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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taatggacttcctgtaatcaagtcttgtttcttgtcgaatcgcaatcattctcacactaactccaaacacttatatcatggcctggggtaatgagtgcagGTTACGGTAACGGCCGTGAGTCTGGATACGAATGTGGAGATTAATACGCGTGGCCAAGTCGAGGATTGGGTAGCCAGTGTAGTTCCAGTCTCCCCTGCTT

Basic information

species Physcomitrella patens
transcript PP1S425_16V6.2
intron # 9
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|37850380|gb|BJ608388.1|BJ608388
EST:     TTGGAGAGGTTGCCCCTGATCATGACTTTGGAGCGTTGGAACTAGGCTAT                         T
genomic: TTGGAGAGGTTGCCCCTGATCATGACTTTGGAGCGTTGGAACTAGGCTATgtaagtagtc ... atgagtgcag-
EST: gi|37850380|gb|BJ608388.1|BJ608388
EST:     TTGGAGAGGTTGCCCCTGATCATGACTTTGGAGCGTTGGAACTAGGCTAT                         T
genomic: TTGGAGAGGTTGCCCCTGATCATGACTTTGGAGCGTTGGAACTAGGCTATgtaagtagtc ... atgagtgcag-
EST: gi|162186159|gb|FC361363.1|FC361363
EST:     TTGGAGAGGTTGCCCCTGATCATGACTTTGGAGCGTTGGAACTAGGCTAT                         GTTACGGTAACGGCCGTGAGTCTGGATACGAATGTGGAGATTAATACGCGT
genomic: TTGGAGAGGTTGCCCCTGATCATGACTTTGGAGCGTTGGAACTAGGCTATgtaagtagtc ... atgagtgcagGTTACGGTAACGGCCGTGAGTCTGGATACGAATGTGGAGATTAATACGCGT
EST: gi|162265881|gb|FC442884.1|FC442884
EST:     TTGGAGAGGTTGCCCCTGATCATGACTTTGGAGCGTTGGAACTAGGCTAT                         GTTACGGTAACGGCCGTGAGTCTGGATACGAATGTGGAGATTAATACGCGT
genomic: TTGGAGAGGTTGCCCCTGATCATGACTTTGGAGCGTTGGAACTAGGCTATgtaagtagtc ... atgagtgcagGTTACGGTAACGGCCGTGAGTCTGGATACGAATGTGGAGATTAATACGCGT
EST: gi|37829212|gb|BJ587224.1|BJ587224
EST:     TTGGAGAGGTTGCCCCTGATCATGACTTTGGAGCGTTGGAACTAGGCTAT                         GTTACGGTAACGGCCGTGAGTCTGGATACGAATGTGGAGATTAATACGCGT
genomic: TTGGAGAGGTTGCCCCTGATCATGACTTTGGAGCGTTGGAACTAGGCTATgtaagtagtc ... atgagtgcagGTTACGGTAACGGCCGTGAGTCTGGATACGAATGTGGAGATTAATACGCGT
EST: gi|37835343|gb|BJ593355.1|BJ593355
EST:     TTGGAGAGGTTGCCCCTGATCATGACTTTGGAGCGTTGGAACTAGGCTAT                         GTTACGGTAACGGCCGTGAGTCTGGATACGAATGTGGAGATTAATACGCGT
genomic: TTGGAGAGGTTGCCCCTGATCATGACTTTGGAGCGTTGGAACTAGGCTATgtaagtagtc ... atgagtgcagGTTACGGTAACGGCCGTGAGTCTGGATACGAATGTGGAGATTAATACGCGT
EST: gi|208367233|gb|DC951221.1|DC951221
EST:     TTGGAGAGGTTGCCCCTGATCATGACTTTGGAGCGTTGGAACTAGGCTAT                         GTTACGGTAACGGCCGTGAGTCTGGATACGAATGTGGAGATTAATACGCGT
genomic: TTGGAGAGGTTGCCCCTGATCATGACTTTGGAGCGTTGGAACTAGGCTATgtaagtagtc ... atgagtgcagGTTACGGTAACGGCCGTGAGTCTGGATACGAATGTGGAGATTAATACGCGT
EST: gi|162173550|gb|FC350124.1|FC350124
EST:     TTGGAGAGGTTGCCCCTGATCATGACTTTGGAGCGTTGGAACTAGGCTAT                         GTTACGGTAACGGCCGTGAGTCTGGATACGAATGTGGAGATTAATACGCGT
genomic: TTGGAGAGGTTGCCCCTGATCATGACTTTGGAGCGTTGGAACTAGGCTATgtaagtagtc ... atgagtgcagGTTACGGTAACGGCCGTGAGTCTGGATACGAATGTGGAGATTAATACGCGT
EST: gi|208346039|gb|DC921284.1|DC921284
EST:     TTGGAGAGGTTGCCCCTGATCATGACTTTGGAGCGTTGGAACTAGGCTAT                         GTTACGGTAACGGCCGTGAGTCTGGATACGAATGTGGAGATTAATACGCGT
genomic: TTGGAGAGGTTGCCCCTGATCATGACTTTGGAGCGTTGGAACTAGGCTATgtaagtagtc ... atgagtgcagGTTACGGTAACGGCCGTGAGTCTGGATACGAATGTGGAGATTAATACGCGT
EST: gi|37832494|gb|BJ590506.1|BJ590506
EST:     TTGGAGAGGTTGCCCCTGATCATGACTTTGGAGCGTTGGAACTAGGCTAT                         GTTACGGTAACGGCCGTGAGTCTGGATACGAATGTGGAGATTAATACGCGT
genomic: TTGGAGAGGTTGCCCCTGATCATGACTTTGGAGCGTTGGAACTAGGCTATgtaagtagtc ... atgagtgcagGTTACGGTAACGGCCGTGAGTCTGGATACGAATGTGGAGATTAATACGCGT
EST: gi|208364864|gb|DC943682.1|DC943682
EST:     TTGGAGAGGTTGCCCCTGATCATGACTTTGGAGCGTTGGAACTAGGCTAT                         GTTACGGTAACGGCCGTGAGTCTGGATACGAATGTGGAGATTAATACGCGT
genomic: TTGGAGAGGTTGCCCCTGATCATGACTTTGGAGCGTTGGAACTAGGCTATgtaagtagtc ... atgagtgcagGTTACGGTAACGGCCGTGAGTCTGGATACGAATGTGGAGATTAATACGCGT
EST: gi|162173551|gb|FC350125.1|FC350125
EST:     TTGGAGAGGTTGCCCCTGATCATGACTTTGGAGCGTTGGAACTAGGCTAT                         GTTACGGTAACGGCCGTGAGTCTGGATACGAATGTGGAGATTAATACGCGT
genomic: TTGGAGAGGTTGCCCCTGATCATGACTTTGGAGCGTTGGAACTAGGCTATgtaagtagtc ... atgagtgcagGTTACGGTAACGGCCGTGAGTCTGGATACGAATGTGGAGATTAATACGCGT
EST: gi|208385034|gb|DC919714.1|DC919714
EST:     TTGGAGAGGTTGCCCCTGATCATGACTTTGGAGCGTTGGAACTAGGCTAT                         GTTACGGTAACGGCCGTGAGTCTGGATACGAATGTGGAGATTAATACGCGT
genomic: TTGGAGAGGTTGCCCCTGATCATGACTTTGGAGCGTTGGAACTAGGCTATgtaagtagtc ... atgagtgcagGTTACGGTAACGGCCGTGAGTCTGGATACGAATGTGGAGATTAATACGCGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcattctcacactaactccaaacacttatatcatggcctggggtaatgagtgcagGTTACGGTAACGGCCGTGAGTCTGGATACGAATGTGGAGATTAATACGCGTGGCCAAGTCGAGGATTGGGTAGCCAGTGTAGTTCCAGTCTCCCCTGCTT
         cactaac  putative branch site (score: 1)
                         ttatatcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taatggacttcctgtaatcaagtcttgtttcttgtcgaatcgcaatcattctcacactaactccaaacacttatatcatggcctggggtaatgagtgcagGTTACGGTAACGGCCGTGAGTCTGGATACGAATGTGGAGATTAATACGCGTGGCCAAGTCGAGGATTGGGTAGCCAGTGTAGTTCCAGTCTCCCCTGCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT