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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttcttgaagttcattctgtagcatgttttgaggctcttttctttcttttttctttttcttgcatctaggatatgctaattatgctgttactgttctcagGATCAGCATCGGGAAAAGTGGGCGGCAAGCAACTTGCGTTGGTGCCTGCTCGAGTCCAACCTCCAGCTGCAGCTCCAATTGTTGGAGCCGCTCCTGCAGT

Basic information

species Physcomitrella patens
transcript PP1S169_73V6.2
intron # 3
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|18350280|gb|BJ182331.1|BJ182331
EST:     CCTTCAAAGCTTGCGAGTCCCTGCGCCAGAACAACCTGGTACAAATGCAG                         GATCAGCATCGGGAAAAGTGGGCGGCAAGCAACTTGCGTTGGTGCCTGCTC
genomic: CCTTCAAAGCTTGCGAGTCCCTGCGCCAGAACAACCTGGTACAAATGCAGgtattttcta ... ctgttctcagGATCAGCATCGGGAAAAGTGGGCGGCAAGCAACTTGCGTTGGTGCCTGCTC
EST: gi|100379420|gb|BY986628.1|BY986628
EST:     CCTTCAAAGCTTGCGAGTCCCTGCGCCAGAACAACCTGGTACAAATGCAG                         GATCAGCATCGGGAAAAGTGGGCGGCAAGCAACTTGCGTTGGTGCCTGCTC
genomic: CCTTCAAAGCTTGCGAGTCCCTGCGCCAGAACAACCTGGTACAAATGCAGgtattttcta ... ctgttctcagGATCAGCATCGGGAAAAGTGGGCGGCAAGCAACTTGCGTTGGTGCCTGCTC
EST: gi|18348253|gb|BJ180300.1|BJ180300
EST:     CCTTCAAAGCTTGCGAGTCCCTGCGCCAGAACAACCTGGTACAAATGCAG                         GATCAGCATCGGGAAAAGTGGGCGGCAAGCAACTTGCGTTGGTGCCTGCTC
genomic: CCTTCAAAGCTTGCGAGTCCCTGCGCCAGAACAACCTGGTACAAATGCAGgtattttcta ... ctgttctcagGATCAGCATCGGGAAAAGTGGGCGGCAAGCAACTTGCGTTGGTGCCTGCTC
EST: gi|162266559|gb|FC442790.1|FC442790
EST:     CCTTCAAAGCTTGCGAGTCCCTGCGCCAGAACAACCTGGTACAAATGCAG                         GATCAGCATCGGGAAAAGTGGGCGGCAAGCAACTTGCGTTGGTGCCTGCTC
genomic: CCTTCAAAGCTTGCGAGTCCCTGCGCCAGAACAACCTGGTACAAATGCAGgtattttcta ... ctgttctcagGATCAGCATCGGGAAAAGTGGGCGGCAAGCAACTTGCGTTGGTGCCTGCTC
EST: gi|162160839|gb|FC337661.1|FC337661
EST:     CCTTCAAAGCTTGCGAGTCCCTGCGCCAGAACAACCTGGTACAAATGCAG                         GATCAGCATCGGGAAAAGTGGGCGGCAAGCAACTTGCGTTGGTGCCTGCTC
genomic: CCTTCAAAGCTTGCGAGTCCCTGCGCCAGAACAACCTGGTACAAATGCAGgtattttcta ... ctgttctcagGATCAGCATCGGGAAAAGTGGGCGGCAAGCAACTTGCGTTGGTGCCTGCTC
EST: gi|162183681|gb|FC359909.1|FC359909
EST:     CCTTCAAAGCTTGCGAGTCCCTGCGCCAGAACAACCTGGTACAAATGCAG                         GATCAGCATCGGGAAAAGTGGGCGGCAAGCAACTTGCGTTGGTGCCTGCTC
genomic: CCTTCAAAGCTTGCGAGTCCCTGCGCCAGAACAACCTGGTACAAATGCAGgtattttcta ... ctgttctcagGATCAGCATCGGGAAAAGTGGGCGGCAAGCAACTTGCGTTGGTGCCTGCTC
EST: gi|18343267|gb|BJ175305.1|BJ175305
EST:     CCTTCAAAGCTTGCGAGTCCCTGCGCCAGAACAACCTGGTACAAATGCAG                         GATCAGCATCGGGAAAAGTGGGCGGCAAGCAACTTGCGTTGGTGCCTGCTC
genomic: CCTTCAAAGCTTGCGAGTCCCTGCGCCAGAACAACCTGGTACAAATGCAGgtattttcta ... ctgttctcagGATCAGCATCGGGAAAAGTGGGCGGCAAGCAACTTGCGTTGGTGCCTGCTC
EST: gi|18349577|gb|BJ181627.1|BJ181627
EST:     CCTTCAAAGCTTGCGAGTCCCTGCGCCAGAACAACCTGGTACAAATGCAG                         GATCAGCATCGGGAAAAGTGGGCGGCAAGCAACTTGCGTTGGTGCCTGCTC
genomic: CCTTCAAAGCTTGCGAGTCCCTGCGCCAGAACAACCTGGTACAAATGCAGgtattttcta ... ctgttctcagGATCAGCATCGGGAAAAGTGGGCGGCAAGCAACTTGCGTTGGTGCCTGCTC
EST: gi|18350303|gb|BJ182354.1|BJ182354
EST:     CCTTCAAAGCTTGCGAGTCCCTGCGCCAGAACAACCTGGTACAAATGCAG                         GATCAGCATCGGGAAAAGTGGGCGGCAAGCAACTTGCGTTGGTGCCTGCTC
genomic: CCTTCAAAGCTTGCGAGTCCCTGCGCCAGAACAACCTGGTACAAATGCAGgtattttcta ... ctgttctcagGATCAGCATCGGGAAAAGTGGGCGGCAAGCAACTTGCGTTGGTGCCTGCTC
EST: gi|18344551|gb|BJ176592.1|BJ176592
EST:     CCTTCAAAGCTTGCGAGTCCCTGCGCCAGAACAACCTGGTACAAATGCAG                         GATCAGCATCGGGAAAAGTGGGCGGCAAGCAACTTGCGTTGGTGCCTGCTC
genomic: CCTTCAAAGCTTGCGAGTCCCTGCGCCAGAACAACCTGGTACAAATGCAGgtattttcta ... ctgttctcagGATCAGCATCGGGAAAAGTGGGCGGCAAGCAACTTGCGTTGGTGCCTGCTC
EST: gi|18344205|gb|BJ176244.1|BJ176244
EST:     CCTTCAAAGCTTGCGAGTCCCTGCGCCAGAACAACCTGGTACAAATGCAG                         GATCAGCATCGGGAAAAGTGGGCGGCAAGCAACTTGCGTTGGTGCCTGCTC
genomic: CCTTCAAAGCTTGCGAGTCCCTGCGCCAGAACAACCTGGTACAAATGCAGgtattttcta ... ctgttctcagGATCAGCATCGGGAAAAGTGGGCGGCAAGCAACTTGCGTTGGTGCCTGCTC
EST: gi|18364666|gb|BJ196739.1|BJ196739
EST:     CCTTCAAAGCTTGCGAGTCCCTGCGCCAGAACAACCTGGTACAAATGCAG                         GATCAGCATCGGGAAAAGTGGGCGGCAAGCAACTTGCGTTGGTGCCTGCTC
genomic: CCTTCAAAGCTTGCGAGTCCCTGCGCCAGAACAACCTGGTACAAATGCAGgtattttcta ... ctgttctcagGATCAGCATCGGGAAAAGTGGGCGGCAAGCAACTTGCGTTGGTGCCTGCTC
EST: gi|18328479|gb|BJ160484.1|BJ160484
EST:     CCTTCAAAGCTTGCGAGTCCCTGCGCCAGAACAACCTGGTACAAATGCAG                         GATCAGCATCGGGAAAAGTGGGCGGCAAGCAACTTGCGTTGGTGCCTGCTC
genomic: CCTTCAAAGCTTGCGAGTCCCTGCGCCAGAACAACCTGGTACAAATGCAGgtattttcta ... ctgttctcagGATCAGCATCGGGAAAAGTGGGCGGCAAGCAACTTGCGTTGGTGCCTGCTC
EST: gi|18352311|gb|BJ184365.1|BJ184365
EST:     CCTTCAAAGCTTGCGAGTCCCTGCGCCAGAACAACCTGGTACAAATGCAG                         GATCAGCATCGGGAAAAGTGGGCGGCAAGCAACTTGCGTTGGTGCCTGCTC
genomic: CCTTCAAAGCTTGCGAGTCCCTGCGCCAGAACAACCTGGTACAAATGCAGgtattttcta ... ctgttctcagGATCAGCATCGGGAAAAGTGGGCGGCAAGCAACTTGCGTTGGTGCCTGCTC
EST: gi|100422342|gb|BY976327.1|BY976327
EST:     CCTTCAAAGCTTGCGAGTCCCTGCGCCAGAACAACCTGGTACAAATGCAG                         GATCAGCATTCGGGAAAAGTGTGCGGCAAGCAACTTTGCGTTGGTGCCTGC
genomic: CCTTCAAAGCTTGCGAGTCCCTGCGCCAGAACAACCTGGTACAAATGCAGgtattttcta ... ctgttctcagGATCAGCAT-CGGGAAAAGTGGGCGGCAAGCAACTT-GCGTTGGTGCCTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttttctttttcttgcatctaggatatgctaattatgctgttactgttctcagGATCAGCATCGGGAAAAGTGGGCGGCAAGCAACTTGCGTTGGTGCCTGCTCGAGTCCAACCTCCAGCTGCAGCTCCAATTGTTGGAGCCGCTCCTGCAGT
                            tgctaat  putative branch site (score: 2)
                                             ctgttctc  putative PPT
                               taattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcttgaagttcattctgtagcatgttttgaggctcttttctttcttttttctttttcttgcatctaggatatgctaattatgctgttactgttctcagGATCAGCATCGGGAAAAGTGGGCGGCAAGCAACTTGCGTTGGTGCCTGCTCGAGTCCAACCTCCAGCTGCAGCTCCAATTGTTGGAGCCGCTCCTGCAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG