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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAATGCGCAGCCCAGATTCCAGTTTGTTGTCATGAATCGTCGTAATACAGgtacgctgcatgaaaattttcttggttttcttagagttgaagtttctataattggctatgttacaacctttgtaaaacctgtgcgtgaaattgtcaatct...

Basic information

species Oryza sativa
transcript LOC_Os07g14580.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g14580.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G101596_T01 (Zea mays), 5'ss of exon 3
GAATGCGCAGCCCAGATTCCAGTTTGTTGTCATGAATCGTCGTAATACAGgtacgctgcatgaaaattttcttggttttcttagagttgaagtttctataattggctatgt---tacaacctttgtaaaacctgtgcgtgaaattgtcaatct
|||||| || ||||||||||||||  |||||||||||||  | ||||||||||   |  || |    ||| |||||  | ||  |  || | |     || ||    ||||   |       ||||| ||   |    |  |  | |      
GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAGgtat--tttatcatgtattttttggtactgtttaatctgcaatacaggtattttatcatgtattttttggtattgtataataaggaattacaggtattgtat-

upper sequence: LOC_Os07g14580.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AT1G08370.1 (Arabidopsis thaliana), 5'ss of exon 3
GAATGCGCAGCCCAGATTCCAGTTTGTTGTCATGAATCGTCGTAATACAGgt-acgctgcatgaaaattttcttggttttcttagagtt-----gaagtttctataattggc--tatgttacaacct-----ttgtaaaacctgtgcgtgaaattgtcaatct----------------------
 | | | || ||  |||| |||||| |||| ||||||||||||||||||||| | | |  ||  ||||    ||||| |   |   ||       ||   | || | || |   ||| || |||  |     ||    |  | ||    | |||  ||| | |                      
AAGTACACAACCTCGATTTCAGTTTATTGTGATGAATCGTCGTAATACAGgtcaggatttattcaaataaagttggtgtgtgtcatgtgtctagaaaaggtttagatttagtaatatattgcaagttcttatttaaggattcagtattagtaatcatcagtgtgttgctgtatttgtctggatag
















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|33675101|gb|CF303340.1|CF303340
EST:     GAATGCGCAGCCCAGATTCCAGTTTGTTGTCATGAATCGTCGTAATACAG                         ATAATTTAGTTGAAGATCTCCTGGGAGATTTTGAATATCAGCTTCAGGTTC
genomic: GAATGCGCAGCCCAGATTCCAGTTTGTTGTCATGAATCGTCGTAATACAGgtacgctgca ... ttatcaacagATAATTTAGTTGAAGATCTCCTGGGAGATTTTGAATATCAGCTTCAGGTTC
EST: gi|117230076|gb|CT853782.1|CT853782
EST:     GAATGCGCAGCCCAGATTCCAGTTTGTTGTCATGAATCGTCGTAATACAG                         ATAATTTAGTTGAAGATCTCCTGGGAGATTTTGAATATCAGCTTCAGGTTC
genomic: GAATGCGCAGCCCAGATTCCAGTTTGTTGTCATGAATCGTCGTAATACAGgtacgctgca ... ttatcaacagATAATTTAGTTGAAGATCTCCTGGGAGATTTTGAATATCAGCTTCAGGTTC
EST: gi|33657056|gb|CF279670.1|CF279670
EST:     GAATGCGCAGCCCAGATTCCAGTTTGTTGTCATGAATCGTCGTAATACAG                         ATAATTTAGTTGAAGATCTCCTGGGAGATTTTGAATATCAGCTTCAGGTTC
genomic: GAATGCGCAGCCCAGATTCCAGTTTGTTGTCATGAATCGTCGTAATACAGgtacgctgca ... ttatcaacagATAATTTAGTTGAAGATCTCCTGGGAGATTTTGAATATCAGCTTCAGGTTC
EST: gi|88358340|gb|CI606849.1|CI606849
EST:     GAATGCGCAGCCCAGGTTCCAGTTTGTTGTCATGAATCGTCGTAATACAG                         ATAATTTAGTTGAAGATCTCCTGGGAGATTTTGAATATCAGCTTCAGGTTC
genomic: GAATGCGCAGCCCAGATTCCAGTTTGTTGTCATGAATCGTCGTAATACAGgtacgctgca ... ttatcaacagATAATTTAGTTGAAGATCTCCTGGGAGATTTTGAATATCAGCTTCAGGTTC
EST: gi|58597046|gb|CK007574.1|CK007574
EST:     GAATGCGCAGCCCAGATTCCAGTTTGTTGTCATGAATCGTCGTAATACAG                         ATAATTTAGTTGAAGATCTCCTGGGAGATTTTGAATATCAGCTTCAGGTTC
genomic: GAATGCGCAGCCCAGATTCCAGTTTGTTGTCATGAATCGTCGTAATACAGgtacgctgca ... ttatcaacagATAATTTAGTTGAAGATCTCCTGGGAGATTTTGAATATCAGCTTCAGGTTC
EST: gi|58690454|gb|CK079141.1|CK079141
EST:     GAATGCGCAGCCCAGATTCCAGTTTGTTGTCATGAATCGTCGTAATACAG                         AT-ATTTAGTTGAAGATCTCCTGGGAGATTTTGAATATCAGCTTCAGGTTC
genomic: GAATGCGCAGCCCAGATTCCAGTTTGTTGTCATGAATCGTCGTAATACAGgtacgctgca ... ttatcaacagATAATTTAGTTGAAGATCTCCTGGGAGATTTTGAATATCAGCTTCAGGTTC
EST: gi|66923810|gb|CX110658.1|CX110658
EST:     GCGCAGCCCAGATTCCAGTTTGTTGTCATGAATCGTCGTAATACAG                         ATAATTTAGTTGAAGATCTCCTGGGAGATTTTGAATATCAGCTTCAGGTTC
genomic: GCGCAGCCCAGATTCCAGTTTGTTGTCATGAATCGTCGTAATACAGgtacgctgca ... ttatcaacagATAATTTAGTTGAAGATCTCCTGGGAGATTTTGAATATCAGCTTCAGGTTC

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: 45 (upstream exon), 63 (downstream exon)
Score: 13

GAATGCGCAGCCCAGATTCCAGTTTGTTGTCATGAATCGTCGTAATACAGgtacgctgca ... ttatcaacagATAATTTAGTTGAAGATCTCCTGGGAGATTTTGAATATCAGCTTCAGGTTCCCTATATAATGTATCGCAATGCTGCACAAGAAGTTATTGGCATTTGGTT




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