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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTTGTCCGCTCGGCTTGGGCGTAAACCAGAGGATATAATCAAGTTGGATGCAAATGAAAATCCATATGGTCCACCTCCGGAGgtgagtttcttgtaatacccaaacaagagtagcatctacctctaatacttgaaacaatacattcttaagaaacagtagtttgaccatgtcaacatgaacc...

Basic information

species Oryza sativa
transcript LOC_Os02g47940.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g47940.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G170595_T01 (Zea mays), 5'ss of exon 2
GTGTTGTCCGCTCGGCTTGGGCGTAAACCAGAGGATATAATCAAGTTGGATGCAAATGAAAATCCATATGGTCCACCTCCGGAGgtgagtttct-tgtaatacccaaacaagagta-gcatctacc-tctaatacttgaaacaatacattcttaagaaacagtagtttgaccatgtcaacatgaacc
||||| || ||||| |||||||||| ||||||||| ||||||||||||||||||||||| ||||||||||||||||| ||||||||||| |    | ||  ||  ||| |   ||  ||| ||    || | |||| ||||  ||| |||||||| || ||| |||| ||| | |  | ||||    
GTGTTATCTGCTCGCCTTGGGCGTAGACCAGAGGACATAATCAAGTTGGATGCAAATGAGAATCCATATGGTCCACCCCCGGAGgtgagctctagtctacaacataaagatcggtttgcacctgtaatccagtactcgaaagcatatattcttaacaatcagaagttagacaacgggagcatgg---

upper sequence: LOC_Os02g47940.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA16G27220.1 (Glycine max), 5'ss of exon 3
GTGTTGTCCGCTCGGCTTGGGCGTAAACCAGAGGATATAATCAAGTTGGATGCAAATGAAAATCCATATGGTCCACCTCCGGAGgtgagtttcttgtaatacccaaacaagagtagcatctacct--ctaatacttgaa-----acaatacattcttaagaaacagtagtttgaccatgtcaacatgaacc
|| || || ||||| ||||| ||||| || ||||||||  | ||||| ||||| ||||||||||| |||||||| ||||| |||||||||| ||| | |||       | |  | | || | ||   ||| |   | ||     | ||||  |  ||   ||   |  |||| || ||| ||   |     
GTTTTATCAGCTCGCCTTGGACGTAAGCCTGAGGATATCGTGAAGTTAGATGCTAATGAAAATCCTTATGGTCCCCCTCCAGAGgtgagtt-cttattatatttttttatgtct-gtatttcccatactattgagtaaacgtgtaaaataattatttggtaatatgatgtttaacaatggcagggt-----
















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|88716981|gb|CI740491.1|CI740491
EST:     ATATAATCAAGTTGGATGCAAATGAAAATCCATATGGTCCACCTCCGGAG                         GTAGCTAAAGCATTAGG
genomic: ATATAATCAAGTTGGATGCAAATGAAAATCCATATGGTCCACCTCCGGAGgtgagtttct ... ttttatacagGTAGCTAAAGCATTAGG
EST: gi|88363721|gb|CI609078.1|CI609078
EST:     ATATAATCAAGTTGGATGCCAATGAAAATC-ATATGGTCCACCTC-GGAG                         GTAGCTAAAGCATT
genomic: ATATAATCAAGTTGGATGCAAATGAAAATCCATATGGTCCACCTCCGGAGgtgagtttct ... ttttatacagGTAGCTAAAGCATT
EST: gi|29641902|gb|CB646909.1|CB646909
EST:     ATATAATCAAGTTGGATGCAAATGAAAATCCATATGGTCCACCTCCGGAG                         GTAGCTAAAGCATTAGGAAATTTGAAGTTTCCCTATGTGTACCCTGATCCT
genomic: ATATAATCAAGTTGGATGCAAATGAAAATCCATATGGTCCACCTCCGGAGgtgagtttct ... ttttatacagGTAGCTAAAGCATTAGGAAATTTGAAGTTTCCCTATGTGTACCCTGATCCT
EST: gi|88303422|gb|CI669070.1|CI669070
EST:     ATATAATCAAGTTGGATGCAAATGAAAATCCATATGGTCCACCTCCGGAG                         GTAGCTAAAGCATTAGGAA
genomic: ATATAATCAAGTTGGATGCAAATGAAAATCCATATGGTCCACCTCCGGAGgtgagtttct ... ttttatacagGTAGCTAAAGCATTAGGAA
EST: gi|88389725|gb|CI603224.1|CI603224
EST:     ATATAATCAAGTTGGATGCAAATGAAAATCCATATGGTCCACCTCCGGAG                         GTAGCTAAAGCATTAGGAAATTTGAAG
genomic: ATATAATCAAGTTGGATGCAAATGAAAATCCATATGGTCCACCTCCGGAGgtgagtttct ... ttttatacagGTAGCTAAAGCATTAGGAAATTTGAAG
EST: gi|88402807|gb|CI613255.1|CI613255
EST:     ATATAATCAAGTTGGATGCAAATGAAAATCCATATGGTCCACCTC-GGAG                         GTAGCTAAAGCATTAGGAAATTTGAAGTTT
genomic: ATATAATCAAGTTGGATGCAAATGAAAATCCATATGGTCCACCTCCGGAGgtgagtttct ... ttttatacagGTAGCTAAAGCATTAGGAAATTTGAAGTTT
EST: gi|88399533|gb|CI606154.1|CI606154
EST:     ATATAATCAAGTTGGATGCAAATGAAAATCCATATGGTCCACCTCCGGAG                         GTAGCTAAAGCATTAGGAAATTTGAAGTTTCCCTATGTGTACCCTGATCCT
genomic: ATATAATCAAGTTGGATGCAAATGAAAATCCATATGGTCCACCTCCGGAGgtgagtttct ... ttttatacagGTAGCTAAAGCATTAGGAAATTTGAAGTTTCCCTATGTGTACCCTGATCCT
EST: gi|88591567|gb|CI709607.1|CI709607
EST:     ATATAATCAAGTTGGATGCAAATGAAAATCCATATGGTCCACCTCCGGAG                         GTAGCTAAAGCATTAGGAAATTTGAAGTTTCCCTATGTG
genomic: ATATAATCAAGTTGGATGCAAATGAAAATCCATATGGTCCACCTCCGGAGgtgagtttct ... ttttatacagGTAGCTAAAGCATTAGGAAATTTGAAGTTTCCCTATGTG
EST: gi|88362101|gb|CI607101.1|CI607101
EST:     ATATAATCAAGTTGGATGCAAATGAAAATCCATATGGTCCACCTCCGGAG                         GTAGCTAAAGCATTAGGAAATTTGAAGTTTCCCTATG
genomic: ATATAATCAAGTTGGATGCAAATGAAAATCCATATGGTCCACCTCCGGAGgtgagtttct ... ttttatacagGTAGCTAAAGCATTAGGAAATTTGAAGTTTCCCTATG

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: 73 (upstream exon), 70 (downstream exon)
Score: 25

GTGTTGTCCGCTCGGCTTGGGCGTAAACCAGAGGATATAATCAAGTTGGATGCAAATGAAAATCCATATGGTCCACCTCCGGAGgtgagtttct ... ttttatacagGTAGCTAAAGCATTAGGAAATTTGAAGTTTCCCTATGTGTACCCTGATCCTGAAAGCCGTCAGTTGCGTGCTGCTCTTGCTGAAGATTCTGGTCTTGAAT




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