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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTTTCTATCACTAACAGgtacttgaattttgttttctagtatataatatgcattatacagatatttgtgatgtaatacatttcagtgccatgttctatgactaatactagtattgta...

Basic information

species Oryza sativa
transcript LOC_Os01g09120.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g09120.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G176506_T04 (Zea mays), 5'ss of exon 3
GACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTTTCTATCACTAACAGgtacttgaattttgttttctagtat-ataatatgcattatacagatatttgtgatgtaatacatttca-gtgcca-tgttctatgactaatactagtattgta
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GACTGACTCCCGCTTGCCTAACATGCCAATTATTTATGCTAGTGATGCTTTTACATCATTAACAGgtaattgt-ttttgactgttagtaccagagtacgcattctagcagtatgtaatatgtgcaacttccaatatattactgttatattttcaata-tattgtttt-
















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|29660689|gb|CB656964.1|CB656964
EST:     GCCTGACATGCCGATCATCTATGCTAGTGATGCTTTTCTATCACTAACAG                         GTTACTCAAGAGAAGAAATCTTGGGCTGTAACTGCAGATTCTTGAATGGTC
genomic: GCCTGACATGCCGATCATCTATGCTAGTGATGCTTTTCTATCACTAACAGgtacttgaat ... tatcatccagGTTACTCAAGAGAAGAAATCTTGGGCTGTAACTGCAGATTCTTGAATGGTC
EST: gi|29660992|gb|CB657267.1|CB657267
EST:     GCCTGACATGCCGATCATCTATGCTAGTGATGCTTTTCTATCACTAACAG                         GTTACTCAAGAGAAGAAATCTTGGGCTGTAACTGCAGATTCTTGAATGGTC
genomic: GCCTGACATGCCGATCATCTATGCTAGTGATGCTTTTCTATCACTAACAGgtacttgaat ... tatcatccagGTTACTCAAGAGAAGAAATCTTGGGCTGTAACTGCAGATTCTTGAATGGTC
EST: gi|29640574|gb|CB645583.1|CB645583
EST:     GCCTGACATGCCGATCATCTATGCTAGTGATGCTTTTCTATCACTAACAG                         GTTACTCAAGAGAAGAAATCTTGGGCTGTAACTGCAGATTCTTGAATGGTC
genomic: GCCTGACATGCCGATCATCTATGCTAGTGATGCTTTTCTATCACTAACAGgtacttgaat ... tatcatccagGTTACTCAAGAGAAGAAATCTTGGGCTGTAACTGCAGATTCTTGAATGGTC
EST: gi|29680769|gb|CB677044.1|CB677044
EST:     GCCTGACATGCCGATCATCTATGCTAGTGATGCTTTTCTATCACTAACAG                         GTTACTCAAGAGAAGAAATCTTGGGCTGTAACTGCAGATTCTTGAATGGTC
genomic: GCCTGACATGCCGATCATCTATGCTAGTGATGCTTTTCTATCACTAACAGgtacttgaat ... tatcatccagGTTACTCAAGAGAAGAAATCTTGGGCTGTAACTGCAGATTCTTGAATGGTC
EST: gi|86505958|gb|CI148591.1|CI148591
EST:     GCCTGACATGCCGATCATCTATGCTAGTGATGCTTTTCTATCACTAACAG                         GTTACTCAAGAGAAGAAATCTTGGGCTGTAACTGCAGATTCTTGAATGGTC
genomic: GCCTGACATGCCGATCATCTATGCTAGTGATGCTTTTCTATCACTAACAGgtacttgaat ... tatcatccagGTTACTCAAGAGAAGAAATCTTGGGCTGTAACTGCAGATTCTTGAATGGTC
EST: gi|86527492|gb|CI167698.1|CI167698
EST:     CCGATCATCTATGCTAGTGATGCTTTTCTATCACTAACAG                         GTTACTCAAGAGAAGAAATCTTGGGCTGTAACTGCAGATTCTTGAATGGTC
genomic: CCGATCATCTATGCTAGTGATGCTTTTCTATCACTAACAGgtacttgaat ... tatcatccagGTTACTCAAGAGAAGAAATCTTGGGCTGTAACTGCAGATTCTTGAATGGTC
EST: gi|31818552|gb|CD645551.1|CD645551
EST:     GCCTGACATGCCGATCATCTATGCTAGTGATGCTTTTCTATCACTAACAG                         GTTACTCAAGAGAAGAAATCTTGGGCTGTAACTGCAGATTCTTGAATGGTC
genomic: GCCTGACATGCCGATCATCTATGCTAGTGATGCTTTTCTATCACTAACAGgtacttgaat ... tatcatccagGTTACTCAAGAGAAGAAATCTTGGGCTGTAACTGCAGATTCTTGAATGGTC
EST: gi|29662742|gb|CB659017.1|CB659017
EST:     GCCTGACATGCCGATCATCTATGCTAGTGATGCTTTTCTATCACTAACAG                         GTTACTCAAGAGAAGAAATCTTGGGCTGTAACTGCAGATTCTTGAATGGTC
genomic: GCCTGACATGCCGATCATCTATGCTAGTGATGCTTTTCTATCACTAACAGgtacttgaat ... tatcatccagGTTACTCAAGAGAAGAAATCTTGGGCTGTAACTGCAGATTCTTGAATGGTC
EST: gi|29657673|gb|CB653948.1|CB653948
EST:     GCCTGACATGCCGATCATCTATGCTAGTGATGCTTTTCTATCACTAACAG                         GTTACTCAAGAGAAGAAATCTTGGGCTGTAACTGCAGATTCTTGAATGGTC
genomic: GCCTGACATGCCGATCATCTATGCTAGTGATGCTTTTCTATCACTAACAGgtacttgaat ... tatcatccagGTTACTCAAGAGAAGAAATCTTGGGCTGTAACTGCAGATTCTTGAATGGTC
EST: gi|14571448|gb|BI118816.1|BI118816
EST:     GCCTGACATGCCGATCATCTATGCTAGTGATGCTTTTCTATCACTAACAG                         GTTACTCAAGAGAAGAAATCTTGGGCTGTAACTGCAGATTCTTGAATGGTC
genomic: GCCTGACATGCCGATCATCTATGCTAGTGATGCTTTTCTATCACTAACAGgtacttgaat ... tatcatccagGTTACTCAAGAGAAGAAATCTTGGGCTGTAACTGCAGATTCTTGAATGGTC
EST: gi|38474285|gb|CF958417.1|CF958417
EST:     GCCTGACATGCCGATCATCTATGCTAGTGATGCTTTTCTATCACTAACAG                         GTTACTCAAGAGAAGAAATCTTGGGCTGTAACTGCAGATTCTTGAATGGTC
genomic: GCCTGACATGCCGATCATCTATGCTAGTGATGCTTTTCTATCACTAACAGgtacttgaat ... tatcatccagGTTACTCAAGAGAAGAAATCTTGGGCTGTAACTGCAGATTCTTGAATGGTC
EST: gi|88228766|gb|CI228246.1|CI228246
EST:     GCCTGACATGCCGATCATCTATGCTAGTGATGCTTTTCTATCACTAACAG                         GTTACTCAAGAGAAGAAATCTTGGGCTGTAACTGCAGATTCTTGAATGGTC
genomic: GCCTGACATGCCGATCATCTATGCTAGTGATGCTTTTCTATCACTAACAGgtacttgaat ... tatcatccagGTTACTCAAGAGAAGAAATCTTGGGCTGTAACTGCAGATTCTTGAATGGTC
EST: gi|29660961|gb|CB657236.1|CB657236
EST:     GCCTGACATGCCGATCATCTATGCTAGTGATGCTTTTCTATCACTAACAG                         GTTACTCAAGAGAAGAAATCTTGGGCTGTAACTGCAGATTCTTGAATGGTC
genomic: GCCTGACATGCCGATCATCTATGCTAGTGATGCTTTTCTATCACTAACAGgtacttgaat ... tatcatccagGTTACTCAAGAGAAGAAATCTTGGGCTGTAACTGCAGATTCTTGAATGGTC
EST: gi|29655805|gb|CB652080.1|CB652080
EST:     GCCTGACATGCCGATCATGTATGGTAGTGATGCTTTTCTATCACTAACAG                         GTTACTCAAGAGAAGAAATCTTGGGCTGTAACTGCAGATTCTTGAATGGTC
genomic: GCCTGACATGCCGATCATCTATGCTAGTGATGCTTTTCTATCACTAACAGgtacttgaat ... tatcatccagGTTACTCAAGAGAAGAAATCTTGGGCTGTAACTGCAGATTCTTGAATGGTC
EST: gi|29638115|gb|CB643124.1|CB643124
EST:     GCCTGACATGCCGATCATCTATGCTAGTGATGCTTTTCTATCACTAACAG                         GTTACTCAAGAGAAGAAATCTTGGGCTGTAACTGCAGATTCTTGAATGGTC
genomic: GCCTGACATGCCGATCATCTATGCTAGTGATGCTTTTCTATCACTAACAGgtacttgaat ... tatcatccagGTTACTCAAGAGAAGAAATCTTGGGCTGTAACTGCAGATTCTTGAATGGTC

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: 56 (upstream exon), 48 (downstream exon)
Score: 18

GACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTTTCTATCACTAACAGgtacttgaat ... tatcatccagGTTACTCAAGAGAAGAAATCTTGGGCTGTAACTGCAGATTCTTGAATGGTCCTGGCACTAGTGTGGAGGTTTTAGAACAG




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