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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggttaattttatagtgttacctttgcagattatacctcgcaacaagtaaaggaggtactgacaagtgtgctgcatgtaattcttggaaggttctaactttactgttaaaactttgcagGGTTGGTGGTTTCTTCATTTTGCTACCTCCAATTTTTTCCAATGCCATCTGATGAAAACG

Basic information

species Oryza sativa
transcript LOC_Os01g49820.2
intron # 6
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|88273527|gb|CI393933.1|CI393933
EST:     ATTGGCCAAAATGTGTTCACCGGTGGAATTTTGG                         GGTTGGTGGTTTCTTCATTTTGCTACCTCCAATTTTTTCCAATGCCATCTG
genomic: ATTGG-CAAGATGTGTTCACCGGTGGAATTTTGGgtaggttaat ... aactttgcagGGTTGGTGGTTTCTTCATTTTGCTACCTCCAATTTTTTCCAATGCCATCTG
EST: gi|33687573|gb|CF315812.1|CF315812
EST:     AGATGACTATTGGCATCATTGGCAAGATGTGTTCACCGGTGGAATTTTGG                         GGTTGGTGGTTTCTTCATTTTGCTACCTCCAATTTTTTCCAATGCCATCTG
genomic: AGATGACTATTGGCATCATTGGCAAGATGTGTTCACCGGTGGAATTTTGGgtaggttaat ... aactttgcagGGTTGGTGGTTTCTTCATTTTGCTACCTCCAATTTTTTCCAATGCCATCTG
EST: gi|27547046|gb|CA765107.2|CA765107
EST:     AGATGACTATTGGCATCATTGGCAAGATGTGTTCACCGGTGGAGTTTTGG                         GGTTGGTGGTTTCTTCATTTTGCTACCTCCAATTTTTTCCAATGCCATCTG
genomic: AGATGACTATTGGCATCATTGGCAAGATGTGTTCACCGGTGGAATTTTGGgtaggttaat ... aactttgcagGGTTGGTGGTTTCTTCATTTTGCTACCTCCAATTTTTTCCAATGCCATCTG
EST: gi|25807069|gb|CA763030.1|CA763030
EST:     AGATGACTATTGGCATCATTGGCAAGATGTGTTCACCGGTGGAATTTTGG                         GGTTGGTGGTTTCTTCATTTTGCTACCTCCAATTTTTTCCAATGCCATCTG
genomic: AGATGACTATTGGCATCATTGGCAAGATGTGTTCACCGGTGGAATTTTGGgtaggttaat ... aactttgcagGGTTGGTGGTTTCTTCATTTTGCTACCTCCAATTTTTTCCAATGCCATCTG
EST: gi|5771042|gb|AU077931.1|AU077931
EST:     AGATGACTATTGGCATCATTGGCAAGATGTGTTCACCGGTGGAATTTTGG                         GGTTGGTGGTTTCTTCATTTTGCTACCTCCAATTTTTTCCAATGCCATCTG
genomic: AGATGACTATTGGCATCATTGGCAAGATGTGTTCACCGGTGGAATTTTGGgtaggttaat ... aactttgcagGGTTGGTGGTTTCTTCATTTTGCTACCTCCAATTTTTTCCAATGCCATCTG

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: 71 (upstream exon), 40 (downstream exon)
Score: 6

ATTATTATTCTCCCTCTGCTCCTTGCAGCCTTGGTTGCTGTTTCTCGGGTAGATGACTATTGGCATCATTGGCAAGATGTGTTCACCGGTGGAATTTTGGgtaggttaat ... aactttgcagGGTTGGTGGTTTCTTCATTTTGCTACCTCCAATTTTTTCCAATGCCATCTGATGAAAACG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtgtgctgcatgtaattcttggaaggttctaactttactgttaaaactttgcagGGTTGGTGGTTTCTTCATTTTGCTACCTCCAATTTTTTCCAATGCCATCTGATGAAAACG
                           ttctaac  putative branch site (score: 6)
 ttaaaacttt  TA-rich tract