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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTACTCCAGCCCTCTTGGTTCTTCCAAGCGCAGCGGTGTCGCCATCAGAGCAATGTCAAGCGAAAGTGGCCCCCAAGGCCTACCAATTGATCTTAGAGgtaactctttagctgcatatctgtagtaatcatgcacctagcaatgctatgtgatcatgttcttttcctttacgcattcatgtttccgtgcaacattttg...

Basic information

species Oryza sativa
transcript LOC_Os08g23810.1
intron # 2
splice site 5'
intron type U2

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|428588|gb|D24740.1|D24740
EST:     GCAATGTCAAGCGAAAGTGGCCCCCAAGGCCTTACCAATTGATCTTAGAG                         GTAAAAGGGCGTTCATTGCTGGAGTTGCTGATGACAATGGCTATGGCTGGG
genomic: GCAATGTCAAGCGAAAGTGGCCCCCAAGGCCT-ACCAATTGATCTTAGAGgtaactcttt ... gatctctcagGTAAAAGGGCGTTCATTGCTGGAGTTGCTGATGACAATGGCTATGGCTGGG
EST: gi|88317317|gb|CI627966.1|CI627966
EST:     AGCAATGTCA-GCGAAAGTGGCCCC-AAGGCCTACCAATTGATCTTAGAG                         GTAAAAGGGCGTTCATTGCTGGAGTTGCTGATGACAATGGCTATGGCTGGG
genomic: AGCAATGTCAAGCGAAAGTGGCCCCCAAGGCCTACCAATTGATCTTAGAGgtaactcttt ... gatctctcagGTAAAAGGGCGTTCATTGCTGGAGTTGCTGATGACAATGGCTATGGCTGGG
EST: gi|58659884|gb|CK048564.1|CK048564
EST:     AGCAATGTCAAGCGAAAGTGGCCCCCAAGGCCTACCAATTGATCTTAGAG                         GTAAAAGGGCGTTCATTGCTGGAGTTGCTGATGACAATGGCTATGGCTGGG
genomic: AGCAATGTCAAGCGAAAGTGGCCCCCAAGGCCTACCAATTGATCTTAGAGgtaactcttt ... gatctctcagGTAAAAGGGCGTTCATTGCTGGAGTTGCTGATGACAATGGCTATGGCTGGG
EST: gi|88294433|gb|CI667407.1|CI667407
EST:     AGCAATGTCAAGCGAAAGTGGCCCCCAAGGCCTACCAATTGATCTTAGAG                         GTAAAAGGGCGTTCATTGCTGGAGTTGCTG
genomic: AGCAATGTCAAGCGAAAGTGGCCCCCAAGGCCTACCAATTGATCTTAGAGgtaactcttt ... gatctctcagGTAAAAGGGCGTTCATTGCTGGAGTTGCTG
EST: gi|88395429|gb|CI612951.1|CI612951
EST:     AGCAATGTCAAGCGAAAGTGGCCCCCAAGGCCTACCAATTGATCTTAGAG                         GTAAAAGGGCGTTCATTGCTGGAGTTGCTGATGACAATGGCTATGGCTGGG
genomic: AGCAATGTCAAGCGAAAGTGGCCCCCAAGGCCTACCAATTGATCTTAGAGgtaactcttt ... gatctctcagGTAAAAGGGCGTTCATTGCTGGAGTTGCTGATGACAATGGCTATGGCTGGG
EST: gi|88307608|gb|CI643459.1|CI643459
EST:     ACCAATGTCAAGCGAAAGTGGCCCCCAAGGCCTACCACTTGATCTTACAG                         GTAAAAGGGCGTTCATTGCTGGAGTTGCTGATGACAATGGCTATGGCTGGG
genomic: AGCAATGTCAAGCGAAAGTGGCCCCCAAGGCCTACCAATTGATCTTAGAGgtaactcttt ... gatctctcagGTAAAAGGGCGTTCATTGCTGGAGTTGCTGATGACAATGGCTATGGCTGGG
EST: gi|88399474|gb|CI606095.1|CI606095
EST:     AGCAATGTCAAGCGAAAGTGGCCCCCAAGGCCTACCAATTGATCTTAGAG                         GTAAAAGGGCGTTCATTGCTGGAGTTGCTGATGACAATGGCTATGGCTGGG
genomic: AGCAATGTCAAGCGAAAGTGGCCCCCAAGGCCTACCAATTGATCTTAGAGgtaactcttt ... gatctctcagGTAAAAGGGCGTTCATTGCTGGAGTTGCTGATGACAATGGCTATGGCTGGG
EST: gi|33795136|gb|CF323441.1|CF323441
EST:     AGCAATGTCAAGCGAAAGTGGCCCCCAAGGCCTACCAATTGATCTTAGAG                         GTAAAAGGGCGTTCATTGCTGGAGTTGCTGATGACAATGGCTATGGCTGGG
genomic: AGCAATGTCAAGCGAAAGTGGCCCCCAAGGCCTACCAATTGATCTTAGAGgtaactcttt ... gatctctcagGTAAAAGGGCGTTCATTGCTGGAGTTGCTGATGACAATGGCTATGGCTGGG
EST: gi|58672850|gb|CK061536.1|CK061536
EST:     AGCAATGTCAAGCGAAAGTGGCCCCCAAGGCCTACCAATTGATCTTAGAG                         GTAAAAGGGCGTTCATTGCTGGAGTTGCTGATGACAATGGCTATGGCTGGG
genomic: AGCAATGTCAAGCGAAAGTGGCCCCCAAGGCCTACCAATTGATCTTAGAGgtaactcttt ... gatctctcagGTAAAAGGGCGTTCATTGCTGGAGTTGCTGATGACAATGGCTATGGCTGGG
EST: gi|571922|gb|D41433.1|D41433
EST:     AGCAATGTCAAGCGAAAGTGGCCCCCAAGGCCTACCAATTGATCTTAGAG                         GTAAAAGGGCGTTCATTGCTGGAGTTGCTGATGACAATGGCTATGGCTGGG
genomic: AGCAATGTCAAGCGAAAGTGGCCCCCAAGGCCTACCAATTGATCTTAGAGgtaactcttt ... gatctctcagGTAAAAGGGCGTTCATTGCTGGAGTTGCTGATGACAATGGCTATGGCTGGG
EST: gi|29613728|gb|CB618741.1|CB618741
EST:     AGCAATGTCAAGCGAAAGTGGCCCCCAAGGCCTACCAATTGATCTTAGAG                         GTAAAAGGGCGTTCATTGCTGGAGTTGCTGATGACAATGGCTATGGCTGGG
genomic: AGCAATGTCAAGCGAAAGTGGCCCCCAAGGCCTACCAATTGATCTTAGAGgtaactcttt ... gatctctcagGTAAAAGGGCGTTCATTGCTGGAGTTGCTGATGACAATGGCTATGGCTGGG
EST: gi|88350148|gb|CI622079.1|CI622079
EST:     AGCAATGTCAAGCGAAAGTGGCCCCCAAGGCCTAACAATTGATCTTAGAG                         GTAAAAGGGCGTTCATTGCTGGAGTTGCTGATGACAATGGCT
genomic: AGCAATGTCAAGCGAAAGTGGCCCCCAAGGCCTACCAATTGATCTTAGAGgtaactcttt ... gatctctcagGTAAAAGGGCGTTCATTGCTGGAGTTGCTGATGACAATGGCT
EST: gi|88574877|gb|CI666646.1|CI666646
EST:     AGCAATGTCAAGCGAAAGTGGCCCCCAAGGCCTACCAATTGATCTTAGAG                         GTAAAAGGGCGTTCATTGCTGGAGTTGCTGATGACAATGGCTATGGCTGGG
genomic: AGCAATGTCAAGCGAAAGTGGCCCCCAAGGCCTACCAATTGATCTTAGAGgtaactcttt ... gatctctcagGTAAAAGGGCGTTCATTGCTGGAGTTGCTGATGACAATGGCTATGGCTGGG
EST: gi|88449350|gb|CI582222.1|CI582222
EST:     AGCAATGTCAAGCGAAAGTGGCCCCCAAGGCCTACCAATTGATCTTAGAG                         GTAAAAGGGCGTTCATTGCTGGAGTTGCTGATGACAATGGCTATGGCTG
genomic: AGCAATGTCAAGCGAAAGTGGCCCCCAAGGCCTACCAATTGATCTTAGAGgtaactcttt ... gatctctcagGTAAAAGGGCGTTCATTGCTGGAGTTGCTGATGACAATGGCTATGGCTG
EST: gi|88370906|gb|CI595018.1|CI595018
EST:     AGCAATGTCAAGCGAAAGTGGCCCCCAAGGCCTACCAATTGATCTTAGAG                         GTAAAAGGGCGTTCATTGCTGGAGTTGCTGATGAC
genomic: AGCAATGTCAAGCGAAAGTGGCCCCCAAGGCCTACCAATTGATCTTAGAGgtaactcttt ... gatctctcagGTAAAAGGGCGTTCATTGCTGGAGTTGCTGATGAC
EST: gi|33691058|gb|CF319297.1|CF319297
EST:     AGCAATGTCAAGCGAAAGTGGCCCCCAAGGCCTACCAATTGATCTTAGAG                         GTAAAAGGGCGTTCATTGCTGGAGTTGCTGATGACAATGGCTATGGCTGGG
genomic: AGCAATGTCAAGCGAAAGTGGCCCCCAAGGCCTACCAATTGATCTTAGAGgtaactcttt ... gatctctcagGTAAAAGGGCGTTCATTGCTGGAGTTGCTGATGACAATGGCTATGGCTGGG
EST: gi|88326669|gb|CI658391.1|CI658391
EST:     AGCAATGTCAAGCGAAAGTGGCCCCCAAGGCCTACCAATTGATCTTAGAG                         GTAAAAGGGCGTTCATTGCTGGAGTTGCTGATGACAATGGC
genomic: AGCAATGTCAAGCGAAAGTGGCCCCCAAGGCCTACCAATTGATCTTAGAGgtaactcttt ... gatctctcagGTAAAAGGGCGTTCATTGCTGGAGTTGCTGATGACAATGGC
EST: gi|88719687|gb|CI743197.1|CI743197
EST:     AGCAATGTCAAGCGAAAGTGGCCCCCAAGGCCTACCAATTGATCTTAGAG                         GTAAAAGGGCGTTCATTGCTGGAGTTGCTGATGACAATGGC
genomic: AGCAATGTCAAGCGAAAGTGGCCCCCAAGGCCTACCAATTGATCTTAGAGgtaactcttt ... gatctctcagGTAAAAGGGCGTTCATTGCTGGAGTTGCTGATGACAATGGC
EST: gi|88330328|gb|CI633530.1|CI633530
EST:     AGCAATGTCAAGCGAAAGTGGCCCCCAAGGCCTACCAATTGATCTTAGAG                         GTAAAAGGGCGTTCATTGCTGGAGTTGCTGATGACAATGGCTATGGCTGGG
genomic: AGCAATGTCAAGCGAAAGTGGCCCCCAAGGCCTACCAATTGATCTTAGAGgtaactcttt ... gatctctcagGTAAAAGGGCGTTCATTGCTGGAGTTGCTGATGACAATGGCTATGGCTGGG
EST: gi|571926|gb|D41437.1|D41437
EST:     AGCAATGTCAAGCGAAAGTGGCCCCCAAGGCCTACCAATTGATCTTAGAG                         GTAAAAGGGCGTTCATTGCTGGAGTTGCTGATGACAATGGCTATGGCTGGG
genomic: AGCAATGTCAAGCGAAAGTGGCCCCCAAGGCCTACCAATTGATCTTAGAGgtaactcttt ... gatctctcagGTAAAAGGGCGTTCATTGCTGGAGTTGCTGATGACAATGGCTATGGCTGGG
EST: gi|58679709|gb|CK068396.1|CK068396
EST:     AGCAATGTCAAGCGAAAGTGGCCCCCAAGGCCTACCAATTGATCTTAGAG                         GTAAAAGGGCGTTCATTGCTGGAGTTGCTGATGACAATGGCTATGGCTGGG
genomic: AGCAATGTCAAGCGAAAGTGGCCCCCAAGGCCTACCAATTGATCTTAGAGgtaactcttt ... gatctctcagGTAAAAGGGCGTTCATTGCTGGAGTTGCTGATGACAATGGCTATGGCTGGG
EST: gi|88333772|gb|CI643804.1|CI643804
EST:     AGCAATGTCAAGCGAAAGTGGCCCCCAAGGCCTACCAATTGATCTTAGAG                         GTAAAAGGGCGTTCATTGCTGGAGTTGCTGATGACAATGGCTATGGCTGGG
genomic: AGCAATGTCAAGCGAAAGTGGCCCCCAAGGCCTACCAATTGATCTTAGAGgtaactcttt ... gatctctcagGTAAAAGGGCGTTCATTGCTGGAGTTGCTGATGACAATGGCTATGGCTGGG
EST: gi|88399311|gb|CI618501.1|CI618501
EST:     AGCAATGTCAAGCGAAAGTGGCCCC-AAGGCCTACCAATTGATCTTAGAG                         GTAAAAGGGCGTTCATTGCTGGAGTTGCTGATGACAATGGCTATGGCTGGG
genomic: AGCAATGTCAAGCGAAAGTGGCCCCCAAGGCCTACCAATTGATCTTAGAGgtaactcttt ... gatctctcagGTAAAAGGGCGTTCATTGCTGGAGTTGCTGATGACAATGGCTATGGCTGGG
EST: gi|58656775|gb|CK045455.1|CK045455
EST:     AGCAATGTCAAGCGAAAGTGGNCCCCAAGGCCTACCAATTGATCTTAGAG                         GTAAAAGGGCGTTCATTGCTGGAGTTGCTGATGACAATGGCTATGGCTGGG
genomic: AGCAATGTCAAGCGAAAGTGGCCCCCAAGGCCTACCAATTGATCTTAGAGgtaactcttt ... gatctctcagGTAAAAGGGCGTTCATTGCTGGAGTTGCTGATGACAATGGCTATGGCTGGG

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: 75 (upstream exon), 75 (downstream exon)
Score: 36

TGCTACTCCAGCCCTCTTGGTTCTTCCAAGCGCAGCGGTGTCGCCATCAGAGCAATGTCAAGCGAAAGTGGCCCCCAAGGCCTACCAATTGATCTTAGAGgtaactcttt ... gatctctcagGTAAAAGGGCGTTCATTGCTGGAGTTGCTGATGACAATGGCTATGGCTGGGCAATTGCAAAGGCTCTTGCTGCTGCTGGTGCTGAAATTCTTGTTGGTAC




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