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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatctcaagttcctccttgaaaattcgcatgaacttcgcattttagaattcgtccagtgtcgaaaatgttttgatggaaatacactgtcagtgtattaatgaagtggtggggttcctatgttagGGACGGAAAAAGATCCAAATGCTGAGGTGCTGCATTGGGTGGAATGCATGCGGCTGGCTAAATGCTGCTACGACTTGGATCCCAGTTTACAGAAGAGACC

Basic information

species Physcomitrella patens
transcript PP1S45_269V6.3
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|162268011|gb|FC444092.1|FC444092
EST:     CCGTCTGAATACGTACACCAATCAGATTCAGGTCACAGTGGCGTCCCTCC                         GGACGGAAAAAGATCCAAATGCTGAGGTGCTGCATTGGGTGGAATGCATGC
genomic: CCGTCTGAATACGTACACCAATCAGATTCAGGTCACAGTGGCGTCCCTCCgtaagatctc ... cctatgttagGGACGGAAAAAGATCCAAATGCTGAGGTGCTGCATTGGGTGGAATGCATGC
EST: gi|162268012|gb|FC444093.1|FC444093
EST:     CCGTCTGAATACGTACACCAATCAGATTCAGGTCACAGTGGCGTCCCTCC                         GGACGGAAAAAGATCCAAATGCTGAGGTGCTGCATTGGGTGGAATGCATGC
genomic: CCGTCTGAATACGTACACCAATCAGATTCAGGTCACAGTGGCGTCCCTCCgtaagatctc ... cctatgttagGGACGGAAAAAGATCCAAATGCTGAGGTGCTGCATTGGGTGGAATGCATGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgatggaaatacactgtcagtgtattaatgaagtggtggggttcctatgttagGGACGGAAAAAGATCCAAATGCTGAGGTGCTGCATTGGGTGGAATGCATGCGGCTGGCTAAATGCTGCTACGACTTGGATCCCAGTTTACAGAAGAGACC
                        tattaat  putative branch site (score: 2)
                                           ttcctat  putative PPT
                        tattaatgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagatctcaagttcctccttgaaaattcgcatgaacttcgcattttagaattcgtccagtgtcgaaaatgttttgatggaaatacactgtcagtgtattaatgaagtggtggggttcctatgttagGGACGGAAAAAGATCCAAATGCTGAGGTGCTGCATTGGGTGGAATGCATGCGGCTGGCTAAATGCTGCTACGACTTGGATCCCAGTTTACAGAAGAGACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA