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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatattgatattacctcttctggaatctgtactcgttattaaatcttattagctgtaaagaaagactaaaggaatatattgcatcctatagtagtcctaaaaaagcctcaagtagctgtttacttaaaatacgagtaaagcaagcgggcaatgatcattctgttgttgcagGTTAAATGTTACATGCAGCAGCTACTCTGTGGCCTTGAGCATTGTCATAGTCGTCACATTCTGCACCGTGACATTAAGGGTTCCAATCTTTTGATTGACA

Basic information

species Oryza sativa
transcript LOC_Os01g10430.2
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|66924685|gb|CX111533.1|CX111533
EST:     ACCTAGCTGGACTAGCTTCTTTTCCTGGAGTGAAATTTACTGAGTCTCAG                         GTTAAATGTTACATGCAGCAGCTACTCTGTGGCCTTGAGCATTGTCATAGT
genomic: ACCTAGCTGGACTAGCTTCTTTTCCTGGAGTGAAATTTACTGAGTCTCAGgtatattgat ... gttgttgcagGTTAAATGTTACATGCAGCAGCTACTCTGTGGCCTTGAGCATTGTCATAGT
EST: gi|33677544|gb|CF305783.1|CF305783
EST:     ACCTAGCTGGACTAGCTTCTTTTCCTGGAGTGAAATTTACTGAGTCTCAG                         GTTAAATGTTACATGCAGCAGCTACTCTGTGGCCTTGAGCATTGTCATAGT
genomic: ACCTAGCTGGACTAGCTTCTTTTCCTGGAGTGAAATTTACTGAGTCTCAGgtatattgat ... gttgttgcagGTTAAATGTTACATGCAGCAGCTACTCTGTGGCCTTGAGCATTGTCATAGT
EST: gi|29619147|gb|CB624159.1|CB624159
EST:     ACCTAGCTGGACTAGCTTCTTTTCCTGGAGTGAAATTTACTGAGTCTCAG                         GTTAAATGTTACATGCAGCAGCTACTCTGTGGCCTTGAGCATTGTCATAGT
genomic: ACCTAGCTGGACTAGCTTCTTTTCCTGGAGTGAAATTTACTGAGTCTCAGgtatattgat ... gttgttgcagGTTAAATGTTACATGCAGCAGCTACTCTGTGGCCTTGAGCATTGTCATAGT
EST: gi|29620850|gb|CB625861.1|CB625861
EST:     ACCTAGCTGGACTAGCTTCTTTTCCTGGAGTGAAATTTACTGAGTCTCAG                         GTTAAATGTTACATGCAGCAGCTACTCTGTGGCCTTGAGCATTGTCATAGT
genomic: ACCTAGCTGGACTAGCTTCTTTTCCTGGAGTGAAATTTACTGAGTCTCAGgtatattgat ... gttgttgcagGTTAAATGTTACATGCAGCAGCTACTCTGTGGCCTTGAGCATTGTCATAGT
EST: gi|58668580|gb|CK057266.1|CK057266
EST:     ACCTAGCTGGACTAGCTTCTTTTCCTGGAGTGAAATTTACTGAGTCTCAG                         GTTAAATGTTACATGCAGCAGCTACTCTGTGGCCTTGAGCATTGTCATAGT
genomic: ACCTAGCTGGACTAGCTTCTTTTCCTGGAGTGAAATTTACTGAGTCTCAGgtatattgat ... gttgttgcagGTTAAATGTTACATGCAGCAGCTACTCTGTGGCCTTGAGCATTGTCATAGT

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: 72 (upstream exon), 64 (downstream exon)
Score: 22

TTCAAGAATGTCTTGTAGCTTATATCTTGTTTTTGAGTACATGGAACATGACCTAGCTGGACTAGCTTCTTTTCCTGGAGTGAAATTTACTGAGTCTCAGgtatattgat ... gttgttgcagGTTAAATGTTACATGCAGCAGCTACTCTGTGGCCTTGAGCATTGTCATAGTCGTCACATTCTGCACCGTGACATTAAGGGTTCCAATCTTTTGATTGACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttacttaaaatacgagtaaagcaagcgggcaatgatcattctgttgttgcagGTTAAATGTTACATGCAGCAGCTACTCTGTGGCCTTGAGCATTGTCATAGTCGTCACATTCTGCACCGTGACATTAAGGGTTCCAATCTTTTGATTGACA
                                         ttctgtt  CT-rich tract
     acttaaaata  TA-rich tract