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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgcagtaatgtcttaactgtgtgcctcacaagaaccaagtaaccttaatatactcgatcttgtgtctcactccatcgccatttgatatttgtagTTTGCATCTGGTAGCTTGGATGGACCGATACGGTACTTCTGAGAATTATAATCCAAGTTTTCTTAATGCTCCCTGCCCTACCAACCTGCACATTCTGCCA

Basic information

species Oryza sativa
transcript LOC_Os03g46740.2
intron # 10
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|38476994|gb|CF961127.1|CF961127
EST:     AAGGAATGACACAAGAATTTACTACATCAACAAATCCTATTGTAAAACAG                         TTTGCATCTGGTAGCTTGGATGGACCGATACGGTACTTCTGAGAATTATAA
genomic: AAGGAATGACACAAGAATTTACTACATCAACAAATCCTATTGTAAAACAGgtaatgcagt ... atatttgtagTTTGCATCTGGTAGCTTGGATGGACCGATACGGTACTTCTGAGAATTATAA
EST: gi|27921057|gb|CB096865.1|CB096865
EST:     AAGGAATGACACAAGAATTTACTACATCAACAAATCCTATTGTAAAACAG                         TTTGCATCTGGTAGCTTGGATGGACCGATACGGTACTTCTGAGAATTATAA
genomic: AAGGAATGACACAAGAATTTACTACATCAACAAATCCTATTGTAAAACAGgtaatgcagt ... atatttgtagTTTGCATCTGGTAGCTTGGATGGACCGATACGGTACTTCTGAGAATTATAA
EST: gi|88252279|gb|CI350707.1|CI350707
EST:     AAGGAATGACACAAGAATTTACTACATCAACAAATCCTATTGTAAAACAC                         TTTGCATCTGGTAGCTTGGATGGACCGATACGGTGCTTCTGAGAATTATAA
genomic: AAGGAATGACACAAGAATTTACTACATCAACAAATCCTATTGTAAAACAGgtaatgcagt ... atatttgtagTTTGCATCTGGTAGCTTGGATGGACCGATACGGTACTTCTGAGAATTATAA
EST: gi|88476696|gb|CI413967.1|CI413967
EST:     AAGGAATGACACAAGAATTTACTACATCAACAAATCCTATTGTAAAACAG                         TTTGCATCTGGTAGCTTGGATGGACCGATACGGTACTTCTGAGAATTATAA
genomic: AAGGAATGACACAAGAATTTACTACATCAACAAATCCTATTGTAAAACAGgtaatgcagt ... atatttgtagTTTGCATCTGGTAGCTTGGATGGACCGATACGGTACTTCTGAGAATTATAA
EST: gi|58691671|gb|CK080358.1|CK080358
EST:     AAGGAATGACACAAGAATTTACTACATCAACAAATCCTATTGTAAAACAG                         TTTGCATCTGGTAGCTTGGATGGACCGATACGGTACTTCTGAGAATTATAA
genomic: AAGGAATGACACAAGAATTTACTACATCAACAAATCCTATTGTAAAACAGgtaatgcagt ... atatttgtagTTTGCATCTGGTAGCTTGGATGGACCGATACGGTACTTCTGAGAATTATAA
EST: gi|88508239|gb|CI435745.1|CI435745
EST:     AAGGAATGACACAAGAATTTACTACATCAACAAATCCTATTGTAAAACAG                         TTTGCATCTGGTAGCTTGGATGGACCGATACGGTACTTCTGAGAATTATAA
genomic: AAGGAATGACACAAGAATTTACTACATCAACAAATCCTATTGTAAAACAGgtaatgcagt ... atatttgtagTTTGCATCTGGTAGCTTGGATGGACCGATACGGTACTTCTGAGAATTATAA
EST: gi|88484975|gb|CI422246.1|CI422246
EST:     AAGGAATGACACAAGAATTTACTACATCAACAAATCCTATTGTAAAACAG                         TTTGCATCTGGTAGCTTGGATGGACCGATACGGTACTTCTGAGAATTATAA
genomic: AAGGAATGACACAAGAATTTACTACATCAACAAATCCTATTGTAAAACAGgtaatgcagt ... atatttgtagTTTGCATCTGGTAGCTTGGATGGACCGATACGGTACTTCTGAGAATTATAA
EST: gi|27547660|gb|CA767399.2|CA767399
EST:     AAGGAATGACACAAGAATTTACTACATCAACAAATCCTATTGTAAAACAG                         TTTGCATCTGGTAGCTTGGATGGACCGACACGGTACTTCTGAGAATTATAA
genomic: AAGGAATGACACAAGAATTTACTACATCAACAAATCCTATTGTAAAACAGgtaatgcagt ... atatttgtagTTTGCATCTGGTAGCTTGGATGGACCGATACGGTACTTCTGAGAATTATAA

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: 32 (upstream exon), 47 (downstream exon)
Score: 2

GTTGTTATTTCTCCATGAGGGGAAGGTAGTGTGGGAAGGAATGACACAAGAATTTACTACATCAACAAATCCTATTGTAAAACAGgtaatgcagt ... atatttgtagTTTGCATCTGGTAGCTTGGATGGACCGATACGGTACTTCTGAGAATTATAATCCAAGTTTTCTTAATGCTCCCTGCCCTACCAACCTGCACATTCTGCCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaccttaatatactcgatcttgtgtctcactccatcgccatttgatatttgtagTTTGCATCTGGTAGCTTGGATGGACCGATACGGTACTTCTGAGAATTATAATCCAAGTTTTCTTAATGCTCCCTGCCCTACCAACCTGCACATTCTGCCA
                                        atttgatatttgta  TA-rich tract