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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtataatgatgtgtgatcgccgatagcgcatcgtggtgctgtactcgaatagggagtatgaatgcctgctgcagtataaagcttaaatgcagtgcatgtaattgcacagaatgcatgcttacttagttagatacagaactgactttcaaaggatgctggattttcagGCCGCTGCTTTGGCCGGTTCGGAGCACCGTCGATCTACCCCGGTATCAAGCCGTCTGGAACAGCAGCAGAAGTACTTGAACCTGCCAATCCTGCCGACGA

Basic information

species Physcomitrella patens
transcript PP1S399_19V6.2
intron # 6
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|162165805|gb|FC341233.1|FC341233
EST:     AATCGAGGAGGAACTCCCCCCGCGTTCATAACAAGGCAGTGAAGGAAGCA                         GCCGCTGCTTTGGCCGGTTCGGAGCACCGTCGATCTACCCCGGTATCAAGC
genomic: AATCGAGGAGGAACTCCCCCCGCGTTCATAACAAGGCAGTGAAGGAAGCAgtaagtataa ... ggattttcagGCCGCTGCTTTGGCCGGTTCGGAGCACCGTCGATCTACCCCGGTATCAAGC
EST: gi|162275290|gb|FC451266.1|FC451266
EST:     AATCGAGGAGGAACTCCCCCCGCGTTCATAACAAGGCAGTGAAGGAAGCA                         GCCGCTGCTTTGGCCGGTTCGGAGCACCGTCGATCTACCCCGGTATCAAGC
genomic: AATCGAGGAGGAACTCCCCCCGCGTTCATAACAAGGCAGTGAAGGAAGCAgtaagtataa ... ggattttcagGCCGCTGCTTTGGCCGGTTCGGAGCACCGTCGATCTACCCCGGTATCAAGC
EST: gi|162156429|gb|FC332661.1|FC332661
EST:     AATCGAGGAGGAACTCCCCCCGCGTTCATAACAAGGCAGTGAAGGAAGCA                         GCCGCTGCTTTGGCCGGTTCGGAGCACCGTCGATCTACCCCGGTATCAAGC
genomic: AATCGAGGAGGAACTCCCCCCGCGTTCATAACAAGGCAGTGAAGGAAGCAgtaagtataa ... ggattttcagGCCGCTGCTTTGGCCGGTTCGGAGCACCGTCGATCTACCCCGGTATCAAGC
EST: gi|162181010|gb|FC358664.1|FC358664
EST:     AATCGAGGAGGAACTCCCCCCGCGTTCATAACAAGGCAGTGAAGGAAGCA                         GCCGCTGCTTTGGCCGGTTCGGAGCACCGTCGATCTACCCCGGTATCAAGC
genomic: AATCGAGGAGGAACTCCCCCCGCGTTCATAACAAGGCAGTGAAGGAAGCAgtaagtataa ... ggattttcagGCCGCTGCTTTGGCCGGTTCGGAGCACCGTCGATCTACCCCGGTATCAAGC
EST: gi|162164320|gb|FC340991.1|FC340991
EST:     AATCGAGGAGGAACTCCCCCCGCGTTCATAACAAGGCAGTGAAGGAAGCA                         GCCGCTGCTTTGGCCGGTTCGGAGCACCGTCGATCTACCCCGGTATCAAGC
genomic: AATCGAGGAGGAACTCCCCCCGCGTTCATAACAAGGCAGTGAAGGAAGCAgtaagtataa ... ggattttcagGCCGCTGCTTTGGCCGGTTCGGAGCACCGTCGATCTACCCCGGTATCAAGC
EST: gi|162171094|gb|FC347708.1|FC347708
EST:     AATCGAGGAGGAACTCCCCCCGCGTTCATAACAAGGCAGTGAAGGAAGCA                         GCCGCTGCTTTGGCCGGTTCGGAGCACCGTCGATCTACCCCGGTATCAAGC
genomic: AATCGAGGAGGAACTCCCCCCGCGTTCATAACAAGGCAGTGAAGGAAGCAgtaagtataa ... ggattttcagGCCGCTGCTTTGGCCGGTTCGGAGCACCGTCGATCTACCCCGGTATCAAGC
EST: gi|162277617|gb|FC453248.1|FC453248
EST:     AATCGAGGAGGAACTCCCCCCGCGTTCATAACAAGGCAGTGAAGGAAGCA                         GCCGCTGCTTTGGCCGGTTCGGAGCACCGTCGATCTACCCCGGTATCAAGC
genomic: AATCGAGGAGGAACTCCCCCCGCGTTCATAACAAGGCAGTGAAGGAAGCAgtaagtataa ... ggattttcagGCCGCTGCTTTGGCCGGTTCGGAGCACCGTCGATCTACCCCGGTATCAAGC
EST: gi|162189799|gb|FC365541.1|FC365541
EST:     AATCGAGGAGGAACTCCCCCCGCGTTCATAACAAGGCAGTGAAGGAAGCA                         GCCGCTGCTTTGGCCGGTTCGGAGCACCGTCGATCTACCCCGGTATCAAGC
genomic: AATCGAGGAGGAACTCCCCCCGCGTTCATAACAAGGCAGTGAAGGAAGCAgtaagtataa ... ggattttcagGCCGCTGCTTTGGCCGGTTCGGAGCACCGTCGATCTACCCCGGTATCAAGC
EST: gi|162160395|gb|FC337396.1|FC337396
EST:     AATCGAGGAGGAACTCCCCCCGCGTTCATAACAAGGCAGTGAAGGAAGCA                         GCCGCTGCTTTGGCCGGTTCGGAGCACCGTCGATCTACCCCGGTATCAAGC
genomic: AATCGAGGAGGAACTCCCCCCGCGTTCATAACAAGGCAGTGAAGGAAGCAgtaagtataa ... ggattttcagGCCGCTGCTTTGGCCGGTTCGGAGCACCGTCGATCTACCCCGGTATCAAGC
EST: gi|162169968|gb|FC345908.1|FC345908
EST:     AATCGAGGAGGAACTCCCCCCGCGTTCATAACAAGGCAGTGAAGGAAGCA                         GCCGCTGCTTTGGCCGGTTCGGAGCACCGTCGATCTACCCCGGTATCAAGC
genomic: AATCGAGGAGGAACTCCCCCCGCGTTCATAACAAGGCAGTGAAGGAAGCAgtaagtataa ... ggattttcagGCCGCTGCTTTGGCCGGTTCGGAGCACCGTCGATCTACCCCGGTATCAAGC
EST: gi|100399159|gb|BY954229.1|BY954229
EST:     AACAAGGCAGTGAAGGAAGCA                         GCCGCTGCTTTGGCCGGTTCGGAGCACCGTCGATCTACCCCGGTATCAAGC
genomic: AACAAGGCAGTGAAGGAAGCAgtaagtataa ... ggattttcagGCCGCTGCTTTGGCCGGTTCGGAGCACCGTCGATCTACCCCGGTATCAAGC
EST: gi|19790140|gb|BQ041713.1|BQ041713
EST:     AATCGAGGAGGAACTCCCCCCGCGTTCATAACAAGGCAGTGAAGGAAGCA                         GCCGCTGCTTTGGCCGGTTCGGAGCACCGTCGATCTACCCCGGTATCAAGC
genomic: AATCGAGGAGGAACTCCCCCCGCGTTCATAACAAGGCAGTGAAGGAAGCAgtaagtataa ... ggattttcagGCCGCTGCTTTGGCCGGTTCGGAGCACCGTCGATCTACCCCGGTATCAAGC
EST: gi|162150213|gb|FC326298.1|FC326298
EST:     AATCGAGGAGGAACTCCCCCCGCGTTCATAACAAGGCAGTGAAGGAAGCA                         GCCGCTGCTTTGGCCGGTTCGGAGCACCGTCGATCTACCCCGGTATCAAGC
genomic: AATCGAGGAGGAACTCCCCCCGCGTTCATAACAAGGCAGTGAAGGAAGCAgtaagtataa ... ggattttcagGCCGCTGCTTTGGCCGGTTCGGAGCACCGTCGATCTACCCCGGTATCAAGC
EST: gi|18326134|gb|BJ158133.1|BJ158133
EST:     AATCGAGGAGGAACTCCCCCCGCGTTCATAACAAGGCAGTGAAGGAAGCA                         GCCGCTGCTTTGGCCGGTTCGGAGCACCGTCGATCTACCCCGGTATCAAGC
genomic: AATCGAGGAGGAACTCCCCCCGCGTTCATAACAAGGCAGTGAAGGAAGCAgtaagtataa ... ggattttcagGCCGCTGCTTTGGCCGGTTCGGAGCACCGTCGATCTACCCCGGTATCAAGC
EST: gi|162179653|gb|FC355711.1|FC355711
EST:     AATCGAGGAGGAACTCCCCCCGCGTTCATAACAAGGCAGTGAAGGAAGCA                         GCCGCTGCTTTGGCCGGTTCGGAGCACCGTCGATCTACCCCGGTATCAAGC
genomic: AATCGAGGAGGAACTCCCCCCGCGTTCATAACAAGGCAGTGAAGGAAGCAgtaagtataa ... ggattttcagGCCGCTGCTTTGGCCGGTTCGGAGCACCGTCGATCTACCCCGGTATCAAGC
EST: gi|162185338|gb|FC360912.1|FC360912
EST:     AATCGAGGAGGAACTCCCCCCGCGTTCATAACAAGGCAGTGAAGGAAGCA                         GCCGCTGCTTTGGCCGGTTCGGAGCACCGTCGATCTACCCCGGTATCAAGC
genomic: AATCGAGGAGGAACTCCCCCCGCGTTCATAACAAGGCAGTGAAGGAAGCAgtaagtataa ... ggattttcagGCCGCTGCTTTGGCCGGTTCGGAGCACCGTCGATCTACCCCGGTATCAAGC
EST: gi|162153731|gb|FC329134.1|FC329134
EST:     GGAACTCCCCCCGCGTTCATAACAAGGCAGTGAAGGAAGCA                         GCCGCTGCTTTGGCCGGTTCGGAGCACCGTCGATCTACCCCGGTATCAAGC
genomic: GGAACTCCCCCCGCGTTCATAACAAGGCAGTGAAGGAAGCAgtaagtataa ... ggattttcagGCCGCTGCTTTGGCCGGTTCGGAGCACCGTCGATCTACCCCGGTATCAAGC
EST: gi|162165513|gb|FC340624.1|FC340624
EST:     AGGCAGTGAAGGAAGCA                         GCCGCTGCTTTGGCCGGTTCGGAGCACCGTCGATCTACCCCGGTATCAAGC
genomic: AGGCAGTGAAGGAAGCAgtaagtataa ... ggattttcagGCCGCTGCTTTGGCCGGTTCGGAGCACCGTCGATCTACCCCGGTATCAAGC
EST: gi|162230917|gb|FC407172.1|FC407172
EST:     AATCGAGGAGGAACTCCCCCCGCGTTCATAACAAGGCAGTGAAGGAAGCA                         GCCGCTGCTTTGGCCGGTTCGGAGCACCGTCGATCTACCCCGGTATCAAGC
genomic: AATCGAGGAGGAACTCCCCCCGCGTTCATAACAAGGCAGTGAAGGAAGCAgtaagtataa ... ggattttcagGCCGCTGCTTTGGCCGGTTCGGAGCACCGTCGATCTACCCCGGTATCAAGC
EST: gi|162152719|gb|FC329725.1|FC329725
EST:     AATCGAGGAGGAACTCCCCCCGCGTTCATAACAAGGCAGTGAAGGAAGCA                         GCCGCTGCTTTGGCCGGTTCGGAGCACCGTCGATCTACCCCGGTATCAAGC
genomic: AATCGAGGAGGAACTCCCCCCGCGTTCATAACAAGGCAGTGAAGGAAGCAgtaagtataa ... ggattttcagGCCGCTGCTTTGGCCGGTTCGGAGCACCGTCGATCTACCCCGGTATCAAGC
EST: gi|162171048|gb|FC346947.1|FC346947
EST:     AATCGAGGAGGAACTCCCCCCGCGTTCATAACAAGGCAGTGAAGGAAGCA                         GCCGCTGCTTTGGCCGGTTCGGAGCACCGTCGATCTACCCCGGTATCAAGC
genomic: AATCGAGGAGGAACTCCCCCCGCGTTCATAACAAGGCAGTGAAGGAAGCAgtaagtataa ... ggattttcagGCCGCTGCTTTGGCCGGTTCGGAGCACCGTCGATCTACCCCGGTATCAAGC
EST: gi|162242611|gb|FC419240.1|FC419240
EST:     AATCGAGGAGGAACTCCCCCCGCGTTCATAACAAGGCAGTGAAGGAAGCA                         GCCGCTGCTTTGGCCGGTTCGGAGCACCGTCGATCTACCCCGGTATCAAGC
genomic: AATCGAGGAGGAACTCCCCCCGCGTTCATAACAAGGCAGTGAAGGAAGCAgtaagtataa ... ggattttcagGCCGCTGCTTTGGCCGGTTCGGAGCACCGTCGATCTACCCCGGTATCAAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatgcttacttagttagatacagaactgactttcaaaggatgctggattttcagGCCGCTGCTTTGGCCGGTTCGGAGCACCGTCGATCTACCCCGGTATCAAGCCGTCTGGAACAGCAGCAGAAGTACTTGAACCTGCCAATCCTGCCGACGA
                        aactgac  putative branch site (score: 2)
                                                ttttc  putative PPT
      ttactta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtataatgatgtgtgatcgccgatagcgcatcgtggtgctgtactcgaatagggagtatgaatgcctgctgcagtataaagcttaaatgcagtgcatgtaattgcacagaatgcatgcttacttagttagatacagaactgactttcaaaggatgctggattttcagGCCGCTGCTTTGGCCGGTTCGGAGCACCGTCGATCTACCCCGGTATCAAGCCGTCTGGAACAGCAGCAGAAGTACTTGAACCTGCCAATCCTGCCGACGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT