Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGCAAGGATAATTTTGTTCATGTACTTGTTTTATCAGATCTTTTTACATTATGATCAGgtacatggtaattcttctggattcaatgtacatgatggctatcaaacacatatttctgacttgatacttgttcgcatacag

Basic information

species Oryza sativa
transcript LOC_Os05g43540.1
intron # 8
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|88466361|gb|CI529770.1|CI529770
EST:     TAATTTTGTTCATGTACTTGTTTTATCAGATCTTTTTACATTATGATCAG                         ATTAAGCAGATGGAGACCTTTGGTTATCTTCTGGTTTGTGTTGTGCCTGCC
genomic: TAATTTTGTTCATGTACTTGTTTTATCAGATCTTTTTACATTATGATCAGgtacatggta ... tcgcatacagATTAAGCAGATGGAGACCTTTGGTTATCTTCTGGTTTGTGTTGTGCCTGCC
EST: gi|88839208|gb|CI378132.1|CI378132
EST:     TAATTTTGTTCATGTACTTGTTTTATCAGATCTTTTTACATTATGATCAG                         ATTAAGCAGATGGAGACCTTTGGTTATCTTCTGGTTTGTGTTGTGCCTGCC
genomic: TAATTTTGTTCATGTACTTGTTTTATCAGATCTTTTTACATTATGATCAGgtacatggta ... tcgcatacagATTAAGCAGATGGAGACCTTTGGTTATCTTCTGGTTTGTGTTGTGCCTGCC
EST: gi|88956742|gb|CI009012.1|CI009012
EST:     TAATTTTGTTCATGTACTTGTTTTATCAGATCTTTTTACATTATGATCAG                         ATTAAGCAGATGGAGACCTTTGGTTATCTTCTGGTTTGTGTTGTGCCTGCC
genomic: TAATTTTGTTCATGTACTTGTTTTATCAGATCTTTTTACATTATGATCAGgtacatggta ... tcgcatacagATTAAGCAGATGGAGACCTTTGGTTATCTTCTGGTTTGTGTTGTGCCTGCC
EST: gi|33691827|gb|CF320066.1|CF320066
EST:     TAATTTTGTTCATGTACTTGTTTTATCAGATCTTTTTACATTATGATCAG                         ATTAAGCAGATGGAGACCTTTGGTTATCTTCTGGTTTGTGTTGTGCCTGCC
genomic: TAATTTTGTTCATGTACTTGTTTTATCAGATCTTTTTACATTATGATCAGgtacatggta ... tcgcatacagATTAAGCAGATGGAGACCTTTGGTTATCTTCTGGTTTGTGTTGTGCCTGCC
EST: gi|88560412|gb|CI491071.1|CI491071
EST:     TAATTTTGTTCATGTACTTGTTTTATCAGATCTTTTTACATTATGATCAG                         ATTAAGCAGATGGAGACCTTTGGTTATCTTCTGGTTTGTGTTGTGCCTGCC
genomic: TAATTTTGTTCATGTACTTGTTTTATCAGATCTTTTTACATTATGATCAGgtacatggta ... tcgcatacagATTAAGCAGATGGAGACCTTTGGTTATCTTCTGGTTTGTGTTGTGCCTGCC
EST: gi|88272939|gb|CI386199.1|CI386199
EST:     TAATTTTGTTCATGTACTTGTTTTATCAGATCTTTTTACATTATGATCAG                         ATTAAGCAGATGGAGACCTTTGGTTATCTTCTGGTTTGTGTTGTGCCTGCC
genomic: TAATTTTGTTCATGTACTTGTTTTATCAGATCTTTTTACATTATGATCAGgtacatggta ... tcgcatacagATTAAGCAGATGGAGACCTTTGGTTATCTTCTGGTTTGTGTTGTGCCTGCC
EST: gi|88296681|gb|CI537648.1|CI537648
EST:     TAATTTTGTTCATGTACTTGTTTTATCAGATCTTTTTACATTATGATCAG                         ATTAAGCAGATGGAGACCTTTGGTTATCTTCTGGTTTGTGTTGTGCCTGCC
genomic: TAATTTTGTTCATGTACTTGTTTTATCAGATCTTTTTACATTATGATCAGgtacatggta ... tcgcatacagATTAAGCAGATGGAGACCTTTGGTTATCTTCTGGTTTGTGTTGTGCCTGCC
EST: gi|14192050|gb|AU184261.1|AU184261
EST:     TAATTTTGTTCATGTACTTGTTTTATCAGATCTTTTTNCATTATGATCAG                         ATTAAGCAGATGGAGACCTTTGGTTATCTTCTGGTTTGTGTTGTGCCTGCC
genomic: TAATTTTGTTCATGTACTTGTTTTATCAGATCTTTTTACATTATGATCAGgtacatggta ... tcgcatacagATTAAGCAGATGGAGACCTTTGGTTATCTTCTGGTTTGTGTTGTGCCTGCC
EST: gi|86820908|gb|CI357642.1|CI357642
EST:     TTTGTTCATGTACTTGTTTTATCAGATCTTTTTACATTATGATCAG                         ATTAAGCAGATGGAGACCTTTGGTTATCTTCTGGTTTGTGTTGTGCCTGCC
genomic: TTTGTTCATGTACTTGTTTTATCAGATCTTTTTACATTATGATCAGgtacatggta ... tcgcatacagATTAAGCAGATGGAGACCTTTGGTTATCTTCTGGTTTGTGTTGTGCCTGCC
EST: gi|88522122|gb|CI449856.1|CI449856
EST:     TAATTTTGTTCATGTACTTGTTTTATCAGATCTTTTTACATTATGATCAG                         ATTAAGCAGATGGAGACCTTTGGTTATCTTCTGGTTTGTGTTGTGCCTGCC
genomic: TAATTTTGTTCATGTACTTGTTTTATCAGATCTTTTTACATTATGATCAGgtacatggta ... tcgcatacagATTAAGCAGATGGAGACCTTTGGTTATCTTCTGGTTTGTGTTGTGCCTGCC
EST: gi|86853806|gb|CI329252.1|CI329252
EST:     GATCTTTTTACATTATGATCAG                         ATTAAGCAGATGGAGACCTTTGGTTATCTTCTGGTTTGTGTTGTGCCTGCC
genomic: GATCTTTTTACATTATGATCAGgtacatggta ... tcgcatacagATTAAGCAGATGGAGACCTTTGGTTATCTTCTGGTTTGTGTTGTGCCTGCC
EST: gi|29666720|gb|CB662995.1|CB662995
EST:     TAATTTTGTTCATGTACTTGTTTTATCAGATCTTTTTACATTATGATCAG                         ATTAAGCAGATGGAGACCTTTGGTTATCTTCTGGTTTGTGTTGTGCCTGCC
genomic: TAATTTTGTTCATGTACTTGTTTTATCAGATCTTTTTACATTATGATCAGgtacatggta ... tcgcatacagATTAAGCAGATGGAGACCTTTGGTTATCTTCTGGTTTGTGTTGTGCCTGCC
EST: gi|5667497|gb|AU077739.1|AU077739
EST:     TTTTACATTATNATCAG                         ATTAAGCAGATGGAGACCTTTGGTTATCTTCTGGTTTGTGTTGTGCCTGCC
genomic: TTTTACATTATGATCAGgtacatggta ... tcgcatacagATTAAGCAGATGGAGACCTTTGGTTATCTTCTGGTTTGTGTTGTGCCTGCC
EST: gi|86860123|gb|CI322021.1|CI322021
EST:     TTTGGTCATGTACTTG-TTTATCAGATCTTTTTACATTATGATCAG                         ATTAAGCAGATGGAAACCTTTGGTTATCTTCTGGTTTGTGTTGTGCCTGCC
genomic: TTTGTTCATGTACTTGTTTTATCAGATCTTTTTACATTATGATCAGgtacatggta ... tcgcatacagATTAAGCAGATGGAGACCTTTGGTTATCTTCTGGTTTGTGTTGTGCCTGCC

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: 60 (upstream exon), 49 (downstream exon)
Score: 27

GTTGCAAGGATAATTTTGTTCATGTACTTGTTTTATCAGATCTTTTTACATTATGATCAGgtacatggta ... tcgcatacagATTAAGCAGATGGAGACCTTTGGTTATCTTCTGGTTTGTGTTGTGCCTGCCATACTGTTCGTGATGAATATGATATGGTTTTCCAAGATCTTAAGGGGCC




<











<


<