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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAAGAACGATCGCCGCCTGGACGATAGTCTTCGGTATTGCCTAGTCAGTGGAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAGgtaagttccagaaactgcgaagcaacgtgacgcaattcaaagtcggttttgaatatgttcctgtgttgtttgaagtatatattcggtatttaagttgagaacctcgaatatcgattttaagtacatgtgctctacaagtctatttgttggcctcacagcgtgtttcggtgaccag

Basic information

species Physcomitrella patens
transcript PP1S201_89V6.1
intron # 2
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|100372876|gb|BY948744.1|BY948744
EST:     GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAG                         GTAGATAAGCAAGAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT
genomic: GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAGgtaagttcca ... cggtgaccagGTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT
EST: gi|100360671|gb|BY984087.1|BY984087
EST:     GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAG                         GTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT
genomic: GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAGgtaagttcca ... cggtgaccagGTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT
EST: gi|100386639|gb|BY970180.1|BY970180
EST:     GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAG                         GTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT
genomic: GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAGgtaagttcca ... cggtgaccagGTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT
EST: gi|162160985|gb|FC337009.1|FC337009
EST:     GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAG                         GTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT
genomic: GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAGgtaagttcca ... cggtgaccagGTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT
EST: gi|208348346|gb|DC905546.1|DC905546
EST:     GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAG                         GTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT
genomic: GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAGgtaagttcca ... cggtgaccagGTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT
EST: gi|162267461|gb|FC444212.1|FC444212
EST:     GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAG                         GTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT
genomic: GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAGgtaagttcca ... cggtgaccagGTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT
EST: gi|100418807|gb|BY975749.1|BY975749
EST:     GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGGAAACTTGAATCAG                         GTAGATAAGCAAAAAGTGGGCGTTCTCGTGG
genomic: GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAGgtaagttcca ... cggtgaccagGTAGATAAGCAAAAGGTGGGCGTTCTCGTGG
EST: gi|162190723|gb|FC367609.1|FC367609
EST:     GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAG                         GTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT
genomic: GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAGgtaagttcca ... cggtgaccagGTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT
EST: gi|100431839|gb|BY978532.1|BY978532
EST:     GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAG                         GTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATNGGTGGGCTT
genomic: GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAGgtaagttcca ... cggtgaccagGTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT
EST: gi|162186065|gb|FC361269.1|FC361269
EST:     GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAG                         GTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT
genomic: GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAGgtaagttcca ... cggtgaccagGTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT
EST: gi|67569629|gb|BJ942453.1|BJ942453
EST:     GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAG                         GTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT
genomic: GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAGgtaagttcca ... cggtgaccagGTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT
EST: gi|162160824|gb|FC336723.1|FC336723
EST:     GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAG                         GTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT
genomic: GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAGgtaagttcca ... cggtgaccagGTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT
EST: gi|162154190|gb|FC330321.1|FC330321
EST:     GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAG                         GTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT
genomic: GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAGgtaagttcca ... cggtgaccagGTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT
EST: gi|162252118|gb|FC428357.1|FC428357
EST:     GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAG                         GTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT
genomic: GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAGgtaagttcca ... cggtgaccagGTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT
EST: gi|162182567|gb|FC357542.1|FC357542
EST:     GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAG                         GTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT
genomic: GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAGgtaagttcca ... cggtgaccagGTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT
EST: gi|162150595|gb|FC326451.1|FC326451
EST:     GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAG                         GTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT
genomic: GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAGgtaagttcca ... cggtgaccagGTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT
EST: gi|162220366|gb|FC395734.1|FC395734
EST:     GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAG                         GTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT
genomic: GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAGgtaagttcca ... cggtgaccagGTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT
EST: gi|100369482|gb|BY948115.1|BY948115
EST:     GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAG                         GTAGATNAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT
genomic: GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAGgtaagttcca ... cggtgaccagGTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT
EST: gi|162193226|gb|FC372014.1|FC372014
EST:     GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAG                         GTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT
genomic: GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAGgtaagttcca ... cggtgaccagGTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT
EST: gi|162163534|gb|FC339444.1|FC339444
EST:     GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAG                         GTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT
genomic: GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAGgtaagttcca ... cggtgaccagGTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT
EST: gi|162182299|gb|FC357170.1|FC357170
EST:     GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAG                         GTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT
genomic: GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAGgtaagttcca ... cggtgaccagGTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT
EST: gi|162277903|gb|FC453826.1|FC453826
EST:     GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAG                         GTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT
genomic: GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAGgtaagttcca ... cggtgaccagGTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT
EST: gi|162221825|gb|FC398392.1|FC398392
EST:     GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAG                         GTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT
genomic: GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAGgtaagttcca ... cggtgaccagGTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT
EST: gi|100447045|gb|CJ971344.1|CJ971344
EST:     GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAG                         GTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT
genomic: GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAGgtaagttcca ... cggtgaccagGTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT
EST: gi|162155216|gb|FC331699.1|FC331699
EST:     GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAG                         GTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT
genomic: GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAGgtaagttcca ... cggtgaccagGTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT
EST: gi|162277039|gb|FC453761.1|FC453761
EST:     GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAG                         GTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT
genomic: GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAGgtaagttcca ... cggtgaccagGTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT
EST: gi|100379105|gb|BY986577.1|BY986577
EST:     GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAG                         GTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT
genomic: GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAGgtaagttcca ... cggtgaccagGTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT
EST: gi|162277398|gb|FC453204.1|FC453204
EST:     GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAG                         GTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT
genomic: GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAGgtaagttcca ... cggtgaccagGTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT
EST: gi|162184292|gb|FC359701.1|FC359701
EST:     GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAG                         GTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT
genomic: GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAGgtaagttcca ... cggtgaccagGTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT
EST: gi|100360911|gb|BY946818.1|BY946818
EST:     GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAG                         GTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT
genomic: GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAGgtaagttcca ... cggtgaccagGTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT
EST: gi|208358490|gb|DC930622.1|DC930622
EST:     GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAG                         GTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGNGTGGGCTT
genomic: GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAGgtaagttcca ... cggtgaccagGTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT
EST: gi|100396938|gb|BY953903.1|BY953903
EST:     GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAANACTTGAATCAG                         GTAGATAAGCAAAAGGTGGGCGTTCTCGTGNGGA-CTGGCATGGGTGGGCT
genomic: GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAGgtaagttcca ... cggtgaccagGTAGATAAGCAAAAGGTGGGCGTTCTCGTG-GGAACTGGCATGGGTGGGCT
EST: gi|162241386|gb|FC415444.1|FC415444
EST:     GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAG                         GTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT
genomic: GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAGgtaagttcca ... cggtgaccagGTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT
EST: gi|100428697|gb|BY959388.1|BY959388
EST:     GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAG                         GTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT
genomic: GAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAGgtaagttcca ... cggtgaccagGTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTT

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), 31 (downstream exon)
Score: 17

TAAGAACGATCGCCGCCTGGACGATAGTCTTCGGTATTGCCTAGTCAGTGGAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAGgtaagttcca ... cggtgaccagGTAGATAAGCAAAAGGTGGGCGTTCTCGTGGGAACTGGCATGGGTGGGCTTACAGTATTCTCAGATGGTGTCCAAGCTTTGGTGGAAAAGGGCCATAAGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAAGAACGATCGCCGCCTGGACGATAGTCTTCGGTATTGCCTAGTCAGTGGAAAAAGAGCGCTTGAAGACGCCGGCCTCGGTGGAGAAAACTTGAATCAGgtaagttccagaaactgcgaagcaacgtgacgcaattcaaagtcggttttgaatatgttcctgtgttgtttgaagtatatattcggtatttaagttgagaacctcgaatatcgattttaagtacatgtgctctacaagtctatttgttggcctcacagcgtgtttcggtgaccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA