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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaaaaaaaaacaaatgaatgactgaatcacaatggatgacattctagtgttctaacttttgtcggtagagcaacagttcactcactcactgctatatgtatccatattgttcttctgattatttttcgcgaacgtgatttttttttcgcgaacgctgttcttctgattagGATGGCGTACGCGTTCTCGAGAGACGGCGCGATGCCATTGTCGTCCGTCTGGCACAAGGTCAACAAGCACGAGGTGCCGATCAACGCCGTCTGGCTCTCG

Basic information

species Oryza sativa
transcript LOC_Os01g42234.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g42234.2 (Oryza sativa), 3'ss of exon 6
lower sequence: AT2G01170.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaaaaaaaaaaacaaatgaatgactgaatcacaatggatgacattctagtgttctaacttttgtcggtagagcaacagttcactcactcactgctatatgtatccatattgttcttctgattatttttcgcgaacgtgatttttttttcgcgaacgctgttcttctgattagGATGGCGTACGCGTTCTCGAGAGACGGCGCGATGCCATTGTCGTCCGTCTGGCACAAGGTCAACAAGCACGAGGTGCCGATCAACGCCGTCTGGCTCTCG
                                                                                               |||||  || ||| ||    |      |||| |    | |  |     ||  | |      | ||||    | || ||||||||||| ||||| |||||||| || ||||||||| ||||| |  | |||||||| || ||||     ||||| || || || || || |||||||| 
------------------------------------------------------------------------------------------gtatatatatacattcatgtttggttaaaacatattctgtctgcatttaggacttgat-catatgtg-tgtttggttaatcagGATGGCGTATGCGTTTTCGAGAGATGGAGCGATGCCAATGTCGCCGTTATGGCACAAAGTGAACAGCAGAGAGGTCCCCATTAATGCGGTTTGGCTCTCT
















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: 74 (upstream exon), 55 (downstream exon)
Score: 8

AGAGCCGGTACGGGAGCGGCATCGGCGGGATCATCTGCCTAGGGATCGTCGCCGTCGCGATATACTTCTGTGGCATGAGCTCGGTAACAAGCAACTCAAGgtaaaaaaaa ... ttctgattagGATGGCGTACGCGTTCTCGAGAGACGGCGCGATGCCATTGTCGTCCGTCTGGCACAAGGTCAACAAGCACGAGGTGCCGATCAACGCCGTCTGGCTCTCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgattatttttcgcgaacgtgatttttttttcgcgaacgctgttcttctgattagGATGGCGTACGCGTTCTCGAGAGACGGCGCGATGCCATTGTCGTCCGTCTGGCACAAGGTCAACAAGCACGAGGTGCCGATCAACGCCGTCTGGCTCTCG
 ttctgat  putative branch site (score: 8)
                                       ctgttcttct  putative PPT
                   tgattttttttt  TA-rich tract