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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caaagaactaagcaatgatatacttgaatagtggccgaaacagatatcacatgcatctaagtctaatgggtcttgattatctcgtaaattatgtgggcagGAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAG

Basic information

species Physcomitrella patens
transcript PP1S215_28V6.1
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|162184664|gb|FC361902.1|FC361902
EST:     CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTG                         GAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
genomic: CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTGgtaagccatt ... atgtgggcagGAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
EST: gi|162207832|gb|FC384125.1|FC384125
EST:     CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTG                         GAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
genomic: CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTGgtaagccatt ... atgtgggcagGAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
EST: gi|208400418|gb|DC908645.1|DC908645
EST:     CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTG                         GAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
genomic: CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTGgtaagccatt ... atgtgggcagGAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
EST: gi|100371525|gb|BY968022.1|BY968022
EST:     CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTG                         GAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
genomic: CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTGgtaagccatt ... atgtgggcagGAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
EST: gi|100395972|gb|BY972219.1|BY972219
EST:     CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTG                         GAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
genomic: CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTGgtaagccatt ... atgtgggcagGAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
EST: gi|162166511|gb|FC343208.1|FC343208
EST:     CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTG                         GAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
genomic: CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTGgtaagccatt ... atgtgggcagGAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
EST: gi|100448661|gb|CJ972960.1|CJ972960
EST:     CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTG                         GAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
genomic: CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTGgtaagccatt ... atgtgggcagGAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
EST: gi|100393479|gb|BY953418.1|BY953418
EST:     CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTG                         GAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
genomic: CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTGgtaagccatt ... atgtgggcagGAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
EST: gi|162214587|gb|FC390618.1|FC390618
EST:     CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTG                         GAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
genomic: CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTGgtaagccatt ... atgtgggcagGAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
EST: gi|100417952|gb|BY993265.1|BY993265
EST:     CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTG                         GAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
genomic: CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTGgtaagccatt ... atgtgggcagGAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
EST: gi|162155910|gb|FC332459.1|FC332459
EST:     CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTG                         GAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
genomic: CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTGgtaagccatt ... atgtgggcagGAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
EST: gi|162151638|gb|FC327767.1|FC327767
EST:     CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTG                         GAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
genomic: CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTGgtaagccatt ... atgtgggcagGAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
EST: gi|162153918|gb|FC329425.1|FC329425
EST:     CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTG                         GAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
genomic: CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTGgtaagccatt ... atgtgggcagGAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
EST: gi|100392222|gb|BY953255.1|BY953255
EST:     CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTG                         GAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
genomic: CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTGgtaagccatt ... atgtgggcagGAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
EST: gi|100384799|gb|BY969534.1|BY969534
EST:     CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTG                         GAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
genomic: CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTGgtaagccatt ... atgtgggcagGAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
EST: gi|162186627|gb|FC363599.1|FC363599
EST:     CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTG                         GAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
genomic: CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTGgtaagccatt ... atgtgggcagGAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
EST: gi|162152068|gb|FC328463.1|FC328463
EST:     CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTG                         GAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
genomic: CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTGgtaagccatt ... atgtgggcagGAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
EST: gi|100437194|gb|BY961398.1|BY961398
EST:     CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTG                         GAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
genomic: CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTGgtaagccatt ... atgtgggcagGAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
EST: gi|162155922|gb|FC332471.1|FC332471
EST:     CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTG                         GAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
genomic: CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTGgtaagccatt ... atgtgggcagGAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
EST: gi|100360719|gb|BY965863.1|BY965863
EST:     CGCAATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTG                         GAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
genomic: CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTGgtaagccatt ... atgtgggcagGAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
EST: gi|100441845|gb|BY981068.1|BY981068
EST:     CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTG                         GAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
genomic: CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTGgtaagccatt ... atgtgggcagGAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
EST: gi|100448584|gb|CJ972883.1|CJ972883
EST:     CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTG                         GAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
genomic: CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTGgtaagccatt ... atgtgggcagGAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
EST: gi|100448006|gb|CJ972305.1|CJ972305
EST:     CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTG                         GAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
genomic: CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTGgtaagccatt ... atgtgggcagGAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
EST: gi|162177756|gb|FC354590.1|FC354590
EST:     CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTG                         GAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
genomic: CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTGgtaagccatt ... atgtgggcagGAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
EST: gi|162178101|gb|FC354403.1|FC354403
EST:     CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTG                         GAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
genomic: CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTGgtaagccatt ... atgtgggcagGAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
EST: gi|162186048|gb|FC361876.1|FC361876
EST:     CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTG                         GAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
genomic: CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTGgtaagccatt ... atgtgggcagGAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
EST: gi|162161643|gb|FC339058.1|FC339058
EST:     CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTG                         GAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
genomic: CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTGgtaagccatt ... atgtgggcagGAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
EST: gi|100390035|gb|BY989115.1|BY989115
EST:     CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTG                         GAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
genomic: CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTGgtaagccatt ... atgtgggcagGAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
EST: gi|100441603|gb|BY981025.1|BY981025
EST:     CGCGATTGCCAA-GCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTG                         GAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
genomic: CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTGgtaagccatt ... atgtgggcagGAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
EST: gi|100425083|gb|BY976964.1|BY976964
EST:     CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTG                         GAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
genomic: CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTGgtaagccatt ... atgtgggcagGAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
EST: gi|162151906|gb|FC328152.1|FC328152
EST:     CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTG                         GAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
genomic: CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTGgtaagccatt ... atgtgggcagGAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
EST: gi|100360291|gb|BY966102.1|BY966102
EST:     CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTG                         GAGCTTACAGTGATTCCAGAGGGCTCCCCTGGTGTGCGGCAGGAGGTTGCA
genomic: CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTGgtaagccatt ... atgtgggcagGAGCTTACAGTGATTCCAGAGGGCTCCC-TGGTGTGCGGCAGGAGGTTGCA
EST: gi|162181637|gb|FC357939.1|FC357939
EST:     CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTG                         GAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
genomic: CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTGgtaagccatt ... atgtgggcagGAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
EST: gi|100418930|gb|BY975809.1|BY975809
EST:     CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTG                         GAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
genomic: CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTGgtaagccatt ... atgtgggcagGAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
EST: gi|100398360|gb|BY972565.1|BY972565
EST:     CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTG                         GAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
genomic: CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTGgtaagccatt ... atgtgggcagGAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
EST: gi|100437396|gb|BY961497.1|BY961497
EST:     CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTG                         GAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA
genomic: CGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTGgtaagccatt ... atgtgggcagGAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAA

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: 52

GCCCCCTTCTTGATGGATGACCCCCATGTTGGGCTACTTTTCCCCGCCGACGCGATTGCCAAAGCCAAGCACTATTTGGCTATGACCTCAGGAGGCGTTGgtaagccatt ... atgtgggcagGAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcacatgcatctaagtctaatgggtcttgattatctcgtaaattatgtgggcagGAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAG
                                       taaattatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caaagaactaagcaatgatatacttgaatagtggccgaaacagatatcacatgcatctaagtctaatgggtcttgattatctcgtaaattatgtgggcagGAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - -cacatgc