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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtagtcgtggaggcgtaaatgaattgtatttagggttattgtcgtggagataggatgatgaactctacttttagtgctctaagatggtgcaacttgccagGGGGCGTACCGTACTGATGAGGGCAAACCATTGGTATTGGAATGCGTGCGTAAAGCTGAAGAAAAGATTGCCGGTTCCAACTTCAT

Basic information

species Physcomitrella patens
transcript PP1S223_31V6.1
intron # 1
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|18343315|gb|BJ175353.1|BJ175353
EST:     CGGAGGCGTTTCTCGCTGATTCTCACCCGGATAAGATGAACGTCGGCGTT                         GGGGCGTACCGTACTGATGAGGGCAAACCATTGGTATTGGAATGCGTGCGT
genomic: CGGAGGCGTTTCTCGCTGATTCTCACCCGGATAAGATGAACGTCGGCGTTgtatgtgctt ... aacttgccagGGGGCGTACCGTACTGATGAGGGCAAACCATTGGTATTGGAATGCGTGCGT
EST: gi|67716236|gb|BJ966496.1|BJ966496
EST:     CGGAGGCGTTTCTCGCTGATTCTCACCCGGATAAGATGAACGTCGGCGTT                         GGGGCGTACCGTACTGATGAGGGCAAACCATTGGTATTGGAATGCGTGCGT
genomic: CGGAGGCGTTTCTCGCTGATTCTCACCCGGATAAGATGAACGTCGGCGTTgtatgtgctt ... aacttgccagGGGGCGTACCGTACTGATGAGGGCAAACCATTGGTATTGGAATGCGTGCGT
EST: gi|67703583|gb|BJ963816.1|BJ963816
EST:     CGGAGGCGTTTCTCGCTGATTCTCACCCGGATAAGATGAACGTCGGCGTT                         GGGGCGTACCGTACTGATGAGGGCAAACCATTGGTATTGGAATGCGTGCGT
genomic: CGGAGGCGTTTCTCGCTGATTCTCACCCGGATAAGATGAACGTCGGCGTTgtatgtgctt ... aacttgccagGGGGCGTACCGTACTGATGAGGGCAAACCATTGGTATTGGAATGCGTGCGT
EST: gi|18348563|gb|BJ180612.1|BJ180612
EST:     CGGAGGCGTTTCTCGCTGATTCTCACCCGGATAAGATGAACGTCGGCGTT                         GGGGCGTACCGTACTGATGAGGGCAAACCATTGGTATTGGAATGCGTGCGT
genomic: CGGAGGCGTTTCTCGCTGATTCTCACCCGGATAAGATGAACGTCGGCGTTgtatgtgctt ... aacttgccagGGGGCGTACCGTACTGATGAGGGCAAACCATTGGTATTGGAATGCGTGCGT
EST: gi|162256780|gb|FC432674.1|FC432674
EST:     CGGAGGCGTTTCTCGCTGATTCTCACCCGGATAAGATGAACGTCGGCGTT                         GGGGCGTACCGTACTGATGAGGGCAAACCATTGGTATTGGAATGCGTGCGT
genomic: CGGAGGCGTTTCTCGCTGATTCTCACCCGGATAAGATGAACGTCGGCGTTgtatgtgctt ... aacttgccagGGGGCGTACCGTACTGATGAGGGCAAACCATTGGTATTGGAATGCGTGCGT
EST: gi|18372779|gb|BJ204381.1|BJ204381
EST:     CGGAGGCGTTTCTCGCTGATTCTCACCCGGATAAGATGAACGTCGGCGTT                         GGGGCGTACCGTACTGATGAGGGCAAACCATTGGTATTGGAATGCGTGCGT
genomic: CGGAGGCGTTTCTCGCTGATTCTCACCCGGATAAGATGAACGTCGGCGTTgtatgtgctt ... aacttgccagGGGGCGTACCGTACTGATGAGGGCAAACCATTGGTATTGGAATGCGTGCGT
EST: gi|208361604|gb|DC942847.1|DC942847
EST:     CGGAGGCGTTTCTCGCTGATTCTCACCCGGATAAGATGAACGTCGGCGTT                         GGGGCGTACCGTACTGATGAGGGCAAACCATTGGTATTGGAATGCGTGCGT
genomic: CGGAGGCGTTTCTCGCTGATTCTCACCCGGATAAGATGAACGTCGGCGTTgtatgtgctt ... aacttgccagGGGGCGTACCGTACTGATGAGGGCAAACCATTGGTATTGGAATGCGTGCGT
EST: gi|162274186|gb|FC449946.1|FC449946
EST:     CGGAGGCGTTTCTCGCTGATTCTCACCCGGATAAGATGAACGTCGGCGTT                         GGGGCGTACCGTACTGATGAGGGCAAACCATTGGTATTGGAATGCGTGCGT
genomic: CGGAGGCGTTTCTCGCTGATTCTCACCCGGATAAGATGAACGTCGGCGTTgtatgtgctt ... aacttgccagGGGGCGTACCGTACTGATGAGGGCAAACCATTGGTATTGGAATGCGTGCGT
EST: gi|162257990|gb|FC434084.1|FC434084
EST:     CGGAGGCGTTTCTCGCTGATTCTCACCCGGATAAGATGAACGTCGGCGTT                         GGGGCGTACCGTACTGATGAGGGCAAACCATTGGTATTGGAATGCGTGCGT
genomic: CGGAGGCGTTTCTCGCTGATTCTCACCCGGATAAGATGAACGTCGGCGTTgtatgtgctt ... aacttgccagGGGGCGTACCGTACTGATGAGGGCAAACCATTGGTATTGGAATGCGTGCGT
EST: gi|162192506|gb|FC371697.1|FC371697
EST:     CGGAGGCGTTTCTCGCTGATTCTCACCCGGATAAGATGAACGTCGGCGTT                         GGGGCGTACCGTACTGATGAGGGCAAACCATTGGTATTGGAATGCGTGCGT
genomic: CGGAGGCGTTTCTCGCTGATTCTCACCCGGATAAGATGAACGTCGGCGTTgtatgtgctt ... aacttgccagGGGGCGTACCGTACTGATGAGGGCAAACCATTGGTATTGGAATGCGTGCGT
EST: gi|18363244|gb|BJ195316.1|BJ195316
EST:     CGGAGGCGTTTCTCGCTGATTCTCACCCGGATAAGATGAACGTCGGCGTT                         GGGGCGTACCGTACTGATGAGGGCAAACCATTGGTATTGGAATGCGTGCGT
genomic: CGGAGGCGTTTCTCGCTGATTCTCACCCGGATAAGATGAACGTCGGCGTTgtatgtgctt ... aacttgccagGGGGCGTACCGTACTGATGAGGGCAAACCATTGGTATTGGAATGCGTGCGT
EST: gi|162198689|gb|FC373470.1|FC373470
EST:     CGGAGGCGTTTCTCGCTGATTCTCACCCGGATAAGATGAACGTCGGCGTT                         GGGGCGTACCGTACTGATGAGGGCAAACCATTGGTATTGGAATGCGTGCGT
genomic: CGGAGGCGTTTCTCGCTGATTCTCACCCGGATAAGATGAACGTCGGCGTTgtatgtgctt ... aacttgccagGGGGCGTACCGTACTGATGAGGGCAAACCATTGGTATTGGAATGCGTGCGT
EST: gi|67716980|gb|BJ967239.1|BJ967239
EST:     CGGAGGCGTTTCTCGCTGATTCTCACCCGGATAAGATGAACGTCGGCGTT                         GGGGCGTACCGTACTGATGAGGGCAAACCATTGGTATTGGAATGCGTGCGT
genomic: CGGAGGCGTTTCTCGCTGATTCTCACCCGGATAAGATGAACGTCGGCGTTgtatgtgctt ... aacttgccagGGGGCGTACCGTACTGATGAGGGCAAACCATTGGTATTGGAATGCGTGCGT
EST: gi|100405509|gb|BY973712.1|BY973712
EST:     CGGAGGCGTTTCTCGCTGATTCTCACCCGGATAAGATGAACGTCGGCGTT                         GGGGCGTACCGTACTGATGAGGGCAAACCATTGGTATTGGAATGCGTGCGT
genomic: CGGAGGCGTTTCTCGCTGATTCTCACCCGGATAAGATGAACGTCGGCGTTgtatgtgctt ... aacttgccagGGGGCGTACCGTACTGATGAGGGCAAACCATTGGTATTGGAATGCGTGCGT
EST: gi|67704142|gb|BJ964375.1|BJ964375
EST:     CGGAGGCGTTTCTCGCTGATTCTCACCCGGATAAGATGAACGTCGGCGTT                         GGGGCGTACCGTACTGATGAGGGCAAACCATTGGTATTGGAATGCGTGCGT
genomic: CGGAGGCGTTTCTCGCTGATTCTCACCCGGATAAGATGAACGTCGGCGTTgtatgtgctt ... aacttgccagGGGGCGTACCGTACTGATGAGGGCAAACCATTGGTATTGGAATGCGTGCGT
EST: gi|100446972|gb|CJ971271.1|CJ971271
EST:     CGGAGGCGTTTCTCGCTGATTCTCACCCGGATAAGATGAACGTCGGCGTT                         GGGGCGTACCGTACTGATGAGGGCAAACCATTGGTATTGGAATGCGTGCGT
genomic: CGGAGGCGTTTCTCGCTGATTCTCACCCGGATAAGATGAACGTCGGCGTTgtatgtgctt ... aacttgccagGGGGCGTACCGTACTGATGAGGGCAAACCATTGGTATTGGAATGCGTGCGT
EST: gi|18361332|gb|BJ193398.1|BJ193398
EST:     CGGAGGCGTTTCTCGCTGATTCTCACCCGGATAAGATGAACGTCGGCGTT                         GGGGCGTACCGTACTGATGAGGGCAAACCATTGGTATTGGAATGCGTGCGT
genomic: CGGAGGCGTTTCTCGCTGATTCTCACCCGGATAAGATGAACGTCGGCGTTgtatgtgctt ... aacttgccagGGGGCGTACCGTACTGATGAGGGCAAACCATTGGTATTGGAATGCGTGCGT
EST: gi|208381144|gb|DC903034.1|DC903034
EST:     CGGAGGCGTTTCTCGCTGATTCTCACCCGGATAAGATGAACGTCGGCGTT                         GGGGCGTACCGTACTGATGAGGGCAAACCATTGGTATTGGAATGCGTGCGT
genomic: CGGAGGCGTTTCTCGCTGATTCTCACCCGGATAAGATGAACGTCGGCGTTgtatgtgctt ... aacttgccagGGGGCGTACCGTACTGATGAGGGCAAACCATTGGTATTGGAATGCGTGCGT
EST: gi|18367140|gb|BJ199221.1|BJ199221
EST:     CGGAGGCGTTTCTCGCTGATTCTCACCCGGATAAGATGAACGTCGGCGTT                         GGGGCGTACCGTACTGATGAGGGCAAACCATTGGTATTGGAATGCGTGCGT
genomic: CGGAGGCGTTTCTCGCTGATTCTCACCCGGATAAGATGAACGTCGGCGTTgtatgtgctt ... aacttgccagGGGGCGTACCGTACTGATGAGGGCAAACCATTGGTATTGGAATGCGTGCGT

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: 29 (upstream exon), 34 (downstream exon)
Score: 5

GTGGTTCGGGCATGTGCAGCCCGCGCCCAAGGACCCTATCCTGGGCGTCACGGAGGCGTTTCTCGCTGATTCTCACCCGGATAAGATGAACGTCGGCGTTgtatgtgctt ... aacttgccagGGGGCGTACCGTACTGATGAGGGCAAACCATTGGTATTGGAATGCGTGCGTAAAGCTGAAGAAAAGATTGCCGGTTCCAACTTCAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggagataggatgatgaactctacttttagtgctctaagatggtgcaacttgccagGGGGCGTACCGTACTGATGAGGGCAAACCATTGGTATTGGAATGCGTGCGTAAAGCTGAAGAAAAGATTGCCGGTTCCAACTTCAT
                    tactttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagtcgtggaggcgtaaatgaattgtatttagggttattgtcgtggagataggatgatgaactctacttttagtgctctaagatggtgcaacttgccagGGGGCGTACCGTACTGATGAGGGCAAACCATTGGTATTGGAATGCGTGCGTAAAGCTGAAGAAAAGATTGCCGGTTCCAACTTCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA