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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgaattctccaatacgcagaacaacttaaaatgtttgaatatatcacctgataacaggttatgtatctaaaggattttctaatttgggttgcatggcagCTACGTGGTTGATGCTGCAGACAAAGACAACGTCGCCATCTCCAGGAATGAGCTGCACGATTTACTGAATAAGCCTTCACTTCATGGTATTCCATTGCTT

Basic information

species Physcomitrella patens
transcript PP1S6_409V6.3
intron # 5
splice site 3'
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|67699163|gb|BJ959396.1|BJ959396
EST:     CGCCTTCGTAGTATGTGGGAGCGCTACTGCCGTGGAGTGTCGGCCATTGT                         CTACGTGGTTGATGCTGCAGACAAAGACAACGTCGCCATCTCCAGGAATGA
genomic: CGCTTTCGTAGTATGTGGGAGCGCTACTGCCGTGGAGTGTCGGCCATTGTgtaagtgcct ... tgcatggcagCTACGTGGTTGATGCTGCAGACAAAGACAACGTCGCCATCTCCAGGAATGA
EST: gi|208364105|gb|DC950397.1|DC950397
EST:     CGCTTTCGTAGTATGTGGGAGCGCTACTGCCGTGGAGTGTCGGCCATTGT                         CTACGTGGTTGATGCTGCAGACAAAGACAACGTCGCCATCTCCAGGAATGA
genomic: CGCTTTCGTAGTATGTGGGAGCGCTACTGCCGTGGAGTGTCGGCCATTGTgtaagtgcct ... tgcatggcagCTACGTGGTTGATGCTGCAGACAAAGACAACGTCGCCATCTCCAGGAATGA
EST: gi|208382259|gb|DC919247.1|DC919247
EST:     CGCTTTCGTAGTATGTGGGAGCGCTACTGCCGTGGAGTGTCGGCCATTGT                         CTACGTGGTTGATGCTGCAGGCAAAGACAACGTCGCCATCTCCAGGAATGA
genomic: CGCTTTCGTAGTATGTGGGAGCGCTACTGCCGTGGAGTGTCGGCCATTGTgtaagtgcct ... tgcatggcagCTACGTGGTTGATGCTGCAGACAAAGACAACGTCGCCATCTCCAGGAATGA
EST: gi|208368100|gb|DC947660.1|DC947660
EST:     TTCGTAGTATGTGGGAGCGCTACTGCCGTGGAGTGTCGGCCATTGT                         NTACGTGGTTGATGCTGCAGACAAAGACAACGTCGCCATCTCCAGGAATGA
genomic: TTCGTAGTATGTGGGAGCGCTACTGCCGTGGAGTGTCGGCCATTGTgtaagtgcct ... tgcatggcagCTACGTGGTTGATGCTGCAGACAAAGACAACGTCGCCATCTCCAGGAATGA
EST: gi|208374248|gb|DC945294.1|DC945294
EST:     CGCTTTCGTAGTATGTGGGAGCGCTACTGCCGTGGAGTGTCGGCCATTGT                         CTACGTGGTTGATGCTGCAGACAAAGACAACGTCGCCATCTCCAGGAATGA
genomic: CGCTTTCGTAGTATGTGGGAGCGCTACTGCCGTGGAGTGTCGGCCATTGTgtaagtgcct ... tgcatggcagCTACGTGGTTGATGCTGCAGACAAAGACAACGTCGCCATCTCCAGGAATGA
EST: gi|67577659|gb|BJ949826.1|BJ949826
EST:     CGCTTTCGTAGTATGTGGGAGCGCTACTGCCGTGGAGTGTCGGCCATTGT                         CTACGTGGTTGATGCTGCAGACAAAGACAACGTCGCCAT
genomic: CGCTTTCGTAGTATGTGGGAGCGCTACTGCCGTGGAGTGTCGGCCATTGTgtaagtgcct ... tgcatggcagCTACGTGGTTGATGCTGCAGACAAAGACAACGTCGCCAT
EST: gi|162203520|gb|FC380436.1|FC380436
EST:     CGCTTTCGTAGTATGTGGGAGCGCTACTGCCGTGGAGTGTCGGCCATNGT                         CTACGTGGTTGATGCTGCAGACAAAGACAACGTCGCCATCTCCAGGAATGA
genomic: CGCTTTCGTAGTATGTGGGAGCGCTACTGCCGTGGAGTGTCGGCCATTGTgtaagtgcct ... tgcatggcagCTACGTGGTTGATGCTGCAGACAAAGACAACGTCGCCATCTCCAGGAATGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacctgataacaggttatgtatctaaaggattttctaatttgggttgcatggcagCTACGTGGTTGATGCTGCAGACAAAGACAACGTCGCCATCTCCAGGAATGAGCTGCACGATTTACTGAATAAGCCTTCACTTCATGGTATTCCATTGCTT
                                ttctaat  putative branch site (score: 2)
                             attttctaattt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgaattctccaatacgcagaacaacttaaaatgtttgaatatatcacctgataacaggttatgtatctaaaggattttctaatttgggttgcatggcagCTACGTGGTTGATGCTGCAGACAAAGACAACGTCGCCATCTCCAGGAATGAGCTGCACGATTTACTGAATAAGCCTTCACTTCATGGTATTCCATTGCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC