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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATCTGCAGAACAATCAATTTACTGGTTATATCAATGTCCTTGCTAATCTCCCCCTTGATGATCTgtaagaaatcaacctataagtaattaatattttatttgcacgtgcagtaccacatctcatatctttgctttcctatag

Basic information

species Oryza sativa
transcript LOC_Os03g08550.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g08550.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G330907_T01 (Zea mays), 5'ss of exon 8
ATATCTGCAGAACAATCAATTTACTGGTTATATCAATGTCCTTGCTAATCTCCCCCTTGATGATCTgtaagaaatcaacc-tataagtaattaatattttatttgcacgtgcagtaccacatctcatatctttgctttcctatag
 ||| |||||||||| |||||||||||||||||||||||| | || || || ||||||||    |||| || |||||||  |  || | | |  |  || ||||||| || |||||||| |||||||| | | ||||  || |||
GTATTTGCAGAACAACCAATTTACTGGTTATATCAATGTCTTAGCCAACCTTCCCCTTGAAACCCTgtgagtaatcaactatgaaattcaatggtgcttcatttgcatgttcagtaccatatctcataacct-gcttgtctctag

upper sequence: LOC_Os03g08550.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G153393_T01 (Zea mays), 5'ss of exon 8
ATATCTGCAGAACAATCAATTTACTGGTTATATCAATGTCCTTGCTAATCTCCCCCTTGATGATCTgtaagaaatcaacc-tataagtaattaatattttatttgcacgtgcagtaccacatctcatatctttgctttcctatag
 ||| |||||||||| |||||||||||| ||||||||||| | || ||||||||||||||   | ||| || |||||||  |  || | | |  |  |||||||||| || || ||||| || ||||| ||| |||| ||| |||
GTATTTGCAGAACAACCAATTTACTGGTAATATCAATGTCTTAGCCAATCTCCCCCTTGAAACTTTgtgagtaatcaactgtgaaattcaatggtgctttatttgcatgttcattaccatatttcataactt-gcttgcctctag
















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|58652520|gb|CK041200.1|CK041200
EST:     CAATTTACTGGTTATATCAATGTCCTTGCTAATCTCCCCCTTGATGATCT                         GAATGTTGCAAACAATCATTTCACTGGCTGGATTCCTAGTCAACTTAAGAA
genomic: CAATTTACTGGTTATATCAATGTCCTTGCTAATCTCCCCCTTGATGATCTgtaagaaatc ... tttcctatagGAATGTTGCAAACAATCATTTCACTGGCTGGATTCCTAGTCAACTTAAGAA
EST: gi|44665230|gb|CR278664.1|CR278664
EST:     CAATTTACTGGTTATATCAATGTCCTTGCTAATCTCCCCCTTGATGATCT                         GAATGTTGCAAACAATCATT
genomic: CAATTTACTGGTTATATCAATGTCCTTGCTAATCTCCCCCTTGATGATCTgtaagaaatc ... tttcctatagGAATGTTGCAAACAATCATT
EST: gi|29644649|gb|CB649656.1|CB649656
EST:     CAATTTACTGGTTATATCAATGTCCTTGCTAATCTCCCCCTTGATGATCT                         GAATGTTGCAAACAATCATTTCACTGGCTGGATTCCTAGTCAACTTAAGAA
genomic: CAATTTACTGGTTATATCAATGTCCTTGCTAATCTCCCCCTTGATGATCTgtaagaaatc ... tttcctatagGAATGTTGCAAACAATCATTTCACTGGCTGGATTCCTAGTCAACTTAAGAA
EST: gi|29624948|gb|CB629959.1|CB629959
EST:     CAATTTACTGGTTATATCAATGTCCTTGCTAATCTCCCCCTTGATGATCT                         GAATGTTGCAAACAATCATTTCACTGGCTGGATTCCTAGTCAACTTAAGAA
genomic: CAATTTACTGGTTATATCAATGTCCTTGCTAATCTCCCCCTTGATGATCTgtaagaaatc ... tttcctatagGAATGTTGCAAACAATCATTTCACTGGCTGGATTCCTAGTCAACTTAAGAA
EST: gi|58661405|gb|CK050085.1|CK050085
EST:     CAATTTACTGGTTATATCAATGTCCTTGCTAATCTCCCCCTTGATGATCT                         GAATGTTGCAAACAATCATTTCACTGGCTGGATTCCTAGTCAACTTAAGAA
genomic: CAATTTACTGGTTATATCAATGTCCTTGCTAATCTCCCCCTTGATGATCTgtaagaaatc ... tttcctatagGAATGTTGCAAACAATCATTTCACTGGCTGGATTCCTAGTCAACTTAAGAA
EST: gi|58658124|gb|CK046804.1|CK046804
EST:     CAATTTACTGGTTATATCAATGTCCTTGCTAATCTCCCCCTTGATGATCT                         GAATGTTGCAAACAATCATTTCACTGGCTGGATTCCTAGTCAACTTAAGAA
genomic: CAATTTACTGGTTATATCAATGTCCTTGCTAATCTCCCCCTTGATGATCTgtaagaaatc ... tttcctatagGAATGTTGCAAACAATCATTTCACTGGCTGGATTCCTAGTCAACTTAAGAA
EST: gi|29681108|gb|CB677383.1|CB677383
EST:     CAATTTACTGGTTATATCAATGTCCTTGCTAATCTCCCCCTTGATGATCT                         GAATGTTGCAAACAATCATTTCACTGGCTGGATTCCTAGTCAACTTAAGAA
genomic: CAATTTACTGGTTATATCAATGTCCTTGCTAATCTCCCCCTTGATGATCTgtaagaaatc ... tttcctatagGAATGTTGCAAACAATCATTTCACTGGCTGGATTCCTAGTCAACTTAAGAA

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: 66 (upstream exon), 66 (downstream exon)
Score: 16

ATATCTGCAGAACAATCAATTTACTGGTTATATCAATGTCCTTGCTAATCTCCCCCTTGATGATCTgtaagaaatc ... tttcctatagGAATGTTGCAAACAATCATTTCACTGGCTGGATTCCTAGTCAACTTAAGAAGATAAACAATCTACA




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