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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGCGTGGAGTTCATGCCGTTCCTGCTCTCCCTGTCCGTGTTCCTGTGCGGCACCTCCTGGTTCATCTACGGCCTGCTCGGCCGCGACCCTTTCATCGCGgtaatttactcatcgtctttcttttcgctgtcaattgctgcaagcctacaagcaacctgtcgacgttgattacagaaagatacgtaacctgacgacgaga...

Basic information

species Oryza sativa
transcript LOC_Os01g65880.3
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g65880.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA13G09140.1 (Glycine max), 5'ss of exon 5
GAGCGTGGAGTTCATGCCGTTCCTGCTCTCCCTGTCCGTGTTCCTGTGCGGCACCTCCTGGTTCATCTACGGCCTGCTCGGCCGCGACCCTTTCATCGCGgtaatttactcatcgtctttcttttcgct-gtcaatt----gctgcaagcctacaagcaacctgtcgacgttgattacagaaagatacgtaacctgacgacgaga
|||||||||||||||||| ||| | ||||| || |  |||||||| || ||||| || |||||||||||||| || || ||||| ||||| ||  | || |||| |  | ||    | || |   || |  ||| ||      || |    |||||   |  |    |   | | ||   ||| ||||   |    |        
GAGCGTGGAGTTCATGCCCTTCTTCCTCTCACTCTTTGTGTTCCTCTGTGGCACATCTTGGTTCATCTACGGGCTACTAGGCCGTGACCCATTTGTGGCTgtaagtagcacactcacattatccacgtttatcagttttcaattggatcaatacaatacaaatacaaaatgtcactatttaaacataccctattgtattg-----

upper sequence: LOC_Os01g65880.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA14G27610.1 (Glycine max), 5'ss of exon 5
GAGCGTGGAGTTCATGCCGTTCCTGCTCTCCCTGTCCGTGTTCCTGTGCGGCACCTCCTGGTTCATCTACGGCCTGCTCGGCCGCGACCCTTTCATCGCGgtaatttactcatcgtctttcttttcgct--gtcaattgctgcaagcctacaagcaacctgtcgacgttgattacagaaagatacgtaacctgacgacgaga----------------------
|||||||||||||||||| ||| | ||||| || |  |||||||| || || || || |||||||||||||| || || ||||| ||||| ||  | || |||| |  | ||    | || |   || |   ||||||       |  |  |  |||           |  | ||      | || || |||   |    |                       
GAGCGTGGAGTTCATGCCCTTCTTCCTCTCACTCTTTGTGTTCCTCTGTGGTACTTCTTGGTTCATCTACGGGCTACTAGGCCGTGACCCATTTGTGGCTgtaagtagcacactaacattatccacgttttatcaattttcaattggatcaatacaatacaatacaaattgtcactattttaaacttaccctcttgggttgcaattggcttgtattgaacgtag
















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|58673060|gb|CK061746.1|CK061746
EST:     GCACCTCCTGGTTCATCTACGGCCTGCTCGGCCGCGACCCTTTCATCGCG                         ATCCCCAATGGATGCGGGAGCTTTCTGGGCTTGATGCAGCTGATCCTCTAC
genomic: GCACCTCCTGGTTCATCTACGGCCTGCTCGGCCGCGACCCTTTCATCGCGgtaatttact ... cgacgtgcagATCCCCAATGGATGCGGGAGCTTTCTGGGCTTGATGCAGCTGATCCTCTAC
EST: gi|11172087|gb|AU164110.1|AU164110
EST:     GCACCTCCTGGTTCATCTACGGCCTGCTCGGCCGCGACCCTTTCATCGCG                         ATCCCCAATGGATGCGGGAGCTTTCTGGGCTTGATGCAGCTGATCCTCTAC
genomic: GCACCTCCTGGTTCATCTACGGCCTGCTCGGCCGCGACCCTTTCATCGCGgtaatttact ... cgacgtgcagATCCCCAATGGATGCGGGAGCTTTCTGGGCTTGATGCAGCTGATCCTCTAC
EST: gi|86598411|gb|CI355028.1|CI355028
EST:     GCACCTCCTGGTTCATGTACGGCCTGCTCGGCCGCGACCCTTTCATCGCG                         ATCCCCAATGGATTCGGGAGCTTTCTGGGCTTGATCCAGCTGATCCTCTAC
genomic: GCACCTCCTGGTTCATCTACGGCCTGCTCGGCCGCGACCCTTTCATCGCGgtaatttact ... cgacgtgcagATCCCCAATGGATGCGGGAGCTTTCTGGGCTTGATGCAGCTGATCCTCTAC
EST: gi|11026129|gb|AU162730.1|AU162730
EST:     GCACCTCCTGGTTCATCTACGGCCTGCTCGGCCGCGACCCTTTCATCGCG                         ATCCCCAATGGATGCGGGAGCTTTCTGGGCTTGATGCAGCTGATCCTCTAC
genomic: GCACCTCCTGGTTCATCTACGGCCTGCTCGGCCGCGACCCTTTCATCGCGgtaatttact ... cgacgtgcagATCCCCAATGGATGCGGGAGCTTTCTGGGCTTGATGCAGCTGATCCTCTAC
EST: gi|88481240|gb|CI418511.1|CI418511
EST:     CGGCCTGCTCGGCCGCGACCCTTTCATCGCG                         ATCCCCAATGGATGCGGGAGCTTTCTGGGCTTGATGCAGCTGATCCTTTAC
genomic: CGGCCTGCTCGGCCGCGACCCTTTCATCGCGgtaatttact ... cgacgtgcagATCCCCAATGGATGCGGGAGCTTTCTGGGCTTGATGCAGCTGATCCTCTAC
EST: gi|58674455|gb|CK063141.1|CK063141
EST:     GCACCTCCTGGTTCATCTACGGCCTGCTCGGCCGCGACCCTTTCATCGCG                         ATCCCCAATGGATGCGGGAGCTTTCTGGGCTTGATGCAGCTGATCCTCTAC
genomic: GCACCTCCTGGTTCATCTACGGCCTGCTCGGCCGCGACCCTTTCATCGCGgtaatttact ... cgacgtgcagATCCCCAATGGATGCGGGAGCTTTCTGGGCTTGATGCAGCTGATCCTCTAC
EST: gi|8856858|gb|AU094176.1|AU094176
EST:     GCACCTCCTGGTTCATCTACGGCCTGCTCGGCCGCGACCCTTTCATCGCG                         ATCCCCAATGGATGCGGGAGCTTTCTGGGCTTGATGCAGCTGATCCTCTAC
genomic: GCACCTCCTGGTTCATCTACGGCCTGCTCGGCCGCGACCCTTTCATCGCGgtaatttact ... cgacgtgcagATCCCCAATGGATGCGGGAGCTTTCTGGGCTTGATGCAGCTGATCCTCTAC

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), 73 (downstream exon)
Score: 23

GAGCGTGGAGTTCATGCCGTTCCTGCTCTCCCTGTCCGTGTTCCTGTGCGGCACCTCCTGGTTCATCTACGGCCTGCTCGGCCGCGACCCTTTCATCGCGgtaatttact ... cgacgtgcagATCCCCAATGGATGCGGGAGCTTTCTGGGCTTGATGCAGCTGATCCTCTACGCGATCTACCGGAACCACAAGGGGGCCACGCCGGCGGCGGCGGCCGGGA




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