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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGCGCCGCGGGGATCCGCCCCGTCCCGCGCATCCACCACGCCCCCGTCCTCCGCGTCGCGCAGGACGATTATTCCGCCTACGCCCTCGCCGTCATGAAGgtgcgttcccttttctcggttcggtttggttggtgggggaagggggtaattctaattctgggcttgctctgcag

Basic information

species Oryza sativa
transcript LOC_Os01g56890.2
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g56890.3 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G127453_T02 (Zea mays), 5'ss of exon 1
CGGCGCCGCGGGGATCCGCCCCGTCCCGCGCATCCACCACGCCCCCGTCCTCCGCGT---CGCGCAGGACGATTATTCCGCCTACGCCCTCGCCGTCATGAAGgtgcgttc----ccttttctcggttcggtttggttggtg--ggggaaggggg-taattctaattctgggct---tgctctgcag
 || || |  |||||||| ||||||||||||||| |||||||| |||||||||||||   | ||||||| || |   ||||||||||||||||| |||||||||| ||| |    |  |  | | | | | || || | |||  || || |  || |||||||     | || |   ||||| ||||
-GGGGCAG--GGGATCCGACCCGTCCCGCGCATCAACCACGCCTCCGTCCTCCGCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAGgtacgtacgcacctgtcccccagcttgattggggttgtgttggtgaggaaggctaattctggaggttggttggttgctccgcag

upper sequence: LOC_Os01g56890.3 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G132978_T01 (Zea mays), 5'ss of exon 1
CGGCGCCGCGGGGATCCGCCCCGTCCCGCGCATCCACCACGCCCCCGTCCTCCGCGTCGC---GCAGGACGATTATTCCGCCTACGCCCTCGCCGTCATGAAGgtgcgttc---ccttttctcggttcggtttggttg--gtgggggaagggggtaattctaattctgg---------gcttgctctgcag
 || || |  |||||||| |||||||||||||||||||| |||||||||||| |||| ||   |||||| || ||  ||||||||||||||| | |||||||||| ||      ||  | |||    | | ||| |||  || |||   | ||| ||  ||||||||||         | |||||| ||||
-GGGGCAG--GGGATCCGACCCGTCCCGCGCATCCACCATGCCCCCGTCCTCAGCGTTGCTACGCAGGAAGACTACGCCGCCTACGCCCTCGACATCATGAAGgtacgcatacacccctcctcccccctgcttgattgaggttgggttggtggggaaggctaattctggaggttggttggttgctccgcag
















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|88827005|gb|CI777570.1|CI777570
EST:     TCCGCGTCGCGCAGGACGATTATTCCGCCTACGCCCTCGCCGTCATGAAG                         CATCCGGATCCGATAGGGG
genomic: TCCGCGTCGCGCAGGACGATTATTCCGCCTACGCCCTCGCCGTCATGAAGgtgcgttccc ... tgctctgcagCATCCGGATCCGATAGGGG
EST: gi|33797362|gb|CF324543.1|CF324543
EST:     GCCGTCATGAAG                         CATCCGGATCCGATAGGGGAGGGGTTGGCCATGGAGGCTATGGTGGAGGCG
genomic: GCCGTCATGAAGgtgcgttccc ... tgctctgcagCATCCGGATCCGATAGGGGAGGGGTTGGCCATGGAGGCTATGGTGGAGGCG
EST: gi|117246753|gb|CT843637.1|CT843637
EST:     TCCGCGTCGCGCAGGACGATTATTCCGCTTACGCCCTCGCCGTCATGAAG                         CATCCGGATCCGATAGGGGAGGGGTTGGCCATGGAGGCTATGGTGGAGGCG
genomic: TCCGCGTCGCGCAGGACGATTATTCCGCCTACGCCCTCGCCGTCATGAAGgtgcgttccc ... tgctctgcagCATCCGGATCCGATAGGGGAGGGGTTGGCCATGGAGGCTATGGTGGAGGCG

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: 63 (upstream exon), 63 (downstream exon)
Score: 8

CGGCGCCGCGGGGATCCGCCCCGTCCCGCGCATCCACCACGCCCCCGTCCTCCGCGTCGCGCAGGACGATTATTCCGCCTACGCCCTCGCCGTCATGAAGgtgcgttccc ... tgctctgcagCATCCGGATCCGATAGGGGAGGGGTTGGCCATGGAGGCTATGGTGGAGGCGGCCGGGCCGGAGTGCATCGTGCCCGGGCAGCAGGCGCCGCTGCGGCTGC




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