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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATGCCACCTTGAACTTTACTTGTGTTGAGCTGCGCACCGCCGATGAAACTGTAAAGTTCCCTGGTGCTTTGGCTGATCCTGAAGGTCTCGTATCGCAGgttataatactttcaccaattcaccattctaattatgtttttccgagccaaagatcaattagtactttgtgaatgccctcgtacactcgaagagcacaagaaaatgattcaacataaatcgactcatcttttacctttcatttcttaattcattttgtgtctcaatctttttcctattag

Basic information

species Physcomitrella patens
transcript PP1S9_318V6.6
intron # 8
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|18341674|gb|BJ173709.1|BJ173709
EST:     CTGTAAAGTTCCCTGGTGCTTTGGCTGATCCTGAAGGTCTCGTATCGCAG                         GTTTTGCGAGCTGCATGGGAGCAGGGTGTGGAGGTGGCTGCCGAGAATGCG
genomic: CTGTAAAGTTCCCTGGTGCTTTGGCTGATCCTGAAGGTCTCGTATCGCAGgttataatac ... ttcctattagGTTTTGCGAGCTGCATGGGAGCAGGGTGTGGAGGTGGCTGCCGAGAATGCG
EST: gi|37846633|gb|BJ604641.1|BJ604641
EST:     CTGTAAAGTTCCCTGGTGCTTTGGCTGATCCTGAAGGTCTCGTATCGCAG                         GTTTTGCGAGCTGCATGGGAGCAGGGTGTGGAGGTGGCTGCCGAGAATGCG
genomic: CTGTAAAGTTCCCTGGTGCTTTGGCTGATCCTGAAGGTCTCGTATCGCAGgttataatac ... ttcctattagGTTTTGCGAGCTGCATGGGAGCAGGGTGTGGAGGTGGCTGCCGAGAATGCG
EST: gi|208382589|gb|DC919785.1|DC919785
EST:     CTGTAAAGTTCCCTGGTGCTTTGGCTGATCCTGAAGGTCTCGTATCGCAG                         GTTTTGCGAGCTGCATGGGAGCAGGGTGTGGAGGTGGCTGCCGAGAATGCG
genomic: CTGTAAAGTTCCCTGGTGCTTTGGCTGATCCTGAAGGTCTCGTATCGCAGgttataatac ... ttcctattagGTTTTGCGAGCTGCATGGGAGCAGGGTGTGGAGGTGGCTGCCGAGAATGCG
EST: gi|67692207|gb|BJ952440.1|BJ952440
EST:     TGTAAAGTTNCCCTGGTGCTTTGGCTGATCCTGAAGGTCTCGTATCGCAG                         GTTTTGCGAGCTGCATGGGAGCAGGGTGTGGAGGTGGCTGCCGAGAATGCG
genomic: TGTAAAGTT-CCCTGGTGCTTTGGCTGATCCTGAAGGTCTCGTATCGCAGgttataatac ... ttcctattagGTTTTGCGAGCTGCATGGGAGCAGGGTGTGGAGGTGGCTGCCGAGAATGCG
EST: gi|67699862|gb|BJ960095.1|BJ960095
EST:     CTGAAGGTCTCGTATCGCAG                         GTTTTGCGAGCTGCATGGGAGCAGGGTGTGGAGGTGGCTGCCGAGAATGCG
genomic: CTGAAGGTCTCGTATCGCAGgttataatac ... ttcctattagGTTTTGCGAGCTGCATGGGAGCAGGGTGTGGAGGTGGCTGCCGAGAATGCG
EST: gi|18335610|gb|BJ167630.1|BJ167630
EST:     TGGTGCTTTGGCTGATCCTGAAGGTCTCGTATCGCAG                         GTTTTGCGAGCTGCATGGGAGCAGGGTGTGGAGGTGGCTGCCGAGAATGCG
genomic: TGGTGCTTTGGCTGATCCTGAAGGTCTCGTATCGCAGgttataatac ... ttcctattagGTTTTGCGAGCTGCATGGGAGCAGGGTGTGGAGGTGGCTGCCGAGAATGCG
EST: gi|162160286|gb|FC336572.1|FC336572
EST:     TCCTGAAGGTCTCGTATCGCAG                         GTTTTGCGAGCTGCATGGGAGCAGGGTTG-GGAGGTGGCTGCCGAGAATGC
genomic: TCCTGAAGGTCTCGTATCGCAGgttataatac ... ttcctattagGTTTTGCGAGCTGCATGGGAGCAGGG-TGTGGAGGTGGCTGCCGAGAATGC
EST: gi|37840414|gb|BJ598422.1|BJ598422
EST:     CTGTAAAGTTCCCTGGTGCTTTGGCTGATCCTGAAGGTCTCGTATCGCAG                         GTTTTGCGAGCTGCATGGGAGCAGGGTGTGGAGGTGGCTGCCGAGAATGCG
genomic: CTGTAAAGTTCCCTGGTGCTTTGGCTGATCCTGAAGGTCTCGTATCGCAGgttataatac ... ttcctattagGTTTTGCGAGCTGCATGGGAGCAGGGTGTGGAGGTGGCTGCCGAGAATGCG
EST: gi|162237714|gb|FC413329.1|FC413329
EST:     CTGTAAAGTTCCCTGGTGCTTTGGCTGATCCTGAAGGTCTCGTATCGCAG                         GTTTTGCGAGCTGCATGGGAGCAGGGTGTGGAGGTGGCTGCCGAGAATGCG
genomic: CTGTAAAGTTCCCTGGTGCTTTGGCTGATCCTGAAGGTCTCGTATCGCAGgttataatac ... ttcctattagGTTTTGCGAGCTGCATGGGAGCAGGGTGTGGAGGTGGCTGCCGAGAATGCG

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: 7

TGATGCCACCTTGAACTTTACTTGTGTTGAGCTGCGCACCGCCGATGAAACTGTAAAGTTCCCTGGTGCTTTGGCTGATCCTGAAGGTCTCGTATCGCAGgttataatac ... ttcctattagGTTTTGCGAGCTGCATGGGAGCAGGGTGTGGAGGTGGCTGCCGAGAATGCGCTATCATTCTACGAAAAGTCTGGCTATGATCAGATCCTTGTACAAGCAA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATGCCACCTTGAACTTTACTTGTGTTGAGCTGCGCACCGCCGATGAAACTGTAAAGTTCCCTGGTGCTTTGGCTGATCCTGAAGGTCTCGTATCGCAGgttataatactttcaccaattcaccattctaattatgtttttccgagccaaagatcaattagtactttgtgaatgccctcgtacactcgaagagcacaagaaaatgattcaacataaatcgactcatcttttacctttcatttcttaattcattttgtgtctcaatctttttcctattag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG