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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCTCAAATCACTGCAATTCATCTTATAATTGGAACCCTTCAACGGATGAATATATTCGGGGTTGAAAATAGAGATACCCTGACTCACAAGACAACAGGGgtaacaattactatgctgtttccttattgaattatgtttttctcttctctctctctctctctctctctcaaatcagtctcttctatgcacataataacatcctgctgaataattgtgcag

Basic information

species Oryza sativa
transcript LOC_Os03g58700.1
intron # 19
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g58700.1 (Oryza sativa), 5'ss of exon 19
lower sequence: GRMZM5G844195_T04 (Zea mays), 5'ss of exon 2
GGCTCAAATCACTGCAATTCATCTTATAATTGGAACCCTTCAACGGATGAATATATTCGGGGTTGAAAATAGAGATACCCTGACTCACAAGACAACAGGGgtaacaattactatgctgtttccttattgaattatgtttttctcttctctctctctctctctctctctcaaatcagtctcttctatgca-cataataacatcctgctgaataattgtgcag------------------------------------------------------------------
|||||| |||||||||||||| || |||||||| |||||||| |||||||||||||| ||||| ||||||||||| ||||| ||||||||||||||||||||||  |||       |||||  |   |   | || ||   |     || | |  ||  || |  |    |||  || | | | | | | | |  || | ||  |     |  |  ||||                                                                   
GGCTCAGATCACTGCAATTCACCTGATAATTGGGACCCTTCAGCGGATGAATATATTTGGGGTGGAAAATAGAGACACCCTCACTCACAAGACAACAGGGgtaatgattct-----tgttttatggctagttcat-ttccccctcaatccccccttcaatccccatggggaatgggtgtatccaaagtagccttgtagcctcgcgagacctgttattgcatgaatcagctttctttaaatgaagtgctagcctctcttgtaaattacattgctactgctttctgcag

upper sequence: LOC_Os03g58700.1 (Oryza sativa), 5'ss of exon 19
lower sequence: GRMZM2G079610_T01 (Zea mays), 5'ss of exon 2
GGCTCAAATCACTGCAATTCATCTTATAATTGGAACCCTTCAACGGATGAATATATTCGGGGTTGAAAATAGAGATACCCTGACTCACAAGACAACAGGGgtaacaattactatgctgtttccttattgaattat--gtttttctcttctctctctctctctctctctctcaaatcagtctcttcta-tgcacataataacatcctgctgaataattgtgcag
||| ||||||| |||||||||  |   | |||| || ||| |  ||||||||||||| |||||  |||||||||| || || ||||||||||||||| || |||  |||  | |    || | ||   ||| | |  | || ||||       ||   |      ||   |||| || | | ||  | |  | |    |   | |                  
GGCCCAAATCATTGCAATTCACTTGGAAGTTGGGACGCTTAAGTGGATGAATATATTTGGGGTGAAAAATAGAGACACTCTCACTCACAAGACAACATGG-

upper sequence: LOC_Os03g58700.1 (Oryza sativa), 5'ss of exon 19
lower sequence: GRMZM5G825524_T02 (Zea mays), 5'ss of exon 19
GGCTCAAATCACTGCAATTCATCTTATAATTGGAACCCTTCAACGGATGAATATATTCGGGGTTGAAAATAGAGATACCCTGACTCACAAGACAACAGGGgtaacaattactatgctgtttccttattgaattatgtttttctcttctctctctctctctctctctctcaaatcagtctcttctatgcacataataacatcctgctgaataattgtgcag
||||||||||||||||||||| || |||||||| |||||||| |||||||||||||| ||||| ||||||||||| || || ||||||||||||||||||||||   ||  | |  | | ||    ||| ||      ||  | |||  |  |              |  | |        |  | |   || ||| |  |||||  | | |        
GGCTCAAATCACTGCAATTCACCTGATAATTGGGACCCTTCAGCGGATGAATATATTTGGGGTGGAAAATAGAGACACTCTCACTCACAAGACAACAGGGgtaatggttcttgttttatgtctagtttggatccatgattcttgttcggttgca-----------ggtggattggaggggattgagggggattatatc--cctgcctatttaa-------

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|25799908|gb|CA755869.1|CA755869
EST:     ATATATTCGGGGTTGAAAATAGAGATACCCTGACTCACAAGACAACAGGG                         TACTCAGCANAACTTCTAAAGAAACCTGACCAATGCCGAGCGGTTTATGCA
genomic: ATATATTCGGGGTTGAAAATAGAGATACCCTGACTCACAAGACAACAGGGgtaacaatta ... aattgtgcagTACTCAGCAAAACTTCTAAAGAAACCTGACCAATGCCGAGCGGTTTATGCA
EST: gi|163927174|gb|EG715195.1|EG715195
EST:     ATATATTCGGGGTTGAAAATAGAGATACCCTGACTCACAAGACAACAGGG                         TACTCAGCAAAACTTCTAAAGAAACCTGACCAATGCCGAGCGGTTTATGCA
genomic: ATATATTCGGGGTTGAAAATAGAGATACCCTGACTCACAAGACAACAGGGgtaacaatta ... aattgtgcagTACTCAGCAAAACTTCTAAAGAAACCTGACCAATGCCGAGCGGTTTATGCA
EST: gi|13420911|gb|AU175001.1|AU175001
EST:     ATATATTCGGGGTTGAAAATAGAGATACCCTGACTCACAAGACAACAGGG                         TACTCAGCAAAACTTCTAAAGGAACCTGACCAAT
genomic: ATATATTCGGGGTTGAAAATAGAGATACCCTGACTCACAAGACAACAGGGgtaacaatta ... aattgtgcagTACTCAGCAAAACTTCTAAAGAAACCTGACCAAT
EST: gi|27576800|gb|CA999494.1|CA999494
EST:     CCTGACTC-CAAGACAACAGGG                         TACTCAGCAAAACTTCTAAAGAAACCTGACCAATGCCGAGCGGTTTATGCA
genomic: CCTGACTCACAAGACAACAGGGgtaacaatta ... aattgtgcagTACTCAGCAAAACTTCTAAAGAAACCTGACCAATGCCGAGCGGTTTATGCA

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: 70 (upstream exon), 73 (downstream exon)
Score: 52

GGCTCAAATCACTGCAATTCATCTTATAATTGGAACCCTTCAACGGATGAATATATTCGGGGTTGAAAATAGAGATACCCTGACTCACAAGACAACAGGGgtaacaatta ... aattgtgcagTACTCAGCAAAACTTCTAAAGAAACCTGACCAATGCCGAGCGGTTTATGCATGTTCACACCTTTTCTGGACTGACGACCAAGACGGAATAATGGATGGTG




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