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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATGTGTTTGACTTCCAACTTATCAAGGGCTTGTTGTCTCGGCCAGATTTCAGgttctgtatatttatttgcttttcacatgttgtttagtcattaataaataatactagagttttggaaatattaatgcctgataatctacatgtgtatttt...

Basic information

species Oryza sativa
transcript LOC_Os10g11140.2
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g11140.2 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G025854_T02 (Zea mays), 5'ss of exon 10
AATGTGTTTGACTTCCAACTTATCAAGGGCTTGTTGTCTCGGCCAGATTTCAGgttctgtatatttatttgcttttcacatgttgtttagtcattaataaataatactaga---gttttggaaatattaatgcctgataatctacatgtgtatttt
||||||||||||||||||||||||||||  ||| | |||||||| ||||||||||  |      |      || |    || || |||    ||| | |  | ||| |      |||     | || |||||   | || |  ||   |  |    
AATGTGTTTGACTTCCAACTTATCAAGGATTTGCTTTCTCGGCCTGATTTCAGgtcttcctctctctgactctctatgtatcttttttttgtatttacattttatagtgagtgtgttacttgagtaataatgta-gctactaaacggttaaacc--
















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|58691145|gb|CK079832.1|CK079832
EST:     GTGTTTGACTTCCAACTTATCAAGGGCTTGTTGTCTCGGCCAGATTTCAGG                         GTTTGTATTTGATGCCATGCATGCTGTGACTGGTGCATATGCGGATCCAT
genomic: GTGTTTGACTTCCAACTTATCAAGGGCTTGTTGTCTCGGCCAGATTTCA-Ggttctgtata ... gattttctagGTTTGTATTTGATGCCATGCATGCTGTGACTGGTGCATATGCGGATCC-T
EST: gi|58676489|gb|CK065176.1|CK065176
EST:     GTGTTTGACTTCCAACTTATCAAGGGCTTGTTGTCTCGGCCAGATTTCAG                         GTTTGTATTTGATGCCATGCATGCTGTGACTGGTGCATATGCGGATCCTAT
genomic: GTGTTTGACTTCCAACTTATCAAGGGCTTGTTGTCTCGGCCAGATTTCAGgttctgtata ... gattttctagGTTTGTATTTGATGCCATGCATGCTGTGACTGGTGCATATGCGGATCCTAT
EST: gi|58608460|gb|CK036493.1|CK036493
EST:     GTGTTTGACTTCCAACTTATCAAGGGCTTGTTGTCTCGGCCAGATTTCAG                         GTTTGTATTTGATGCCATGCATGCTGTGACTGGTGC
genomic: GTGTTTGACTTCCAACTTATCAAGGGCTTGTTGTCTCGGCCAGATTTCAGgttctgtata ... gattttctagGTTTGTATTTGATGCCATGCATGCTGTGACTGGTGC
EST: gi|33796171|gb|CF323951.1|CF323951
EST:     GTGTTTGACTTCCAACTTATCAAGGGCTTGTTGTCTCGGCCAGATTTCAG                         GTTTGTATTTGATGCCATGCATGCTGTGACTGGTGCATATGCGGATCCTAT
genomic: GTGTTTGACTTCCAACTTATCAAGGGCTTGTTGTCTCGGCCAGATTTCAGgttctgtata ... gattttctagGTTTGTATTTGATGCCATGCATGCTGTGACTGGTGCATATGCGGATCCTAT
EST: gi|29681950|gb|CB678225.1|CB678225
EST:     GTGTTTGACTTCCAACTTATCAAGGGCTTGTTGTCTCGGCCAGATTTCAG                         GTTTGTATTTGATGCCATGCATGCTGTGACTGGTGCATATGCGGATCCTAT
genomic: GTGTTTGACTTCCAACTTATCAAGGGCTTGTTGTCTCGGCCAGATTTCAGgttctgtata ... gattttctagGTTTGTATTTGATGCCATGCATGCTGTGACTGGTGCATATGCGGATCCTAT

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: 65 (upstream exon), 75 (downstream exon)
Score: 61

AATGTGTTTGACTTCCAACTTATCAAGGGCTTGTTGTCTCGGCCAGATTTCAGgttctgtata ... gattttctagGTTTGTATTTGATGCCATGCATGCTGTGACTGGTGCATATGCGGATCCTATTTTTGTTGAGAAACTTGGAGCTGATCCG




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