Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgcaatccgaaccatcacgaagtcgcatctaaaattgttgattaaattcccaaaatgtgattgtgcattgaaatcaaccaataagctggtggtgtgcagGCCGCTGAAGCTCTAGCAAAAGTAAATAAATGGGCGAAAGACGAGACGCACGGGAAAATTGAGAATCTCCTTCCTGCAGGTTCAGTGGACCACGACACAC

Basic information

species Physcomitrella patens
transcript PP1S61_265V6.3
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|18349588|gb|BJ181638.1|BJ181638
EST:     TTCANGAGAGCTACGGATCTGAAGCTGCCTCGGTAGACTTCATCTCTAAG                         GCCGCTGAAGCTCTAGCAAAAGTAAATAAATGGGCGAAAGACGAG
genomic: TTCAGGAGAGCTACGGATCTGAAGCTGCCTCGGTAGACTTCATCTCTAAGgtactgaaat ... tggtgtgcagGCCGCTGAAGCTCTAGCAAAAGTAAATAAATGGGCGAAAGACGAG
EST: gi|18371868|gb|BJ203470.1|BJ203470
EST:     TTCAGGAGAGCTACGGATCTGAAGCTGCCTCGGTAGACTTCATCTCTAAG                         GCCGCTGAAGCTCTAGC
genomic: TTCAGGAGAGCTACGGATCTGAAGCTGCCTCGGTAGACTTCATCTCTAAGgtactgaaat ... tggtgtgcagGCCGCTGAAGCTCTAGC
EST: gi|208391738|gb|DC937956.1|DC937956
EST:     TTCAGGAGAGCTACGGATCTGAAGCTGCCTCGGTAGACTTCATCTCTAAG                         GCCGCTGAAGCTCTAGCAAAAGTAAATAAATGGGCGAAAGACGAGACGCAC
genomic: TTCAGGAGAGCTACGGATCTGAAGCTGCCTCGGTAGACTTCATCTCTAAGgtactgaaat ... tggtgtgcagGCCGCTGAAGCTCTAGCAAAAGTAAATAAATGGGCGAAAGACGAGACGCAC
EST: gi|162193124|gb|FC371990.1|FC371990
EST:     TTCAGGAGAGCTACGGATCTGAAGCTGCCTCGGTAGACTTCATCTCTAAG                         GCCGCTGAAGCTCTAGCAAAAGTAAATAAATGGGCGAAAGACGAGACGCAC
genomic: TTCAGGAGAGCTACGGATCTGAAGCTGCCTCGGTAGACTTCATCTCTAAGgtactgaaat ... tggtgtgcagGCCGCTGAAGCTCTAGCAAAAGTAAATAAATGGGCGAAAGACGAGACGCAC
EST: gi|18366405|gb|BJ198484.1|BJ198484
EST:     TTCAGGAGAGCTACGGATCTGAAGCTGCCTCGGTAGACTTCATCTCTAAG                         GCCGCTGAAGCTCTAGCAAAAGTAAATAAATGGGCGAAAGACGAGACGCAC
genomic: TTCAGGAGAGCTACGGATCTGAAGCTGCCTCGGTAGACTTCATCTCTAAGgtactgaaat ... tggtgtgcagGCCGCTGAAGCTCTAGCAAAAGTAAATAAATGGGCGAAAGACGAGACGCAC
EST: gi|18331537|gb|BJ163548.1|BJ163548
EST:     TTCAGGAGAGCTACGGATCTGAAGCTGCCTCGGTAGACTTCATCTCTAAN                         GCCGCTGAAGCTCTAGCA
genomic: TTCAGGAGAGCTACGGATCTGAAGCTGCCTCGGTAGACTTCATCTCTAAGgtactgaaat ... tggtgtgcagGCCGCTGAAGCTCTAGCA
EST: gi|100371412|gb|BY967968.1|BY967968
EST:     TCAGGAGAGCTACGGATCTGAGGCTGCCTCGGTAGACTTCATCTTCTA-G                         GCCGCTGAAGCTCTAGCAAAAGTAAATAAATGGGCGAAAAAACGAGACGC
genomic: TCAGGAGAGCTACGGATCTGAAGCTGCCTCGGTAGACTTCATCT-CTAAGgtactgaaat ... tggtgtgcagGCCGCTGAAGCTCTAGCAAAAGTAAATAAATGGGCGAAAGA-CGAGACGC
EST: gi|100365013|gb|BY966767.1|BY966767
EST:     TTCAGGAGAGCTACGGATCTGAAGCTGCCTCGGTAGACTTCATCTCTAAG                         GCCGCTGAAGCTCTAGCAAAAGTAAATAAATGGGCGAAAGACGAGACGCAC
genomic: TTCAGGAGAGCTACGGATCTGAAGCTGCCTCGGTAGACTTCATCTCTAAGgtactgaaat ... tggtgtgcagGCCGCTGAAGCTCTAGCAAAAGTAAATAAATGGGCGAAAGACGAGACGCAC
EST: gi|100430543|gb|BY959922.1|BY959922
EST:     TTCAGGAGAGCTACGGATCTGAAGCTGCCTCGGTAGACTTCATCTCTAAG                         GCCGCTGAAGCTCTAGCAAAAGTAAATAAATGGGCGAAAGACGAGACGCAC
genomic: TTCAGGAGAGCTACGGATCTGAAGCTGCCTCGGTAGACTTCATCTCTAAGgtactgaaat ... tggtgtgcagGCCGCTGAAGCTCTAGCAAAAGTAAATAAATGGGCGAAAGACGAGACGCAC
EST: gi|100442013|gb|BY981236.1|BY981236
EST:     TTCAGGAGAGCTACGGATCTGAAGCTGCCTCGGTAGACTTCATCTCTAAG                         GCCGCTGAAGCTCTAGCAAAAGTAAAATAAATGGGCGGAAGACGAGACGCA
genomic: TTCAGGAGAGCTACGGATCTGAAGCTGCCTCGGTAGACTTCATCTCTAAGgtactgaaat ... tggtgtgcagGCCGCTGAAGCTCTAGCAAAAGTAAA-TAAATGGGCGAAAGACGAGACGCA
EST: gi|18360126|gb|BJ192188.1|BJ192188
EST:     TTCAGGAGAGCTACGGATCTGAAGCTGCCTCGGTAGACTTCATCTCTAAG                         GCCGCTGAAGCTCTAGCAAAAGTAAATAAATGGGCGAAAGACGAGACGCAC
genomic: TTCAGGAGAGCTACGGATCTGAAGCTGCCTCGGTAGACTTCATCTCTAAGgtactgaaat ... tggtgtgcagGCCGCTGAAGCTCTAGCAAAAGTAAATAAATGGGCGAAAGACGAGACGCAC
EST: gi|18366667|gb|BJ198746.1|BJ198746
EST:     TTCAGGAGAGCTACGGATCTGAAGCTGCCTCGGTAGGCTTCATCTCTAAG                         GCCGCTGAAGCTCTAGCAAAAGTAAATAAATGGGCGAAAGACGAGACGCAC
genomic: TTCAGGAGAGCTACGGATCTGAAGCTGCCTCGGTAGACTTCATCTCTAAGgtactgaaat ... tggtgtgcagGCCGCTGAAGCTCTAGCAAAAGTAAATAAATGGGCGAAAGACGAGACGCAC

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: 21 (upstream exon), 35 (downstream exon)
Score: 6

TTTGTGGGTGGAGCAATCAGTGAAACTGAAACCTGCATTCCAGAAAATTCTTCAGGAGAGCTACGGATCTGAAGCTGCCTCGGTAGACTTCATCTCTAAGgtactgaaat ... tggtgtgcagGCCGCTGAAGCTCTAGCAAAAGTAAATAAATGGGCGAAAGACGAGACGCACGGGAAAATTGAGAATCTCCTTCCTGCAGGTTCAGTGGACCACGACACAC




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattcccaaaatgtgattgtgcattgaaatcaaccaataagctggtggtgtgcagGCCGCTGAAGCTCTAGCAAAAGTAAATAAATGGGCGAAAGACGAGACGCACGGGAAAATTGAGAATCTCCTTCCTGCAGGTTCAGTGGACCACGACACAC
                      attgaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgcaatccgaaccatcacgaagtcgcatctaaaattgttgattaaattcccaaaatgtgattgtgcattgaaatcaaccaataagctggtggtgtgcagGCCGCTGAAGCTCTAGCAAAAGTAAATAAATGGGCGAAAGACGAGACGCACGGGAAAATTGAGAATCTCCTTCCTGCAGGTTCAGTGGACCACGACACAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA