Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGGGCCACTGGCATTCATCTAGGTAACCTGTCTAAGGGAATCACCTATTCGCTTCACAGAAACATCGGGATCACAGTATTTGCGCTTGGTACCCTACAGgtatgttctattgcacacattgttatgacctctttatctgccaatatttcaagcccattttgtgcaattgtacgatcatactgattgttctatgtgcactctttcttgaag

Basic information

species Oryza sativa
transcript LOC_Os08g41280.1
intron # 2
splice site 5'
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|3766685|gb|AU030795.1|AU030795
EST:     CGCTTCACAGAAACATCGGGATCACAGTATTTGCGCTTGGTACCCTACAG                         ATCTTTGCGCTTTTCCTGAGGCCCAAGAAGGATCACAAATACCGTATCTAC
genomic: CGCTTCACAGAAACATCGGGATCACAGTATTTGCGCTTGGTACCCTACAGgtatgttcta ... tttcttgaagATCTTTGCGCTTTTCCTGAGGCCCAAGAAGGATCACAAATACCGTATCTAC
EST: gi|58678237|gb|CK066924.1|CK066924
EST:     CGCTTCACAGAAACATCGGGATCACAGTATTTGCGCTTGGTACCCTACAG                         ATCTTTGCGCTTTTCCTGAGGCCCAAGAAGGATCACAAATACCGTATCTAC
genomic: CGCTTCACAGAAACATCGGGATCACAGTATTTGCGCTTGGTACCCTACAGgtatgttcta ... tttcttgaagATCTTTGCGCTTTTCCTGAGGCCCAAGAAGGATCACAAATACCGTATCTAC
EST: gi|29688474|gb|CB684749.1|CB684749
EST:     CGCTTCACAGAAACATCGGGATCACAGTATTTGCGCTTGGTACCCTACAG                         ATCTTTGCGCTTTTCCTGAGGCCCAAGAAGGATCACAAATACCGTATCTAC
genomic: CGCTTCACAGAAACATCGGGATCACAGTATTTGCGCTTGGTACCCTACAGgtatgttcta ... tttcttgaagATCTTTGCGCTTTTCCTGAGGCCCAAGAAGGATCACAAATACCGTATCTAC
EST: gi|86251691|gb|CI018883.1|CI018883
EST:     CGCTTCACAGAAACATCGGGATCACAGTATTTGCGCTTGGTACCCTACAG                         ATCTTTGCGCTTTTCCTGAGGCCCAAGAAGGATCACAAATACCGTATCTAC
genomic: CGCTTCACAGAAACATCGGGATCACAGTATTTGCGCTTGGTACCCTACAGgtatgttcta ... tttcttgaagATCTTTGCGCTTTTCCTGAGGCCCAAGAAGGATCACAAATACCGTATCTAC
EST: gi|87029326|gb|CI250259.1|CI250259
EST:     GAAACATCGGGATCACAGTATTTGCGCTTGGTACCCTACAG                         ATCTTTGCGCTTTTCCTGAGGCCCAAGAAGGATCACAAATACCGTATCTAC
genomic: GAAACATCGGGATCACAGTATTTGCGCTTGGTACCCTACAGgtatgttcta ... tttcttgaagATCTTTGCGCTTTTCCTGAGGCCCAAGAAGGATCACAAATACCGTATCTAC
EST: gi|29620247|gb|CB625259.1|CB625259
EST:     CGCTTCACAGAAACATCGGGATCACAGTATTTGCGCTTGGTACCCTACAG                         ATCTTTGCGCTTTTCCTGAGGCCCAAGAAGGATCACAAATACCGTATCTAC
genomic: CGCTTCACAGAAACATCGGGATCACAGTATTTGCGCTTGGTACCCTACAGgtatgttcta ... tttcttgaagATCTTTGCGCTTTTCCTGAGGCCCAAGAAGGATCACAAATACCGTATCTAC
EST: gi|88467215|gb|CI696577.1|CI696577
EST:     CGCTTCACAGAAACATCGGGATCACAGTATTTGCGCTTGGTACCCTACAG                         ATCTTTGCGCTTTTCCTGAGGCCCAAGAAGGATCACAAATACCGTATCTAC
genomic: CGCTTCACAGAAACATCGGGATCACAGTATTTGCGCTTGGTACCCTACAGgtatgttcta ... tttcttgaagATCTTTGCGCTTTTCCTGAGGCCCAAGAAGGATCACAAATACCGTATCTAC
EST: gi|218478572|gb|FG959944.1|FG959944
EST:     CGCTTCACAGAAACATCGGGATCACAGTATTTGCGCTTGGTACCCTACAG                         ATCTTTGCGCTTTTCCTGAGGC
genomic: CGCTTCACAGAAACATCGGGATCACAGTATTTGCGCTTGGTACCCTACAGgtatgttcta ... tttcttgaagATCTTTGCGCTTTTCCTGAGGC
EST: gi|88205261|gb|CI204647.1|CI204647
EST:     ATTTGCGCTTGGTACCCTACAG                         ATCTTTGCGCTTTTCCTGAGGCCCAAGAAGGATCACAAATACCGTATCTAC
genomic: ATTTGCGCTTGGTACCCTACAGgtatgttcta ... tttcttgaagATCTTTGCGCTTTTCCTGAGGCCCAAGAAGGATCACAAATACCGTATCTAC
EST: gi|66924746|gb|CX111594.1|CX111594
EST:     CGCTTCACAGAAACATCGGGATCACAGTATTTGCGCTTGGTACCCTACAG                         ATCTTTGCGCTTTTCCTGAGGCCCAAGAAGGATCACAAATACCGTATCTAC
genomic: CGCTTCACAGAAACATCGGGATCACAGTATTTGCGCTTGGTACCCTACAGgtatgttcta ... tttcttgaagATCTTTGCGCTTTTCCTGAGGCCCAAGAAGGATCACAAATACCGTATCTAC

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: 69 (upstream exon), 70 (downstream exon)
Score: 27

CTGGGCCACTGGCATTCATCTAGGTAACCTGTCTAAGGGAATCACCTATTCGCTTCACAGAAACATCGGGATCACAGTATTTGCGCTTGGTACCCTACAGgtatgttcta ... tttcttgaagATCTTTGCGCTTTTCCTGAGGCCCAAGAAGGATCACAAATACCGTATCTACTGGAACGCCTACCACCACTCGGTCGGTTACACCATCATCATACTCGGCA




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