGTCCTCTTCGGCAACGCGCCCAACGCCAATTCCCTCAT                         GTTAGAGCTGTGGCGTGAGCAGCATGTTGAGTATTTGACGAGAGGGCTGAA
genomic: GAAATCTACCGCGTCCTCTTCGGCAACGCGCCCAACGCCAATTCCCTCATgtaagcgaac ... actgcttcagGTTAGAGCTGTGGCGTGAGCAGCATGTTGAGTATTTGACGAGAGGGCTGAA
EST: gi|29674619|gb|CB670894.1|CB670894
EST:     CAATTCCCTCAT                         GTTACATCTGTGGCGTGAGCAGCATGTTGAGTATTTGACGAGAGGGCTGAA
genomic: CAATTCCCTCATgtaagcgaac ... actgcttcagGTTAGAGCTGTGGCGTGAGCAGCATGTTGAGTATTTGACGAGAGGGCTGAA
EST: gi|29674660|gb|CB670935.1|CB670935
EST:     CAATTCCCTCAT                         GTTAGAGCTGTGGCGTGAGCAGCATGTTGAGTATTTGACGAGAGGGCTGAA
genomic: CAATTCCCTCATgtaagcgaac ... actgcttcagGTTAGAGCTGTGGCGTGAGCAGCATGTTGAGTATTTGACGAGAGGGCTGAA

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), 65 (downstream exon)
Score: 14

GGCTGACTGTGACGCAGGTGGAGCAGATGAAGGTGGAGGCGAAGGTGGGCGAAATCTACCGCGTCCTCTTCGGCAACGCGCCCAACGCCAATTCCCTCATgtaagcgaac ... actgcttcagGTTAGAGCTGTGGCGTGAGCAGCATGTTGAGTATTTGACGAGAGGGCTGAAACATCTTGGACCAAGCTTCCATGTGCTCGATGCCAA




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