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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGTTGTTCACCCTTTGAAGGTCTCCTTGGAAGAACTTTACAATGGCACATCAAAGAAACTGTCATTGTCGAGGAACATTATTTGCTCAAAGTGCAAAGGgtaaagctcgttgctgtgcatctcgttacagattatgtcttaattggaacattcaacgtaaggttcatttcagtatcaagaaaaattcccgcttttcttg...

Basic information

species Physcomitrella patens
transcript PP1S342_16V6.1
intron # 3
splice site 5'
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|162279815|gb|FC455099.1|FC455099
EST:     TCAAAGAAACTGTCATTGTCGAGGAACATTATTTGCTCAAAGTGCAAAGG                         GAAAGGTTCCAAATCCGGTGCATCCAGTCGGTGTGCAGGATGTCAAGGTTC
genomic: TCAAAGAAACTGTCATTGTCGAGGAACATTATTTGCTCAAAGTGCAAAGGgtaaagctcg ... gaatttgcagGAAAGGTTCCAAATCCGGTGCATCCAGTCGGTGTGCAGGATGTCAAGGTTC
EST: gi|100401219|gb|BY990892.1|BY990892
EST:     TCAAAGAAACTGTCATTGTCGAGGAACATTATTTGCTCAAAGTGCAAAGG                         GAAAGGTTCCAAATCCGGTGCATCCAGTCGGTGTGCAGGGTGTCAAGGTTC
genomic: TCAAAGAAACTGTCATTGTCGAGGAACATTATTTGCTCAAAGTGCAAAGGgtaaagctcg ... gaatttgcagGAAAGGTTCCAAATCCGGTGCATCCAGTCGGTGTGCAGGATGTCAAGGTTC
EST: gi|100414304|gb|BY992711.1|BY992711
EST:     TCAAAGAAACTGTCATTGTCGAGGAACATTATTTGCTCAAAGTGCAAAGG                         GAAAGGTTCCAAATCCGGTGCATCCAGTCGGTGTGCAGGATGTCAAGGTTC
genomic: TCAAAGAAACTGTCATTGTCGAGGAACATTATTTGCTCAAAGTGCAAAGGgtaaagctcg ... gaatttgcagGAAAGGTTCCAAATCCGGTGCATCCAGTCGGTGTGCAGGATGTCAAGGTTC
EST: gi|19778134|gb|BQ039262.1|BQ039262
EST:     TCAAAGAAACTGTCATTGTCGAGGAACATTATTTGCTCAAAGTGCAAAGG                         GAAAGGTTCCAAATCCGGTGCATCCAGTCGGTGTGCAGGATGTCAAGGTTC
genomic: TCAAAGAAACTGTCATTGTCGAGGAACATTATTTGCTCAAAGTGCAAAGGgtaaagctcg ... gaatttgcagGAAAGGTTCCAAATCCGGTGCATCCAGTCGGTGTGCAGGATGTCAAGGTTC
EST: gi|162174909|gb|FC351701.1|FC351701
EST:     TCANAGAAACTGTCATTGTCGAGGAACATTATTTGCTCAAAGTGCANAGG                         GAAAGGTTCCAAATCCGGTGCATCCAGTCGGTGTGCAGGATGTCAAGGTTC
genomic: TCAAAGAAACTGTCATTGTCGAGGAACATTATTTGCTCAAAGTGCAAAGGgtaaagctcg ... gaatttgcagGAAAGGTTCCAAATCCGGTGCATCCAGTCGGTGTGCAGGATGTCAAGGTTC
EST: gi|162189947|gb|FC365611.1|FC365611
EST:     TCAAAGAAACTGTCATTGTCGAGGAACATTATTTGCTCAAAGTGCAAAGG                         GAAAGGTTCCAAATCCGGTGCATCCAGTCGGTGTGCAGGATGTCAAGGTTC
genomic: TCAAAGAAACTGTCATTGTCGAGGAACATTATTTGCTCAAAGTGCAAAGGgtaaagctcg ... gaatttgcagGAAAGGTTCCAAATCCGGTGCATCCAGTCGGTGTGCAGGATGTCAAGGTTC
EST: gi|162242594|gb|FC414985.1|FC414985
EST:     TCAAAGAAACTGTCATTGTCGAGGAACATTATTTGCTCAAAGTGCAAAGG                         GAAAGGTTCCAAATCCGGTGCATCCAGTCGGTGTGCAGGATGTCAAGGTTC
genomic: TCAAAGAAACTGTCATTGTCGAGGAACATTATTTGCTCAAAGTGCAAAGGgtaaagctcg ... gaatttgcagGAAAGGTTCCAAATCCGGTGCATCCAGTCGGTGTGCAGGATGTCAAGGTTC
EST: gi|162195909|gb|FC375642.1|FC375642
EST:     TCAAAGAAACTGTCATTGTCGAGGAACATTATTTGCTCAAAGTGCAAAGG                         GAAAGGTTCCAAATCCGGTGCATCCAGTCGGTGTGCAGGATGTCAAGGTTC
genomic: TCAAAGAAACTGTCATTGTCGAGGAACATTATTTGCTCAAAGTGCAAAGGgtaaagctcg ... gaatttgcagGAAAGGTTCCAAATCCGGTGCATCCAGTCGGTGTGCAGGATGTCAAGGTTC
EST: gi|100357768|gb|BY946564.1|BY946564
EST:     TCAAAGAAACTGTCATTGTCGAGGAACATTATTTGCTCAAAGTGCAAAGG                         GAAAGGTTCCAAATCCGGTGCATCCAGTCGGTGTGCAGGATGTCAAGGTTC
genomic: TCAAAGAAACTGTCATTGTCGAGGAACATTATTTGCTCAAAGTGCAAAGGgtaaagctcg ... gaatttgcagGAAAGGTTCCAAATCCGGTGCATCCAGTCGGTGTGCAGGATGTCAAGGTTC
EST: gi|162152418|gb|FC327981.1|FC327981
EST:     TCAAAGAAACTGTCATTGTCGAGGAACATTATTTGCTCAAAGTGCAAAGG                         GAAAGGTTCCAAATCCGGTGCATCCAGTCGGTGTGCAGGATGTCAAGGTTC
genomic: TCAAAGAAACTGTCATTGTCGAGGAACATTATTTGCTCAAAGTGCAAAGGgtaaagctcg ... gaatttgcagGAAAGGTTCCAAATCCGGTGCATCCAGTCGGTGTGCAGGATGTCAAGGTTC
EST: gi|100409753|gb|BY956088.1|BY956088
EST:     TCAAAGAAACTGTCATTGTCGAGGAACATTATTTGCTCAAAGTGCAAAGG                         GAAAGGTTCCAAATCCGGTGCATCCAGTCGGTGTGCAGGATGTCAAGGTTC
genomic: TCAAAGAAACTGTCATTGTCGAGGAACATTATTTGCTCAAAGTGCAAAGGgtaaagctcg ... gaatttgcagGAAAGGTTCCAAATCCGGTGCATCCAGTCGGTGTGCAGGATGTCAAGGTTC
EST: gi|100415464|gb|BY992856.1|BY992856
EST:     TCANAGAAACTGTCATTGTCGAGGAACATTATTTGCTCAAAGTGCAAAGG                         GGAAGGTTCCAAATCCGGTGCATCCAGTCGGTGTGCAGGATGTCA-GGTTT
genomic: TCAAAGAAACTGTCATTGTCGAGGAACATTATTTGCTCAAAGTGCAAAGGgtaaagctcg ... gaatttgcagGAAAGGTTCCAAATCCGGTGCATCCAGTCGGTGTGCAGGATGTCAAGGTT-
EST: gi|162157608|gb|FC332930.1|FC332930
EST:     TCAAAGAAACTGTCATTGTCGAGGAACATTATTTGCTCAAAGTGCAAAGG                         GAAAGGTTCCAAATCCGGTGCATCCAGTCGGTGTGCAGGATGTCAAGGTTC
genomic: TCAAAGAAACTGTCATTGTCGAGGAACATTATTTGCTCAAAGTGCAAAGGgtaaagctcg ... gaatttgcagGAAAGGTTCCAAATCCGGTGCATCCAGTCGGTGTGCAGGATGTCAAGGTTC
EST: gi|162185740|gb|FC362088.1|FC362088
EST:     TCAAAGAAACTGTCATTGTCGAGGAACATTATTTGCTCAAAGTGCAAAGG                         GAAAGGTTCCAAATCCGGTGCATCCAGTCGGTGTGCAGGATGTCAAGGTTC
genomic: TCAAAGAAACTGTCATTGTCGAGGAACATTATTTGCTCAAAGTGCAAAGGgtaaagctcg ... gaatttgcagGAAAGGTTCCAAATCCGGTGCATCCAGTCGGTGTGCAGGATGTCAAGGTTC
EST: gi|100448738|gb|CJ973037.1|CJ973037
EST:     TCAAAGAAACTGTCATTGTCGAGGAACATTATTTGCTCAAAGTGCAAAGG                         GAAAGGTTCCAAATCCGGTGCATCCAGTCGGTGTGCAGGATGTCAAGGTTC
genomic: TCAAAGAAACTGTCATTGTCGAGGAACATTATTTGCTCAAAGTGCAAAGGgtaaagctcg ... gaatttgcagGAAAGGTTCCAAATCCGGTGCATCCAGTCGGTGTGCAGGATGTCAAGGTTC
EST: gi|162254102|gb|FC429626.1|FC429626
EST:     TCAAAGAAACTGTCATTGTCGAGGAACATTATTTGCTCAAAGTGCAAAGG                         GAAAGGTTCCAAATCCGGTGCATCCAGTCGGTGTGCAGGATGTCAAGGTTC
genomic: TCAAAGAAACTGTCATTGTCGAGGAACATTATTTGCTCAAAGTGCAAAGGgtaaagctcg ... gaatttgcagGAAAGGTTCCAAATCCGGTGCATCCAGTCGGTGTGCAGGATGTCAAGGTTC
EST: gi|162162054|gb|FC338845.1|FC338845
EST:     TCAAAGAAACTGTCATTGTCGAGGAACATTATTTGCTCAAAGTGCAAAGG                         GAAAGGTTCCAAATCCGGTGCATCCAGTCGGTGTGCAGGATGTCAAGGTTC
genomic: TCAAAGAAACTGTCATTGTCGAGGAACATTATTTGCTCAAAGTGCAAAGGgtaaagctcg ... gaatttgcagGAAAGGTTCCAAATCCGGTGCATCCAGTCGGTGTGCAGGATGTCAAGGTTC

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: 70

ATGTTGTTCACCCTTTGAAGGTCTCCTTGGAAGAACTTTACAATGGCACATCAAAGAAACTGTCATTGTCGAGGAACATTATTTGCTCAAAGTGCAAAGGgtaaagctcg ... gaatttgcagGAAAGGTTCCAAATCCGGTGCATCCAGTCGGTGTGCAGGATGTCAAGGTTCAGGTGTGAAGGTCTCAGTGCGTCAGCTCGGCCCTGGTATGATACAGCAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGTTGTTCACCCTTTGAAGGTCTCCTTGGAAGAACTTTACAATGGCACATCAAAGAAACTGTCATTGTCGAGGAACATTATTTGCTCAAAGTGCAAAGGgtaaagctcgttgctgtgcatctcgttacagattatgtcttaattggaacattcaacgtaaggttcatttcagtatcaagaaaaattcccgcttttcttg

- - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caagaaaa