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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCAATCTCAACATAACATTTTTAAAGCCCCCCATCGTCACTCTGCCTTCTTGTCCTACCCCTTGCCTTCGCTGCACCCTATGCCCGCCACCACTGAAGgtgcacgctcatctttccctccgttcacagcaacattcttctcagccgtaggtggtgtctttgcctgtgttgaaacgagcttttacacgacagcatccat...

Basic information

species Physcomitrella patens
transcript PP1S55_112V6.1
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|37848627|gb|BJ606635.1|BJ606635
EST:     TACCCCTTGCCTTCGCTGCACCCTATGCCCGCCACCACTGAAG                         AGTGGAGCCTCGATAAATCTTTGCAAGTGAAAGAGCGTGAAAGCCTTTAAC
genomic: TACCCCTTGCCTTCGCTGCACCCTATGCCCGCCACCACTGAAGgtgcacgctc ... tctgctgcagAGTGGAGCCTCGATAAATCTTTGCAAGTGAAAGAGCGTGAAAGCCTTTAAC
EST: gi|67569562|gb|BJ942386.1|BJ942386
EST:     CCTTCGCTGCACCCTATGCCCGCCACCACTGAAG                         AGTGGAGCCTCGATAAATCTTTGCAAGTGAAAGAGCGTGAAAGCCTTTAAC
genomic: CCTTCGCTGCACCCTATGCCCGCCACCACTGAAGgtgcacgctc ... tctgctgcagAGTGGAGCCTCGATAAATCTTTGCAAGTGAAAGAGCGTGAAAGCCTTTAAC
EST: gi|208373359|gb|DC941012.1|DC941012
EST:     CTACCCCTTGCCTTCGCTGCACCCTATGCCCGCCACCACTGAAG                         AGTGGAGCCTCGATAAATCTTTGCAAGTGAAAGAGCGTGAAAGCCTTTAAC
genomic: CTACCCCTTGCCTTCGCTGCACCCTATGCCCGCCACCACTGAAGgtgcacgctc ... tctgctgcagAGTGGAGCCTCGATAAATCTTTGCAAGTGAAAGAGCGTGAAAGCCTTTAAC
EST: gi|7286411|gb|AW598840.1|AW598840
EST:     CTTGTCCTACCCCTTGCCTTCGCTGCACCCTATGCCCGCCACCACTGAAG                         AGTGGAGCCTCGATAAATCTTTGCAAGTGAAAGAGCGTGAAAGCCTTTAAC
genomic: CTTGTCCTACCCCTTGCCTTCGCTGCACCCTATGCCCGCCACCACTGAAGgtgcacgctc ... tctgctgcagAGTGGAGCCTCGATAAATCTTTGCAAGTGAAAGAGCGTGAAAGCCTTTAAC
EST: gi|37846028|gb|BJ604036.1|BJ604036
EST:     GCCTTCGCTGCACCCTATGCCCGCCACCACTGAAG                         AGTGGAGCCTCGATAAATCTTTGCAAGTGAAAGAGCGTGAAAGCCTTTAAC
genomic: GCCTTCGCTGCACCCTATGCCCGCCACCACTGAAGgtgcacgctc ... tctgctgcagAGTGGAGCCTCGATAAATCTTTGCAAGTGAAAGAGCGTGAAAGCCTTTAAC
EST: gi|208359460|gb|DC954013.1|DC954013
EST:     CTACCCCTTGCCTTCGCTGCACCCTATGCCCGCCACCACTGAAG                         AGTGGAGCCTCGATAAATCTTTGCAAGTGAAAGAGCGTGAAAGCCTTTAAC
genomic: CTACCCCTTGCCTTCGCTGCACCCTATGCCCGCCACCACTGAAGgtgcacgctc ... tctgctgcagAGTGGAGCCTCGATAAATCTTTGCAAGTGAAAGAGCGTGAAAGCCTTTAAC
EST: gi|162207988|gb|FC384734.1|FC384734
EST:     CTTCGCTGCACCCTATGCCCGCCACCACTGAAG                         AGTGGAGCCTCGATAAATCTTTGCAAGTGAAAGAGCGTGAAAGCCTTTAAC
genomic: CTTCGCTGCACCCTATGCCCGCCACCACTGAAGgtgcacgctc ... tctgctgcagAGTGGAGCCTCGATAAATCTTTGCAAGTGAAAGAGCGTGAAAGCCTTTAAC
EST: gi|18374856|gb|BJ206434.1|BJ206434
EST:     TACCCCTTGCCTTCGCTGCACCCTATGCCCGCCACCACTGAAG                         AGTGGAGCCTCGATAAATCTTTGCAAGTGAAAGAGCGTGAAAGCCTTTAAC
genomic: TACCCCTTGCCTTCGCTGCACCCTATGCCCGCCACCACTGAAGgtgcacgctc ... tctgctgcagAGTGGAGCCTCGATAAATCTTTGCAAGTGAAAGAGCGTGAAAGCCTTTAAC
EST: gi|67692830|gb|BJ953063.1|BJ953063
EST:     CTTGTCCTACCCCTTGCCTTCGCTGCACCCTATGCCCGCCACCACTGAAG                         AGTGGAGCCTCGATAAATCTTTGCAAGTGAAAGAGCGTGAAAGCCTTTAAC
genomic: CTTGTCCTACCCCTTGCCTTCGCTGCACCCTATGCCCGCCACCACTGAAGgtgcacgctc ... tctgctgcagAGTGGAGCCTCGATAAATCTTTGCAAGTGAAAGAGCGTGAAAGCCTTTAAC
EST: gi|18363419|gb|BJ195491.1|BJ195491
EST:     CTACCCCTTGCCTTCGCTGCACCCTATGCCCGCCACCACTGAAG                         AGTGGAGCCTCGATAAATCTTTGCAAGTGAAAGAGCGTGAAAGCCTTTAAC
genomic: CTACCCCTTGCCTTCGCTGCACCCTATGCCCGCCACCACTGAAGgtgcacgctc ... tctgctgcagAGTGGAGCCTCGATAAATCTTTGCAAGTGAAAGAGCGTGAAAGCCTTTAAC
EST: gi|162215209|gb|FC390795.1|FC390795
EST:     TGCCTTCGCTGCACCCTATGCCCGCCACCACTGAAG                         AGTGGAGCCTCGATAAATCTTTGCAAGTGAAAGAGCGTGAAAGCCTTTAAC
genomic: TGCCTTCGCTGCACCCTATGCCCGCCACCACTGAAGgtgcacgctc ... tctgctgcagAGTGGAGCCTCGATAAATCTTTGCAAGTGAAAGAGCGTGAAAGCCTTTAAC

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: 32 (upstream exon), 14 (downstream exon)
Score: 3

CTCAATCTCAACATAACATTTTTAAAGCCCCCCATCGTCACTCTGCCTTCTTGTCCTACCCCTTGCCTTCGCTGCACCCTATGCCCGCCACCACTGAAGgtgcacgctc ... tctgctgcagAGTGGAGCCTCGATAAATCTTTGCAAGTGAAAGAGCGTGAAAGCCTTTAACAACCATGAGTTCTCCCGGTGCTACTCCTGGAGGCCGCGGGAAGTCCAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCAATCTCAACATAACATTTTTAAAGCCCCCCATCGTCACTCTGCCTTCTTGTCCTACCCCTTGCCTTCGCTGCACCCTATGCCCGCCACCACTGAAGgtgcacgctcatctttccctccgttcacagcaacattcttctcagccgtaggtggtgtctttgcctgtgttgaaacgagcttttacacgacagcatccat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG