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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttaaatgggaaggcgacatgctgtgcaacgtagagtgcccatgctcatatatgctacagcttgtccagcagctgacttgagtaaactctgtatgacagGCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATG

Basic information

species Physcomitrella patens
transcript PP1S90_28V6.4
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|100355472|gb|BY945951.1|BY945951
EST:     TAAAACTGGGATTACAACCTGGGGAACTGACCATTTTCTCCAAAGAAGCG                         GCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAT
genomic: TAAAACTGGGATTACAACCTGGGGAACTGACCATTTTCTCCAAAGAAGCGgtatattgct ... tgtatgacagGCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAT
EST: gi|100391837|gb|BY989572.1|BY989572
EST:     TAAAACTGGGATTACAACCTGGGGAACTGACCATTTTCTCCAAAGAAGCG                         ACGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAC
genomic: TAAAACTGGGATTACAACCTGGGGAACTGACCATTTTCTCCAAAGAAGCGgtatattgct ... tgtatgacagGCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAT
EST: gi|67573440|gb|BJ946264.1|BJ946264
EST:     TAAAACTGGGATTACAACCTGGGGAACTGACCATTTTCTCCAAAGAAGCG                         GCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAT
genomic: TAAAACTGGGATTACAACCTGGGGAACTGACCATTTTCTCCAAAGAAGCGgtatattgct ... tgtatgacagGCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAT
EST: gi|18365163|gb|BJ197237.1|BJ197237
EST:     TAAAACTGGGATTACAACCTGGGGAACTGACCATTTTCTCCAAAGAAGCG                         GCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAT
genomic: TAAAACTGGGATTACAACCTGGGGAACTGACCATTTTCTCCAAAGAAGCGgtatattgct ... tgtatgacagGCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAT
EST: gi|100377879|gb|BY986439.1|BY986439
EST:     TAAAACTGGGATTACAACCTGGGGAACTGACCATTTTCTCCAAAGAAGCG                         GCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAT
genomic: TAAAACTGGGATTACAACCTGGGGAACTGACCATTTTCTCCAAAGAAGCGgtatattgct ... tgtatgacagGCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAT
EST: gi|162278698|gb|FC454808.1|FC454808
EST:     T-AAACTGGGATTACAACCTGGGGAACTGACCATTTTCTCCAAAGAAGCG                         GCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAT
genomic: TAAAACTGGGATTACAACCTGGGGAACTGACCATTTTCTCCAAAGAAGCGgtatattgct ... tgtatgacagGCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAT
EST: gi|100361319|gb|BY965781.1|BY965781
EST:     TAAAACTGGGATTACAACCTGGGGAACTGACCATTTTCTCCAAAGAAGCG                         GCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAT
genomic: TAAAACTGGGATTACAACCTGGGGAACTGACCATTTTCTCCAAAGAAGCGgtatattgct ... tgtatgacagGCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAT
EST: gi|18356191|gb|BJ188250.1|BJ188250
EST:     TAAAACTGGGATTACAACCTGGGGAACTGACCATTTTCTCCAAGGAAGCG                         GCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAT
genomic: TAAAACTGGGATTACAACCTGGGGAACTGACCATTTTCTCCAAAGAAGCGgtatattgct ... tgtatgacagGCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAT
EST: gi|208385252|gb|DC915052.1|DC915052
EST:     TAAAACTGGGATTACAACCTGGGGAACTGACCATTTTCTCCAAAGAAGCG                         GCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAT
genomic: TAAAACTGGGATTACAACCTGGGGAACTGACCATTTTCTCCAAAGAAGCGgtatattgct ... tgtatgacagGCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAT
EST: gi|208361425|gb|DC935112.1|DC935112
EST:     TAAAACTGGGATTACAACCTGGGGAACTGACCATTTTCTCCAAAGAAGCG                         GCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAT
genomic: TAAAACTGGGATTACAACCTGGGGAACTGACCATTTTCTCCAAAGAAGCGgtatattgct ... tgtatgacagGCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAT
EST: gi|100386104|gb|BY970043.1|BY970043
EST:     TAAAACTGGGATTACAACCTGGGGAACTGACCATTTTCTCCAAAGAAGCG                         GCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAT
genomic: TAAAACTGGGATTACAACCTGGGGAACTGACCATTTTCTCCAAAGAAGCGgtatattgct ... tgtatgacagGCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAT
EST: gi|18331507|gb|BJ163518.1|BJ163518
EST:     TAAAACTGGGATTACAACCTGGGGAACTGACCATTTTCTCCAAAGAAGCG                         GCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAT
genomic: TAAAACTGGGATTACAACCTGGGGAACTGACCATTTTCTCCAAAGAAGCGgtatattgct ... tgtatgacagGCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAT
EST: gi|100363976|gb|BY966264.1|BY966264
EST:     TAAAACTGGGATTACAACCTGGGGAACTGACCATTTTCTCCAAAGAAGCG                         GCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAT
genomic: TAAAACTGGGATTACAACCTGGGGAACTGACCATTTTCTCCAAAGAAGCGgtatattgct ... tgtatgacagGCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAT
EST: gi|208375453|gb|DC936996.1|DC936996
EST:     TAAAACTGGGATTACAACCTGGGGAACTGACCATTTTCTCCAAAGAAGCG                         GCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAT
genomic: TAAAACTGGGATTACAACCTGGGGAACTGACCATTTTCTCCAAAGAAGCGgtatattgct ... tgtatgacagGCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAT
EST: gi|162225064|gb|FC401688.1|FC401688
EST:     TGACCATTTTCTCCAAAGAAGCG                         GCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAT
genomic: TGACCATTTTCTCCAAAGAAGCGgtatattgct ... tgtatgacagGCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAT
EST: gi|100378191|gb|BY949726.1|BY949726
EST:     TAAAACTGGGATTACAACCTGGGGAACTGACCATTTTCTCCAAAGAAGCG                         GCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAT
genomic: TAAAACTGGGATTACAACCTGGGGAACTGACCATTTTCTCCAAAGAAGCGgtatattgct ... tgtatgacagGCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAT
EST: gi|18360912|gb|BJ192976.1|BJ192976
EST:     TAAAACTGGGATTACAACCTGGGGAACTGACCATTTTCTCCAAAGAAGCG                         GCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAT
genomic: TAAAACTGGGATTACAACCTGGGGAACTGACCATTTTCTCCAAAGAAGCGgtatattgct ... tgtatgacagGCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAT
EST: gi|100365162|gb|BY966841.1|BY966841
EST:     TAAAACTGGGATTACAACCTGGGGAACTGACCATTTTCTCCAAAGAAGCG                         GCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAT
genomic: TAAAACTGGGATTACAACCTGGGGAACTGACCATTTTCTCCAAAGAAGCGgtatattgct ... tgtatgacagGCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAT
EST: gi|18364385|gb|BJ196458.1|BJ196458
EST:     TAAAACTGGGATTACAACCTGGGGAACTGACCATTTTCTCCAAAGAAGCG                         GCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAT
genomic: TAAAACTGGGATTACAACCTGGGGAACTGACCATTTTCTCCAAAGAAGCGgtatattgct ... tgtatgacagGCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAT
EST: gi|100448660|gb|CJ972959.1|CJ972959
EST:     TAAAACTGGGATTACAACCTGGGGAACTGACCATTTTCTCCAAAGAAGCG                         GCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAT
genomic: TAAAACTGGGATTACAACCTGGGGAACTGACCATTTTCTCCAAAGAAGCGgtatattgct ... tgtatgacagGCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAT
EST: gi|100375395|gb|BY948855.1|BY948855
EST:     TAAAACTGGGATTACAACCTGGGGAACTGACCATTTTCTCCAAAGAAGCG                         GCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAT
genomic: TAAAACTGGGATTACAACCTGGGGAACTGACCATTTTCTCCAAAGAAGCGgtatattgct ... tgtatgacagGCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAT
EST: gi|18359114|gb|BJ191174.1|BJ191174
EST:     TAAAACTGGGATTACAACCTGGGGAACTGACCATTTTCTCCAAAGAAGCG                         GCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAT
genomic: TAAAACTGGGATTACAACCTGGGGAACTGACCATTTTCTCCAAAGAAGCGgtatattgct ... tgtatgacagGCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAT
EST: gi|162237033|gb|FC413192.1|FC413192
EST:     TGGGATT-CAACCTGGGGAACTGACCATTTTCTCCAAAGAAGCG                         GCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAT
genomic: TGGGATTACAACCTGGGGAACTGACCATTTTCTCCAAAGAAGCGgtatattgct ... tgtatgacagGCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAT
EST: gi|18349313|gb|BJ181362.1|BJ181362
EST:     TAAAACTGGGATTACAACCTGGGGAACTGACCATTTTCTCCAAAGAAGCG                         GCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAT
genomic: TAAAACTGGGATTACAACCTGGGGAACTGACCATTTTCTCCAAAGAAGCGgtatattgct ... tgtatgacagGCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAT
EST: gi|100406861|gb|BY955754.1|BY955754
EST:     TAAAACTGGGATTACAACCTGGGGAACTGACCATTTTCTCCAAAGAAGCG                         GCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAT
genomic: TAAAACTGGGATTACAACCTGGGGAACTGACCATTTTCTCCAAAGAAGCGgtatattgct ... tgtatgacagGCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAT
EST: gi|100444932|gb|BY982760.1|BY982760
EST:     TAAAACTGGGATTACAACCTGGGGAACTGACCATTTTCTCCAAAGAAGCG                         GCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAT
genomic: TAAAACTGGGATTACAACCTGGGGAACTGACCATTTTCTCCAAAGAAGCGgtatattgct ... tgtatgacagGCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAT
EST: gi|100388010|gb|BY988483.1|BY988483
EST:     TAAAACTGGGATTACAACCTGGGGAACTGACCATTTTCTCCAAAGAAGCG                         GCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAT
genomic: TAAAACTGGGATTACAACCTGGGGAACTGACCATTTTCTCCAAAGAAGCGgtatattgct ... tgtatgacagGCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAT
EST: gi|100385258|gb|BY950850.1|BY950850
EST:     TAAAACTGGGATTACAACCTGGGGAACTGACCATTTTCTCCAAAGAAGCG                         GCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAT
genomic: TAAAACTGGGATTACAACCTGGGGAACTGACCATTTTCTCCAAAGAAGCGgtatattgct ... tgtatgacagGCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAT
EST: gi|100418007|gb|BY993291.1|BY993291
EST:     TAAAACTGGGATTACAACCTGGGGAACTGACCATTTTCTCCAAAGAAGCG                         GCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAT
genomic: TAAAACTGGGATTACAACCTGGGGAACTGACCATTTTCTCCAAAGAAGCGgtatattgct ... tgtatgacagGCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAT
EST: gi|18369448|gb|BJ201535.1|BJ201535
EST:     TAAAACTGGGATTACAACCTGGGGAACTGACCATTTTCTCCAAAGAAGCG                         GCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAT
genomic: TAAAACTGGGATTACAACCTGGGGAACTGACCATTTTCTCCAAAGAAGCGgtatattgct ... tgtatgacagGCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAT
EST: gi|162158960|gb|FC334820.1|FC334820
EST:     TAAAACTGGGATTACAACCTGGGGAACTGACCATTTTCTCCAAAGAAGCG                         GCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAT
genomic: TAAAACTGGGATTACAACCTGGGGAACTGACCATTTTCTCCAAAGAAGCGgtatattgct ... tgtatgacagGCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGAT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 35 (upstream exon), 35 (downstream exon)
Score: 40

GGCTACGCTGCACGAGAGTTTGTAAAACTGGGATTACAACCTGGGGAACTGACCATTTTCTCCAAAGAAGCGgtatattgct ... tgtatgacagGCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcatatatgctacagcttgtccagcagctgacttgagtaaactctgtatgacagGCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATG
                          agctgac  putative branch site (score: 40)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttaaatgggaaggcgacatgctgtgcaacgtagagtgcccatgctcatatatgctacagcttgtccagcagctgacttgagtaaactctgtatgacagGCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG