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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGTCACCGACGGCGGGAGCTACGACTACGACCTGTTCGTGATCGGCGCCGGGAGCGGCGGCGTCCGGGGCTCTCGCACCTCCGCGTCCTTCGGGGCTAAGgtttgacttttctcctctcccccgctccccatttttgcgaggaaacgtgttggatttttattttttttcgtgtgatttgattcggtgtgtggcgcggttcag

Basic information

species Oryza sativa
transcript LOC_Os02g56850.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g56850.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM5G806449_T02 (Zea mays), 5'ss of exon 2
CGTCACCGACGGCGGGAGCTACGACTACGACCTGTTCGTGATCGGCGCCGGGAGCGGCGGCGTCCGGGGCTCTCGCACCTCCGCGTCCTTCGGGGCTAAGgtttgacttttctcctctcccc--cgctccccatttttgcgaggaaacgtgttggatttt-tattttttttcgtgtgat-ttgattcggtgtgtggcgcggttcag
|||| | || || |||  ||| |||||||| || ||||| ||||| || || ||||||||||| || |||||||||||| |||| |||||||| ||||||||| |    ||| || | ||||  |    || ||   ||    ||  | |  | |   |  ||        | | |  | | |  ||| ||       ||      
CGTCGCGGATGGTGGGCACTATGACTACGATCTCTTCGTCATCGGGGCGGGCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAGgttcgttgcttccccacaccccaccagctcctatgcctgacgtgatgcctcctagccgtgatacccgagcccatctactgtcgcctcgctgctctatccg------
















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|88366537|gb|CI612361.1|CI612361
EST:     GGAGCGGCGGCGTCCGGGGCTCTCGCACCTCCGCGTCCTTCGGGGCTAAG                         GTTGCGATTTGCGAGCTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGA
genomic: GGAGCGGCGGCGTCCGGGGCTCTCGCACCTCCGCGTCCTTCGGGGCTAAGgtttgacttt ... cgcggttcagGTTGCGATTTGCGAGCTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGA
EST: gi|88314032|gb|CI600034.1|CI600034
EST:     GGAGCGGCGGCGTCCGGGGCTCTCGCACCTCCGCGTCCTTCGGGGCTAAG                         GTTGCGATTTGCGAGCTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGA
genomic: GGAGCGGCGGCGTCCGGGGCTCTCGCACCTCCGCGTCCTTCGGGGCTAAGgtttgacttt ... cgcggttcagGTTGCGATTTGCGAGCTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGA
EST: gi|29670415|gb|CB666690.1|CB666690
EST:     GGAGCGGCGGCGTCCGGGGCTCTCGCACCTCCGCGTCCTTCGGGGCTAAG                         GTTGCGATTTGCGAGCTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGA
genomic: GGAGCGGCGGCGTCCGGGGCTCTCGCACCTCCGCGTCCTTCGGGGCTAAGgtttgacttt ... cgcggttcagGTTGCGATTTGCGAGCTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGA
EST: gi|88417483|gb|CI579144.1|CI579144
EST:     GGAGCGGCGGCGTCCGGGGCTCTCGCACCTCCGCGTCCTTCGGGGCTAAG                         GTTGCGATTTGCGAGCTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGA
genomic: GGAGCGGCGGCGTCCGGGGCTCTCGCACCTCCGCGTCCTTCGGGGCTAAGgtttgacttt ... cgcggttcagGTTGCGATTTGCGAGCTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGA
EST: gi|88760896|gb|CI770452.1|CI770452
EST:     GGAGCGGCGGCGTCCGGGGCTCTCGCACCTCCGCGTCCTTCGGGGCTAAG                         GTTGCGATTTGCGAGCTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGA
genomic: GGAGCGGCGGCGTCCGGGGCTCTCGCACCTCCGCGTCCTTCGGGGCTAAGgtttgacttt ... cgcggttcagGTTGCGATTTGCGAGCTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGA
EST: gi|88352021|gb|CI626021.1|CI626021
EST:     GGAGCGGCGGCGTCCGGGGCTCTCGCACCTCCGCGTCCTTCGGGGCTAAG                         GTTGCGATTTGCGAGCTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGA
genomic: GGAGCGGCGGCGTCCGGGGCTCTCGCACCTCCGCGTCCTTCGGGGCTAAGgtttgacttt ... cgcggttcagGTTGCGATTTGCGAGCTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGA
EST: gi|88337120|gb|CI628206.1|CI628206
EST:     GGAGCGGCGGCGTCCGGGGCTCTCGCACCTCCGCGTCCTTCGGGGCTAAG                         GTTGCGATTTGCGAGCTCCCGTTCCATCCCATCAGCTCGGATTGGCGAGGA
genomic: GGAGCGGCGGCGTCCGGGGCTCTCGCACCTCCGCGTCCTTCGGGGCTAAGgtttgacttt ... cgcggttcagGTTGCGATTTGCGAGCTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGA
EST: gi|88430778|gb|CI596892.1|CI596892
EST:     GGAGCGGCGGCGTCCGGGGCTCTCGCACCTCCGCGTCCTTCGGGGCTAAG                         GTTGCGATTTGCGAGCTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGA
genomic: GGAGCGGCGGCGTCCGGGGCTCTCGCACCTCCGCGTCCTTCGGGGCTAAGgtttgacttt ... cgcggttcagGTTGCGATTTGCGAGCTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGA
EST: gi|2443112|gb|C74883.1|C74883
EST:     GGAGCGGCGGCGTCCGGGGCTCTCGCACCTCCGCGTCCTTCGGGGCTAAG                         GTTGCGATTTGCGAGCTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGA
genomic: GGAGCGGCGGCGTCCGGGGCTCTCGCACCTCCGCGTCCTTCGGGGCTAAGgtttgacttt ... cgcggttcagGTTGCGATTTGCGAGCTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGA
EST: gi|33658225|gb|CF280839.1|CF280839
EST:     GGAGCGGCGGCGTCCGGGGCTCTCGCACCTCCGCGTCCTTCGGGGCTAAG                         GTTGCGATTTGCGAGCTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGA
genomic: GGAGCGGCGGCGTCCGGGGCTCTCGCACCTCCGCGTCCTTCGGGGCTAAGgtttgacttt ... cgcggttcagGTTGCGATTTGCGAGCTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGA
EST: gi|38469842|gb|CF953973.1|CF953973
EST:     GGAGCGGCGGCGTCCGGGGCTCTCGCAGCTCCGCGTCCTTCGGGGCTAAG                         GTTGCGATTTGCGAGCTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGA
genomic: GGAGCGGCGGCGTCCGGGGCTCTCGCACCTCCGCGTCCTTCGGGGCTAAGgtttgacttt ... cgcggttcagGTTGCGATTTGCGAGCTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGA
EST: gi|88723894|gb|CI745591.1|CI745591
EST:     GGAGCGGCGGCGTCCGGGGCTCTCGCACCTCCGCGTCCTTCGGGGCTAAG                         GTTGCGATTTGCGAGCTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGA
genomic: GGAGCGGCGGCGTCCGGGGCTCTCGCACCTCCGCGTCCTTCGGGGCTAAGgtttgacttt ... cgcggttcagGTTGCGATTTGCGAGCTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGA
EST: gi|88760244|gb|CI769800.1|CI769800
EST:     GGAGCGGCGGCGTCCGGGGCTCTCGCACCTCCGCGTCCTTCGGGGCTAAG                         GTTGCGATTTGCGAGCTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGA
genomic: GGAGCGGCGGCGTCCGGGGCTCTCGCACCTCCGCGTCCTTCGGGGCTAAGgtttgacttt ... cgcggttcagGTTGCGATTTGCGAGCTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGA
EST: gi|88416046|gb|CI594158.1|CI594158
EST:     GGAGCGGCGGCGTCCGGGGCTCTCGCACCTCCGCGTCCTTCGGGGCTAAG                         GTTGCGATTTGCGAGCTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGA
genomic: GGAGCGGCGGCGTCCGGGGCTCTCGCACCTCCGCGTCCTTCGGGGCTAAGgtttgacttt ... cgcggttcagGTTGCGATTTGCGAGCTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGA
EST: gi|426418|gb|D22281.1|D22281
EST:     GGAGCGGCGGCGTCCGGGGCTCTCGCACCTCCGCGTCCTTCGGGGCTAAG                         GTTGCGATTTGCGAGCTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGA
genomic: GGAGCGGCGGCGTCCGGGGCTCTCGCACCTCCGCGTCCTTCGGGGCTAAGgtttgacttt ... cgcggttcagGTTGCGATTTGCGAGCTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGA
EST: gi|88396564|gb|CI601047.1|CI601047
EST:     GGAGCGGCGGCGTCCGGGGCTCTCGCACCTCCGCGTCCTTCGGGGCTAAG                         GTTGCGATTTGCGAGCTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGA
genomic: GGAGCGGCGGCGTCCGGGGCTCTCGCACCTCCGCGTCCTTCGGGGCTAAGgtttgacttt ... cgcggttcagGTTGCGATTTGCGAGCTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGA
EST: gi|29680732|gb|CB677007.1|CB677007
EST:     GGAGCGGCGGCGTCCGGGGCTCTCGCACCTCCGCGTCCTTCGGGGCTAAG                         GTTGCGATTTGCGAGCTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGA
genomic: GGAGCGGCGGCGTCCGGGGCTCTCGCACCTCCGCGTCCTTCGGGGCTAAGgtttgacttt ... cgcggttcagGTTGCGATTTGCGAGCTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGA
EST: gi|88694888|gb|CI738926.1|CI738926
EST:     GGAGCGGCGGCGTCCGGGGCTCTCGCACCTCCGCGTCCTTCGGGGCTAAG                         GTTGCGATTTGCGAGCTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGA
genomic: GGAGCGGCGGCGTCCGGGGCTCTCGCACCTCCGCGTCCTTCGGGGCTAAGgtttgacttt ... cgcggttcagGTTGCGATTTGCGAGCTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGA
EST: gi|25802825|gb|CA758786.1|CA758786
EST:     GGAGCGGCGGCGTCCGGGGCTCTCGCACCTCCGCGTCCTTCGGGGCTAAG                         GTTGCGATTTGCGAGCTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGA
genomic: GGAGCGGCGGCGTCCGGGGCTCTCGCACCTCCGCGTCCTTCGGGGCTAAGgtttgacttt ... cgcggttcagGTTGCGATTTGCGAGCTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGA
EST: gi|29675048|gb|CB671323.1|CB671323
EST:     GGAGCGGCGGCGTCCGGGGCTCTCGCACCTCCGCGTCCTTCGGGGCTAAG                         GTTGCGATTTGCGAGCTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGA
genomic: GGAGCGGCGGCGTCCGGGGCTCTCGCACCTCCGCGTCCTTCGGGGCTAAGgtttgacttt ... cgcggttcagGTTGCGATTTGCGAGCTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGA
EST: gi|88726529|gb|CI750184.1|CI750184
EST:     GGAGCGGCGGCGTCCGGGGCTCTCGCACCTCCGCGTCCTTCGGGGCTAAG                         GTTGCGATTTGCGAGCTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGA
genomic: GGAGCGGCGGCGTCCGGGGCTCTCGCACCTCCGCGTCCTTCGGGGCTAAGgtttgacttt ... cgcggttcagGTTGCGATTTGCGAGCTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGA
EST: gi|88389287|gb|CI598085.1|CI598085
EST:     GGAGCGGCGGCGTCCGGGGCTCTCGCACCTCCGCGTCCTTCGGGGCTAAG                         GTTGCGATTTGCGAGCTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGA
genomic: GGAGCGGCGGCGTCCGGGGCTCTCGCACCTCCGCGTCCTTCGGGGCTAAGgtttgacttt ... cgcggttcagGTTGCGATTTGCGAGCTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGA
EST: gi|88417209|gb|CI576283.1|CI576283
EST:     GGAGCGGCGGCGTCCGGGGCTCTCGCACCTCCGCGTCCTTCGGGGCTAAG                         GTTGCGATTTGCGAGCTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGA
genomic: GGAGCGGCGGCGTCCGGGGCTCTCGCACCTCCGCGTCCTTCGGGGCTAAGgtttgacttt ... cgcggttcagGTTGCGATTTGCGAGCTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGA
EST: gi|88744812|gb|CI768172.1|CI768172
EST:     GGAGCGGCGGCGTCCGGGGCTCTCGCACCTCCGCGTCCTTCGGGGCTAAG                         GTTGCGATTTGCGAGCTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGA
genomic: GGAGCGGCGGCGTCCGGGGCTCTCGCACCTCCGCGTCCTTCGGGGCTAAGgtttgacttt ... cgcggttcagGTTGCGATTTGCGAGCTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGA

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: 55 (upstream exon), 63 (downstream exon)
Score: 15

CGTCACCGACGGCGGGAGCTACGACTACGACCTGTTCGTGATCGGCGCCGGGAGCGGCGGCGTCCGGGGCTCTCGCACCTCCGCGTCCTTCGGGGCTAAGgtttgacttt ... cgcggttcagGTTGCGATTTGCGAGCTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGAC




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