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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttcaattcacagttctagtggaattctcatcaagggtcgcattagacttcctttgtggtctttcggtgtcttcacatcgaagctctcgcttaacatgtaaagtaagtcattgcatcagagaatagttgaaggtgactgaagacttaatgatgtttctgtatgtacagGGGCCTGCAAGTCATAATCCTTTGGCTTATAAATACTATAATGCTGAGGAACTGATTTTTGGCAAGAAGATGAAG

Basic information

species Physcomitrella patens
transcript PP1S180_53V6.2
intron # 4
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|18324844|gb|BJ156839.1|BJ156839
EST:     AAGAGTGGGAAGGGGAATTCTTCCCTAACATTTCGTACATCAAATATGAG                         GGGCCTGCAAGTCATAATCCTTTGGCTTATAAATACTATAATGCTGAGGAA
genomic: AAGAGTGGGAAGGGGAATTCTTCCCTAACATTTCGTACATCAAATATGAGgtatttcaat ... gtatgtacagGGGCCTGCAAGTCATAATCCTTTGGCTTATAAATACTATAATGCTGAGGAA
EST: gi|208374343|gb|DC941156.1|DC941156
EST:     AAGAGTGGGAAGGGGAATTCTTCCCTAACATTTCGTACATCAAATATGAG                         GGGCCTGCAAGTCATAATCCTTTGGCTTATAAATACTATAATGCTGAGGAA
genomic: AAGAGTGGGAAGGGGAATTCTTCCCTAACATTTCGTACATCAAATATGAGgtatttcaat ... gtatgtacagGGGCCTGCAAGTCATAATCCTTTGGCTTATAAATACTATAATGCTGAGGAA
EST: gi|100392407|gb|BY953347.1|BY953347
EST:     AAGAGTGGGAAGGGGAATTCTTCCCTAACATTTCGTACATCAAATATGAG                         GGGCCTGCAAGTCATAATCCTTTGGCTTATAAATACTATAATGCTGAGGAA
genomic: AAGAGTGGGAAGGGGAATTCTTCCCTAACATTTCGTACATCAAATATGAGgtatttcaat ... gtatgtacagGGGCCTGCAAGTCATAATCCTTTGGCTTATAAATACTATAATGCTGAGGAA
EST: gi|100358061|gb|BY965452.1|BY965452
EST:     AAGAGTGGGAAGGGGAATTCTTCCCTAACATTTCGTACATCAAATATGAG                         GGGCCTGCAAGTCATAATCCTTTGGCTTATAAATACTATAATGCTGAGGAA
genomic: AAGAGTGGGAAGGGGAATTCTTCCCTAACATTTCGTACATCAAATATGAGgtatttcaat ... gtatgtacagGGGCCTGCAAGTCATAATCCTTTGGCTTATAAATACTATAATGCTGAGGAA
EST: gi|100404244|gb|BY955328.1|BY955328
EST:     AAGAGTGGGAAGGGGAATTCTTCCCTAACATTTCGTACATCAAATATGAG                         GGGCCTGCAAGTCATAATCCTTTGGCTTATAAATACTATAATGCTGAGGAA
genomic: AAGAGTGGGAAGGGGAATTCTTCCCTAACATTTCGTACATCAAATATGAGgtatttcaat ... gtatgtacagGGGCCTGCAAGTCATAATCCTTTGGCTTATAAATACTATAATGCTGAGGAA
EST: gi|208376225|gb|DC914510.1|DC914510
EST:     AAGAGTGGGAAGGGGAATTCTTCCCTAACATTTCGTACATCAAATATGAG                         GGGCCTGCAAGTCATAATCCTTTGGCTTATAAATACTATAATGCTGAGGAA
genomic: AAGAGTGGGAAGGGGAATTCTTCCCTAACATTTCGTACATCAAATATGAGgtatttcaat ... gtatgtacagGGGCCTGCAAGTCATAATCCTTTGGCTTATAAATACTATAATGCTGAGGAA
EST: gi|100398077|gb|BY954076.1|BY954076
EST:     AAGAGTGGGAAGGGGAATTCTTCCCTAACATTTCGTACATCAAATATGAG                         GGGCCTGCAAGTCATAATCCTTTGGCTTATAAATACTATAATGCTGAGGAA
genomic: AAGAGTGGGAAGGGGAATTCTTCCCTAACATTTCGTACATCAAATATGAGgtatttcaat ... gtatgtacagGGGCCTGCAAGTCATAATCCTTTGGCTTATAAATACTATAATGCTGAGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catcagagaatagttgaaggtgactgaagacttaatgatgtttctgtatgtacagGGGCCTGCAAGTCATAATCCTTTGGCTTATAAATACTATAATGCTGAGGAACTGATTTTTGGCAAGAAGATGAAG
                             acttaat  putative branch site (score: 4)
                                        tttctgt  putative PPT
                               ttaatgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttcaattcacagttctagtggaattctcatcaagggtcgcattagacttcctttgtggtctttcggtgtcttcacatcgaagctctcgcttaacatgtaaagtaagtcattgcatcagagaatagttgaaggtgactgaagacttaatgatgtttctgtatgtacagGGGCCTGCAAGTCATAATCCTTTGGCTTATAAATACTATAATGCTGAGGAACTGATTTTTGGCAAGAAGATGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG