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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCGGCAACGTTTCTTGCTTTCCATCCTCAAGATAACAACATTATAGCAATTGGAATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAGgtattagcacatctaatggcattgctctgcgttattcttataaaaaatggaacaagattcaatcaattttttttttgattctttgcacag

Basic information

species Oryza sativa
transcript LOC_Os03g14980.1
intron # 22
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g14980.1 (Oryza sativa), 5'ss of exon 22
lower sequence: GRMZM2G550865_T02 (Zea mays), 5'ss of exon 8
GGCGGCAACGTTTCTTGCTTTCCATCCTCAAGATAACAACATTATAGCAATTGGAATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAGgtattagcacatctaatggcattgctctgcgttattcttataaaaaatggaacaagattcaatcaattttttttttgattctttgcacag
||| ||||| |||||||| || || || |||||||||||||| || ||||||||||||||||||||||||||||||||||| ||||| |||||||||||||||||  ||       |||| ||| | |      |  ||  |   ||  | |||   || | |  ||   || ||| |||||||| ||||
GGCAGCAACTTTTCTTGCATTTCACCCCCAAGATAACAACATAATTGCAATTGGAATGGATGACTCAACCATCCAAATCTATAATGTCCGAATTGATGAGgtattcaca------gtggctttgtttt------tctttccattgaacaggacacagtt-agtatatggcttattt-attctttgtacag

upper sequence: LOC_Os03g14980.1 (Oryza sativa), 5'ss of exon 22
lower sequence: GRMZM2G030422_T03 (Zea mays), 5'ss of exon 23
GGCGGCAACGTTTCTTGCTTTCCATCCTCAAGATAACAACATTATAGCAATTGGAATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAGgtattagcacatctaatggcattgctctgcgttattcttataaaaaatggaacaagattcaatcaattttttttttgattctttgcacag
||| ||||| |||||||| || ||||| |||||||||||||| || ||||||||||||||||||||||||||||||||||| ||||| |||||||||||||||||        |  |||| ||| | | | ||    ||  | | |  | |   |  |   |   ||||          |||||| ||||
GGCAGCAACTTTTCTTGCATTTCATCCCCAAGATAACAACATAATTGCAATTGGAATGGATGACTCAACCATCCAAATCTATAATGTCCGAATTGATGAGgtattca------tggtggctttgtttttcttt--cattgcacagatagaagttaagtatgacttattt--------gctctttgtacag

upper sequence: LOC_Os03g14980.1 (Oryza sativa), 5'ss of exon 22
lower sequence: PP1S316_34V6.1 (Physcomitrella patens), 5'ss of exon 21
GGCGGCAACGTTTCTTGCTTTCCATCCTCAAGATAACAACATTATAGCAATTGGAATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAGgtattagcacatctaatggcattgctctgcgttattcttataaaaaatggaacaagattcaatcaattttttttttgattctttgcacag------------------------------
 || || || |||||||| |||||||| ||||| |||||||| || || || |||||||| || ||||| || || || || ||||||||  | |||||||||||    ||      |   || || || | | | |       |  | ||     ||||      || | || | ||| |     |  |                              
AGCAGCTACTTTTCTTGCGTTCCATCCCCAAGACAACAACATCATTGCCATAGGAATGGAGGATTCAACAATACAGATTTATAATGTTCGTGTAGATGAGgtattttaccag--gccgttctttctttgtgatctcccgtacctatgttgatttgtattcgtcagtttgtattctagatcccgaataatgtgcctaattagagctttctgctgttggcag

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|27554431|gb|CA998331.1|CA998331
EST:     TTGGAATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAG                         GTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
genomic: TTGGAATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAGgtattagcac ... ctttgcacagGTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
EST: gi|58657128|gb|CK045808.1|CK045808
EST:     TTGGAATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAG                         GTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
genomic: TTGGAATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAGgtattagcac ... ctttgcacagGTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
EST: gi|58677432|gb|CK066119.1|CK066119
EST:     TTGGAATGGATGAGTCAACCATCCAAATCTACAATGTTCGAATTGATGAG                         GTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
genomic: TTGGAATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAGgtattagcac ... ctttgcacagGTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
EST: gi|58655231|gb|CK043911.1|CK043911
EST:     TTGGAATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAG                         GTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
genomic: TTGGAATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAGgtattagcac ... ctttgcacagGTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
EST: gi|58691548|gb|CK080235.1|CK080235
EST:     TTGGAATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAG                         GTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
genomic: TTGGAATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAGgtattagcac ... ctttgcacagGTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
EST: gi|58594272|gb|CF992580.1|CF992580
EST:     TTGGAATGGATGACTCAACCATCCAAATGTACAATGTTCGAATTGATGAG                         GTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
genomic: TTGGAATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAGgtattagcac ... ctttgcacagGTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
EST: gi|58657970|gb|CK046650.1|CK046650
EST:     TTGGAATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAG                         GTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
genomic: TTGGAATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAGgtattagcac ... ctttgcacagGTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
EST: gi|163926688|gb|EG713704.1|EG713704
EST:     TTGGAATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAG                         GTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
genomic: TTGGAATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAGgtattagcac ... ctttgcacagGTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
EST: gi|58656462|gb|CK045142.1|CK045142
EST:     TTGGAATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAG                         GTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
genomic: TTGGAATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAGgtattagcac ... ctttgcacagGTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
EST: gi|218501279|gb|FG957977.1|FG957977
EST:     GGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAG                         GTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
genomic: GGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAGgtattagcac ... ctttgcacagGTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
EST: gi|218487225|gb|FG954419.1|FG954419
EST:     TTGGAATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAG                         GTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
genomic: TTGGAATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAGgtattagcac ... ctttgcacagGTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
EST: gi|29680680|gb|CB676955.1|CB676955
EST:     TTGGAATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAG                         GTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
genomic: TTGGAATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAGgtattagcac ... ctttgcacagGTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
EST: gi|58689471|gb|CK078158.1|CK078158
EST:     TTGGAATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAG                         GTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
genomic: TTGGAATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAGgtattagcac ... ctttgcacagGTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
EST: gi|58694923|gb|CK083610.1|CK083610
EST:     TTGGAATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAG                         GTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
genomic: TTGGAATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAGgtattagcac ... ctttgcacagGTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
EST: gi|29673860|gb|CB670135.1|CB670135
EST:     TTGGAATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAG                         GTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
genomic: TTGGAATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAGgtattagcac ... ctttgcacagGTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
EST: gi|58590233|gb|CF988541.1|CF988541
EST:     TTGGGATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAG                         GTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
genomic: TTGGAATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAGgtattagcac ... ctttgcacagGTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT

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: 72 (upstream exon), 73 (downstream exon)
Score: 65

GGCGGCAACGTTTCTTGCTTTCCATCCTCAAGATAACAACATTATAGCAATTGGAATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAGgtattagcac ... ctttgcacagGTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTTTCAAATGTATTAAATGTGTTAGTCTCTTCTGGAGCTGATGCGCAG




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