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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATGTCGACCCAATCGAATTGGTAGTGTGGTTGCCCGCGCTTTGTCGCAAGATGAATGTGCCATATGCCATCGTCAAAGGAAAATCACGCTTAGGACAGgtaaagtgtgtcaattatgttcgcagtaaacatttcgtatagtagtaaggatagcaatggtgctgggaagtggtgtttttgatttcgtaataccttcagcctgggttgttgccgcgtggatatagtagtaacggtaattgtgttgcgcag

Basic information

species Physcomitrella patens
transcript PP1S90_23V6.1
intron # 5
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|18338430|gb|BJ170454.1|BJ170454
EST:     AGATGAATGTGCCATATGCCATCGTCAAAGGAAAATCACGCTTAGGACAG                         ATTGTGCATGCCAAGACCGCCACGGCTCTTTGTTTGACGTCAGTGAAAAAC
genomic: AGATGAATGTGCCATATGCCATCGTCAAAGGAAAATCACGCTTAGGACAGgtaaagtgtg ... tgttgcgcagATTGTGCATGCCAAGACCGCCACGGCTCTTTGTTTGACGTCAGTGAAAAAC
EST: gi|67726326|gb|BJ976585.1|BJ976585
EST:     AGATGAATGTGCCATATGCCATCGTCAAAGGAAAATCACGCTTAGGACAG                         ATTGTGCATGCCAAGACCGCCACGGCTCTTTGTTTGACGTCAGTGAAAAAC
genomic: AGATGAATGTGCCATATGCCATCGTCAAAGGAAAATCACGCTTAGGACAGgtaaagtgtg ... tgttgcgcagATTGTGCATGCCAAGACCGCCACGGCTCTTTGTTTGACGTCAGTGAAAAAC
EST: gi|37826868|gb|BJ584880.1|BJ584880
EST:     AGATGAATGTGCCATATGCCATCGTCAAAGGAAAATCACGCTTAGGACAG                         ATTGTGCATGCCAAGACCGCCACGGCTTCTTTGTTTGACGTCAGTGAAAAA
genomic: AGATGAATGTGCCATATGCCATCGTCAAAGGAAAATCACGCTTAGGACAGgtaaagtgtg ... tgttgcgcagATTGTGCATGCCAAGACCGCCACGGCT-CTTTGTTTGACGTCAGTGAAAAA
EST: gi|162272266|gb|FC448164.1|FC448164
EST:     AGATGAATGTGCCATATGCCATCGTCAAAGGAAAATCACGCTTAGGACAG                         ATTGTGCATGCCAAGACCGCCACGGCTCTTTGTTTGACGTCAGTGAAAAAC
genomic: AGATGAATGTGCCATATGCCATCGTCAAAGGAAAATCACGCTTAGGACAGgtaaagtgtg ... tgttgcgcagATTGTGCATGCCAAGACCGCCACGGCTCTTTGTTTGACGTCAGTGAAAAAC
EST: gi|161984007|gb|EE296457.1|EE296457
EST:     AGATGAATGTGCCATATGCCATCGTCAAAGGAAAATCACGCTTAGGACAG                         ATTGTGCATGCCAAGACCGCCACGGCTCTTTGTTTGACGTCAGTGAAAAAC
genomic: AGATGAATGTGCCATATGCCATCGTCAAAGGAAAATCACGCTTAGGACAGgtaaagtgtg ... tgttgcgcagATTGTGCATGCCAAGACCGCCACGGCTCTTTGTTTGACGTCAGTGAAAAAC
EST: gi|67727722|gb|BJ977981.1|BJ977981
EST:     AGATGAATGTGCCATATGCCATCGTCAAAGGAAAATCACGCTTAGGACAG                         ATTGTGCATGCCAAGACCGCCACGGCTCTTTGTTTGACGTCAGTGAAAAAC
genomic: AGATGAATGTGCCATATGCCATCGTCAAAGGAAAATCACGCTTAGGACAGgtaaagtgtg ... tgttgcgcagATTGTGCATGCCAAGACCGCCACGGCTCTTTGTTTGACGTCAGTGAAAAAC
EST: gi|37835624|gb|BJ593636.1|BJ593636
EST:     AGATGAATGTGCCATATGCCATCGTCAAAGGAAAATCACGCTTAGGACAG                         ATTGTGCATGCCAAGACCGCCACGGCTCTTTGTTTGACGTCAGTGAAAAAC
genomic: AGATGAATGTGCCATATGCCATCGTCAAAGGAAAATCACGCTTAGGACAGgtaaagtgtg ... tgttgcgcagATTGTGCATGCCAAGACCGCCACGGCTCTTTGTTTGACGTCAGTGAAAAAC
EST: gi|208390668|gb|DC937824.1|DC937824
EST:     AGATGAATGTGCCATATGCCATCGTCAAAGGAAAATCACGCTTAGGACAG                         ATTGTGCATGCCAAG
genomic: AGATGAATGTGCCATATGCCATCGTCAAAGGAAAATCACGCTTAGGACAGgtaaagtgtg ... tgttgcgcagATTGTGCATGCCAAG
EST: gi|162272267|gb|FC448165.1|FC448165
EST:     AGATGAATGTGCCATATGCCATCGTCAAAGGAAAATCACGCTTAGGACAG                         ATTGTGCATGCCAAGACCGCCACGGCTCTTTGTTTGACGTCAGTGAAAAAC
genomic: AGATGAATGTGCCATATGCCATCGTCAAAGGAAAATCACGCTTAGGACAGgtaaagtgtg ... tgttgcgcagATTGTGCATGCCAAGACCGCCACGGCTCTTTGTTTGACGTCAGTGAAAAAC
EST: gi|162238124|gb|FC418708.1|FC418708
EST:     AGATGAATGTGCCATATGCCATCGTCAAAGGAAAATCACGCTTAGGACAG                         ATTGTGCATGCCAAGACCGCCACGGCTCTTTGTTTGACGTCAGTGAAAAAC
genomic: AGATGAATGTGCCATATGCCATCGTCAAAGGAAAATCACGCTTAGGACAGgtaaagtgtg ... tgttgcgcagATTGTGCATGCCAAGACCGCCACGGCTCTTTGTTTGACGTCAGTGAAAAAC
EST: gi|162262188|gb|FC437099.1|FC437099
EST:     AGATGAATGTGCCATATGCCATCGTCAAAGGAAAATCACGCTTAGGACAG                         ATTGTGCATGCCAAGACCGCCACGGCTCTTTGTTTGACGTCAGTGAAAAAC
genomic: AGATGAATGTGCCATATGCCATCGTCAAAGGAAAATCACGCTTAGGACAGgtaaagtgtg ... tgttgcgcagATTGTGCATGCCAAGACCGCCACGGCTCTTTGTTTGACGTCAGTGAAAAAC
EST: gi|162273488|gb|FC449633.1|FC449633
EST:     AGATGAATGTGCCATATGCCATCGTCAAAGGAAAATCACGCTTAGGACAG                         ATTGTGCATGCCAAGACCGCCACGGCTCTTTGTTTGACGTCAGTGAAAAAC
genomic: AGATGAATGTGCCATATGCCATCGTCAAAGGAAAATCACGCTTAGGACAGgtaaagtgtg ... tgttgcgcagATTGTGCATGCCAAGACCGCCACGGCTCTTTGTTTGACGTCAGTGAAAAAC
EST: gi|208363293|gb|DC935474.1|DC935474
EST:     NNATGAATGTGCCNTATGCCATCNTCAAAGGAAAATCACGCTTANGACAN                         ATTGTGCATGCC
genomic: AGATGAATGTGCCATATGCCATCGTCAAAGGAAAATCACGCTTAGGACAGgtaaagtgtg ... tgttgcgcagATTGTGCATGCC
EST: gi|162238125|gb|FC418709.1|FC418709
EST:     AGATGAATGTGCCATATGCCATCGTCAAAGGAAAATCACGCTTAGGACAG                         ATTGTGCATGCCAAGACCGCCACGGCTCTTTGTTTGACGTCAGTGAAAAAC
genomic: AGATGAATGTGCCATATGCCATCGTCAAAGGAAAATCACGCTTAGGACAGgtaaagtgtg ... tgttgcgcagATTGTGCATGCCAAGACCGCCACGGCTCTTTGTTTGACGTCAGTGAAAAAC
EST: gi|208387273|gb|DC933024.1|DC933024
EST:     AGATGAATGTGCCATATGCCATCGTCAAAGGAAAATCACGCTTAGGACAG                         ATTGTGCATGCCAAGACCGCCACGGCTCTTTGTTTGACGTCAGTGAAAAAC
genomic: AGATGAATGTGCCATATGCCATCGTCAAAGGAAAATCACGCTTAGGACAGgtaaagtgtg ... tgttgcgcagATTGTGCATGCCAAGACCGCCACGGCTCTTTGTTTGACGTCAGTGAAAAAC
EST: gi|67720719|gb|BJ970978.1|BJ970978
EST:     AGATGAATGTGCCATATGCCATCGTCAAAGGAAAATCACGCTTAGGACAG                         ATTGTGCATGCCAAGACCGCCACGGCTCTTTGTTTGACGTCAGTGAAAAAC
genomic: AGATGAATGTGCCATATGCCATCGTCAAAGGAAAATCACGCTTAGGACAGgtaaagtgtg ... tgttgcgcagATTGTGCATGCCAAGACCGCCACGGCTCTTTGTTTGACGTCAGTGAAAAAC
EST: gi|208365421|gb|DC950888.1|DC950888
EST:     AGATGAATGTGCCATATGCCATCGTCAAAGGAAAATCACGCTTAGGACAG                         ATTGTGCATGCCAAGACCGCCACGGCTCTTTGTTTGACGTCAGTGAAAAAC
genomic: AGATGAATGTGCCATATGCCATCGTCAAAGGAAAATCACGCTTAGGACAGgtaaagtgtg ... tgttgcgcagATTGTGCATGCCAAGACCGCCACGGCTCTTTGTTTGACGTCAGTGAAAAAC
EST: gi|208386526|gb|DC956860.1|DC956860
EST:     AGATGAATGTGCCATATGCCATCGTCAAAGGAAAATCACGCTTAGGACAG                         ATTGTGCATGCCAAGACCACCACGGCTCTTTGTTTGACGTCAGTGAAAAAC
genomic: AGATGAATGTGCCATATGCCATCGTCAAAGGAAAATCACGCTTAGGACAGgtaaagtgtg ... tgttgcgcagATTGTGCATGCCAAGACCGCCACGGCTCTTTGTTTGACGTCAGTGAAAAAC
EST: gi|208362679|gb|DC947170.1|DC947170
EST:     AGATGAATGTGCCATATGCCATCGTCAAAGGAAAATCACGCTTAGGACAG                         ATTGTGCATGCCAAGACCGCCACGGCTCTTTGTTTGACGTCAGTGAAAAAC
genomic: AGATGAATGTGCCATATGCCATCGTCAAAGGAAAATCACGCTTAGGACAGgtaaagtgtg ... tgttgcgcagATTGTGCATGCCAAGACCGCCACGGCTCTTTGTTTGACGTCAGTGAAAAAC
EST: gi|162262187|gb|FC437098.1|FC437098
EST:     AGATGAATGTGCCATATGCCATCGTCAAAGGAAAATCACGCTTAGGACAG                         ATTGTGCATGCCAAGACCGCCACGGCTCTTTGTTTGACGTCAGTGAAAAAC
genomic: AGATGAATGTGCCATATGCCATCGTCAAAGGAAAATCACGCTTAGGACAGgtaaagtgtg ... tgttgcgcagATTGTGCATGCCAAGACCGCCACGGCTCTTTGTTTGACGTCAGTGAAAAAC
EST: gi|37835974|gb|BJ593986.1|BJ593986
EST:     AGATGAATGTGCCATATGCCATCGTCAAAGGAAAATCACGCTTAGGACAG                         ATTGTGCATGCCAAGACCGCCACGGCTCTTTGTTTGACGTCAGTGAAAAAC
genomic: AGATGAATGTGCCATATGCCATCGTCAAAGGAAAATCACGCTTAGGACAGgtaaagtgtg ... tgttgcgcagATTGTGCATGCCAAGACCGCCACGGCTCTTTGTTTGACGTCAGTGAAAAAC
EST: gi|67717819|gb|BJ968078.1|BJ968078
EST:     AGATGAATGTGCCATATGCCATCGTCAAAGGAAAATCACGCTTAGGACAG                         ATTGTGCATGCCAAGACCGCCACGGCTCTTTGTTTGACGTCAGTGAAAA
genomic: AGATGAATGTGCCATATGCCATCGTCAAAGGAAAATCACGCTTAGGACAGgtaaagtgtg ... tgttgcgcagATTGTGCATGCCAAGACCGCCACGGCTCTTTGTTTGACGTCAGTGAAAA
EST: gi|67719439|gb|BJ969698.1|BJ969698
EST:     AGATGAATGTGCCATATGCCATCGTCAAAGGAAAATCACGCTTAGGACAG                         ATTGTGCATGCCAAGACCGCCACGGCTCTTTGTTTGACGTCAGTGAAAAAC
genomic: AGATGAATGTGCCATATGCCATCGTCAAAGGAAAATCACGCTTAGGACAGgtaaagtgtg ... tgttgcgcagATTGTGCATGCCAAGACCGCCACGGCTCTTTGTTTGACGTCAGTGAAAAAC
EST: gi|162273489|gb|FC449634.1|FC449634
EST:     AGATGAATGTGCCATATGCCATCGTCAAAGGAAAATCACGCTTAGGACAG                         ATTGTGCATGCCAAGACCGCCACGGCTCTTTGTTTGACGTCAGTGAAAAAC
genomic: AGATGAATGTGCCATATGCCATCGTCAAAGGAAAATCACGCTTAGGACAGgtaaagtgtg ... tgttgcgcagATTGTGCATGCCAAGACCGCCACGGCTCTTTGTTTGACGTCAGTGAAAAAC
EST: gi|37824459|gb|BJ582525.1|BJ582525
EST:     AGATGAATGTGCCATATGCCATCGTCAAAGGAAAATCACGCTTAGGACAG                         ATTGTGCATGCCAAGACCGCCACGGCTCTTTGTTTGACGTCAGTGAAAAAC
genomic: AGATGAATGTGCCATATGCCATCGTCAAAGGAAAATCACGCTTAGGACAGgtaaagtgtg ... tgttgcgcagATTGTGCATGCCAAGACCGCCACGGCTCTTTGTTTGACGTCAGTGAAAAAC
EST: gi|18338854|gb|BJ170879.1|BJ170879
EST:     AGATGAATGTGCCATATGCCATCGTCAAAGGAAAATCACGCTTAGGACAG                         ATTGTGCATGCCAAGACCGCCACGGCTCTTTGTTTGACGTCAGTGAAAAAC
genomic: AGATGAATGTGCCATATGCCATCGTCAAAGGAAAATCACGCTTAGGACAGgtaaagtgtg ... tgttgcgcagATTGTGCATGCCAAGACCGCCACGGCTCTTTGTTTGACGTCAGTGAAAAAC

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: 31 (upstream exon), 35 (downstream exon)
Score: 24

TGATGTCGACCCAATCGAATTGGTAGTGTGGTTGCCCGCGCTTTGTCGCAAGATGAATGTGCCATATGCCATCGTCAAAGGAAAATCACGCTTAGGACAGgtaaagtgtg ... tgttgcgcagATTGTGCATGCCAAGACCGCCACGGCTCTTTGTTTGACGTCAGTGAAAAACGAAGACAAGCATGAGTTCTCCAAGATCATCGAGGCTGTTAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATGTCGACCCAATCGAATTGGTAGTGTGGTTGCCCGCGCTTTGTCGCAAGATGAATGTGCCATATGCCATCGTCAAAGGAAAATCACGCTTAGGACAGgtaaagtgtgtcaattatgttcgcagtaaacatttcgtatagtagtaaggatagcaatggtgctgggaagtggtgtttttgatttcgtaataccttcagcctgggttgttgccgcgtggatatagtagtaacggtaattgtgttgcgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA