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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcatttgatgtctactttctagaatgttgtttgatagcctgacaaaaattcacatgggtctcacaacaatgctttgtcatgttgattagATTGGTTAGAGCTGCCTGGTGCTGTGATCCTTCTCATTGCTGTTGCCCCGAACCTGTTTGCGAGCACCTTCCGAGGCGACTTAGTTGGCATCTTCATATG

Basic information

species Oryza sativa
transcript LOC_Os03g55850.1
intron # 3
splice site 3'
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|29656136|gb|CB652411.1|CB652411
EST:     TGCGATCATTGCTGTCATCCTTCGTCTCTTCTTTCCTCGCCATTTCCCTG                         ATTGGTTAGAGCTGCCTGGTGCTGTGATCCTTCTCATTGCTGTTGCCCCGA
genomic: TGCGATCATTGCTGTCATCCTTCGTCTCTTCTTTCCTCGCCATTTCCCTGgtatcatttg ... tgttgattagATTGGTTAGAGCTGCCTGGTGCTGTGATCCTTCTCATTGCTGTTGCCCCGA
EST: gi|218505408|gb|FG953377.1|FG953377
EST:     TGCGATCATTGCTGTCATCCTTCGTCTCTTCTTTCCTCGCCATTTCCCTG                         ATTGGTTCGAGCTGCCTGGTGCTGTGATCCTTCTCATTGCTGTTGCCCCGA
genomic: TGCGATCATTGCTGTCATCCTTCGTCTCTTCTTTCCTCGCCATTTCCCTGgtatcatttg ... tgttgattagATTGGTTAGAGCTGCCTGGTGCTGTGATCCTTCTCATTGCTGTTGCCCCGA
EST: gi|119002221|gb|CU234192.1|CU234192
EST:     TGCGATCATTGCTGTCATCCTTCGTCTCTTCTTTCCTCGCCATTTCCCTG                         ATTGGTTAGAGCTGCCTGGTGCTGTGATCCTTCTCATTGCTGTTGCCCCGA
genomic: TGCGATCATTGCTGTCATCCTTCGTCTCTTCTTTCCTCGCCATTTCCCTGgtatcatttg ... tgttgattagATTGGTTAGAGCTGCCTGGTGCTGTGATCCTTCTCATTGCTGTTGCCCCGA
EST: gi|87019196|gb|CI277912.1|CI277912
EST:     CTGTCATCCTTCGTCTCTTCTTTCCTCGCCATTTCCCTG                         ATTGGTTAGAGCTGCCTGGTGCTGTGATCCTTCTCATTGCTGTTGCCCCGA
genomic: CTGTCATCCTTCGTCTCTTCTTTCCTCGCCATTTCCCTGgtatcatttg ... tgttgattagATTGGTTAGAGCTGCCTGGTGCTGTGATCCTTCTCATTGCTGTTGCCCCGA
EST: gi|29667854|gb|CB664129.1|CB664129
EST:     TGCGATCATTGCTGTCATCCTTCGTCTCTTCTTTCCTCGCCATTTCCCTG                         ATTGGTTAGAGCTGCCTGGTGCTGTGATCCTTCTCATTGCTGTTGCCCCGA
genomic: TGCGATCATTGCTGTCATCCTTCGTCTCTTCTTTCCTCGCCATTTCCCTGgtatcatttg ... tgttgattagATTGGTTAGAGCTGCCTGGTGCTGTGATCCTTCTCATTGCTGTTGCCCCGA
EST: gi|58591798|gb|CF990106.1|CF990106
EST:     TGCGATCATTGCTGTCATCCTTCGTCTCTTCTTTCCTCGCCATTTCCCTG                         ATTGGTTAGAGCTGCCTGGTGCTGTGATCCTTCTCATTGCTGTTGCCCCGA
genomic: TGCGATCATTGCTGTCATCCTTCGTCTCTTCTTTCCTCGCCATTTCCCTGgtatcatttg ... tgttgattagATTGGTTAGAGCTGCCTGGTGCTGTGATCCTTCTCATTGCTGTTGCCCCGA
EST: gi|86494252|gb|CI136885.1|CI136885
EST:     TGCGATCATTGCTGTCATCCTTCGTCTCTTCTTTCCTCGCCATTTCCCTG                         ATTGGTTAGAGCTGCCTGGTGCTGTGATCCTTCTCATTGCTGTTGCCCCGA
genomic: TGCGATCATTGCTGTCATCCTTCGTCTCTTCTTTCCTCGCCATTTCCCTGgtatcatttg ... tgttgattagATTGGTTAGAGCTGCCTGGTGCTGTGATCCTTCTCATTGCTGTTGCCCCGA
EST: gi|86509585|gb|CI152218.1|CI152218
EST:     TCATCCTTCGTCTCTTCTTTCCTCGCCATTTCCCTG                         ATTGGTTAGAGCTGCCTGGTGCTGTGATCCTTCTCATTGCTGTTGCCCCGA
genomic: TCATCCTTCGTCTCTTCTTTCCTCGCCATTTCCCTGgtatcatttg ... tgttgattagATTGGTTAGAGCTGCCTGGTGCTGTGATCCTTCTCATTGCTGTTGCCCCGA
EST: gi|88835395|gb|CI005085.1|CI005085
EST:     TGCGATCATTGCTGTCATCCTTCGTCTCTTCTTTCCTCGCCATTTCCCTG                         ATTGGTTAGAGCTGCCTGGTGCTGTGATCCTTCTCATTGCTGTTGCCCCGA
genomic: TGCGATCATTGCTGTCATCCTTCGTCTCTTCTTTCCTCGCCATTTCCCTGgtatcatttg ... tgttgattagATTGGTTAGAGCTGCCTGGTGCTGTGATCCTTCTCATTGCTGTTGCCCCGA
EST: gi|119002222|gb|CU234193.1|CU234193
EST:     CATCCTTCGTCTCTTCTTTCCTCGCCATTTCCCTG                         ATTGGTTAGAGCTGCCTGGTGCTGTGATCCTTCTCATTGCTGTTGCCCCGA
genomic: CATCCTTCGTCTCTTCTTTCCTCGCCATTTCCCTGgtatcatttg ... tgttgattagATTGGTTAGAGCTGCCTGGTGCTGTGATCCTTCTCATTGCTGTTGCCCCGA
EST: gi|29667853|gb|CB664128.1|CB664128
EST:     TGCGATCATTGCTGTCATCCTTCGTCTCTTCTTTCCTCGCCATTTCCCTG                         ATTGGTTAGAGCTGCCTGGTGCTGTGATCCTTCTCATTGCTGTTGCCCCGA
genomic: TGCGATCATTGCTGTCATCCTTCGTCTCTTCTTTCCTCGCCATTTCCCTGgtatcatttg ... tgttgattagATTGGTTAGAGCTGCCTGGTGCTGTGATCCTTCTCATTGCTGTTGCCCCGA
EST: gi|58591068|gb|CF989376.1|CF989376
EST:     TGCGATCATTGCTGTCATCCTTCGTCTCTTCTTTCCTCGCCATTTCCCTG                         ATTGGTTAGAGCTGCCTGGTGCTGTGATCCTTCTCATTGCTGTTGCCCCGA
genomic: TGCGATCATTGCTGTCATCCTTCGTCTCTTCTTTCCTCGCCATTTCCCTGgtatcatttg ... tgttgattagATTGGTTAGAGCTGCCTGGTGCTGTGATCCTTCTCATTGCTGTTGCCCCGA
EST: gi|38473864|gb|CF957996.1|CF957996
EST:     TGCGATCATTGCTGTCATCCTTCGTCTCTTCTTTCCTCGCCATTTCCCTG                         ATTGGTTAGAGCTGCCTGGTGCTGTGATCCTTCTCATTGCTGTTGCCCCGA
genomic: TGCGATCATTGCTGTCATCCTTCGTCTCTTCTTTCCTCGCCATTTCCCTGgtatcatttg ... tgttgattagATTGGTTAGAGCTGCCTGGTGCTGTGATCCTTCTCATTGCTGTTGCCCCGA
EST: gi|29626644|gb|CB631655.1|CB631655
EST:     TGCGATCATTGCTGTCATCCTTCGTCTCTTCTTTCCTCGCCATTTCCCTG                         ATTGGTTAGAGCTGCCTGGTGCTGTGATCCTTCTCATTGCTGTTGCCCCGA
genomic: TGCGATCATTGCTGTCATCCTTCGTCTCTTCTTTCCTCGCCATTTCCCTGgtatcatttg ... tgttgattagATTGGTTAGAGCTGCCTGGTGCTGTGATCCTTCTCATTGCTGTTGCCCCGA
EST: gi|88234313|gb|CI234162.1|CI234162
EST:     TGCGATCATTGCTGTCATCCTTCGTCTCTTCTTTCCTCGCCATTTCCCTG                         ATTGGTTAGAGCTGCCTGGTGCTGTGATCCTTCTCATTGCTGTTGCCCCGA
genomic: TGCGATCATTGCTGTCATCCTTCGTCTCTTCTTTCCTCGCCATTTCCCTGgtatcatttg ... tgttgattagATTGGTTAGAGCTGCCTGGTGCTGTGATCCTTCTCATTGCTGTTGCCCCGA
EST: gi|88202868|gb|CI200720.1|CI200720
EST:     CTTTCCTCGCCATTTGCCTG                         ATTGGTTAGAGCTGCCTGGTGCTGTGATCCTTCTCATTGCTGTTGCCCCGA
genomic: CTTTCCTCGCCATTTCCCTGgtatcatttg ... tgttgattagATTGGTTAGAGCTGCCTGGTGCTGTGATCCTTCTCATTGCTGTTGCCCCGA
EST: gi|58586796|gb|CF985104.1|CF985104
EST:     TGCGATCATTGCTGTCATCCTTCGTCTCTTCTTTCCTCGCCATTTCCCTG                         ATTGGTTAGAGCTGCCTGGTGCTGTGATCCTTCTCATTGCTGTTGCCCCGA
genomic: TGCGATCATTGCTGTCATCCTTCGTCTCTTCTTTCCTCGCCATTTCCCTGgtatcatttg ... tgttgattagATTGGTTAGAGCTGCCTGGTGCTGTGATCCTTCTCATTGCTGTTGCCCCGA
EST: gi|66913495|gb|CX100343.1|CX100343
EST:     TGCGATCATTGCTGTCATCCTTCGTCTCTTCTTTCCTCGCCATTTCCCTG                         ATTGGTTAGAGCTGCCTGGTGCTGTGATCCTTCTCATTGCTGTTGCCCCGA
genomic: TGCGATCATTGCTGTCATCCTTCGTCTCTTCTTTCCTCGCCATTTCCCTGgtatcatttg ... tgttgattagATTGGTTAGAGCTGCCTGGTGCTGTGATCCTTCTCATTGCTGTTGCCCCGA
EST: gi|88836869|gb|CI014870.1|CI014870
EST:     CGATCATTGCTGTCATCCTTCGTCTCTTCGTTCGTCGCCATTTCCCTG                         ATTGGTTAGAGCTGCCTGGTTCTGTGATCCTTCTCATTGCTGTTGCCCCGA
genomic: CGATCATTGCTGTCATCCTTCGTCTCTTCTTTCCTCGCCATTTCCCTGgtatcatttg ... tgttgattagATTGGTTAGAGCTGCCTGGTGCTGTGATCCTTCTCATTGCTGTTGCCCCGA
EST: gi|88829782|gb|CI004820.1|CI004820
EST:     CTTCTTTCCTCGCCATTTCCCTG                         ATTGGTTAGAGCTGCCTGGTGCTGTGATCCTTCTCATTGCTGTTGCCCCGA
genomic: CTTCTTTCCTCGCCATTTCCCTGgtatcatttg ... tgttgattagATTGGTTAGAGCTGCCTGGTGCTGTGATCCTTCTCATTGCTGTTGCCCCGA
EST: gi|86259012|gb|CI004556.1|CI004556
EST:     TGCGATCATTGCTGTCATCCTTCGTCTCTTCTTTCCTCGCCATTTCCCTG                         ATTGGTTAGAGCTGCCTGGTGCTGTGATCCTTCTCATTGCTGTTGCCCCGA
genomic: TGCGATCATTGCTGTCATCCTTCGTCTCTTCTTTCCTCGCCATTTCCCTGgtatcatttg ... tgttgattagATTGGTTAGAGCTGCCTGGTGCTGTGATCCTTCTCATTGCTGTTGCCCCGA
EST: gi|88201754|gb|CI202109.1|CI202109
EST:     TGCGATCATTGCTGTCATCCTTCGTCTCTTCTTTCCTCGCCATTTCCCTG                         ATTGGTTAGAGCTGCCTGGTGCTGTGATCCTTCTCATTGCTGTTGCCCCGA
genomic: TGCGATCATTGCTGTCATCCTTCGTCTCTTCTTTCCTCGCCATTTCCCTGgtatcatttg ... tgttgattagATTGGTTAGAGCTGCCTGGTGCTGTGATCCTTCTCATTGCTGTTGCCCCGA
EST: gi|86496839|gb|CI139472.1|CI139472
EST:     TGCGATCATTGCTGTCATCCTTCGTCTCTTCTTTCCTCGCCATTTCCCTG                         ATTGGTTAGAGCTGCCTGGTGCTGTGATCCTTCTCATTGCTGTTGCCCCGA
genomic: TGCGATCATTGCTGTCATCCTTCGTCTCTTCTTTCCTCGCCATTTCCCTGgtatcatttg ... tgttgattagATTGGTTAGAGCTGCCTGGTGCTGTGATCCTTCTCATTGCTGTTGCCCCGA
EST: gi|88844292|gb|CI005665.1|CI005665
EST:     TGCGATCATTGCTGTCATCCTTCGTCTCTTCTTTCCTCGCCATTTCCCTG                         ATTGGTTAGAGCTGCCTGGTGCTGTGATCCTTCTCATTGCTGTTGCCCCGA
genomic: TGCGATCATTGCTGTCATCCTTCGTCTCTTCTTTCCTCGCCATTTCCCTGgtatcatttg ... tgttgattagATTGGTTAGAGCTGCCTGGTGCTGTGATCCTTCTCATTGCTGTTGCCCCGA
EST: gi|88201039|gb|CI201394.1|CI201394
EST:     TTTCCTCGCCATTTCCCTG                         ATTGGTTAGAGCTGCCTGGTGCTGTGATCCTTCTCATTGCTGTTGCCCCGA
genomic: TTTCCTCGCCATTTCCCTGgtatcatttg ... tgttgattagATTGGTTAGAGCTGCCTGGTGCTGTGATCCTTCTCATTGCTGTTGCCCCGA
EST: gi|29626645|gb|CB631656.1|CB631656
EST:     TGCGATCATTGCTGTCATCCTTCGTCTCTTCTTTCCTCGCCATTTCCCTG                         ATTGGTTAGAGCTGCCTGGTGCTGTGATCCTTCTCATTGCTGTTGCCCCGA
genomic: TGCGATCATTGCTGTCATCCTTCGTCTCTTCTTTCCTCGCCATTTCCCTGgtatcatttg ... tgttgattagATTGGTTAGAGCTGCCTGGTGCTGTGATCCTTCTCATTGCTGTTGCCCCGA
EST: gi|88211193|gb|CI210833.1|CI210833
EST:     GCTGTCATCCTTCGTCTCTTCTGTCCTCGCCATTTCCCTG                         ATTGGTTAGAGCTGCCTGGTGCTGTGATCCTTCTCATTGCTGTTGCCCCGA
genomic: GCTGTCATCCTTCGTCTCTTCTTTCCTCGCCATTTCCCTGgtatcatttg ... tgttgattagATTGGTTAGAGCTGCCTGGTGCTGTGATCCTTCTCATTGCTGTTGCCCCGA
EST: gi|218480554|gb|FG955808.1|FG955808
EST:     TGCGATCATTGCTGTCATCCTTCGTCTCTTCTTTCCTCGCCATTTCCCTG                         ATTGGTTAGAGCTGCCTGGTGCTGTGATCCTTCTCATTGCTGTTGCCCCGA
genomic: TGCGATCATTGCTGTCATCCTTCGTCTCTTCTTTCCTCGCCATTTCCCTGgtatcatttg ... tgttgattagATTGGTTAGAGCTGCCTGGTGCTGTGATCCTTCTCATTGCTGTTGCCCCGA
EST: gi|87033828|gb|CI188452.1|CI188452
EST:     GTCATCCTTCGTCTCTTCTTTCCTCGCCATTTCCCTG                         ATTGGTTAGAGCTGCCTGGTGCTGTGATCCTTCTCATTGCTGTTGCCCCGA
genomic: GTCATCCTTCGTCTCTTCTTTCCTCGCCATTTCCCTGgtatcatttg ... tgttgattagATTGGTTAGAGCTGCCTGGTGCTGTGATCCTTCTCATTGCTGTTGCCCCGA
EST: gi|38480635|gb|CF964724.1|CF964724
EST:     TGCGATCATTGCTGTCATCCTTCGTCTCTTCTTTCCTCGCCATTTCCCTG                         ATTGGTTAGAGCTGCCTGGTGCGGTGATCCTTCTCATTGCTGTTGCCCCGA
genomic: TGCGATCATTGCTGTCATCCTTCGTCTCTTCTTTCCTCGCCATTTCCCTGgtatcatttg ... tgttgattagATTGGTTAGAGCTGCCTGGTGCTGTGATCCTTCTCATTGCTGTTGCCCCGA

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: 71 (upstream exon), 75 (downstream exon)
Score: 115

GGGAGAAATTGGAAAATGGATTGCGATCATTGCTGTCATCCTTCGTCTCTTCTTTCCTCGCCATTTCCCTGgtatcatttg ... tgttgattagATTGGTTAGAGCTGCCTGGTGCTGTGATCCTTCTCATTGCTGTTGCCCCGAACCTGTTTGCGAGCACCTTCCGAGGCGACTTAGTTGGCATCTTCATATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagcctgacaaaaattcacatgggtctcacaacaatgctttgtcatgttgattagATTGGTTAGAGCTGCCTGGTGCTGTGATCCTTCTCATTGCTGTTGCCCCGAACCTGTTTGCGAGCACCTTCCGAGGCGACTTAGTTGGCATCTTCATATG
                       gtctcac  putative branch site (score: 115)
       acaaaaatt  TA-rich tract