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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggtgcacgttatttttggttcttcagagatagcctttccttgtctgttcatccctatccttagagtgcaatactctccaacctggtgaaacaaacacaattgttttccatttttgttttcagCTGGTTGATTTTGAGTGCTGGAAAATGATGTTCACCAAACAAAAACATGAGAAGGCTCCTGGCCGCATCAATAACAAATCCTCTTTCCCTGGCCACTTGG

Basic information

species Oryza sativa
transcript LOC_Os04g58700.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g58700.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G119759_T06 (Zea mays), 3'ss of exon 10
--------gtaaggtgca-cgttattt-ttggttcttcagagatagcctttccttgtctgttcatcc---ctatccttagagtgcaatactctccaacctggtgaaaca--aacacaattgttttccatttttgttttcagCTGGTTGATTTTGAGTGCTGGAAAATGATGTTCACCAAACA---------AAAACATGAGAAGGCTCCTGGCCGCATCAATAACAAATCCTCTTTCCCTGGCCACTTGG
           |  |||| | || ||  |||||||  ||     ||  || | |  | | ||    |    ||   |||   |||| | ||      | |||| | |||  ||      | |  | | | | ||||| |||||||| |||||||| |||||||||||||||||| | | |||          | | | |||||||||| ||| | | | || | |||||||||||| || |         
gtatgtcctgcacatgcatccttgttcgttggttcagcaactgaagatttgcatgatgttttggctcgtcttacatttatcatgca-tccttgttcgcttggtcagacagtaatttgtctctgctacgtgtctgtttgcagCTGGTGGATTTTGAATGCTGGAAAATGATGTTCTCGAGACACTCCATCTCGAGAGACGAGAAGGCTCGTGGGCACTTGAACAGCAAATCCTCTTTTCCCG---------
















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), 74 (downstream exon)
Score: 10

GCAGGGTCTAAGATACCTGCATACCGAGTTGCAGCCTCCATTTGCTATCTCTGAGCTGAATTCCAACTCTGTATATGTTACTGAAGATTTTACTCCAAAGgtaaggtgca ... ttgttttcagCTGGTTGATTTTGAGTGCTGGAAAATGATGTTCACCAAACAAAAACATGAGAAGGCTCCTGGCCGCATCAATAACAAATCCTCTTTCCCTGGCCACTTGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatactctccaacctggtgaaacaaacacaattgttttccatttttgttttcagCTGGTTGATTTTGAGTGCTGGAAAATGATGTTCACCAAACAAAAACATGAGAAGGCTCCTGGCCGCATCAATAACAAATCCTCTTTCCCTGGCCACTTGG
                                ttgttttccatttttg  CT-rich tract
                                         atttttgtttt  TA-rich tract