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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagctctctgcttgtatattgtgtaagaagaactatttccattgagcaattgtattagacctttgttttgctgcatgattattttcagTTGTGGGGAGCCGCATCGCAAGCATCAATACAAGGGAGCCATGCTCTTCCTTCAAATCATGGCTCAAATATATTGGCAGGAACACTAGCATCACAGAGAC

Basic information

species Oryza sativa
transcript LOC_Os05g45840.1
intron # 7
splice site 3'
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|157650138|gb|EX449772.1|EX449772
EST:     CTTACAGTTCTCCACTAAACAGAGCTAATAGTGCTCCGGTTAATAGCCAG                         TTGTGGGGAGCCGCATCGCAAGCATCAATACAAGGGAGCCATGCTCTTCCT
genomic: CTTACAGTTCTCCACTAAACAGAGCTAATAGTGCTCCGGTTAATAGCCAGgttagctctc ... ttattttcagTTGTGGGGAGCCGCATCGCAAGCATCAATACAAGGGAGCCATGCTCTTCCT
EST: gi|8954449|gb|BE228360.1|BE228360
EST:     CTTACAGTTCTCCACTAAACAGANCTAATAGTGCTCCGGTTAATAACCAG                         TTGTGGGGAGCCGCATCGCAAGCATCAATACAAGGGAGCCATGCTCTTCCT
genomic: CTTACAGTTCTCCACTAAACAGAGCTAATAGTGCTCCGGTTAATAGCCAGgttagctctc ... ttattttcagTTGTGGGGAGCCGCATCGCAAGCATCAATACAAGGGAGCCATGCTCTTCCT

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: 57 (upstream exon), 75 (downstream exon)
Score: 6

CGGCAGTCAGCAGAACCAGTTCTTTTTCCGCCCCACAGATAATATCCAGTCTTACAGTTCTCCACTAAACAGAGCTAATAGTGCTCCGGTTAATAGCCAGgttagctctc ... ttattttcagTTGTGGGGAGCCGCATCGCAAGCATCAATACAAGGGAGCCATGCTCTTCCTTCAAATCATGGCTCAAATATATTGGCAGGAACACTAGCATCACAGAGAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttccattgagcaattgtattagacctttgttttgctgcatgattattttcagTTGTGGGGAGCCGCATCGCAAGCATCAATACAAGGGAGCCATGCTCTTCCTTCAAATCATGGCTCAAATATATTGGCAGGAACACTAGCATCACAGAGAC
                                             ttattttc  CT-rich tract
                                         atgattatttt  TA-rich tract