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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTTGGAACAATATGAAGGAATCCTCTGCACATCTGTTGGATTGAACAACGTCTGGGGACAAATTTTACCAGATCCTTTTCTCAGGCGCCTGATCGTCAGgtacctttttccatatatctccacattcaatgttttgactatctgccatttggttggaaggttagcattgcatcatcgcttgaagatagtatcttgacct...

Basic information

species Oryza sativa
transcript LOC_Os09g29470.3
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g29470.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G115304_T01 (Zea mays), 5'ss of exon 8
CTTTGGAACAATATGAAGGAATCCTCTGCACATCTGTTGGATTGAACAACGTCTGGGGACAAATTTTACCAGATCCTTTTCTCAGGCGCCTGATCGTCAGgtacctttttc-catatatct-ccacattcaatgtttt--gactatctgccatttggttggaaggttagcattgcatcatcgcttgaagatagtatcttgacct
|||||||| ||||||||||||| |||||||| ||||||||||| ||||| |||||||| |||||||||||||| || |||||||| || |||||  ||||||||||| | |  |||||| | |||||||||| | | |  ||  ||||| ||||| | || ||  | |   | |||   |  |||| | |  || | |||    
CTTTGGAAGAATATGAAGGAATACTCTGCACTTCTGTTGGATTAAACAATGTCTGGGGGCAAATTTTACCAGACCCATTTCTCAGACGGCTGATTCTCAGgtaccttgtacatatatatttgccacattcaaagctatatgaacatctggcatttagctgtaacatcaatttagcaatgtaacttggaaagggtgtattg----
















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|29623684|gb|CB628695.1|CB628695
EST:     GTCTGGGGACAAATTTTACCAGATCCTTTTCTCAGGCGCCTGATCGTCAG                         GTTTATTTTCTGCCGAGCAGTTATCTTCTATTTTCACCCTGAGGAGAATGG
genomic: GTCTGGGGACAAATTTTACCAGATCCTTTTCTCAGGCGCCTGATCGTCAGgtaccttttt ... taatttgcagGTTTATTTTCTGCCGAGCAGTTATATTCTATTTTCACCCTGAGGAGAATGG
EST: gi|29637840|gb|CB642849.1|CB642849
EST:     GTCTGGGGACAAATTTTACCAGATCCTTTTCTCAGGCGCCTGATCGTCAG                         GTTTATTTTCTGCCGAGCAGTTATATTCTATTTTCACCCTGAGGAGAATGG
genomic: GTCTGGGGACAAATTTTACCAGATCCTTTTCTCAGGCGCCTGATCGTCAGgtaccttttt ... taatttgcagGTTTATTTTCTGCCGAGCAGTTATATTCTATTTTCACCCTGAGGAGAATGG
EST: gi|218494056|gb|FG946879.1|FG946879
EST:     GTCTGGGGACAAATTTTACCAGATCCTTTTCTCAGGCGCCTGATCGTCAG                         GTTTATTTTCTGCCGAGCAGTTATCTTCTATTTTCACCCTGAGGAGAATGG
genomic: GTCTGGGGACAAATTTTACCAGATCCTTTTCTCAGGCGCCTGATCGTCAGgtaccttttt ... taatttgcagGTTTATTTTCTGCCGAGCAGTTATATTCTATTTTCACCCTGAGGAGAATGG
EST: gi|29677428|gb|CB673703.1|CB673703
EST:     GTCTGGGGACAAATTTTACCAGATCCTTTTCTCAGGCGCCTGATCGTCAG                         GTTTATTTTCTGCCGAGCAGTTATATTCTATTTTCACCCTGAGGAGAATGG
genomic: GTCTGGGGACAAATTTTACCAGATCCTTTTCTCAGGCGCCTGATCGTCAGgtaccttttt ... taatttgcagGTTTATTTTCTGCCGAGCAGTTATATTCTATTTTCACCCTGAGGAGAATGG

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), 45 (downstream exon)
Score: 10

CTTTGGAACAATATGAAGGAATCCTCTGCACATCTGTTGGATTGAACAACGTCTGGGGACAAATTTTACCAGATCCTTTTCTCAGGCGCCTGATCGTCAGgtaccttttt ... taatttgcagGTTTATTTTCTGCCGAGCAGTTATATTCTATTTTCACCCTGAGGAGAATGGTGAACATATACCAATCTGCCTACCCAGTCTTCCAGAATCAGTCGCGCCA




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