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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaactggtttggccctatagttgttacactttccttgtgagtttccttttcatgtattcggttgttgtgcactggctaatgcagtggatggctttcgcagGGCAACTCTGACTTGTCTCATAATTGTCTTATTGTACATCATCATTTCGTTCTTCTGTGGTGGAATTTTCCTTCGAAGCTGCCGTGGATAATGGCCACCG

Basic information

species Physcomitrella patens
transcript PP1S52_233V6.1
intron # 5
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|37836310|gb|BJ594318.1|BJ594318
EST:     AGTCACGTCGACTGCGACAAGCCCATGTGGATAAAAAACGCCAAACTTTT                         GGCAACTCTGACTTGTCTCATAATTGTCTTATTGTACATCATCATTTCGTT
genomic: AGTCACGTCGACTGCGACAAG-CCATGTGGATAAAAAACGCCAAACTTTTgtaagttttg ... gctttcgcagGGCAACTCTGACTTGTCTCATAATTGTCTTATTGTACATCATCATTTCGTT
EST: gi|162205012|gb|FC381721.1|FC381721
EST:     GCGACAAGCCATGTGGATAAAAAACGCCAAACTTTT                         GGCAACTCTGACTTGTCTCATAATTGTCTTATTGTACATCATCATTTCGTT
genomic: GCGACAAGCCATGTGGATAAAAAACGCCAAACTTTTgtaagttttg ... gctttcgcagGGCAACTCTGACTTGTCTCATAATTGTCTTATTGTACATCATCATTTCGTT
EST: gi|162193407|gb|FC370973.1|FC370973
EST:     CAGTCACGTCGACTGCGACAAGCCATGTGGATAAAAAACGCCAAACTTTT                         GGCAACTCTGACTTGTCTCATAATTGTCTTATTGTACATCATCATTTCGTT
genomic: CAGTCACGTCGACTGCGACAAGCCATGTGGATAAAAAACGCCAAACTTTTgtaagttttg ... gctttcgcagGGCAACTCTGACTTGTCTCATAATTGTCTTATTGTACATCATCATTTCGTT
EST: gi|37831140|gb|BJ589152.1|BJ589152
EST:     GTGGATAAAAAACGCCAANCTTTT                         GGCAACTCTGACTTGTCTCATAATTGTCTTATNGTACATCATCATTTCGTT
genomic: GTGGATAAAAAACGCCAAACTTTTgtaagttttg ... gctttcgcagGGCAACTCTGACTTGTCTCATAATTGTCTTATTGTACATCATCATTTCGTT
EST: gi|208347434|gb|DC917225.1|DC917225
EST:     CAGTCACGTCGACTGCGACAAGCCATGTGGATAAAAAACGCCAAACTTTT                         GGCAACTCTGACTTGTCTCATAATTGTCTTATTGTACATCATCATTTCGTT
genomic: CAGTCACGTCGACTGCGACAAGCCATGTGGATAAAAAACGCCAAACTTTTgtaagttttg ... gctttcgcagGGCAACTCTGACTTGTCTCATAATTGTCTTATTGTACATCATCATTTCGTT
EST: gi|162219104|gb|FC394687.1|FC394687
EST:     CAGTCACGTCGACTGCGACAAGCCATGTGGATAAAAAACGCCAAACTTTT                         GGCAACTCTGACTTGTCTCATAATTGTCTTATTGTACATCATCATTTCGTT
genomic: CAGTCACGTCGACTGCGACAAGCCATGTGGATAAAAAACGCCAAACTTTTgtaagttttg ... gctttcgcagGGCAACTCTGACTTGTCTCATAATTGTCTTATTGTACATCATCATTTCGTT
EST: gi|18333344|gb|BJ165358.1|BJ165358
EST:     CAGTCACGTCGACTGCGACAAGCCATGTGGATAAAAAACGCCAAACTTTT                         GGCAACTCTGACTTGTCTCATAATTGTCTTATTGTACATCATCATTTCGTT
genomic: CAGTCACGTCGACTGCGACAAGCCATGTGGATAAAAAACGCCAAACTTTTgtaagttttg ... gctttcgcagGGCAACTCTGACTTGTCTCATAATTGTCTTATTGTACATCATCATTTCGTT
EST: gi|37825390|gb|BJ583456.1|BJ583456
EST:     AGTCACGTCGACTGCGACAAGCCCATGTGGATAAAAAACGCCAAACTTTT                         GGCAACTCTGACTTGTCTCATAATTGTCTTATTGTACATCATCATTTCGTT
genomic: AGTCACGTCGACTGCGACAAG-CCATGTGGATAAAAAACGCCAAACTTTTgtaagttttg ... gctttcgcagGGCAACTCTGACTTGTCTCATAATTGTCTTATTGTACATCATCATTTCGTT
EST: gi|162219105|gb|FC394688.1|FC394688
EST:     CAGTCACGTCGACTGCGACAAGCCATGTGGATAAAAAACGCCAAACTTTT                         GGCAACTCTGACTTGTCTCATAATTGTCTTATTGTACATCATCATTTCGTT
genomic: CAGTCACGTCGACTGCGACAAGCCATGTGGATAAAAAACGCCAAACTTTTgtaagttttg ... gctttcgcagGGCAACTCTGACTTGTCTCATAATTGTCTTATTGTACATCATCATTTCGTT
EST: gi|18338519|gb|BJ170543.1|BJ170543
EST:     CAGTCACGTCGACTGCGACAAGCCATGTGGATAAAAAACGCCAAACTTTT                         GGCAACTCTGACTTGTCTCATAATTGTCTTATTGTACATCATCATTTCGTT
genomic: CAGTCACGTCGACTGCGACAAGCCATGTGGATAAAAAACGCCAAACTTTTgtaagttttg ... gctttcgcagGGCAACTCTGACTTGTCTCATAATTGTCTTATTGTACATCATCATTTCGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttcatgtattcggttgttgtgcactggctaatgcagtggatggctttcgcagGGCAACTCTGACTTGTCTCATAATTGTCTTATTGTACATCATCATTTCGTTCTTCTGTGGTGGAATTTTCCTTCGAAGCTGCCGTGGATAATGGCCACCG
                            ggctaat  putative branch site (score: 3)
                                              ctttcgc  putative PPT
      atgtatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaactggtttggccctatagttgttacactttccttgtgagtttccttttcatgtattcggttgttgtgcactggctaatgcagtggatggctttcgcagGGCAACTCTGACTTGTCTCATAATTGTCTTATTGTACATCATCATTTCGTTCTTCTGTGGTGGAATTTTCCTTCGAAGCTGCCGTGGATAATGGCCACCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC