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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGAGAAGAGAGGAAGCAACTAATTGGTATGGCGCGAGCAACTTCAGACCATGCCTTTAATGCTACCATTTGGGATGTTCTCGTTGACCCTTCATATCAGgtgaattgatgaacttgaattcactgttttggcatgtaaggttacttataatggtttatacctgttttaacattttcag

Basic information

species Oryza sativa
transcript LOC_Os05g40260.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g40260.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv08s0056g00580.t01 (Vitis vinifera), 5'ss of exon 4
GGGAGAAGAGAGGAAGCAACTAATTGGTATGGCGCGAGCAACTTCAGACCATGCCTTTAATGCTACCATTTGGGATGTTCTCGTTGACCCTTCATATCAGgtgaattgatgaactt------------gaattcactgttttgg-catgtaaggttacttataat-----ggtttatacctgttttaacattttcag---
| |  | |||   ||| | || ||||| ||||| || || || ||||| |||||||| ||||| || ||||||||||| || ||||| ||||||||||||||    |    | |||            ||  ||   ||| ||| ||| |||||  | || |  |     |    | |  |||  ||||||   ||    
GAGGAATGAGCAAAAGAAGCTTATTGGCATGGCCCGTGCTACATCAGATCATGCCTTCAATGCCACAATTTGGGATGTCCTTGTTGATCCTTCATATCAGgtattcttcatatctttgccttggaaaagagatcctggttgtggacatttaaggagaattttccttctcagacccaaaattgtaataacatgaacatgtt
















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|11026174|gb|AU162775.1|AU162775
EST:     ATGCCTTTAATGCTACCATTTGGGATGTTCTCGTTGACCCTTCATATCAG                         GGTCAANGTCTTGGTAAAGCGTTAATGGAGAAAGTAATC
genomic: ATGCCTTTAATGCTACCATTTGGGATGTTCTCGTTGACCCTTCATATCAGgtgaattgat ... acattttcagGGTCAAGGTCTTGGTAAAGCGTTAATGGAGAAAGTAATC
EST: gi|86865983|gb|CI336760.1|CI336760
EST:     TGTTGTCGTTGACCCTTCATATCAG                         GGTCAAGGTCTTGGTAAAGCGTTAAT-GAGAAAGTAATCCGAACTTTGCTC
genomic: TGTTCTCGTTGACCCTTCATATCAGgtgaattgat ... acattttcagGGTCAAGGTCTTGGTAAAGCGTTAATGGAGAAAGTAATCCGAACTTTGCTC
EST: gi|4716609|gb|AU057725.1|AU057725
EST:     ATGCCTTTAATGCTACCATTTGGGATGTTCTCGTTGACCCTTCATATCAG                         GGTCAAGGTCTTGGTAAAGCGTTAATGGAGAAAGTAATCCGAACTTTGCTC
genomic: ATGCCTTTAATGCTACCATTTGGGATGTTCTCGTTGACCCTTCATATCAGgtgaattgat ... acattttcagGGTCAAGGTCTTGGTAAAGCGTTAATGGAGAAAGTAATCCGAACTTTGCTC
EST: gi|88452543|gb|CI558204.1|CI558204
EST:     ATGCCTTTAATGCTACCATTTGGGATGTTCTCGTTGACCCTTCATATCAG                         GGTCAAGGTCTTGGTAAAGCGTTAATGGAGAAAGTAATCCGAACTTTGCTC
genomic: ATGCCTTTAATGCTACCATTTGGGATGTTCTCGTTGACCCTTCATATCAGgtgaattgat ... acattttcagGGTCAAGGTCTTGGTAAAGCGTTAATGGAGAAAGTAATCCGAACTTTGCTC
EST: gi|89167805|gb|CI021504.1|CI021504
EST:     ATGCCTTTAATGCTACCATTTGGGATGTTCTCGTTGACCCTTCATATCAG                         GGTCAAGGTCTTGGTAAAGCGTTAATGGAGAAAGTAATCCGAACTTTGCTC
genomic: ATGCCTTTAATGCTACCATTTGGGATGTTCTCGTTGACCCTTCATATCAGgtgaattgat ... acattttcagGGTCAAGGTCTTGGTAAAGCGTTAATGGAGAAAGTAATCCGAACTTTGCTC
EST: gi|88456659|gb|CI544596.1|CI544596
EST:     CCATTTGGGATGTTCTCGTTGACCCTTCATATCAG                         GGTCAAGGTCTTGGTAAAGCGTTAATGGAGAAAGTAATCCGAACTTTGCTC
genomic: CCATTTGGGATGTTCTCGTTGACCCTTCATATCAGgtgaattgat ... acattttcagGGTCAAGGTCTTGGTAAAGCGTTAATGGAGAAAGTAATCCGAACTTTGCTC
EST: gi|88995783|gb|CI037135.1|CI037135
EST:     ATGCCTTTAATGCTACCATTTGGGATGTTCTCGTTGACCCTTCATATCAG                         GGTCAAGGTCTTGGTAAAGCGTTAATGGAGAAAGTAATCCGAACTTTGCTC
genomic: ATGCCTTTAATGCTACCATTTGGGATGTTCTCGTTGACCCTTCATATCAGgtgaattgat ... acattttcagGGTCAAGGTCTTGGTAAAGCGTTAATGGAGAAAGTAATCCGAACTTTGCTC
EST: gi|89189069|gb|CI012219.1|CI012219
EST:     ATGCCTTTAATGCTACCATTTGGGATGTTCTCGTTGACCCTTCATATCAG                         GGTCAAGGTCTTGGTAAAGCGTTAATGGAGAAAGTAATCCGAACTTTGCTC
genomic: ATGCCTTTAATGCTACCATTTGGGATGTTCTCGTTGACCCTTCATATCAGgtgaattgat ... acattttcagGGTCAAGGTCTTGGTAAAGCGTTAATGGAGAAAGTAATCCGAACTTTGCTC

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: 70 (upstream exon), 59 (downstream exon)
Score: 13

GGGAGAAGAGAGGAAGCAACTAATTGGTATGGCGCGAGCAACTTCAGACCATGCCTTTAATGCTACCATTTGGGATGTTCTCGTTGACCCTTCATATCAGgtgaattgat ... acattttcagGGTCAAGGTCTTGGTAAAGCGTTAATGGAGAAAGTAATCCGAACTTTGCTCCAGAGAGACATCAGCAATATTACGCTGTTTGCAGATAACAAAG




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