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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agggtttaatctcaattaggaatagcatgtttactactactgttagctgacatattcgctcttttaatatttatttatttatatcgctgtccttttgcagACTGGTGGTTATAGCGAAGATATGATTCCCACC

Basic information

species Physcomitrella patens
transcript PP1S6_409V6.3
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|208364105|gb|DC950397.1|DC950397
EST:     ATGTTATTGCG                         ACTGGTGGTTATAGCGAAGATATGATTCCCACC
genomic: ATGTTATTGCGgtatgtatct ... ccttttgcagACTGGTGGTTATAGCGAAGATATGATTCCCACC
EST: gi|208382259|gb|DC919247.1|DC919247
EST:     TGATANGTCTGCAGAACGCTGGGAAAACATCGCTTGTCAATGTTATTGCG                         ACTGGTGGTTATAGCGAAGATATGATTCCCACC
genomic: TGATAGGTCTGCAGAACGCTGGGAAAACATCGCTTGTCAATGTTATTGCGgtatgtatct ... ccttttgcagACTGGTGGTTATAGCGAAGATATGATTCCCACC
EST: gi|208374248|gb|DC945294.1|DC945294
EST:     TGATAGGTNTGCAGAACGCTGGGAAAACATCGCTTGTCAATGTTATTGCG                         ACTGGTGGTTATAGCGAAGATATGATTCCCACC
genomic: TGATAGGTCTGCAGAACGCTGGGAAAACATCGCTTGTCAATGTTATTGCGgtatgtatct ... ccttttgcagACTGGTGGTTATAGCGAAGATATGATTCCCACC
EST: gi|67577659|gb|BJ949826.1|BJ949826
EST:     TGATAGGTCTGCAGAACGCTGGGAAAACATCGCTTGTCAATGTTATTGCG                         ACTGGTGGTTATAGCGAAGATATGATTCCCACC
genomic: TGATAGGTCTGCAGAACGCTGGGAAAACATCGCTTGTCAATGTTATTGCGgtatgtatct ... ccttttgcagACTGGTGGTTATAGCGAAGATATGATTCCCACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctgacatattcgctcttttaatatttatttatttatatcgctgtccttttgcagACTGGTGGTTATAGCGAAGATATGATTCCCACC
                ttttaat  putative branch site (score: 3)
                                         ctgtcctttt  putative PPT
      atattcgctcttttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agggtttaatctcaattaggaatagcatgtttactactactgttagctgacatattcgctcttttaatatttatttatttatatcgctgtccttttgcagACTGGTGGTTATAGCGAAGATATGATTCCCACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA