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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCATGGGCATGGCAGGCTTGCCAGCTTCCCTTGTATTGTAGCAGTCGTGCGCTCTTTTCCCACACCCGTAGCATTGCAAGCCCTCGCTCGCAGCTTTTCGgtctgtgctctctcgcagattcaacagtcattttcattcatttattttattctttctcctttcagtttctgggtgggtgtgattcatgtatccgcacctt...

Basic information

species Physcomitrella patens
transcript PP1S331_37V6.1
intron # 1
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|18375012|gb|BJ206590.1|BJ206590
EST:     GCTCTTTTCCCACACCCGTAGCATTGCAAGCCCTCGCTCGCAGCTTTTCG                         GGCACAGTCTGCAAGTGGTGATTGTGCGGATTGATTGATTGAATCTGCGGG
genomic: GCTCTTTTCCCACACCCGTAGCATTGCAAGCCCTCGCTCGCAGCTTTTCGgtctgtgctc ... tgtgggtcagGGCACAGTCTGCAAGTGGTGATTGTGCGGATTGATTGATTGAATCTGCGGG
EST: gi|18368738|gb|BJ200823.1|BJ200823
EST:     GCTCTTTTCCCACACCCGTAGCATTGCAAGCCCTCGCTCGCAGCTTTTCG                         GGCACAGTCTGCAAGTGGTGATTGTGCGGATTGATTGATTGAATCTGCGGG
genomic: GCTCTTTTCCCACACCCGTAGCATTGCAAGCCCTCGCTCGCAGCTTTTCGgtctgtgctc ... tgtgggtcagGGCACAGTCTGCAAGTGGTGATTGTGCGGATTGATTGATTGAATCTGCGGG
EST: gi|18368772|gb|BJ200857.1|BJ200857
EST:     GCTCTTTTCCCACACCCGTAGCATTGCAAGCCCTCGCTCGCAGCTTTTCG                         GGCACAGTCTGCAAGTGGTGATTGTGCGGATTGATTGATTGAATCTGCGGG
genomic: GCTCTTTTCCCACACCCGTAGCATTGCAAGCCCTCGCTCGCAGCTTTTCGgtctgtgctc ... tgtgggtcagGGCACAGTCTGCAAGTGGTGATTGTGCGGATTGATTGATTGAATCTGCGGG
EST: gi|18326718|gb|BJ158717.1|BJ158717
EST:     GCTCTTTTCCCACACCCGTAGCATTGCAAGCCCTCGCTCGCAGCTTTTCG                         GGCACAGTCTGCAAGTGGTGATTGTGCGGATTGATTGATTGAATCTGCGGG
genomic: GCTCTTTTCCCACACCCGTAGCATTGCAAGCCCTCGCTCGCAGCTTTTCGgtctgtgctc ... tgtgggtcagGGCACAGTCTGCAAGTGGTGATTGTGCGGATTGATTGATTGAATCTGCGGG
EST: gi|67508531|gb|BJ941395.1|BJ941395
EST:     GCTCTTTTCCCACACCCGTAGCATTGCAAGCCCTCGCTCGCAGCTTTTCG                         GGCACAGTCTGCAAGTGGTGATTGTGCGGATTGATTGATTGAATCTGCGGG
genomic: GCTCTTTTCCCACACCCGTAGCATTGCAAGCCCTCGCTCGCAGCTTTTCGgtctgtgctc ... tgtgggtcagGGCACAGTCTGCAAGTGGTGATTGTGCGGATTGATTGATTGAATCTGCGGG
EST: gi|100370097|gb|BY967517.1|BY967517
EST:     GCTCTTTTCCCACACCCGTAGCATTGCAAGCCCTCGCTCGCAGCTTTTCG                         GGCACAGTCTGCAAGTGGTGATTGTGCGGATTGATTGATTGAATCTGCGGG
genomic: GCTCTTTTCCCACACCCGTAGCATTGCAAGCCCTCGCTCGCAGCTTTTCGgtctgtgctc ... tgtgggtcagGGCACAGTCTGCAAGTGGTGATTGTGCGGATTGATTGATTGAATCTGCGGG
EST: gi|208354789|gb|DC934349.1|DC934349
EST:     GCTCTTTTCCCACACCCGTAGCATTGCAAGCCCTCGCTCGCTGCTTTTCG                         GGCACAGTCTGCAAGTGGTGATTGTGCGGATTGATTGATTGAATCTGCGGG
genomic: GCTCTTTTCCCACACCCGTAGCATTGCAAGCCCTCGCTCGCAGCTTTTCGgtctgtgctc ... tgtgggtcagGGCACAGTCTGCAAGTGGTGATTGTGCGGATTGATTGATTGAATCTGCGGG
EST: gi|100387776|gb|BY951776.1|BY951776
EST:     GCTCTTTTCCCACACCCGTAGCATTGCAAGCCCTCGCTCGCAGCTTTTCG                         GGCACAGTCTGCAAGTGGTGATTGTGCGGATTGATTGATTGAATCTGCGGG
genomic: GCTCTTTTCCCACACCCGTAGCATTGCAAGCCCTCGCTCGCAGCTTTTCGgtctgtgctc ... tgtgggtcagGGCACAGTCTGCAAGTGGTGATTGTGCGGATTGATTGATTGAATCTGCGGG
EST: gi|18342344|gb|BJ174379.1|BJ174379
EST:     GCTCTTTTCCCACACCCGTAGCATTGCAAGCCCTCGCTCGCAGCTTTTCG                         GGCACAGTCTGCAAGTGGTGATTGTGCGGATTGATTGATTGAATCTGCGGG
genomic: GCTCTTTTCCCACACCCGTAGCATTGCAAGCCCTCGCTCGCAGCTTTTCGgtctgtgctc ... tgtgggtcagGGCACAGTCTGCAAGTGGTGATTGTGCGGATTGATTGATTGAATCTGCGGG
EST: gi|18341937|gb|BJ173972.1|BJ173972
EST:     GCTCTTTTCCCACACCCGTAGCATTGCAAGCCCTCGCTCGCAGCTTTTCG                         GGCACAGTCTGCAAGTGGTGATTGTGCGGATTGATTGATTGAATCTGCGGG
genomic: GCTCTTTTCCCACACCCGTAGCATTGCAAGCCCTCGCTCGCAGCTTTTCGgtctgtgctc ... tgtgggtcagGGCACAGTCTGCAAGTGGTGATTGTGCGGATTGATTGATTGAATCTGCGGG
EST: gi|100450289|gb|CJ974188.1|CJ974188
EST:     GCTCTTTTCCCACACCCGTAGCATTGCAAGCCCTCGCTCGCAGCTTTTCG                         GGCACAGTCTGCAAGTGGTGATTGTGCGGATTGATTGATTGAATCTGCGGG
genomic: GCTCTTTTCCCACACCCGTAGCATTGCAAGCCCTCGCTCGCAGCTTTTCGgtctgtgctc ... tgtgggtcagGGCACAGTCTGCAAGTGGTGATTGTGCGGATTGATTGATTGAATCTGCGGG
EST: gi|18343798|gb|BJ175836.1|BJ175836
EST:     GCTCTTTTCCCACACCCGTAGCATTGCAAGCCCTCGCTCGCAGCTTTTCG                         GGCACAGTCTGCAAGTGGTGATTGTGCGGATTGATTGATTGAATCTGCGGG
genomic: GCTCTTTTCCCACACCCGTAGCATTGCAAGCCCTCGCTCGCAGCTTTTCGgtctgtgctc ... tgtgggtcagGGCACAGTCTGCAAGTGGTGATTGTGCGGATTGATTGATTGAATCTGCGGG
EST: gi|100383743|gb|BY969272.1|BY969272
EST:     GCTCTTTTCCCACACCCGTAGCATTGCAAGCCCTCGCTCGCAGCTTTTCG                         GGCACAGTCTGCAAGTGGTGATTGTGCGGATTGATTGATTGAATCTGCGGG
genomic: GCTCTTTTCCCACACCCGTAGCATTGCAAGCCCTCGCTCGCAGCTTTTCGgtctgtgctc ... tgtgggtcagGGCACAGTCTGCAAGTGGTGATTGTGCGGATTGATTGATTGAATCTGCGGG
EST: gi|100394409|gb|BY972054.1|BY972054
EST:     GCTCTTTTCCCACACCCGTAGCATTGCAAGCCCTCGCTCGCAGCTTTTCG                         GGCACAGTCTGCAAGTGGTGATTGTGCGGATTGATTGATTGAATCTGCGGG
genomic: GCTCTTTTCCCACACCCGTAGCATTGCAAGCCCTCGCTCGCAGCTTTTCGgtctgtgctc ... tgtgggtcagGGCACAGTCTGCAAGTGGTGATTGTGCGGATTGATTGATTGAATCTGCGGG

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), 34 (downstream exon)
Score: 36

TCATGGGCATGGCAGGCTTGCCAGCTTCCCTTGTATTGTAGCAGTCGTGCGCTCTTTTCCCACACCCGTAGCATTGCAAGCCCTCGCTCGCAGCTTTTCGgtctgtgctc ... tgtgggtcagGGCACAGTCTGCAAGTGGTGATTGTGCGGATTGATTGATTGAATCTGCGGGTGGGGAGTAAGTGACTTGTTGTGATGGAGGCAGCAGCGGCGTCTTTGAC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCATGGGCATGGCAGGCTTGCCAGCTTCCCTTGTATTGTAGCAGTCGTGCGCTCTTTTCCCACACCCGTAGCATTGCAAGCCCTCGCTCGCAGCTTTTCGgtctgtgctctctcgcagattcaacagtcattttcattcatttattttattctttctcctttcagtttctgggtgggtgtgattcatgtatccgcacctt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT