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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cacatttcttattataatctatacacgacaagtatcagcccatggcacatctttgatgcactaaaccccagtctaaagtttatgtttgatgagttttcagGGAGAAACCGCAGATGAATTACCAGAGCGGCTTATCGGTGTTGGACGCTGCTCTCACATTCAACTGGACAAGGCCGTAGATCTTTCTGCAACCTAGGGGT

Basic information

species Physcomitrella patens
transcript PP1S425_13V6.1
intron # 21
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|162156859|gb|FC332805.1|FC332805
EST:     TTTTTGGTTATATATCTGCCCTCGTCGTAGACATGGCCTTTTTCATTAGG                         GGAGAAACCGCAGATGAATTACCAGAGCGGCTTATCGGTGTTGGACGCTGC
genomic: TTTTTGGTTATATATCTGCCCTCGTCGTAGACATGGCCTTTTTCATTAGGgtacttgtgt ... gagttttcagGGAGAAACCGCAGATGAATTACCAGAGCGGCTTATCGGTGTTGGACGCTGC
EST: gi|37829391|gb|BJ587403.1|BJ587403
EST:     TTTTTGGTTATATATCTGCCCTCGTCGTAGACATGGCCTTTTTCATTAGG                         GGAGAAACCGCAGATGAATTACCAGAGCGGCTTATCGGTGTTGGACGCTGC
genomic: TTTTTGGTTATATATCTGCCCTCGTCGTAGACATGGCCTTTTTCATTAGGgtacttgtgt ... gagttttcagGGAGAAACCGCAGATGAATTACCAGAGCGGCTTATCGGTGTTGGACGCTGC
EST: gi|19777603|gb|BQ039203.1|BQ039203
EST:     TTTTTGGTTATATATCTGCCCTCGTCGTAGACATGGCCTTTTTCATTAGG                         GGAGAAACCGCAGATGAATTACCAGAGCGGCTTATCGGTGTTGGACGCTGC
genomic: TTTTTGGTTATATATCTGCCCTCGTCGTAGACATGGCCTTTTTCATTAGGgtacttgtgt ... gagttttcagGGAGAAACCGCAGATGAATTACCAGAGCGGCTTATCGGTGTTGGACGCTGC
EST: gi|37845266|gb|BJ603274.1|BJ603274
EST:     TTTTTGGTTATATATCTGCCCTCGTCGTAGACATGGCCTTTTTCATTAGG                         GGAGAAACCGCAGATGAATTACCAGAGCGGCTTATCGGTGTTGGACGCTGC
genomic: TTTTTGGTTATATATCTGCCCTCGTCGTAGACATGGCCTTTTTCATTAGGgtacttgtgt ... gagttttcagGGAGAAACCGCAGATGAATTACCAGAGCGGCTTATCGGTGTTGGACGCTGC
EST: gi|37828876|gb|BJ586888.1|BJ586888
EST:     TTTTTGGTTATATATCTGCCCTCGTCGTAGACATGGCCTTTTTCATTAGG                         GGAGAAACCGCAGATGAATTACCAGAGCGGCTTATCGGTGTTGGACGCTGC
genomic: TTTTTGGTTATATATCTGCCCTCGTCGTAGACATGGCCTTTTTCATTAGGgtacttgtgt ... gagttttcagGGAGAAACCGCAGATGAATTACCAGAGCGGCTTATCGGTGTTGGACGCTGC
EST: gi|67692290|gb|BJ952523.1|BJ952523
EST:     TTTTTGGTTATATATCTGCCCTCGTCGTAGACATGGCCTTTTTCATTAGG                         GGAGAAACCGCAGATGAATTACCAGAGCGGCTTATCGGTGTTGGACGCTGC
genomic: TTTTTGGTTATATATCTGCCCTCGTCGTAGACATGGCCTTTTTCATTAGGgtacttgtgt ... gagttttcagGGAGAAACCGCAGATGAATTACCAGAGCGGCTTATCGGTGTTGGACGCTGC

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: 31 (upstream exon), 32 (downstream exon)
Score: 7

AGACCTAAATCTTGGATCCTCAGGGGTGGTCCGAGGAGTTCTGAGCTTAGTTTTTGGTTATATATCTGCCCTCGTCGTAGACATGGCCTTTTTCATTAGGgtacttgtgt ... gagttttcagGGAGAAACCGCAGATGAATTACCAGAGCGGCTTATCGGTGTTGGACGCTGCTCTCACATTCAACTGGACAAGGCCGTAGATCTTTCTGCAACCTAGGGGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacatctttgatgcactaaaccccagtctaaagtttatgtttgatgagttttcagGGAGAAACCGCAGATGAATTACCAGAGCGGCTTATCGGTGTTGGACGCTGCTCTCACATTCAACTGGACAAGGCCGTAGATCTTTCTGCAACCTAGGGGT
                                                ttttc  CT-rich tract
                            taaagtttatgttt  TA-rich tract