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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCTGGCAATTTTAAGCTGGGTGAGGGGAAGCCAGAAAACCAAAATCATGCCATAATATTCACCCGTGGAAATGCAGTGCAAACCATTGATATGAATCAGgtatgctgttgtctttatattttgattattgacgagctctcgtacgaagtttggtccttatacatataggagcaaatattatgtatattatatttatttg...

Basic information

species Oryza sativa
transcript LOC_Os03g02756.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g02756.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA20G38860.1 (Glycine max), 5'ss of exon 38
GCCTGGCAATTTTAAGCTGGGTGAGGGGAAGCCAGAAAACCAAAATCATGCCATAATATTCACCCGTGGAAATGCAGTGCAAACCATTGATATGAATCAGgtatgctgttgtctttatattttgattattgacgagctctcgtacgaagtttggtccttatacatataggagcaaatattatgtatattatatttatttg-
 ||||| |||   ||  |||| || |||||||| || || ||||||||||| || ||||| || |||||||||||||| ||||| ||||| |||||||||||    | ||    | || |  | || || ||     |   |  | | | |   | ||  |   | |     |   |||| |||     ||  |   ||  
ACCTGGAAATCCCAAATTGGGAGAAGGGAAGCCCGAGAATCAAAATCATGCAATTATATTTACGCGTGGAAATGCAGTCCAAACAATTGACATGAATCAGgtgaagtttttgactaatttcatcataatagattgtgtaaggacccatgctgtattctcctgt-tgtgccccctcctattttgttagccattctgtcttat

upper sequence: LOC_Os03g02756.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA10G44150.2 (Glycine max), 5'ss of exon 36
GCCTGGCAATTTTAAGCTGGGTGAGGGGAAGCCAGAAAACCAAAATCATGCCATAATATTCACCCGTGGAAATGCAGTGCAAACCATTGATATGAATCAGgtatgctgttgtctttatattttgattattgacgagctc--tcgtacgaagtttggtccttatacatataggagcaaatatt-atgtatattatatttatttg
|||||| |||   ||  ||||||| |||||||| || || ||||||||||| ||  |||| || |||||||||||||| ||||| ||||| |||||||||||    | ||     ||  | |   || ||||| |  |   || ||  |  ||  ||    |  ||| | | |       ||  ||              || 
GCCTGGAAATCCCAAATTGGGTGAAGGGAAGCCCGAGAATCAAAATCATGCAATTGTATTTACGCGTGGAAATGCAGTCCAAACAATTGACATGAATCAGgtgaagttttaa---tagctgtctgtttttgactaatttcatcataatagattgtgtaaggacccatgttgtattttccctttgtgccccccccccccccttt

upper sequence: LOC_Os03g02756.2 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S160_88V6.1 (Physcomitrella patens), 5'ss of exon 36
GCCTGGCAATTTTAAGCTGGGTGAGGGGAAGCCAGAAAACCAAAATCATGCCATAATATTCACCCGTGGAAATGCAGTGCAAACCATTGATATGAATCAGgtatgctgttgtctttatattttgattattgacgagctctcgtacgaagtttggtccttatacatataggagcaaatattatg---tatattatatttatttg
 |||||    ||||| || || || || || |||||||| ||||||||||| || ||||| |  |||||  ||||||| ||||||||||||||||| ||||| |  ||   |  || | ||||  ||  | |    ||||| | || | | |  |   |       |   | |  || ||| |   | || ||||  | ||  
CCCTGGGCCGTTTAAACTCGGAGAAGGAAAACCAGAAAATCAAAATCATGCTATCATATTTAGTCGTGGGGATGCAGTTCAAACCATTGATATGAACCAGgtttcatgcgcttcttttctttt--ttcctcattc-ctctcctccggattgttctagatgcgtccttcttaacttatgttaagggctgtactataaattttct

upper sequence: LOC_Os03g02756.2 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S67_70V6.1 (Physcomitrella patens), 5'ss of exon 31
GCCTGGCAATTTTAAGCTGGGTGAGGGGAAGCCAGAAAACCAAAATCATGCCATAATATTCACCCGTGGAAATGCAGTGCAAACCATTGATATGAATCAGgtatgctgttgtctttatattttgattattgacgagctctcgtacgaagtttggtccttatacatataggagcaaatattatgtatattatatttatttg
 |||||    ||||| || || ||||| || ||||| ||||||||||||||||| |||||||  || ||  |||| || ||||| ||||||||||| ||||| || ||   |  || | |  |  |  |        |     | | |  |   |  || |    ||    | |||| || |       | ||  ||  |
TCCTGGGCCATTTAAACTTGGAGAGGGAAAACCAGAGAACCAAAATCATGCCATTATATTCAGTCGGGGGGATGCTGTTCAAACTATTGATATGAACCAGgtttgatgcccttcttttctccttgtcctcactctctttgtagatgcatctaaatttttctctggattatggtaaatttttttctctaaacatcgatggg

upper sequence: LOC_Os03g02756.2 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ05083 (Selaginella moellendorffii), 5'ss of exon 35
GCCTGGCAATTTTAAGCTGGGTGAGGGGAAGCCAGAAAACCAAAATCATGCCATAATATTCACCCGTGGAAATGCAGTGCAAACCATTGATATGAATCAGgtatgctgttgtctttatattttgatt-attgacgagctctcgtacgaagtttggtccttatacatataggagcaaatattatgtatattatatttatttg
 || || |||   || || || || || ||||| ||||| ||||||||||| || || || ||||||||| ||||| | |||||||| |||||||| ||||||     |||  || || || | |   | | || |  | |  |  | ||                                                   
ACCGGGAAATCCAAAACTTGGAGAAGGCAAGCCTGAAAATCAAAATCATGCGATTATTTTTACCCGTGGAGATGCAATACAAACCATAGATATGAACCAGgtactactttgcattcattttctcacagacttacca-ttttattttgcag---------------------------------------------------

upper sequence: LOC_Os03g02756.2 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ07568 (Selaginella moellendorffii), 5'ss of exon 35
GCCTGGCAATTTTAAGCTGGGTGAGGGGAAGCCAGAAAACCAAAATCATGCCATAATATTCACCCGTGGAAATGCAGTGCAAACCATTGATATGAATCAGgtatgctgttgtctttatattttgatt-attgacgagctctcgtacgaagtttggtccttatacatataggagcaaatattatgtatattatatttatttg
 || || |||   || || || || || ||||| ||||| ||||||||||| || || || ||||||||| ||||| | |||||||| |||||||| ||||||     |||  || || || | |   | | || |  | |  |  | ||                                                   
ACCGGGAAATCCAAAACTTGGAGAAGGCAAGCCTGAAAATCAAAATCATGCGATTATTTTTACCCGTGGAGATGCAATACAAACCATAGATATGAACCAGgtactactttgcattcattttctcacagacttacca-ttttactttgcag---------------------------------------------------

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|300216075|gb|HO088701.1|HO088701
EST:     CCATAATATTCACCCGTGGAAATGCAGTGCAAACCATTGATATGAATCAG                         GATAACTATTTTGAGGAGGCACTCAAAATGAGAAACCTGCTTGAGGAATTC
genomic: CCATAATATTCACCCGTGGAAATGCAGTGCAAACCATTGATATGAATCAGgtatgctgtt ... cctattgaagGATAACTATTTTGAGGAGGCACTCAAAATGAGAAACCTGCTTGAGGAATTC
EST: gi|88399969|gb|CI588273.1|CI588273
EST:     TGCAAACCATTGATATGAATCAG                         GATAACTATTTTGAGGAGGCACTCAAAATGAGAAACCTGCTTGAGGAATTC
genomic: TGCAAACCATTGATATGAATCAGgtatgctgtt ... cctattgaagGATAACTATTTTGAGGAGGCACTCAAAATGAGAAACCTGCTTGAGGAATTC
EST: gi|33679231|gb|CF307470.1|CF307470
EST:     CCATAATATTCACCCGTGGAAATGCAGTGCTTTCCATTGATATGAATCAG                         GATAACTATTTTGAGGAGGCACTCATAATGAGAAACCTGCTTGAGGAATTC
genomic: CCATAATATTCACCCGTGGAAATGCAGTGCAAACCATTGATATGAATCAGgtatgctgtt ... cctattgaagGATAACTATTTTGAGGAGGCACTCAAAATGAGAAACCTGCTTGAGGAATTC
EST: gi|29675246|gb|CB671521.1|CB671521
EST:     CCATAATATTCACCCGTGGAAATGCAGTGCAAACCATTGATATGAATCAG                         GATAACTATTTTGAGGAGGCACTCAAAATGAGAAACCTGCTTGAGGAATTC
genomic: CCATAATATTCACCCGTGGAAATGCAGTGCAAACCATTGATATGAATCAGgtatgctgtt ... cctattgaagGATAACTATTTTGAGGAGGCACTCAAAATGAGAAACCTGCTTGAGGAATTC

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: 74 (upstream exon), 62 (downstream exon)
Score: 64

GCCTGGCAATTTTAAGCTGGGTGAGGGGAAGCCAGAAAACCAAAATCATGCCATAATATTCACCCGTGGAAATGCAGTGCAAACCATTGATATGAATCAGgtatgctgtt ... cctattgaagGATAACTATTTTGAGGAGGCACTCAAAATGAGAAACCTGCTTGAGGAATTCTATCAGAATCATGGCAAGCACAAGCCTTCAATTCTTGGTGTTAGAGAAC




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