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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCACTGTATCTGTACCCTTTCTTGAATACTACTAGCAAGACAAGGCCTTTTGAGTACTTGAGGCTTACCAGCTTGGGTGTCATTGGCGCACTTGTGAAGgtaattgcaagccagaactttatgaaaattatgagggatatgggtgtgtttcttgagtggaagcgtagatttttaaagctagaccattttctgatctact...

Basic information

species Oryza sativa
transcript LOC_Os03g57130.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g57130.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA08G43220.1 (Glycine max), 5'ss of exon 5
CCCACTGTATCTGTACCCTTTCTTGAATACTACTAGCAAGACAAGGCCTTTTGAGTACTTGAGGCTTACCAGCTTGGGTGTCATTGGCGCACTTGTGAAGgtaattgcaagccagaactttatgaaaattatgagggatatgggtgtgtttcttgagtggaagcgtagatttttaaa---gctagaccattttctgatctact----
 ||  | |||||||| || ||| | ||||| || |||||| |||| || |||||||||||||||||||||||  | ||||| ||||| ||| | ||||||||| || |   |  |  | || |    ||| |   ||||       | |   || |    ||   ||      || |   | | ||  ||| | ||     |     
ACCTTTATATCTGTATCCCTTCCTTAATACAACAAGCAAGTCAAGACCATTTGAGTACTTGAGGCTTACCAGTCTTGGTGTAATTGGTGCATTGGTGAAGgtattt-cttccttgctcattct----attgtt--ggatgcaaacatctacattaaaaaaaattatatgacaatatacatgattgatgattatatggcaagcaatat

upper sequence: LOC_Os03g57130.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA18G10400.1 (Glycine max), 5'ss of exon 5
CCCACTGTATCTGTACCCTTTCTTGAATACTACTAGCAAGACAAGGCCTTTTGAGTACTTGAGGCTTACCAGCTTGGGTGTCATTGGCGCACTTGTGAAGgtaattgcaagccagaactttatgaaaattatgagggatatgggtgtgtttcttgagtggaagcgta-gatttttaaagctagaccattttctgatctact------
 || || |||||||| || ||| | ||||| || |||||| |||| || |||||||||||||||||||||||| | ||||||||||| ||| | ||||||||| ||             | || ||     ||  ||||     | |        |    ||   || |    | ||   |  |  |  || | | | |        
ACCTCTATATCTGTATCCCTTCCTTAATACAACAAGCAAGTCAAGACCATTTGAGTACTTGAGGCTTACCAGCCTTGGTGTCATTGGTGCATTGGTGAAGgtattttttccttg----ctcattaagt---tgttggatgcaaatatcacaagaaaacaaaattatatggcaatcaatattgaaaaaacttatcaccaaaatccttg

upper sequence: LOC_Os03g57130.1 (Oryza sativa), 5'ss of exon 5
lower sequence: AT3G20800.1 (Arabidopsis thaliana), 5'ss of exon 5
CCCACTGTATCTGTACCCTTTCTTGAATACTACTAGCAAGACAAGGCCTTTTGAGTACTTGAGGCTTACCAGCTTGGGTGTCATTGGCGCACTTGTGAAGgta----attgcaagccagaactttatgaaaattatgagggatatgggtgtgtttc--------ttgagtggaagcgtagatttttaaagctagaccattttctgatctact--------------------------------------------------------------------------------------
|||  |||| || || || ||| | ||||| || || ||| | || ||||| || |||||| ||||||| ||| | |||||||| || |||||||||||||||    ||  |   ||    || |       || |    | | | | |||    |        ||   || ||||  ||   |  |||    |    |  |||    | ||                                                                                      
CCCGTTGTACCTTTATCCCTTCCTTAATACAACGAGTAAGTCCAGACCTTTCGAATACTTGCGGCTTACTAGCCTAGGTGTCATCGGTGCACTTGTGAAGgtacaccatcccgtcccttttctgttccttgtttctctttggttttgatgttccccacctactttttgctgaaagcaaaggactaaaaattgtgttagtggtcttggtttctaaagtagagaatttatattcttttttggtggttagtgtatgaaataagaaaggttcatcggatccttatttcactttgttttccag

upper sequence: LOC_Os03g57130.1 (Oryza sativa), 5'ss of exon 5
lower sequence: AT5G12980.1 (Arabidopsis thaliana), 5'ss of exon 5
CCCACTGTATCTGTACCCTTTCTTGAATACTACTAGCAAGACAAGGCCTTTTGAGTACTTGAGGCTTACCAGCTTGGGTGTCATTGGCGCACTTGTGAAGgtaattgc--aagccagaactttatgaaaattatgagggatatgggtgtgtttcttgagtggaagcgtagat-----ttttaaagctagaccattttctgatctact
 ||| |||| |||||  |||||||||||||  | |||||  |||| || ||||||||| || |||| || |||||||| || ||||| |||||||| ||||||  |    |     ||  ||| |          ||  || | | | ||||| |       | ||    |      ||||| |     || | | | ||       
GCCATTGTACCTGTATGCTTTCTTGAATACATCAAGCAAATCAAGACCGTTTGAGTACCTGCGGCTGACTAGCTTGGGGGTTATTGGTGCACTTGTTAAGgtatgtattgatatttgagttttgtttcctcgtctagttatttag-tatgtttatgccaaaaaggcaggaacacttcttttacatgctaacaactgtttgg------

upper sequence: LOC_Os03g57130.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv19s0090g00930.t01 (Vitis vinifera), 5'ss of exon 7
CCCACTGTATCTGTACCCTTTCTTGAATACTACTAGCAAGACAAGGCCTTTTGAGTACTTGAGGCTTACCAGCTTGGGTGTCATTGGCGCACTTGTGAAGgtaattgcaagccagaactttatgaaaattatgagggatatgggtgtgtttcttgagtggaagcgtagatttttaaagct--agaccattttctgatctact
 ||  |||| |||||||||||| | ||||| | ||||||  | |||||||||||||||||||| || || ||| | ||||| ||||| ||  | |||||||||  |          |  ||||  |  || | |   || | | |||  ||      ||  |    |   |||| |   |  |       ||   || |   
ACCCTTGTACCTGTACCCTTTCCTCAATACCAATAGCAAATCTAGGCCTTTTGAGTACTTGAGACTAACTAGCCTAGGTGTTATTGGTGCTTTGGTGAAGgtacgttgtccttgctaagttat--agtttttaaattatgttgttgttctttccatatgacactaaaatattttgatttttaaagttgcatttacatttgtc

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|218481822|gb|FG963644.1|FG963644
EST:     TTGAGTACTTGAGGCTTACCAGCTTGGGTGTCATTGGCGCACTTGTGAAG                         GTTGATGATTCTGAAGTCATTGGGTTTCTGCTGCAAACTGAAATAATTCCT
genomic: TTGAGTACTTGAGGCTTACCAGCTTGGGTGTCATTGGCGCACTTGTGAAGgtaattgcaa ... atatatgcagGTTGATGATTCTGAAGTCATTGGGTTTCTGCTGCAAACTGAAATAATTCCT
EST: gi|44678276|gb|CR291710.1|CR291710
EST:     TTGAGTACTTGAGGCTTACCAGCTTGGGTGTCATTGGCGCACTTGTGAAG                         GTTGATGATTCTGAAGTCATTGGGTTTCTGCTGCAAACTGAAATAATTCCT
genomic: TTGAGTACTTGAGGCTTACCAGCTTGGGTGTCATTGGCGCACTTGTGAAGgtaattgcaa ... atatatgcagGTTGATGATTCTGAAGTCATTGGGTTTCTGCTGCAAACTGAAATAATTCCT
EST: gi|58688549|gb|CK077236.1|CK077236
EST:     TTGAGTACTTGAGGCTTACCAGCTTGGGTGTCATTGGCGCACTTGTGAAG                         GTTGATGATTCTGAAGTCATTGGGTTTCTGCTGCAAACTGCAATAATTCCT
genomic: TTGAGTACTTGAGGCTTACCAGCTTGGGTGTCATTGGCGCACTTGTGAAGgtaattgcaa ... atatatgcagGTTGATGATTCTGAAGTCATTGGGTTTCTGCTGCAAACTGAAATAATTCCT
EST: gi|33800042|gb|CF325887.1|CF325887
EST:     TTGAGTACTTGAGGCTTACCAGCTTGGGTGTCATTGGCGCACTTGTGAAG                         GTTGATGATTCTGAAGTCATTGGGTTTCTGCTGCAAACTGAAATAATTCCT
genomic: TTGAGTACTTGAGGCTTACCAGCTTGGGTGTCATTGGCGCACTTGTGAAGgtaattgcaa ... atatatgcagGTTGATGATTCTGAAGTCATTGGGTTTCTGCTGCAAACTGAAATAATTCCT

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: 75 (upstream exon), 43 (downstream exon)
Score: 37

CCCACTGTATCTGTACCCTTTCTTGAATACTACTAGCAAGACAAGGCCTTTTGAGTACTTGAGGCTTACCAGCTTGGGTGTCATTGGCGCACTTGTGAAGgtaattgcaa ... atatatgcagGTTGATGATTCTGAAGTCATTGGGTTTCTGCTGCAAACTGAAATAATTCCTCTGTGTCTCCGTACTATGGAGATGGGCAGTGAACTTTCGAAAACG




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