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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagggacttcgacttttctcgttgcatttggacagtgtatgtgattcatgtgtttgtttgttatttcaaaggtattttcaatagtttagacttgacaatatttttattcgtctcttacttgtcatcgctgcgatttgaatcatacctgcagGTCTACTAGAAAATGGGAGTGAGGTTACTGTTGACGAGTTGGCTGTGTCTCTGAAGAAGGATACCAACATATTTTCTCACGTTTTCTGGAATACCAAGAA

Basic information

species Physcomitrella patens
transcript PP1S497_3V6.2
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|37821575|gb|BJ579641.1|BJ579641
EST:     GGCTAACGACCAGATTAAAGAATTTAGGCAGAAGCTTCGGGAAGCCACTG                         GTCTACTAGAAAATGGGAGTGAGGTTACTGTTGACGAGTTGGCTGTGTCTC
genomic: GGCTAACGACCAGATTAAAGAATTTAGGCAGAAGCTTCGGGAAGCCACTGgtagggactt ... atacctgcagGTCTACTAGAAAATGGGAGTGAGGTTACTGTTGACGAGTTGGCTGTGTCTC
EST: gi|208381290|gb|DC919180.1|DC919180
EST:     GGCTAACGACCAGATTAAAGAATTTAGGCAGAAGCTTCGGGAAGCCACTG                         GTCTACTAGAAAATGGGAGTGAGGTTACTGTTGACGAGTTGGCTGTGTCTC
genomic: GGCTAACGACCAGATTAAAGAATTTAGGCAGAAGCTTCGGGAAGCCACTGgtagggactt ... atacctgcagGTCTACTAGAAAATGGGAGTGAGGTTACTGTTGACGAGTTGGCTGTGTCTC
EST: gi|208368792|gb|DC943792.1|DC943792
EST:     GGCTAACGACCAGATTAAAGAATTTAGGCAGAAGCTTCGGGAAGCCACTG                         GTCTACTAGAAAATGGGAGTGAGGTTACTGTTGACGAGTTGGCTGTGTCTC
genomic: GGCTAACGACCAGATTAAAGAATTTAGGCAGAAGCTTCGGGAAGCCACTGgtagggactt ... atacctgcagGTCTACTAGAAAATGGGAGTGAGGTTACTGTTGACGAGTTGGCTGTGTCTC
EST: gi|37841425|gb|BJ599433.1|BJ599433
EST:     TTAGGCAGAAGCTTCGGGAAGCCACTG                         GTCTACTAGAAAATGGGAGTGAGGTTACTGTTGACGAGTTGGCTGTGTCTC
genomic: TTAGGCAGAAGCTTCGGGAAGCCACTGgtagggactt ... atacctgcagGTCTACTAGAAAATGGGAGTGAGGTTACTGTTGACGAGTTGGCTGTGTCTC
EST: gi|208362303|gb|DC954549.1|DC954549
EST:     TTCGGGAAGCCACTG                         GTCTACTAGAAAATGGGAGTGAGGTTACTGTTGACGAGTTGGCTGTGTCTC
genomic: TTCGGGAAGCCACTGgtagggactt ... atacctgcagGTCTACTAGAAAATGGGAGTGAGGTTACTGTTGACGAGTTGGCTGTGTCTC
EST: gi|100404070|gb|BY955240.1|BY955240
EST:     GGCTAACGACCAGATTAAAGAATTTAGGCAGAAGCTTCGGGAAGCCACTG                         GTCTACTAGAAAATGGGAGTGAGGTTACTGTTGACGAGTTGGCTGTGTCTC
genomic: GGCTAACGACCAGATTAAAGAATTTAGGCAGAAGCTTCGGGAAGCCACTGgtagggactt ... atacctgcagGTCTACTAGAAAATGGGAGTGAGGTTACTGTTGACGAGTTGGCTGTGTCTC
EST: gi|208378412|gb|DC923055.1|DC923055
EST:     GGCTAACGACCAGATTAAAGAATTTAGGCAGAAGCTTCGGGAAGCCACTG                         GTCTACTAGAAAATGGGAGTGAGGTTACTGTTGACGAGTTGGCTGTGTCTC
genomic: GGCTAACGACCAGATTAAAGAATTTAGGCAGAAGCTTCGGGAAGCCACTGgtagggactt ... atacctgcagGTCTACTAGAAAATGGGAGTGAGGTTACTGTTGACGAGTTGGCTGTGTCTC
EST: gi|208362361|gb|DC954607.1|DC954607
EST:     GGCTAACGACCAGATTAAAGAATTTAGGCAGAAGCTTCGGGAAGCCACTG                         GTCTACTAGAAAATGGGAGTGAGGTTACTGTTGACGAGTTGGCTGTGTCTC
genomic: GGCTAACGACCAGATTAAAGAATTTAGGCAGAAGCTTCGGGAAGCCACTGgtagggactt ... atacctgcagGTCTACTAGAAAATGGGAGTGAGGTTACTGTTGACGAGTTGGCTGTGTCTC
EST: gi|37845662|gb|BJ603670.1|BJ603670
EST:     GGCTAACGACCAGATTAAAGAATTTAGGCAGAAGCTTCGGGAAGCCACTG                         GTCTACTAGAAAATGGGAGTGAGGTTACTGTTGACGAGTTGGCTGTGTCTC
genomic: GGCTAACGACCAGATTAAAGAATTTAGGCAGAAGCTTCGGGAAGCCACTGgtagggactt ... atacctgcagGTCTACTAGAAAATGGGAGTGAGGTTACTGTTGACGAGTTGGCTGTGTCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatatttttattcgtctcttacttgtcatcgctgcgatttgaatcatacctgcagGTCTACTAGAAAATGGGAGTGAGGTTACTGTTGACGAGTTGGCTGTGTCTCTGAAGAAGGATACCAACATATTTTCTCACGTTTTCTGGAATACCAAGAA
               ctcttac  putative branch site (score: 3)
     ttttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagggacttcgacttttctcgttgcatttggacagtgtatgtgattcatgtgtttgtttgttatttcaaaggtattttcaatagtttagacttgacaatatttttattcgtctcttacttgtcatcgctgcgatttgaatcatacctgcagGTCTACTAGAAAATGGGAGTGAGGTTACTGTTGACGAGTTGGCTGTGTCTCTGAAGAAGGATACCAACATATTTTCTCACGTTTTCTGGAATACCAAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG