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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtcttttttgcactgaacagtcctcaagttctagatgtaacacgaagtggatgaatctatgtgcgcttttacagtgcaagtcctaggcatgtcatacagtagttattctctttacttaattgttgaagcttggtctttaacgtcaaggctgtggtcttcaactgagatttgggtgggacgctcgcagGAAATGTTGGATTTAGCAATCAAGTACAATAAAGCTGTGCAGGAGGAAGACCAGCTTAGTCCAGAGAAATTGGCTATTGTCAATGTGGGGCGTCAAGATG

Basic information

species Physcomitrella patens
transcript PP1S46_324V6.1
intron # 5
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|67692976|gb|BJ953209.1|BJ953209
EST:     CTCTTCAGCGATATGACGAGCATGGAAAAACTAATGAAGCCACAGTGAAA                         GAAATGTTGGATTTAGCAATCAAGTACAATAAAGCTGTGCAGGAGGAAGAC
genomic: CTCTTCAGCGATATGACGAGCATGGAAAAACTAATGAAGCCACAGTGAAAgtgagtcttt ... acgctcgcagGAAATGTTGGATTTAGCAATCAAGTACAATAAAGCTGTGCAGGAGGAAGAC
EST: gi|162224586|gb|FC400482.1|FC400482
EST:     CTCTTCAGCGATATGACGAGCATGGAAAAACTAATGAAGCCACAGTGAAA                         GAAATGTTGGATTTAGCAATCAAGTACAATAAAGCTGTGCAGGAGGAAGAC
genomic: CTCTTCAGCGATATGACGAGCATGGAAAAACTAATGAAGCCACAGTGAAAgtgagtcttt ... acgctcgcagGAAATGTTGGATTTAGCAATCAAGTACAATAAAGCTGTGCAGGAGGAAGAC
EST: gi|18337375|gb|BJ169399.1|BJ169399
EST:     CTCTTCAGCGATATGACGAGCATGGAAAAACTAATGAAGCCACAGTGAAA                         GAAATGTTGGATTTAGCAATCAAGTACAATAAAGCTGTGCAGGAGGAAGAC
genomic: CTCTTCAGCGATATGACGAGCATGGAAAAACTAATGAAGCCACAGTGAAAgtgagtcttt ... acgctcgcagGAAATGTTGGATTTAGCAATCAAGTACAATAAAGCTGTGCAGGAGGAAGAC
EST: gi|67693371|gb|BJ953604.1|BJ953604
EST:     CTCTTCAGCGATATGACGAGCATGGAAAAACTAATGAAGCCACAGTGAAA                         GAAATGTTGGATTTAGCAATCAAGTACAATAAAGCTGTGCAGGAGGAAGAC
genomic: CTCTTCAGCGATATGACGAGCATGGAAAAACTAATGAAGCCACAGTGAAAgtgagtcttt ... acgctcgcagGAAATGTTGGATTTAGCAATCAAGTACAATAAAGCTGTGCAGGAGGAAGAC
EST: gi|208378926|gb|DC922772.1|DC922772
EST:     CTCTTCAGCGATATGACGAGCATGGAAAAACTAATGAAGCCACAGTGAAA                         GAAATGTTGGATTTAGCAATCAAGTACAATAAAGCTGTGCAGGAGGAAGAC
genomic: CTCTTCAGCGATATGACGAGCATGGAAAAACTAATGAAGCCACAGTGAAAgtgagtcttt ... acgctcgcagGAAATGTTGGATTTAGCAATCAAGTACAATAAAGCTGTGCAGGAGGAAGAC
EST: gi|162224587|gb|FC400483.1|FC400483
EST:     CTCTTCAGCGATATGACGAGCATGGAAAAACTAATGAAGCCACAGTGAAA                         GAAATGTTGGATTTAGCAATCAAGTACAATAAAGCTGTGCAGGAGGAAGAC
genomic: CTCTTCAGCGATATGACGAGCATGGAAAAACTAATGAAGCCACAGTGAAAgtgagtcttt ... acgctcgcagGAAATGTTGGATTTAGCAATCAAGTACAATAAAGCTGTGCAGGAGGAAGAC
EST: gi|208395571|gb|DC928986.1|DC928986
EST:     CTCTTCAGCGATATGACGAGCATGGAAAAACTAATGAAGCCACAGTGAAA                         GAAATGTTGGATTTAGCAATCAAGTACAATAAAGCTGTGCAGGAGGAAGAC
genomic: CTCTTCAGCGATATGACGAGCATGGAAAAACTAATGAAGCCACAGTGAAAgtgagtcttt ... acgctcgcagGAAATGTTGGATTTAGCAATCAAGTACAATAAAGCTGTGCAGGAGGAAGAC
EST: gi|208368927|gb|DC947485.1|DC947485
EST:     CTCTTCAGCGATATGACGAGCATGGAAAAACTAATGAAGCCACAGTGAAA                         GAAATGTTGGATTTAGCAATCAAGTACAATAAAGCTGTGCAGGAGGAAGAC
genomic: CTCTTCAGCGATATGACGAGCATGGAAAAACTAATGAAGCCACAGTGAAAgtgagtcttt ... acgctcgcagGAAATGTTGGATTTAGCAATCAAGTACAATAAAGCTGTGCAGGAGGAAGAC
EST: gi|208362822|gb|DC950622.1|DC950622
EST:     CTCTTCAGCAATATGACGAGCATGGAAAAACTAATGAAGCCACAGTGAAA                         GAAATGTTGGATTTAGCAATCAAGTACAATAAAGCTGTGCAGGAGGAAGAC
genomic: CTCTTCAGCGATATGACGAGCATGGAAAAACTAATGAAGCCACAGTGAAAgtgagtcttt ... acgctcgcagGAAATGTTGGATTTAGCAATCAAGTACAATAAAGCTGTGCAGGAGGAAGAC
EST: gi|37843465|gb|BJ601473.1|BJ601473
EST:     CTCTTCAGCGATATGACGAGCATGGAAAAACTAATGAAGCCACAGTGAAA                         GAAATGTTGGATTTAGCAATCAAGTACAATAAAGCTGTGCAGGAGGAAGAC
genomic: CTCTTCAGCGATATGACGAGCATGGAAAAACTAATGAAGCCACAGTGAAAgtgagtcttt ... acgctcgcagGAAATGTTGGATTTAGCAATCAAGTACAATAAAGCTGTGCAGGAGGAAGAC
EST: gi|67696853|gb|BJ957086.1|BJ957086
EST:     CTCTTCAGCGATATGACGAGCATGGAAAAACTAATGAAGCCACAGTGAAA                         GAAATGTTGGATTTAGCAATCAAGTACAATAAAGCTGTGCAGGAGGAAGAC
genomic: CTCTTCAGCGATATGACGAGCATGGAAAAACTAATGAAGCCACAGTGAAAgtgagtcttt ... acgctcgcagGAAATGTTGGATTTAGCAATCAAGTACAATAAAGCTGTGCAGGAGGAAGAC
EST: gi|208369314|gb|DC955859.1|DC955859
EST:     CTCTTCAGCGATATGACGAGCATGGAAAAACTAATGAAGCCACAGTGAAA                         GAAATGTTGGATTTAGCAATCAAGTACAATAAAGCTGTGCAGGAGGAAGAC
genomic: CTCTTCAGCGATATGACGAGCATGGAAAAACTAATGAAGCCACAGTGAAAgtgagtcttt ... acgctcgcagGAAATGTTGGATTTAGCAATCAAGTACAATAAAGCTGTGCAGGAGGAAGAC
EST: gi|162150909|gb|FC327389.1|FC327389
EST:     CTCTTCAGCGATATGACGAGCATGGAAAAACTAATGAAGCCACAGTGAAA                         GAAATGTTGGATTTAGCAATCAAGTACAATAAAGCTGTGCAGGAGGAAGAC
genomic: CTCTTCAGCGATATGACGAGCATGGAAAAACTAATGAAGCCACAGTGAAAgtgagtcttt ... acgctcgcagGAAATGTTGGATTTAGCAATCAAGTACAATAAAGCTGTGCAGGAGGAAGAC
EST: gi|18335934|gb|BJ167955.1|BJ167955
EST:     CTCTTCAGCGATATGACGAGCATGGAAAAACTAATGAAGCCACAGTGAAA                         GAAATGTTGGATTTAGCAATCAAGTACAATAAAGCTGTGCAGGAGGAAGAC
genomic: CTCTTCAGCGATATGACGAGCATGGAAAAACTAATGAAGCCACAGTGAAAgtgagtcttt ... acgctcgcagGAAATGTTGGATTTAGCAATCAAGTACAATAAAGCTGTGCAGGAGGAAGAC
EST: gi|208364180|gb|DC947284.1|DC947284
EST:     CTCTTCAGCGATATGACGAGCATGGAAAAACTAATGAAGCCACAGTGAAA                         GAAATGTTGGATTTAGCAATCAAGTACAATAAAGCTGTGCAGGAGGAAGAC
genomic: CTCTTCAGCGATATGACGAGCATGGAAAAACTAATGAAGCCACAGTGAAAgtgagtcttt ... acgctcgcagGAAATGTTGGATTTAGCAATCAAGTACAATAAAGCTGTGCAGGAGGAAGAC

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: 34 (upstream exon), 35 (downstream exon)
Score: 7

AGAGAAAATGCTTTTGAACCTTCACAAGAAGAAGTGGACTGATGGACTTACTCTTCAGCGATATGACGAGCATGGAAAAACTAATGAAGCCACAGTGAAAgtgagtcttt ... acgctcgcagGAAATGTTGGATTTAGCAATCAAGTACAATAAAGCTGTGCAGGAGGAAGACCAGCTTAGTCCAGAGAAATTGGCTATTGTCAATGTGGGGCGTCAAGATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtctttaacgtcaaggctgtggtcttcaactgagatttgggtgggacgctcgcagGAAATGTTGGATTTAGCAATCAAGTACAATAAAGCTGTGCAGGAGGAAGACCAGCTTAGTCCAGAGAAATTGGCTATTGTCAATGTGGGGCGTCAAGATG
  ctttaac  putative branch site (score: 7)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtcttttttgcactgaacagtcctcaagttctagatgtaacacgaagtggatgaatctatgtgcgcttttacagtgcaagtcctaggcatgtcatacagtagttattctctttacttaattgttgaagcttggtctttaacgtcaaggctgtggtcttcaactgagatttgggtgggacgctcgcagGAAATGTTGGATTTAGCAATCAAGTACAATAAAGCTGTGCAGGAGGAAGACCAGCTTAGTCCAGAGAAATTGGCTATTGTCAATGTGGGGCGTCAAGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG