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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTAGGGTTTTTGCGGTCTGAGAAGATGAAATTGCTGTCTCCGATCGTCGGTGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTGgtgatttttttatttttacttattttttcttgatttttggttccccttcaaactgtgaaatttagacactgagtggttatgattaaatttagtgcttatg...

Basic information

species Physcomitrella patens
transcript PP1S41_313V6.1
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|18347919|gb|BJ179966.1|BJ179966
EST:     TGCCGCGTCCCAACGGTTTGATGATGCGTTTAAGGAGCCTGCTTACTCTG                         ATTCGGAAACGGAGGCGGGCGCTAGTGAGGTCTCTCCTGATTCCCTGGACA
genomic: TGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTGgtgatttttt ... tgaatggcagATTCGGAAACGGAGGCGGGCGCTAGTGAGGTCTCTCCTGATTCCCTGGACA
EST: gi|18330507|gb|BJ162513.1|BJ162513
EST:     TGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTG                         ATTCGGAAACGGA
genomic: TGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTGgtgatttttt ... tgaatggcagATTCGGAAACGGA
EST: gi|162255371|gb|FC432097.1|FC432097
EST:     TGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTG                         ATTCGGAAACGGAGGCGGGCGCTAGTGAGGTCTCTCCTGATTCCCTGGACA
genomic: TGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTGgtgatttttt ... tgaatggcagATTCGGAAACGGAGGCGGGCGCTAGTGAGGTCTCTCCTGATTCCCTGGACA
EST: gi|162268052|gb|FC443522.1|FC443522
EST:     TGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTG                         ATTCGGAAACGGAGGCGGGCGCTAGTGAGGTCTCTCCTGATTCCCTGGACA
genomic: TGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTGgtgatttttt ... tgaatggcagATTCGGAAACGGAGGCGGGCGCTAGTGAGGTCTCTCCTGATTCCCTGGACA
EST: gi|19778728|gb|BQ039350.1|BQ039350
EST:     TGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTG                         ATTCGGAAACGGAGGCGGGCGCTAGTGAGGTCTCTCCTGATTCCCTGGACA
genomic: TGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTGgtgatttttt ... tgaatggcagATTCGGAAACGGAGGCGGGCGCTAGTGAGGTCTCTCCTGATTCCCTGGACA
EST: gi|162225323|gb|FC400841.1|FC400841
EST:     TGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTG                         ATTCGGAAACGGAGGCGGGCGCTAGTGAGGCCTCTCCTGATTCCCTGGACA
genomic: TGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTGgtgatttttt ... tgaatggcagATTCGGAAACGGAGGCGGGCGCTAGTGAGGTCTCTCCTGATTCCCTGGACA
EST: gi|100416872|gb|BY993131.1|BY993131
EST:     TGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTG                         ATTCGGAAACGGAGGCGGGCGCTAGTGAGGTCTCTCCTGATTCCCTGGACA
genomic: TGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTGgtgatttttt ... tgaatggcagATTCGGAAACGGAGGCGGGCGCTAGTGAGGTCTCTCCTGATTCCCTGGACA
EST: gi|100394920|gb|BY989991.1|BY989991
EST:     TGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTG                         ATTCGGAAACGGAGGCGGGCGCTAGTGAGGTCTCTCCTGATTCCCTGGACA
genomic: TGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTGgtgatttttt ... tgaatggcagATTCGGAAACGGAGGCGGGCGCTAGTGAGGTCTCTCCTGATTCCCTGGACA
EST: gi|162219476|gb|FC396954.1|FC396954
EST:     TGCCGCGTCCCAACGGTTTGATGATGCGTNTGAGGAGCCTGCTTACTCTG                         ATTCGGAAACGGAGGCGGGCGCTAGTGAGGCCTCTCCTGATTCCCTGGACA
genomic: TGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTGgtgatttttt ... tgaatggcagATTCGGAAACGGAGGCGGGCGCTAGTGAGGTCTCTCCTGATTCCCTGGACA
EST: gi|100406705|gb|BY955703.1|BY955703
EST:     TGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTG                         ATTCGGAAACGGAGGCGGGCGCTAGTGAGGTCTCTCCTGATTCCCTGGACA
genomic: TGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTGgtgatttttt ... tgaatggcagATTCGGAAACGGAGGCGGGCGCTAGTGAGGTCTCTCCTGATTCCCTGGACA
EST: gi|162225322|gb|FC400840.1|FC400840
EST:     GGTTTGATGATGCGTNTGAGGAGCCTGCTTACTCTG                         ATTCGGAAACGGAGGCGGGCGCTAGTGAGGCCTCTCCTGATTCCCTGGACA
genomic: GGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTGgtgatttttt ... tgaatggcagATTCGGAAACGGAGGCGGGCGCTAGTGAGGTCTCTCCTGATTCCCTGGACA
EST: gi|162230598|gb|FC407461.1|FC407461
EST:     TGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTG                         ATTCGGAAACGGAGGCGGGCGCTAGTGAGGCCTCTCCTGATTCCCTGGACA
genomic: TGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTGgtgatttttt ... tgaatggcagATTCGGAAACGGAGGCGGGCGCTAGTGAGGTCTCTCCTGATTCCCTGGACA
EST: gi|208395960|gb|DC915720.1|DC915720
EST:     TGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTG                         ATTCGGAAACGGAGGCGGGCGCTAGTGAGGTCTCTCCTGATTCCCTGGACA
genomic: TGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTGgtgatttttt ... tgaatggcagATTCGGAAACGGAGGCGGGCGCTAGTGAGGTCTCTCCTGATTCCCTGGACA
EST: gi|162236522|gb|FC413097.1|FC413097
EST:     TGCCGCGTCCCAACGGTTTGATGATGCGTNTGAGGAGCCTGCTTACTCTG                         ATTCGGAAACGGAGGCGGGCGCTAGTGAGGCCTCTCCTGATTCCCTGGACA
genomic: TGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTGgtgatttttt ... tgaatggcagATTCGGAAACGGAGGCGGGCGCTAGTGAGGTCTCTCCTGATTCCCTGGACA
EST: gi|162268053|gb|FC443523.1|FC443523
EST:     TGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTG                         ATTCGGAAACGGAGGCGGGCGCTAGTGAGGTCTCTCCTGATTCCCTGGACA
genomic: TGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTGgtgatttttt ... tgaatggcagATTCGGAAACGGAGGCGGGCGCTAGTGAGGTCTCTCCTGATTCCCTGGACA
EST: gi|208371538|gb|DC936259.1|DC936259
EST:     TGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTG                         ATTCGGAAACGGAGGCGGGCGCTAGTGAGGTCTCTCCTGATTCCCTGGACA
genomic: TGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTGgtgatttttt ... tgaatggcagATTCGGAAACGGAGGCGGGCGCTAGTGAGGTCTCTCCTGATTCCCTGGACA
EST: gi|67698881|gb|BJ959114.1|BJ959114
EST:     TGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTG                         ATTCGGAAACGGAGGCGGGCGCTAGTGAGGTCTCTCCTGATTCCCTGGACA
genomic: TGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTGgtgatttttt ... tgaatggcagATTCGGAAACGGAGGCGGGCGCTAGTGAGGTCTCTCCTGATTCCCTGGACA
EST: gi|18345723|gb|BJ177766.1|BJ177766
EST:     GCCGCGTCCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTG                         ATTCGGAAACGGAGGCGGGCGCTAGTGAGGTCTCTCCTGATTCCCTGGACA
genomic: GCCGCGTCCC-AACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTGgtgatttttt ... tgaatggcagATTCGGAAACGGAGGCGGGCGCTAGTGAGGTCTCTCCTGATTCCCTGGACA
EST: gi|67573226|gb|BJ946050.1|BJ946050
EST:     TGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTG                         ATTCGGAAACGGAGGCGGGCGCTAGTGAGGTCTCTCCTGATTCCCTGGACA
genomic: TGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTGgtgatttttt ... tgaatggcagATTCGGAAACGGAGGCGGGCGCTAGTGAGGTCTCTCCTGATTCCCTGGACA
EST: gi|162236523|gb|FC413098.1|FC413098
EST:     TGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTG                         ATTCGGAAACGGAGGCGGGCGCTAGTGAGGCCTCTCCTGATTCCCTGGACA
genomic: TGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTGgtgatttttt ... tgaatggcagATTCGGAAACGGAGGCGGGCGCTAGTGAGGTCTCTCCTGATTCCCTGGACA
EST: gi|67696780|gb|BJ957013.1|BJ957013
EST:     TGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTG                         ATTCGGAAACGGAGGCGGGCGCTAGTGAGGTCTCTCCTGATTCCCTGGACA
genomic: TGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTGgtgatttttt ... tgaatggcagATTCGGAAACGGAGGCGGGCGCTAGTGAGGTCTCTCCTGATTCCCTGGACA
EST: gi|67573399|gb|BJ946223.1|BJ946223
EST:     TGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTG                         ATTCGGAAACGGAGGCGGGCGCTAGTGAGGTCTCTCCTGATTCCCTGGACA
genomic: TGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTGgtgatttttt ... tgaatggcagATTCGGAAACGGAGGCGGGCGCTAGTGAGGTCTCTCCTGATTCCCTGGACA
EST: gi|162228314|gb|FC404068.1|FC404068
EST:     TGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTG                         ATTCGGAAACGGAGGCGGGCGCTAGTGAGGCCTCTCCTGATTCCCTGGACA
genomic: TGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTGgtgatttttt ... tgaatggcagATTCGGAAACGGAGGCGGGCGCTAGTGAGGTCTCTCCTGATTCCCTGGACA
EST: gi|208360491|gb|DC950065.1|DC950065
EST:     AACGGTTTGATGATGCGNTTGAGGAGCCTGCTTACTCTG                         ATTCGGAAACGGAGGCGGGCGCTAGTGAGGTCTCTCCTGATTCCCTGGACA
genomic: AACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTGgtgatttttt ... tgaatggcagATTCGGAAACGGAGGCGGGCGCTAGTGAGGTCTCTCCTGATTCCCTGGACA
EST: gi|67578152|gb|BJ950319.1|BJ950319
EST:     TGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTG                         ATTCGGAAACGGAGGCGGGCGCTAGTGAGGTCTCTCCTGATTCCCTGGACA
genomic: TGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTGgtgatttttt ... tgaatggcagATTCGGAAACGGAGGCGGGCGCTAGTGAGGTCTCTCCTGATTCCCTGGACA
EST: gi|162228315|gb|FC404069.1|FC404069
EST:     TGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTG                         ATTCGGAAACGGAGGCGGGCGCTAGTGAGGCCTCTCCTGATTCCCTGGACA
genomic: TGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTGgtgatttttt ... tgaatggcagATTCGGAAACGGAGGCGGGCGCTAGTGAGGTCTCTCCTGATTCCCTGGACA
EST: gi|162242371|gb|FC416127.1|FC416127
EST:     TGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTG                         ATTCGGAAACGGAGGCGGGCGCTAGTGAGGCCTCTCCTGATTCCCTGGACA
genomic: TGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTGgtgatttttt ... tgaatggcagATTCGGAAACGGAGGCGGGCGCTAGTGAGGTCTCTCCTGATTCCCTGGACA
EST: gi|67696610|gb|BJ956843.1|BJ956843
EST:     TGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTG                         ATTCGGAAACGGAGGCGGGCGCTAGTGAGGTCTCTCCTGATTCCCTGGACA
genomic: TGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTGgtgatttttt ... tgaatggcagATTCGGAAACGGAGGCGGGCGCTAGTGAGGTCTCTCCTGATTCCCTGGACA
EST: gi|162230599|gb|FC407462.1|FC407462
EST:     TGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTG                         ATTCGGAAACGGAGGCGGGCGCTAGTGAGGCCTCTCCTGATTCCCTGGACA
genomic: TGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTGgtgatttttt ... tgaatggcagATTCGGAAACGGAGGCGGGCGCTAGTGAGGTCTCTCCTGATTCCCTGGACA
EST: gi|100444973|gb|BY982801.1|BY982801
EST:     TGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTG                         ATTCGGAAACGGAGGCGGGCGCTAGTGAGGTCTCTCCTGATTCCCTGGACA
genomic: TGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTGgtgatttttt ... tgaatggcagATTCGGAAACGGAGGCGGGCGCTAGTGAGGTCTCTCCTGATTCCCTGGACA
EST: gi|67575414|gb|BJ948238.1|BJ948238
EST:     TGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTG                         ATTCGGAAACGGAGGCGGGCGCTAGTGAGGTCTCTCCTGATTCCCTGGACA
genomic: TGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTGgtgatttttt ... tgaatggcagATTCGGAAACGGAGGCGGGCGCTAGTGAGGTCTCTCCTGATTCCCTGGACA
EST: gi|208363770|gb|DC931094.1|DC931094
EST:     TGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTG                         ATTCGGAAACGGAGGCGGGCGCTAGTGAGGTCTCTCCTGATTCCCTGGACA
genomic: TGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTGgtgatttttt ... tgaatggcagATTCGGAAACGGAGGCGGGCGCTAGTGAGGTCTCTCCTGATTCCCTGGACA
EST: gi|208388333|gb|DC945609.1|DC945609
EST:     TGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTG                         ATTCGGAAACGGAGGCGGGCGCTAGTGAGGTCTCTCCTGATTCCCTGGACA
genomic: TGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTGgtgatttttt ... tgaatggcagATTCGGAAACGGAGGCGGGCGCTAGTGAGGTCTCTCCTGATTCCCTGGACA
EST: gi|162219477|gb|FC396955.1|FC396955
EST:     TGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTG                         ATTCGGAAACGGAGGCGGGCGCTAGTGAGGCCTCTCCTGATTCCCTGGACA
genomic: TGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTGgtgatttttt ... tgaatggcagATTCGGAAACGGAGGCGGGCGCTAGTGAGGTCTCTCCTGATTCCCTGGACA

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: 30 (upstream exon), 32 (downstream exon)
Score: 35

CTAGGGTTTTTGCGGTCTGAGAAGATGAAATTGCTGTCTCCGATCGTCGGTGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTGgtgatttttt ... tgaatggcagATTCGGAAACGGAGGCGGGCGCTAGTGAGGTCTCTCCTGATTCCCTGGACAAAGAGGAGATTTCTCCTGAGGCAGGTGCTATTGTTGTGTCGTCGTTGTC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTAGGGTTTTTGCGGTCTGAGAAGATGAAATTGCTGTCTCCGATCGTCGGTGCCGCGTCCCAACGGTTTGATGATGCGTTTGAGGAGCCTGCTTACTCTGgtgatttttttatttttacttattttttcttgatttttggttccccttcaaactgtgaaatttagacactgagtggttatgattaaatttagtgcttatg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG