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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttttattgactgttttttctgacgcctccttgtaattaatttataaatttgatgcttatttgtgactacacagaataagtttctttagggaaacacttcaagtgaatttacgagatgttatattttcactctttgaccagtttgcattcattgccatcttttcatgcagGATCCTTGATAACCTGCCAGTGGCGATGGTCCACTTTGTAAACCGAATTAAGACTTATGACCGAGGATTTCCTGTTGGTCAAAAGCTATCCTTGTCTGAT

Basic information

species Physcomitrella patens
transcript PP1S24_182V6.1
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|100422504|gb|BY976406.1|BY976406
EST:     TCTGCCAAGCTCTTCAAAGAAAGGATTAAGTATGACTACCGTGTAAACAT                         GATCCTTGATAACCTGCCAGTGGCGATGGTCCACTTTGTAAACCGAATTAA
genomic: TCTGCCAAGCTCTTCAAAGAAAGGATTAAGTATGACTACCGTGTAAACATgtaagtttta ... tttcatgcagGATCCTTGATAACCTGCCAGTGGCGATGGTCCACTTTGTAAACCGAATTAA
EST: gi|18325719|gb|BJ157716.1|BJ157716
EST:     TCTGCCAAGCTCTTCAAA-A--GGATTAAGTATGACTACCGTGTAAACAT                         GATCCTTGATAACCTGCCAGTGGCGATGGTC
genomic: TCTGCCAAGCTCTTCAAAGAAAGGATTAAGTATGACTACCGTGTAAACATgtaagtttta ... tttcatgcagGATCCTTGATAACCTGCCAGTGGCGATGGTC
EST: gi|208350408|gb|DC906110.1|DC906110
EST:     TCTGCCAAGCTCTTCAAAGAAAGGATTAAGTATGACTACCGTGTAAACAT                         GATCCTTGATAACCTGCCAGTGGCGATGGTCCACTTTGTAAACCGAATTAA
genomic: TCTGCCAAGCTCTTCAAAGAAAGGATTAAGTATGACTACCGTGTAAACATgtaagtttta ... tttcatgcagGATCCTTGATAACCTGCCAGTGGCGATGGTCCACTTTGTAAACCGAATTAA
EST: gi|18344133|gb|BJ176172.1|BJ176172
EST:     TCTGCCAAGCTCTTCNAAGAAAGGATTAAGTATGACTACCGTGTAAACAT                         GATCCTTGGTAACCTG
genomic: TCTGCCAAGCTCTTCAAAGAAAGGATTAAGTATGACTACCGTGTAAACATgtaagtttta ... tttcatgcagGATCCTTGATAACCTG
EST: gi|18325392|gb|BJ157388.1|BJ157388
EST:     TCTGCCAAGCTCTTCAAAGAAAGGATTAAGTATGACTACCGTGTAAACAT                         GATCCTTGATAAC
genomic: TCTGCCAAGCTCTTCAAAGAAAGGATTAAGTATGACTACCGTGTAAACATgtaagtttta ... tttcatgcagGATCCTTGATAAC
EST: gi|162256884|gb|FC432986.1|FC432986
EST:     TCTGCCAAGCTCTTCAAAGAAAGGATTAAGTATGACTACCGTGTAAACAT                         GATCCTTGATAACCTGCCAGTGGCGATGGTCCACTTTGTAAACCGAATTAA
genomic: TCTGCCAAGCTCTTCAAAGAAAGGATTAAGTATGACTACCGTGTAAACATgtaagtttta ... tttcatgcagGATCCTTGATAACCTGCCAGTGGCGATGGTCCACTTTGTAAACCGAATTAA
EST: gi|100405258|gb|BY955435.1|BY955435
EST:     TCTGCCAAGCTCTTCAAAGAAAGGATTAAGTATGACTACCGTGTAAACAT                         GATCCTTGATAACCTGCCAGTGGCGATGGTCCACTTTGTAAACCGAATTAA
genomic: TCTGCCAAGCTCTTCAAAGAAAGGATTAAGTATGACTACCGTGTAAACATgtaagtttta ... tttcatgcagGATCCTTGATAACCTGCCAGTGGCGATGGTCCACTTTGTAAACCGAATTAA
EST: gi|208352204|gb|DC906307.1|DC906307
EST:     TCTGCCAAGCTCTTCAAAGAAAGGATTAAGTATGACTACCGTGTAAACAT                         GATCCTTGATAACCTGCCANTGGCGATGGTCCACTTTGTAAACCGAATTAA
genomic: TCTGCCAAGCTCTTCAAAGAAAGGATTAAGTATGACTACCGTGTAAACATgtaagtttta ... tttcatgcagGATCCTTGATAACCTGCCAGTGGCGATGGTCCACTTTGTAAACCGAATTAA
EST: gi|18362890|gb|BJ194962.1|BJ194962
EST:     TCTGCCAAGCTCTTCAAAGAAAGGATTAAGTATGACTACCGTGTAAACAT                         GATCCTTGATAACCTGCCAGTGGCCGATGGTCCACTTTGTAA
genomic: TCTGCCAAGCTCTTCAAAGAAAGGATTAAGTATGACTACCGTGTAAACATgtaagtttta ... tttcatgcagGATCCTTGATAACCTGCCAGTGGC-GATGGTCCACTTTGTAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgttatattttcactctttgaccagtttgcattcattgccatcttttcatgcagGATCCTTGATAACCTGCCAGTGGCGATGGTCCACTTTGTAAACCGAATTAAGACTTATGACCGAGGATTTCCTGTTGGTCAAAAGCTATCCTTGTCTGAT
                ctttgac  putative branch site (score: 4)
 ccatcttttc  putative PPT
 atattttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttttattgactgttttttctgacgcctccttgtaattaatttataaatttgatgcttatttgtgactacacagaataagtttctttagggaaacacttcaagtgaatttacgagatgttatattttcactctttgaccagtttgcattcattgccatcttttcatgcagGATCCTTGATAACCTGCCAGTGGCGATGGTCCACTTTGTAAACCGAATTAAGACTTATGACCGAGGATTTCCTGTTGGTCAAAAGCTATCCTTGTCTGAT

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