Skip to another splice site:
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacactcttatcttttctttacgttatagtgtggtgctcgtcaccttctcttcggatcatctctaaaatggttgattttcagGGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGAGGGGCTTTCAGTGACCCTGACCACCACCAAGACGAAGAAGAGGAATCAGCCCGCTAAGGC

Basic information

species Physcomitrella patens
transcript PP1S98_65V6.1
intron # 2
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|162277980|gb|FC454111.1|FC454111
EST:     CAGCTCAGAGCCCAACAACCTTTACAACTTGAACACCTTCAAGTACTCAG                         GGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGAGGGGCTTTCAG
genomic: CAGCTCAGAGCCCAACAACCTTTACAACTTGAACACCTTCAAGTACTCAGgtacactctt ... tgattttcagGGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGAGGGGCTTTCAG
EST: gi|162277981|gb|FC454112.1|FC454112
EST:     CAGCTCAGAGCCCAACAACCTTTACAACTTGAACACCTTCAAGTACTCAG                         GGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGAGGGGCTTTCAG
genomic: CAGCTCAGAGCCCAACAACCTTTACAACTTGAACACCTTCAAGTACTCAGgtacactctt ... tgattttcagGGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGAGGGGCTTTCAG
EST: gi|162266208|gb|FC441737.1|FC441737
EST:     CAGCTCAGAGCCCAACAACCTTTACAACTTGAACACCTTCAAGTACTCAG                         GGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGAGGGGCTTTCAG
genomic: CAGCTCAGAGCCCAACAACCTTTACAACTTGAACACCTTCAAGTACTCAGgtacactctt ... tgattttcagGGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGAGGGGCTTTCAG
EST: gi|18359055|gb|BJ191115.1|BJ191115
EST:     CAGCTCAGAGCCCAACAACCTTTACAACTTGAACACCTTCAAGTACTCAG                         GGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGAGGGGCTTTCAG
genomic: CAGCTCAGAGCCCAACAACCTTTACAACTTGAACACCTTCAAGTACTCAGgtacactctt ... tgattttcagGGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGAGGGGCTTTCAG
EST: gi|162276139|gb|FC452831.1|FC452831
EST:     CAGCTCAGAGCCCAACAACCTTTACAACTTGAACACCTTCAAGTACTCAG                         GGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGAGGGGCTTTCAG
genomic: CAGCTCAGAGCCCAACAACCTTTACAACTTGAACACCTTCAAGTACTCAGgtacactctt ... tgattttcagGGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGAGGGGCTTTCAG
EST: gi|162266846|gb|FC441738.1|FC441738
EST:     CAGCTCAGAGCCCAACAACCTTTACAACTTGAACACCTTCAAGTACTCAG                         GGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGAGGGGCTTTCAG
genomic: CAGCTCAGAGCCCAACAACCTTTACAACTTGAACACCTTCAAGTACTCAGgtacactctt ... tgattttcagGGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGAGGGGCTTTCAG
EST: gi|18331139|gb|BJ163146.1|BJ163146
EST:     CCCAACAACCTTTACAACTTGAACACCTTCAAGTACTCAG                         GGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGAGGGGCTTTCAG
genomic: CCCAACAACCTTTACAACTTGAACACCTTCAAGTACTCAGgtacactctt ... tgattttcagGGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGAGGGGCTTTCAG
EST: gi|162276138|gb|FC452830.1|FC452830
EST:     CAGCTCAGAGCCCAACAACCTTTACAACTTGAACACCTTCAAGTACTCAG                         GGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGAGGGGCTTTCAG
genomic: CAGCTCAGAGCCCAACAACCTTTACAACTTGAACACCTTCAAGTACTCAGgtacactctt ... tgattttcagGGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGAGGGGCTTTCAG
EST: gi|162209251|gb|FC385171.1|FC385171
EST:     CAGCTCAGAGCCCAACAACCTTTACAACTTGAACACCTTCAAGTACTCAG                         GGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGAGGGGCTTTCAG
genomic: CAGCTCAGAGCCCAACAACCTTTACAACTTGAACACCTTCAAGTACTCAGgtacactctt ... tgattttcagGGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGAGGGGCTTTCAG
EST: gi|162261514|gb|FC437531.1|FC437531
EST:     CAGCTCAGAGCCCAACAACCTTTACAACTTGAACACCTTCAAGTACTCAG                         GGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGAGGGGCTTTCAG
genomic: CAGCTCAGAGCCCAACAACCTTTACAACTTGAACACCTTCAAGTACTCAGgtacactctt ... tgattttcagGGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGAGGGGCTTTCAG
EST: gi|67574153|gb|BJ946977.1|BJ946977
EST:     CAGCTCAGAGCCCAACAACCTTTACAACTTGAACACCTTCAAGTACTCAG                         GGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGAGGGGCTTTCAG
genomic: CAGCTCAGAGCCCAACAACCTTTACAACTTGAACACCTTCAAGTACTCAGgtacactctt ... tgattttcagGGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGAGGGGCTTTCAG
EST: gi|162273848|gb|FC449779.1|FC449779
EST:     CAGCTCAGAGCCCAACAACCTTTACAACTTGAACACCTTCAAGTACTCAG                         GGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGAGGGGCTTTCAG
genomic: CAGCTCAGAGCCCAACAACCTTTACAACTTGAACACCTTCAAGTACTCAGgtacactctt ... tgattttcagGGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGAGGGGCTTTCAG
EST: gi|18344706|gb|BJ176747.1|BJ176747
EST:     CAGCTCAGAGCCCAACAACCTTTACAACTTGAACACCTTCAAGTACTCAG                         GGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGA-GGGTTTTCAG
genomic: CAGCTCAGAGCCCAACAACCTTTACAACTTGAACACCTTCAAGTACTCAGgtacactctt ... tgattttcagGGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGAGGGGCTTTCAG
EST: gi|37823910|gb|BJ581976.1|BJ581976
EST:     CAGCTCAGAGCCCAACAACCTTTACAACTTGAACACCTTCAAGTACTCAG                         GGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGA-GGGTTTTCAG
genomic: CAGCTCAGAGCCCAACAACCTTTACAACTTGAACACCTTCAAGTACTCAGgtacactctt ... tgattttcagGGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGAGGGGCTTTCAG
EST: gi|162215347|gb|FC391115.1|FC391115
EST:     CAGCTCAGAGCCCAACAACCTTTACAACTTGAACACCTTCAAGTACTCAG                         GGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGAGGGGCTTTCAG
genomic: CAGCTCAGAGCCCAACAACCTTTACAACTTGAACACCTTCAAGTACTCAGgtacactctt ... tgattttcagGGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGAGGGGCTTTCAG
EST: gi|162213765|gb|FC390380.1|FC390380
EST:     CAGCTCAGAGCCCAACAACCTTTACAACTTGAACACCTTCAAGTACTCAG                         GGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGAGGGGCTTTCAG
genomic: CAGCTCAGAGCCCAACAACCTTTACAACTTGAACACCTTCAAGTACTCAGgtacactctt ... tgattttcagGGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGAGGGGCTTTCAG
EST: gi|162213766|gb|FC390381.1|FC390381
EST:     CAGCTCAGAGCCCAACAACCTTTACAACTTGAACACCTTCAAGTACTCAG                         GGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGAGGGGCTTTCAG
genomic: CAGCTCAGAGCCCAACAACCTTTACAACTTGAACACCTTCAAGTACTCAGgtacactctt ... tgattttcagGGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGAGGGGCTTTCAG
EST: gi|37852452|gb|BJ610460.1|BJ610460
EST:     CAGCTCAGAGCCCAACAACCTTTACAACTTGAACACCTTCAAGTACTCAG                         GGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGAGGGGCTTTCAG
genomic: CAGCTCAGAGCCCAACAACCTTTACAACTTGAACACCTTCAAGTACTCAGgtacactctt ... tgattttcagGGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGAGGGGCTTTCAG
EST: gi|162261513|gb|FC437530.1|FC437530
EST:     CAGCTCAGAGCCCAACAACCTTTACAACTTGAACACCTTCAAGTACTCAG                         GGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGAGGGGCTTTCAG
genomic: CAGCTCAGAGCCCAACAACCTTTACAACTTGAACACCTTCAAGTACTCAGgtacactctt ... tgattttcagGGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGAGGGGCTTTCAG
EST: gi|162273849|gb|FC449780.1|FC449780
EST:     CAGCTCAGAGCCCAACAACCTTTACAACTTGAACACCTTCAAGTACTCAG                         GGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGAGGGGCTTTCAG
genomic: CAGCTCAGAGCCCAACAACCTTTACAACTTGAACACCTTCAAGTACTCAGgtacactctt ... tgattttcagGGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGAGGGGCTTTCAG
EST: gi|19777228|gb|BQ039161.1|BQ039161
EST:     CAGCTCAGAGCCCAACAACCTTTACAACTTGAACACCTTCAAGTACTCAG                         GGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGAGGGGCTTTCAG
genomic: CAGCTCAGAGCCCAACAACCTTTACAACTTGAACACCTTCAAGTACTCAGgtacactctt ... tgattttcagGGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGAGGGGCTTTCAG
EST: gi|18340471|gb|BJ172499.1|BJ172499
EST:     CAGCTCAGAGCCCAACAACCTTTACAACTTGAACACCTTCAAGTACTCAG                         GGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGAGGGGCTTTCAG
genomic: CAGCTCAGAGCCCAACAACCTTTACAACTTGAACACCTTCAAGTACTCAGgtacactctt ... tgattttcagGGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGAGGGGCTTTCAG
EST: gi|7147930|gb|AW509852.1|AW509852
EST:     CAGCTCAGAGCCCAACAACCTTTACAACTTGAACACCTTCAAGTACTCAG                         GGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGAGGGGCTTTCAG
genomic: CAGCTCAGAGCCCAACAACCTTTACAACTTGAACACCTTCAAGTACTCAGgtacactctt ... tgattttcagGGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGAGGGGCTTTCAG
EST: gi|162262080|gb|FC436861.1|FC436861
EST:     CAGCTCAGAGCCCAACAACCTTTACAACTTGAACACCTTCAAGTACTCAG                         GGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGAGGGGCTTTCAG
genomic: CAGCTCAGAGCCCAACAACCTTTACAACTTGAACACCTTCAAGTACTCAGgtacactctt ... tgattttcagGGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGAGGGGCTTTCAG
EST: gi|162209250|gb|FC385170.1|FC385170
EST:     CAGCTCAGAGCCCAACAACCTTTACAACTTGAACACCTTCAAGTACTCAG                         GGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGAGGGGCTTTCAG
genomic: CAGCTCAGAGCCCAACAACCTTTACAACTTGAACACCTTCAAGTACTCAGgtacactctt ... tgattttcagGGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGAGGGGCTTTCAG
EST: gi|162274650|gb|FC450456.1|FC450456
EST:     CAGCTCAGAGCCCAACAACCTTTACAACTTGAACACCTTCAAGTACTCAG                         GGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGAGGGGCTTTCAG
genomic: CAGCTCAGAGCCCAACAACCTTTACAACTTGAACACCTTCAAGTACTCAGgtacactctt ... tgattttcagGGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGAGGGGCTTTCAG
EST: gi|162241490|gb|FC414664.1|FC414664
EST:     CAGCTCAGAGCCCAACAACCTTTACAACTTGAACACCTTCAAGTACTCAG                         GGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGAGGGGCTTTCAG
genomic: CAGCTCAGAGCCCAACAACCTTTACAACTTGAACACCTTCAAGTACTCAGgtacactctt ... tgattttcagGGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGAGGGGCTTTCAG
EST: gi|162251344|gb|FC425516.1|FC425516
EST:     CAGCTCAGAGCCCAACAACCTTTACAACTTGAACACCTTCAAGTACTCAG                         GGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGAGGGGCTTTCAG
genomic: CAGCTCAGAGCCCAACAACCTTTACAACTTGAACACCTTCAAGTACTCAGgtacactctt ... tgattttcagGGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGAGGGGCTTTCAG
EST: gi|19785084|gb|BQ040267.1|BQ040267
EST:     CAGCTCAGAGCCCAACAACCTTTACAACTTGAACACCTTCAAGTACTCAG                         GGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGAGGGGCTTTCAG
genomic: CAGCTCAGAGCCCAACAACCTTTACAACTTGAACACCTTCAAGTACTCAGgtacactctt ... tgattttcagGGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGAGGGGCTTTCAG

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: 32

AACAGGTTCTTGGTGAAGAGAAATGGAAATAATAACAACAGTGTTCAGTTCAGCTCAGAGCCCAACAACCTTTACAACTTGAACACCTTCAAGTACTCAGgtacactctt ... tgattttcagGGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGAGGGGCTTTCAGTGACCCTGACCACCACCAAGACGAAGAAGAGGAATCAGCCCGCTAAGGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtgtggtgctcgtcaccttctcttcggatcatctctaaaatggttgattttcagGGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGAGGGGCTTTCAGTGACCCTGACCACCACCAAGACGAAGAAGAGGAATCAGCCCGCTAAGGC
                                                ttttc  CT-rich tract
                                  tctaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacactcttatcttttctttacgttatagtgtggtgctcgtcaccttctcttcggatcatctctaaaatggttgattttcagGGTTGGCAAACAAGAAAACTGTGGCCATTGCTCCCAATGAGGGGCTTTCAGTGACCCTGACCACCACCAAGACGAAGAAGAGGAATCAGCCCGCTAAGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA