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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggaactgtctttcccatctctctttatggctcacccacaacactatgtggcatgcatcatctcacttaatttggttcaacagGCCCTGGTGCTCCTGCTGTCTTCAACGTT

Basic information

species Oryza sativa
transcript LOC_Os04g59040.1
intron # 2
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|87023771|gb|CI288124.1|CI288124
EST:     CTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCG                         GCCCTGGTGCTCCTGCTGTCTTCAACGTT
genomic: CTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCGgtatggaact ... ggttcaacagGCCCTGGTGCTCCTGCTGTCTTCAACGTT
EST: gi|55433781|gb|CV730004.1|CV730004
EST:     CTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCG                         GCCCTGGTGCTCCTGCTGTCTTCAACGTT
genomic: CTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCGgtatggaact ... ggttcaacagGCCCTGGTGCTCCTGCTGTCTTCAACGTT
EST: gi|3768324|gb|AU032351.1|AU032351
EST:     CTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCG                         GCCCTGGTGCTCCTGCTGTCTTCAACGTT
genomic: CTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCGgtatggaact ... ggttcaacagGCCCTGGTGCTCCTGCTGTCTTCAACGTT
EST: gi|33794379|gb|CF323075.1|CF323075
EST:     CTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCG                         GCCCTGGTGCTCCTGCTGTCTTCAACGTT
genomic: CTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCGgtatggaact ... ggttcaacagGCCCTGGTGCTCCTGCTGTCTTCAACGTT
EST: gi|88423146|gb|CI613447.1|CI613447
EST:     CTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCG                         GCCCTGGTGCTCCTGCTGTCTTCAACGTT
genomic: CTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCGgtatggaact ... ggttcaacagGCCCTGGTGCTCCTGCTGTCTTCAACGTT
EST: gi|33681023|gb|CF309262.1|CF309262
EST:     CTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCG                         GCCCTGGTGCTCCTGCTGTCTTCAACGTT
genomic: CTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCGgtatggaact ... ggttcaacagGCCCTGGTGCTCCTGCTGTCTTCAACGTT
EST: gi|88732604|gb|CI755781.1|CI755781
EST:     CTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCG                         GCCCTGGTGCTCCTGCTGTCTTCAACGTT
genomic: CTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCGgtatggaact ... ggttcaacagGCCCTGGTGCTCCTGCTGTCTTCAACGTT
EST: gi|88300646|gb|CI587450.1|CI587450
EST:     CTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCG                         GCCCTGGTGCTCCTGCTGTCTTCAACGTT
genomic: CTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCGgtatggaact ... ggttcaacagGCCCTGGTGCTCCTGCTGTCTTCAACGTT
EST: gi|88427290|gb|CI586838.1|CI586838
EST:     CTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCG                         GCCCTGGTGCTCCTGCTGTCTTCAACGTT
genomic: CTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCGgtatggaact ... ggttcaacagGCCCTGGTGCTCCTGCTGTCTTCAACGTT
EST: gi|88721865|gb|CI743377.1|CI743377
EST:     CTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCG                         GCCCTGGTGCTCCTGCTGTCTTCAACGTT
genomic: CTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCGgtatggaact ... ggttcaacagGCCCTGGTGCTCCTGCTGTCTTCAACGTT
EST: gi|33686066|gb|CF314305.1|CF314305
EST:     CTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCG                         GCCCTGGTGCTCCTGCTGTCTTCAACGTT
genomic: CTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCGgtatggaact ... ggttcaacagGCCCTGGTGCTCCTGCTGTCTTCAACGTT
EST: gi|58602895|gb|CK013423.1|CK013423
EST:     CTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCG                         GCCCTGGTGCTCCTGCTGTCTTCAACGTT
genomic: CTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCGgtatggaact ... ggttcaacagGCCCTGGTGCTCCTGCTGTCTTCAACGTT
EST: gi|286879|gb|D15686.1|D15686
EST:     CTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCG                         GCCCTGGTGCTCCTGCTGTCTTCAACGTT
genomic: CTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCGgtatggaact ... ggttcaacagGCCCTGGTGCTCCTGCTGTCTTCAACGTT
EST: gi|66915284|gb|CX102132.1|CX102132
EST:     CTTGTCGAGGAGATCAGTAGCTGCACATCCGGGGCATGATCTTGAGATCG                         GCCCTGGTGCTCCTGCTGTCTTCAACGTT
genomic: CTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCGgtatggaact ... ggttcaacagGCCCTGGTGCTCCTGCTGTCTTCAACGTT
EST: gi|88726501|gb|CI750156.1|CI750156
EST:     CTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCG                         GCCCTGGTGCTCCTGCTGTCTTCAACGTT
genomic: CTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCGgtatggaact ... ggttcaacagGCCCTGGTGCTCCTGCTGTCTTCAACGTT
EST: gi|27554006|gb|CA997906.1|CA997906
EST:     CTTGTCGAGGAGATCATTTGCTGCACATCCGTGGCATGATCTTGAGATCG                         GCCCTGGTGCTCCTGCTGTCTTCAACGTT
genomic: CTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCGgtatggaact ... ggttcaacagGCCCTGGTGCTCCTGCTGTCTTCAACGTT
EST: gi|55433023|gb|CV729535.1|CV729535
EST:     CTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCG                         GCCCTGGTGCTCCTGCTGTCTTCAACGTT
genomic: CTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCGgtatggaact ... ggttcaacagGCCCTGGTGCTCCTGCTGTCTTCAACGTT
EST: gi|86907275|gb|CI292840.1|CI292840
EST:     CTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCG                         GCCCTGGTGCTCCTGCTGTCTTCAACGTT
genomic: CTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCGgtatggaact ... ggttcaacagGCCCTGGTGCTCCTGCTGTCTTCAACGTT
EST: gi|32948454|gb|BP185026.1|BP185026
EST:     CTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCG                         GCCCTGGTGCTCCTGCTGTCTTCAACGTT
genomic: CTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCGgtatggaact ... ggttcaacagGCCCTGGTGCTCCTGCTGTCTTCAACGTT
EST: gi|58599062|gb|CK009590.1|CK009590
EST:     CTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCG                         GGCCTGGTGCTCCTGCTGTCTTCAACGTT
genomic: CTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCGgtatggaact ... ggttcaacagGCCCTGGTGCTCCTGCTGTCTTCAACGTT
EST: gi|4878364|gb|AU062663.1|AU062663
EST:     CTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCG                         GCCCTGGTGCTNCTGATGTCTTNAACGTTGTTGTT
genomic: CTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCGgtatggaact ... ggttcaacagGCCCTGGTGCTCCTGCTGTCTTCAACGTTGTTGTT
EST: gi|55409712|gb|CV722088.1|CV722088
EST:     CTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCG                         GCCCTGGTGCTCCTGCTGTCTTCAACGTT
genomic: CTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCGgtatggaact ... ggttcaacagGCCCTGGTGCTCCTGCTGTCTTCAACGTT
EST: gi|33693190|gb|CF321429.1|CF321429
EST:     CTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCG                         GCCCTGGTGCTCCTGCTGTCTTCAACGTT
genomic: CTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCGgtatggaact ... ggttcaacagGCCCTGGTGCTCCTGCTGTCTTCAACGTT
EST: gi|58671895|gb|CK060581.1|CK060581
EST:     CTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCG                         GCCCTGGTGCTCCTGCTGTCTTCAACGTT
genomic: CTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCGgtatggaact ... ggttcaacagGCCCTGGTGCTCCTGCTGTCTTCAACGTT
EST: gi|88742766|gb|CI766274.1|CI766274
EST:     CTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCG                         GCCCTGGTGCTCCTGCTGTCTTCAACGTT
genomic: CTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCGgtatggaact ... ggttcaacagGCCCTGGTGCTCCTGCTGTCTTCAACGTT
EST: gi|163927162|gb|EG710251.1|EG710251
EST:     CTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCG                         GCCCTGGTGCTCCTGCTGTCTTCAACGTT
genomic: CTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCGgtatggaact ... ggttcaacagGCCCTGGTGCTCCTGCTGTCTTCAACGTT
EST: gi|88405920|gb|CI591315.1|CI591315
EST:     CTTGTCGAGGAGATCAGTAGCTGAACATCCGTGGCATGATCTTGAGATCG                         GCCCTGGTGCTCCTGCTGTCTTCAACGTT
genomic: CTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCGgtatggaact ... ggttcaacagGCCCTGGTGCTCCTGCTGTCTTCAACGTT
EST: gi|25799147|gb|CA755108.1|CA755108
EST:     CTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCG                         GCCCTGGTGCTCCTGCTGTCTTCAACGTT
genomic: CTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCGgtatggaact ... ggttcaacagGCCCTGGTGCTCCTGCTGTCTTCAACGTT
EST: gi|55434349|gb|CV730296.1|CV730296
EST:     CTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCG                         GCCCTGGTGCTCCTGCTGTCTTCAACGTT
genomic: CTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCGgtatggaact ... ggttcaacagGCCCTGGTGCTCCTGCTGTCTTCAACGTT
EST: gi|163925905|gb|EG712281.1|EG712281
EST:     CTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCG                         GCCCTGGTGCTCCTGCTGTCTTCAACGTT
genomic: CTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCGgtatggaact ... ggttcaacagGCCCTGGTGCTCCTGCTGTCTTCAACGTT
EST: gi|86848615|gb|CI293930.1|CI293930
EST:     CTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCG                         GCCCTGGTGCTCCTGCTGTCTTCAACGTT
genomic: CTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCGgtatggaact ... ggttcaacagGCCCTGGTGCTCCTGCTGTCTTCAACGTT

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: 73 (upstream exon), 71 (downstream exon)
Score: 117

GCTGGGCAGCCCAGGCGCGCCCCTAAGCTCAACGAGAGGATCCTGTCCTCCTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCGgtatggaact ... ggttcaacagGCCCTGGTGCTCCTGCTGTCTTCAACGTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggctcacccacaacactatgtggcatgcatcatctcacttaatttggttcaacagGCCCTGGTGCTCCTGCTGTCTTCAACGTT
                                    acttaattt  TA-rich tract