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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catttggaattcgtggtttcggaggtcgaagtgctgtctcagaaatagctgacgtttgtttccgatctgaacttaaggctttctgttactgtaattgcagACTGGCATCGAGCCGCAGTTTATTCTATTCTTTGACTGCCCGGAGGACGAAATGGAGAGACGTCTTTTGGGTCGCAACCAG

Basic information

species Physcomitrella patens
transcript PP1S83_28V6.2
intron # 4
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|162264424|gb|FC440590.1|FC440590
EST:     AGTGCTTTGACGAAGTG                         ACTGGCATCGAGCCGCAGTTTATTCTATTCTTTGACTGCCCGGAGGACGAA
genomic: AGTGCTTTGACGAAGTGgtaagcagag ... gtaattgcagACTGGCATCGAGCCGCAGTTTATTCTATTCTTTGACTGCCCGGAGGACGAA
EST: gi|162221997|gb|FC398564.1|FC398564
EST:     TTGATGGGTTCCCCCGCAACTTAGATAACCGCAAGTGCTTTGACGAAGTG                         ACTGGCATCGAGCCGCAGTTTATTCTATTCTTTGACTGCCCGGAGGACGAA
genomic: TTGATGGGTTCCCCCGCAACTTAGATAACCGCAAGTGCTTTGACGAAGTGgtaagcagag ... gtaattgcagACTGGCATCGAGCCGCAGTTTATTCTATTCTTTGACTGCCCGGAGGACGAA
EST: gi|18373209|gb|BJ204811.1|BJ204811
EST:     TGATGGGTTCCCCCGCAACTTAGATAACCCGCAAGTGCTTTGACGAAGTG                         ACTGGCATCGAGC
genomic: TGATGGGTTCCCCCGCAACTTAGATAACC-GCAAGTGCTTTGACGAAGTGgtaagcagag ... gtaattgcagACTGGCATCGAGC
EST: gi|18338935|gb|BJ170961.1|BJ170961
EST:     TTGATGGGTTCCCCCGCAACTTAGATAACCGCAAGTGCTTTGACGAAGTG                         ACTGGCATCGAGCCGCAGTTTATTCTATTCTTTGACTGCCCGGAGGACGAA
genomic: TTGATGGGTTCCCCCGCAACTTAGATAACCGCAAGTGCTTTGACGAAGTGgtaagcagag ... gtaattgcagACTGGCATCGAGCCGCAGTTTATTCTATTCTTTGACTGCCCGGAGGACGAA
EST: gi|162173421|gb|FC349800.1|FC349800
EST:     TTGATGGGTTCCCCCGCAACTTAGATAACCGCAAGTGCTTTGACGAAGTG                         ACTGGCATCGAGCCGCAGTTTATTCTATTCTTTGACTGCCCGGAGGACGAA
genomic: TTGATGGGTTCCCCCGCAACTTAGATAACCGCAAGTGCTTTGACGAAGTGgtaagcagag ... gtaattgcagACTGGCATCGAGCCGCAGTTTATTCTATTCTTTGACTGCCCGGAGGACGAA
EST: gi|37843731|gb|BJ601739.1|BJ601739
EST:     TTGATGGGTTCCCCCGCAACTTAGATAACCGCAAGTGCTTTGACGAAGTG                         ACTGGCATCGAGCCGCAGTTTATTCTATTCTTTGACTGCCCGGAGGACGAA
genomic: TTGATGGGTTCCCCCGCAACTTAGATAACCGCAAGTGCTTTGACGAAGTGgtaagcagag ... gtaattgcagACTGGCATCGAGCCGCAGTTTATTCTATTCTTTGACTGCCCGGAGGACGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagctgacgtttgtttccgatctgaacttaaggctttctgttactgtaattgcagACTGGCATCGAGCCGCAGTTTATTCTATTCTTTGACTGCCCGGAGGACGAAATGGAGAGACGTCTTTTGGGTCGCAACCAG
 agctgac  putative branch site (score: 3)
         tttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catttggaattcgtggtttcggaggtcgaagtgctgtctcagaaatagctgacgtttgtttccgatctgaacttaaggctttctgttactgtaattgcagACTGGCATCGAGCCGCAGTTTATTCTATTCTTTGACTGCCCGGAGGACGAAATGGAGAGACGTCTTTTGGGTCGCAACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA