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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttttgaatacggtttgatatatcactcgcttaccctaccgcattttggtttgttgcattttgtggcattttaagcgagtcctgtgctcttgcaacgcagGTTGACAAGCAAAAGGTCGGTGTTCTCGTCGGAACTGGCATGGGTGGGCTCACTGTGTTCTCTGATGGAGTTCAAGCTTTGGTAGAGAAGGGTCACAAGA

Basic information

species Physcomitrella patens
transcript PP1S52_45V6.1
intron # 2
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|100396986|gb|BY953927.1|BY953927
EST:     GCAAACGAGCGCTTGAAGATGCTGGGCTCGGTGGGGAAAACCTGAACCAG                         GTTGACAAGCAAAAGGTCGGTGTTCTCGTCGGAACTGGCATGGGTGGGCTC
genomic: GCAAACGAGCGCTTGAAGATGCTGGGCTCGGTGGGGAAAACCTGAACCAGgtgaatttca ... tgcaacgcagGTTGACAAGCAAAAGGTCGGTGTTCTCGTCGGAACTGGCATGGGTGGGCTC
EST: gi|208390334|gb|DC929282.1|DC929282
EST:     GCAAACGAGCGCTTGAAGATGCTGGGCTCGGTGGGGAAAACCTGAACCAG                         GTTGACAAGCAAAAGGTCGGTGTTCTCGTCGGAACTGGCATGGGTGGGCTC
genomic: GCAAACGAGCGCTTGAAGATGCTGGGCTCGGTGGGGAAAACCTGAACCAGgtgaatttca ... tgcaacgcagGTTGACAAGCAAAAGGTCGGTGTTCTCGTCGGAACTGGCATGGGTGGGCTC
EST: gi|162231218|gb|FC407005.1|FC407005
EST:     GCAAACGAGCGCTTGAAGATGCTGGGCTCGGTGGGGAAAACCTGAACCAG                         GTTGACAAGCAAAAGGTCGGTGTTCTCGTCGGAACTGGCATGGGTGGGCTC
genomic: GCAAACGAGCGCTTGAAGATGCTGGGCTCGGTGGGGAAAACCTGAACCAGgtgaatttca ... tgcaacgcagGTTGACAAGCAAAAGGTCGGTGTTCTCGTCGGAACTGGCATGGGTGGGCTC
EST: gi|208375556|gb|DC940526.1|DC940526
EST:     GCAAACGAGCGCTTGAAGATGCTGGGCTCGGTGGGGAAAACCTGAACCAG                         GTTGACAAGCAAAAGGTCGGTGTTCTCGTCGGAACTGGCATGGGTGGGCTC
genomic: GCAAACGAGCGCTTGAAGATGCTGGGCTCGGTGGGGAAAACCTGAACCAGgtgaatttca ... tgcaacgcagGTTGACAAGCAAAAGGTCGGTGTTCTCGTCGGAACTGGCATGGGTGGGCTC
EST: gi|208372128|gb|DC940310.1|DC940310
EST:     GCAAACGAGCGCTTGAAGATGCTGGGCTCGGTGGGGAAAACCTGAACCAG                         GTTGACAAGCAAAAGGTCGGTGTTCTCGTCGGAACTGGCATGGGTGGGCTC
genomic: GCAAACGAGCGCTTGAAGATGCTGGGCTCGGTGGGGAAAACCTGAACCAGgtgaatttca ... tgcaacgcagGTTGACAAGCAAAAGGTCGGTGTTCTCGTCGGAACTGGCATGGGTGGGCTC
EST: gi|67718918|gb|BJ969177.1|BJ969177
EST:     GCAAACGAGCGCTTGAAGATGCTGGGCTCGGTGGGGAAAACCTGAACCAG                         GTTGACAAGCAAAAGGTCGGTGTTCTCGTCGGAACTGGCATGGGTGGGCTC
genomic: GCAAACGAGCGCTTGAAGATGCTGGGCTCGGTGGGGAAAACCTGAACCAGgtgaatttca ... tgcaacgcagGTTGACAAGCAAAAGGTCGGTGTTCTCGTCGGAACTGGCATGGGTGGGCTC
EST: gi|208371639|gb|DC932468.1|DC932468
EST:     GCAAACGAGCGCTTGAAGATGCTGGGCTCGGTGGGGAAAACCTGAACCAG                         GTTGACAAGCAAAANGTCGGTGTTCTCGTCGGAACTGGCATGGGTGGGCTC
genomic: GCAAACGAGCGCTTGAAGATGCTGGGCTCGGTGGGGAAAACCTGAACCAGgtgaatttca ... tgcaacgcagGTTGACAAGCAAAAGGTCGGTGTTCTCGTCGGAACTGGCATGGGTGGGCTC
EST: gi|100394380|gb|BY972040.1|BY972040
EST:     CAAACGAGCGCTTGAAGATGCTGGGGCTCGGTGGG-AAAACCTGAACCAG                         GTTGACAAGCAAAAGGTCGGTGTTCTCGTCGGAACTGGCATGGGTGGGCTC
genomic: CAAACGAGCGCTTGAAGATGCTGGG-CTCGGTGGGGAAAACCTGAACCAGgtgaatttca ... tgcaacgcagGTTGACAAGCAAAAGGTCGGTGTTCTCGTCGGAACTGGCATGGGTGGGCTC
EST: gi|208376991|gb|DC911059.1|DC911059
EST:     GCAAACGAGCGCTTGAAGATGCTGGGCTCGGTGGGGAAAACCTGAACCAG                         GTTGACAAGCAAAAGGTCGGTGTTCTCGTCGGAACTGGCATGGGTGGGCTC
genomic: GCAAACGAGCGCTTGAAGATGCTGGGCTCGGTGGGGAAAACCTGAACCAGgtgaatttca ... tgcaacgcagGTTGACAAGCAAAAGGTCGGTGTTCTCGTCGGAACTGGCATGGGTGGGCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggtttgttgcattttgtggcattttaagcgagtcctgtgctcttgcaacgcagGTTGACAAGCAAAAGGTCGGTGTTCTCGTCGGAACTGGCATGGGTGGGCTCACTGTGTTCTCTGATGGAGTTCAAGCTTTGGTAGAGAAGGGTCACAAGA
                                       tgctctt  CT-rich tract
                      attttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttttgaatacggtttgatatatcactcgcttaccctaccgcattttggtttgttgcattttgtggcattttaagcgagtcctgtgctcttgcaacgcagGTTGACAAGCAAAAGGTCGGTGTTCTCGTCGGAACTGGCATGGGTGGGCTCACTGTGTTCTCTGATGGAGTTCAAGCTTTGGTAGAGAAGGGTCACAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - -tgttgca