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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcgtagtttaaataaataatatctccatcacttgtaatacaattttgtgctgaattgaatgttgaataactctgtcttggtttcttttgattttcctcagGCGATGCATATTGCAGCAGCTATAGAGGCTACCAGTAGGCTACTTCCCCATTTGCATGCCCTGCACGAAGCGCTTATTGAGAAG

Basic information

species Physcomitrella patens
transcript PP1S49_154V6.1
intron # 4
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|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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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgctgaattgaatgttgaataactctgtcttggtttcttttgattttcctcagGCGATGCATATTGCAGCAGCTATAGAGGCTACCAGTAGGCTACTTCCCCATTTGCATGCCCTGCACGAAGCGCTTATTGAGAAG
                                   tttcttttgattttcc  CT-rich tract
                                   tttcttttgatttt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcgtagtttaaataaataatatctccatcacttgtaatacaattttgtgctgaattgaatgttgaataactctgtcttggtttcttttgattttcctcagGCGATGCATATTGCAGCAGCTATAGAGGCTACCAGTAGGCTACTTCCCCATTTGCATGCCCTGCACGAAGCGCTTATTGAGAAG

- - - - - - - - - - - - - - - - - - - - - - - -tgctgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgaa