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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttcgaataggtgcaattgtgcagtctttttacgcctctacctctaccaattgcatttttaatgtgaatgaaatccccacaaccacttatttcttgcagGTGGAGGATGCAACAACTTGGTCATAGGGCCAGTGGCAAGAAGGTCAGTACTGGTGAGAGCTGCAGCAGCTCCTACCAAAAAACCTGACCAAGCTGCCAA

Basic information

species Physcomitrella patens
transcript PP1S94_105V6.1
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|18368670|gb|BJ200755.1|BJ200755
EST:     GCGTTGCTCCGTAGTCCTGCAGTCTACATTTGTGGGCTCGTGTTTGCTGA                         GTGGAGGATGCAACAACTTGGTCATAGGGCCAGTGGCAAGAAGGTCAGTAC
genomic: GCGTTGCTCCGTAGTCCTGCAGTCTACATTTGTGGGCTCGTGTTTGCTGAgtaagtgtgt ... tttcttgcagGTGGAGGATGCAACAACTTGGTCATAGGGCCAGTGGCAAGAAGGTCAGTAC
EST: gi|162203478|gb|FC380394.1|FC380394
EST:     GCGTTGCTCCGTAGTCCTGCAGTCTACATTTGTGGGCTCGTGTTTGCTGA                         GTGGAGGATGCAACAGCTTGGTCATAGGGCCAGTGGCAAGAAGGTCAGTAC
genomic: GCGTTGCTCCGTAGTCCTGCAGTCTACATTTGTGGGCTCGTGTTTGCTGAgtaagtgtgt ... tttcttgcagGTGGAGGATGCAACAACTTGGTCATAGGGCCAGTGGCAAGAAGGTCAGTAC
EST: gi|162203477|gb|FC380393.1|FC380393
EST:     GCGTTGCTCCGTAGTCCTGCAGTCTACATTTGTGGGCTCGTGTTTGCTGA                         GTGGAGGATGCAACAGCTTGGTCATAGGGCCAGTGGCAAGAAGGTCAGTAC
genomic: GCGTTGCTCCGTAGTCCTGCAGTCTACATTTGTGGGCTCGTGTTTGCTGAgtaagtgtgt ... tttcttgcagGTGGAGGATGCAACAACTTGGTCATAGGGCCAGTGGCAAGAAGGTCAGTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taccaattgcatttttaatgtgaatgaaatccccacaaccacttatttcttgcagGTGGAGGATGCAACAACTTGGTCATAGGGCCAGTGGCAAGAAGGTCAGTACTGGTGAGAGCTGCAGCAGCTCCTACCAAAAAACCTGACCAAGCTGCCAA
            ttttaat  putative branch site (score: 3)
                                         cttatttctt  putative PPT
          atttttaatgtgaat  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttcgaataggtgcaattgtgcagtctttttacgcctctacctctaccaattgcatttttaatgtgaatgaaatccccacaaccacttatttcttgcagGTGGAGGATGCAACAACTTGGTCATAGGGCCAGTGGCAAGAAGGTCAGTACTGGTGAGAGCTGCAGCAGCTCCTACCAAAAAACCTGACCAAGCTGCCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC