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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATCTAAATGGAAGGAAACGCCAAATGGACAGCATGTTGATTATGATCAAAGGCCAGACATATTTAGgttaatttttatctgatgactttttttggttatattttttgcaactttcctccatatttatcatctgccttcttttggacag

Basic information

species Oryza sativa
transcript LOC_Os01g56580.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g56580.2 (Oryza sativa), 5'ss of exon 9
lower sequence: AT3G03940.1 (Arabidopsis thaliana), 5'ss of exon 9
CATCTAAATGGAAGGAAACGCCAAATGGACAGCATGTTGATTATGATCAAAGGCCAGACATATTTAGgt----taatttttatctgatgactttttt--tggttatattttttgcaactttcctccatatttatcatctgccttcttttggacag
|||| | |||||| ||  | |    ||| ||||||||||| |||||||||||||||||  |||||||||    | |||  | | || |  ||||  |  |  |  |  | | |  |  || |   ||| ||| | |     | | |   |     
CATCAAGATGGAAAGATTCACACTCTGGCCAGCATGTTGAATATGATCAAAGGCCAGATGTATTTAGgtattttgattggtgtatgttatctttcctactattgttggtatatatattttgctcacatctttgttacgcttcatatgcag-----

upper sequence: LOC_Os01g56580.2 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv08s0007g07420.t01 (Vitis vinifera), 5'ss of exon 9
CATCTAAATGGAAGGAAACGCCAAATGGACAGCATGTTGATTATGATCAAAGGCCAGACATATTTAGgttaatttttatctgatgactttttttggttatattttttgcaactttcctccatatttatcatctgccttcttttggacag
| ||||||||||| || ||  ||  ||| || ||||||||||||||||| ||||| |||||||| |||||  |   | ||||     |  |       | |     |||      | |    || ||| |    |||  |||  | |||
CCTCTAAATGGAAAGACACCACATCTGGTCAACATGTTGATTATGATCAGAGGCCTGACATATTCAGgtttgtggatttctggatgttcataaaaaaaaaaaaaaatgctttgacctttataatatattaatctcctctttt--ggcag
















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|29629024|gb|CB634035.1|CB634035
EST:     ACGCCAAATGGACAGCATGTTGATTATGATCAAAGGCCAGACATATTTAG                         GGGTACAATAAGATATGCT
genomic: ACGCCAAATGGACAGCATGTTGATTATGATCAAAGGCCAGACATATTTAGgttaattttt ... ttttggacagGGGTACAATAAGATATGCT
EST: gi|29623307|gb|CB628318.1|CB628318
EST:     ACGCCAAATGGACAGCATGTTGATTATGATCAAAGGCCAGACATATTTAG                         GGGTACAATAAGATATGCTAGTGTCCATGCCCATTTAGGCCGTACTGGTAG
genomic: ACGCCAAATGGACAGCATGTTGATTATGATCAAAGGCCAGACATATTTAGgttaattttt ... ttttggacagGGGTACAATAAGATATGCTAGTGTCCATGCCCATTTAGGCCGTACTGGTAG

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: 62 (upstream exon), 75 (downstream exon)
Score: 49

CATCTAAATGGAAGGAAACGCCAAATGGACAGCATGTTGATTATGATCAAAGGCCAGACATATTTAGgttaattttt ... ttttggacagGGGTACAATAAGATATGCTAGTGTCCATGCCCATTTAGGCCGTACTGGTAGCAGAAGGGATGATCTGGAATCATTAGCATATACATTAATATTTCTTCTC




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