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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagcatttgatgaatgtagttgctaggtgttggaatctaaatatcttgaattggttggaagtaaggaatcatatattatcttggggattctttcttgcatattttgacgtttatttacatttcaatttattgcagGAACATACCCACCCAGGTCACAAAGAACATTCAATAATGTTGGTGCGGGTGCGAGCTGCTGGTCCACACATTGTTGTAGCTGTACAACTAGAGCCG

Basic information

species Physcomitrella patens
transcript PP1S100_30V6.1
intron # 14
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|162161220|gb|FC337283.1|FC337283
EST:     CAACGAGAGTTATGAATGAGAAGAATGCCGAACTTAAAGGGCGGGGAGTTCAG                       
genomic: CAACGAGAGTTATGAATGAGAAGAATGCCGAACTTAAAGGGCGGGGAGTTCAGgtaacctaat ... ttcatgac
EST: gi|162256364|gb|FC432374.1|FC432374
EST:     CAACGAGAGTTATGAATGAGAAGAATGCCGAACTTAAAGGGCGGGGAGTTCAG                       
genomic: CAACGAGAGTTATGAATGAGAAGAATGCCGAACTTAAAGGGCGGGGAGTTCAGgtaacctaat ... ttcatgac
EST: gi|100393142|gb|BY989764.1|BY989764
EST:     ATGAGAAGAATGCCGAACTTAAAGGGCGGGGAGTTCAG                       
genomic: ATGAGAAGAATGCCGAACTTAAAGGGCGGGGAGTTCAGgtaacctaat ... ttcatgac
EST: gi|162185667|gb|FC362054.1|FC362054
EST:     CAACGAGAGTTATGAATGAGAAGAATGCCGAACTTAAAGGGCGGGGAGTTCAG                       
genomic: CAACGAGAGTTATGAATGAGAAGAATGCCGAACTTAAAGGGCGGGGAGTTCAGgtaacctaat ... ttcatgac
EST: gi|162180210|gb|FC355527.1|FC355527
EST:     CAACGAGAGTTATGAATGAGAAGAATGCCGAACTTAAAGGGCGGGGAGTTCAG                       
genomic: CAACGAGAGTTATGAATGAGAAGAATGCCGAACTTAAAGGGCGGGGAGTTCAGgtaacctaat ... ttcatgac
EST: gi|162222679|gb|FC397491.1|FC397491
EST:     CAACGAGAGTTATGAATGAGAAGAATGCCGAACTTAAAGGGCGGGGAGTTCAG                       
genomic: CAACGAGAGTTATGAATGAGAAGAATGCCGAACTTAAAGGGCGGGGAGTTCAGgtaacctaat ... ttcatgac
EST: gi|162255247|gb|FC431557.1|FC431557
EST:     CAACGAGAGTTATGAATGAGAAGAATGCCGAACTTAAAGGGCGGGGAGTTCAG                       
genomic: CAACGAGAGTTATGAATGAGAAGAATGCCGAACTTAAAGGGCGGGGAGTTCAGgtaacctaat ... ttcatgac
EST: gi|162199756|gb|FC375829.1|FC375829
EST:     CAACGAGAGTTATGAATGAGAAGAATGCCGAACTTAAAGGGCGGGGAGTTCAG                       
genomic: CAACGAGAGTTATGAATGAGAAGAATGCCGAACTTAAAGGGCGGGGAGTTCAGgtaacctaat ... ttcatgac


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggggattctttcttgcatattttgacgtttatttacatttcaatttattgcagGAACATACCCACCCAGGTCACAAAGAACATTCAATAATGTTGGTGCGGGTGCGAGCTGCTGGTCCACACATTGTTGTAGCTGTACAACTAGAGCCG
                     ttttgac  putative branch site (score: 3)
                             tttatttacatttcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagcatttgatgaatgtagttgctaggtgttggaatctaaatatcttgaattggttggaagtaaggaatcatatattatcttggggattctttcttgcatattttgacgtttatttacatttcaatttattgcagGAACATACCCACCCAGGTCACAAAGAACATTCAATAATGTTGGTGCGGGTGCGAGCTGCTGGTCCACACATTGTTGTAGCTGTACAACTAGAGCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT