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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagcctggcctacccttgctggagacactctttgaccccaaagttcatagaagcattcggactctttgaacaattaatacttgtgtgttgaggtctgcagGAGCTGGGACTATAGGCGTAAATTATGGCGTGCTAGGAAATAATCTGCCGACGCCTGCTGCTACCACTAAACTCATTCTGTCCACAACTATTCGTAATGT

Basic information

species Physcomitrella patens
transcript PP1S6_62V6.2
intron # 1
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|18360682|gb|BJ192745.1|BJ192745
EST:     TCACTTCATATCGTTTTTGTCGTGTTTGGCGGCATGTATTCCTCTCTCAG                         GAGCTGGGACTATAGGCGTAAATTATGGCGTGCT
genomic: TCACTTCATATCGTTTTTGTCGTGTTTGGCGGCATGTATTCCTCTCTCAGgtatgtgtta ... aggtctgcagGAGCTGGGACTATAGGCGTAAATTATGGCGTGCT
EST: gi|18341889|gb|BJ173924.1|BJ173924
EST:     TCACTTCATATCGTTTTTGTCGTGTTTGGCGGCATGTATTCCTCTCTCAG                         GAGCTGGGACTATAGGCGTAAATTATGGCGTGCTAGGAAATAATCTGCCGA
genomic: TCACTTCATATCGTTTTTGTCGTGTTTGGCGGCATGTATTCCTCTCTCAGgtatgtgtta ... aggtctgcagGAGCTGGGACTATAGGCGTAAATTATGGCGTGCTAGGAAATAATCTGCCGA
EST: gi|100386890|gb|BY988159.1|BY988159
EST:     TCACTTCATATCGTTTTTGTCGTGTTTGGCGGCATGTATTCCTCTCTCAG                         GAGCTGGGACTATAGGCGTAAATTATGGCGTGCTAGGAAATAATCTGCCGA
genomic: TCACTTCATATCGTTTTTGTCGTGTTTGGCGGCATGTATTCCTCTCTCAGgtatgtgtta ... aggtctgcagGAGCTGGGACTATAGGCGTAAATTATGGCGTGCTAGGAAATAATCTGCCGA
EST: gi|18355494|gb|BJ187553.1|BJ187553
EST:     TCACTTCATATCGTTTTTGTCGTGTTTGGCGGCATGTATTCCTCTCTCAG                         GAGCTGGGACTATAGGCGTAAATTATGGCGTGCTAGGAAATAATCTGCCGA
genomic: TCACTTCATATCGTTTTTGTCGTGTTTGGCGGCATGTATTCCTCTCTCAGgtatgtgtta ... aggtctgcagGAGCTGGGACTATAGGCGTAAATTATGGCGTGCTAGGAAATAATCTGCCGA
EST: gi|208380392|gb|DC907717.1|DC907717
EST:     TCACTTCATATCGTTTTTGTCGTGTTTGGCGGCATGTATTCCTCTCTCAG                         GAGCTGGGACTATAGGCGTAAATTATGGCGTGCTAGGAAATAATCTGCCGA
genomic: TCACTTCATATCGTTTTTGTCGTGTTTGGCGGCATGTATTCCTCTCTCAGgtatgtgtta ... aggtctgcagGAGCTGGGACTATAGGCGTAAATTATGGCGTGCTAGGAAATAATCTGCCGA
EST: gi|18347191|gb|BJ179237.1|BJ179237
EST:     TCACTTCATATCGTTTTTGTCGTGTTTGGCGGCATGTATTCCTCTCTCAG                         GAGCTGGGACTATAGGCGTAAATTATGGCGTGCTAGGAAATAATCTGCCGA
genomic: TCACTTCATATCGTTTTTGTCGTGTTTGGCGGCATGTATTCCTCTCTCAGgtatgtgtta ... aggtctgcagGAGCTGGGACTATAGGCGTAAATTATGGCGTGCTAGGAAATAATCTGCCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catagaagcattcggactctttgaacaattaatacttgtgtgttgaggtctgcagGAGCTGGGACTATAGGCGTAAATTATGGCGTGCTAGGAAATAATCTGCCGACGCCTGCTGCTACCACTAAACTCATTCTGTCCACAACTATTCGTAATGT
                          aattaat  putative branch site (score: 3)
                   tttgaacaattaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagcctggcctacccttgctggagacactctttgaccccaaagttcatagaagcattcggactctttgaacaattaatacttgtgtgttgaggtctgcagGAGCTGGGACTATAGGCGTAAATTATGGCGTGCTAGGAAATAATCTGCCGACGCCTGCTGCTACCACTAAACTCATTCTGTCCACAACTATTCGTAATGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT