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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atacagtatcccttgggctcctgtatatgatatgggcgcatatcaatgcttttatagtgaatgatgtgtgtcatttagtcagtaacatgtatttttgcagGTTCAAGACAATCTACGAGGGCCATTTCTCCCCGAAGCTGATGATATTGATAACTCTTGGTTTTCCCTCAGTCTTGGCGGAGGAGAAAACTTGGCAGAAC

Basic information

species Physcomitrella patens
transcript PP1S94_39V6.1
intron # 15
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|162263011|gb|FC439326.1|FC439326
EST:     ATGCTTCGCCTCTGCAAAATTTTCTGCCATCTCAACCAGCACGAGCTGAG                         GTTCAAGACAATCTACGAGGGCCATTTCTCCCCGAAGCTGATGATATTGAT
genomic: ATGCTTCGCCTCTGCAAAATTTTCTGCCATCTCAACCAGCACGAGCTGAGgtattgttgt ... atttttgcagGTTCAAGACAATCTACGAGGGCCATTTCTCCCCGAAGCTGATGATATTGAT
EST: gi|162174140|gb|FC350343.1|FC350343
EST:     ATGCTTCGCCTCTGCAAA-TTTTCTGCCATCTCAAC-AGCACGAGCTGAG                         GTTCAAGAACA-TCTACGAGGGCCATTTCTC
genomic: ATGCTTCGCCTCTGCAAAATTTTCTGCCATCTCAACCAGCACGAGCTGAGgtattgttgt ... atttttgcagGTTCAAGA-CAATCTACGAGGGCCATTTCTC
EST: gi|162185258|gb|FC361768.1|FC361768
EST:     TGCTTCGCCTCTGCAAAATTTTCTGCCATCTNCA-CCAGCACGAGCTGAG                         GTTCAAGACAATCTACGAAGGCCATTTCTCTCCGAAGCTGATGATATTGAT
genomic: TGCTTCGCCTCTGCAAAATTTTCTGCCATCT-CAACCAGCACGAGCTGAGgtattgttgt ... atttttgcagGTTCAAGACAATCTACGAGGGCCATTTCTCCCCGAAGCTGATGATATTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgcttttatagtgaatgatgtgtgtcatttagtcagtaacatgtatttttgcagGTTCAAGACAATCTACGAGGGCCATTTCTCCCCGAAGCTGATGATATTGATAACTCTTGGTTTTCCCTCAGTCTTGGCGGAGGAGAAAACTTGGCAGAAC
                                  cagtaac  putative branch site (score: 2)
                                            tattttt  putative PPT
                                     taacatgtattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atacagtatcccttgggctcctgtatatgatatgggcgcatatcaatgcttttatagtgaatgatgtgtgtcatttagtcagtaacatgtatttttgcagGTTCAAGACAATCTACGAGGGCCATTTCTCCCCGAAGCTGATGATATTGATAACTCTTGGTTTTCCCTCAGTCTTGGCGGAGGAGAAAACTTGGCAGAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA