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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCGTGCGGGTGAGATTATCGGTATCCCTATTGGCAGCAAGGGGGTCCATCCCAACGATCACGTTAACATGAGTCAATCCTCAAATGACACCTTTCCAACGgttcgtagccacactctgttgtaattcaacttaaaataatgggaacttatcttggtctgaaacaagtagctattgctagttgcaggtggtttacttcatc...

Basic information

species Physcomitrella patens
transcript PP1S49_154V6.1
intron # 4
splice site 5'
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|208363600|gb|DC939777.1|DC939777
EST:     CCAACGATCACGTTAACATGAGTCAATCCTCAAATGACACCTTTCCAACG                         GCGATGCATATTGCAGCAGCTATAGAGGCTACCAGTANGCTACTTCCCCAT
genomic: CCAACGATCACGTTAACATGAGTCAATCCTCAAATGACACCTTTCCAACGgttcgtagcc ... ttttcctcagGCGATGCATATTGCAGCAGCTATAGAGGCTACCAGTAGGCTACTTCCCCAT
EST: gi|100377587|gb|BY986312.1|BY986312
EST:     CCAACGATCACGTTAACATGAGTCAATCCTCAAATGACACCTTTCCAACG                         GCGATGCATATTGCAGCAGCTATAGAGGCTA
genomic: CCAACGATCACGTTAACATGAGTCAATCCTCAAATGACACCTTTCCAACGgttcgtagcc ... ttttcctcagGCGATGCATATTGCAGCAGCTATAGAGGCTA
EST: gi|18365619|gb|BJ197696.1|BJ197696
EST:     CCAACGATCACGTTAACATGAGTCAATCCTCAAATGACACCTTTCCAACG                         GCGATGCATATTGCAGCAGCTATAG
genomic: CCAACGATCACGTTAACATGAGTCAATCCTCAAATGACACCTTTCCAACGgttcgtagcc ... ttttcctcagGCGATGCATATTGCAGCAGCTATAG
EST: gi|7047501|gb|AW477395.1|AW477395
EST:     CCAACGATCACGTTAACATGAGTGAATCCTCAAATGACACCTTTCCAACG                         GCGATGCATATTGCAGCAGCTATAGAGGCTACCAGTAGGCTACTTCCCCAT
genomic: CCAACGATCACGTTAACATGAGTCAATCCTCAAATGACACCTTTCCAACGgttcgtagcc ... ttttcctcagGCGATGCATATTGCAGCAGCTATAGAGGCTACCAGTAGGCTACTTCCCCAT
EST: gi|67569924|gb|BJ942748.1|BJ942748
EST:     ATCCTCAAATGACACCTTTCC-ACG                         GCGATGCATATTGCAGCAGCTATAGAGGCTACCAGTAGGCTACTTCCCCAT
genomic: ATCCTCAAATGACACCTTTCCAACGgttcgtagcc ... ttttcctcagGCGATGCATATTGCAGCAGCTATAGAGGCTACCAGTAGGCTACTTCCCCAT
EST: gi|208358694|gb|DC942916.1|DC942916
EST:     CCAACGATCACGTTAACATGAGTCAATCCTCAAATGACACCTTTCCAACG                         GCGATGCATATTGCAGCAGCTATAGAGGCTACCAGTAGGCTACTTCCCCAT
genomic: CCAACGATCACGTTAACATGAGTCAATCCTCAAATGACACCTTTCCAACGgttcgtagcc ... ttttcctcagGCGATGCATATTGCAGCAGCTATAGAGGCTACCAGTAGGCTACTTCCCCAT
EST: gi|18326303|gb|BJ158302.1|BJ158302
EST:     CCAACGATCACGTTAACATGAGTCAATCCTCAAATGACACCTTTCCAACG                         GCGATGCATATTGCAGCAGCTATAG
genomic: CCAACGATCACGTTAACATGAGTCAATCCTCAAATGACACCTTTCCAACGgttcgtagcc ... ttttcctcagGCGATGCATATTGCAGCAGCTATAG
EST: gi|18343443|gb|BJ175481.1|BJ175481
EST:     CCAACGATCACGTTAACATGAGTCAATCCTCAAATGACACCTTTCCAACG                         GCGATGCATATTGCAGCAGCTATAGAGGCTACCAG
genomic: CCAACGATCACGTTAACATGAGTCAATCCTCAAATGACACCTTTCCAACGgttcgtagcc ... ttttcctcagGCGATGCATATTGCAGCAGCTATAGAGGCTACCAG
EST: gi|18366250|gb|BJ198328.1|BJ198328
EST:     CCAACGATCACGTTAACATGAGTCAATCCTCAAATGACACCTTTCCAACG                         GCGATGCATATTGCAGCAGCTAT
genomic: CCAACGATCACGTTAACATGAGTCAATCCTCAAATGACACCTTTCCAACGgttcgtagcc ... ttttcctcagGCGATGCATATTGCAGCAGCTAT

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: 34 (upstream exon), 31 (downstream exon)
Score: 10

TCGTGCGGGTGAGATTATCGGTATCCCTATTGGCAGCAAGGGGGTCCATCCCAACGATCACGTTAACATGAGTCAATCCTCAAATGACACCTTTCCAACGgttcgtagcc ... ttttcctcagGCGATGCATATTGCAGCAGCTATAGAGGCTACCAGTAGGCTACTTCCCCATTTGCATGCCCTGCACGAAGCGCTTATTGAGAAG




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