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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttagttctctaattcttgttttggaacgtaatggatgtcttgtctgcacaaatgttggatctcttgttctcatgatttagactttttttacgaatcttagGCTCTAGCTCAGTGTGAGCAAGGATTGACGAAGTTAGGTGTGGCTCGAGAAGCTGTAGATGATACTGCCGGAGCTGCACAG

Basic information

species Physcomitrella patens
transcript PP1S84_76V6.1
intron # 4
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|37851942|gb|BJ609950.1|BJ609950
EST:     TCCCTGGTGTGAAAAAGGAGGAATTATTACGAGTTGTCAGTCATCCACAG                         GCTCTAGCTCAGTGTGAGCAAGGATTGACGAAGTTAGGTGTGGCTCGAGAA
genomic: TCCCTGGTGTGAAAAAGGAGGAATTATTACGAGTTGTCAGTCATCCACAGgtacatgata ... cgaatcttagGCTCTAGCTCAGTGTGAGCAAGGATTGACGAAGTTAGGTGTGGCTCGAGAA
EST: gi|208360945|gb|DC946634.1|DC946634
EST:     TCCCTGGTGTGAAAAAGGAGGAATTATTACGAGTTGTCAGTCATCCACAG                         GCTCTAGCTCAGTGTGAGCAAGGATTGACGAAGTTAGGTGTGGCTCGAGAA
genomic: TCCCTGGTGTGAAAAAGGAGGAATTATTACGAGTTGTCAGTCATCCACAGgtacatgata ... cgaatcttagGCTCTAGCTCAGTGTGAGCAAGGATTGACGAAGTTAGGTGTGGCTCGAGAA
EST: gi|162182473|gb|FC357448.1|FC357448
EST:     TCCCTGGTGTGAAAAAGGAGGAATTATTACGAGTTGTCAGTCATCCACAG                         GCTCTAGCTCAGTGTGAGCAAGGATTGACGAAGTTAGGTGTGGCTCGAGAA
genomic: TCCCTGGTGTGAAAAAGGAGGAATTATTACGAGTTGTCAGTCATCCACAGgtacatgata ... cgaatcttagGCTCTAGCTCAGTGTGAGCAAGGATTGACGAAGTTAGGTGTGGCTCGAGAA
EST: gi|162258880|gb|FC434887.1|FC434887
EST:     AAAAAGGAGGAATTATTACGAGTTGTCAGTCATCCACAG                         GCTCTAGCTCAGTGTGAGCAAGGATTGACGAAGTTAGGTGTGGCTCGAGAA
genomic: AAAAAGGAGGAATTATTACGAGTTGTCAGTCATCCACAGgtacatgata ... cgaatcttagGCTCTAGCTCAGTGTGAGCAAGGATTGACGAAGTTAGGTGTGGCTCGAGAA
EST: gi|162196647|gb|FC374937.1|FC374937
EST:     TCCCTGGTGTGAAAAAGGAGGAATTATTACGAGTTGTCAGTCATCCACAG                         GCTCTAGCTCAGTGTGAGCAAGGATTGA
genomic: TCCCTGGTGTGAAAAAGGAGGAATTATTACGAGTTGTCAGTCATCCACAGgtacatgata ... cgaatcttagGCTCTAGCTCAGTGTGAGCAAGGATTGA
EST: gi|208372438|gb|DC952282.1|DC952282
EST:     TCCCTGGTGTGAAAAAGGAGGAATTATTACGAGTTGTCAGTCATCCACAG                         GCTCTAGCTCAGTGTGAGCAAGGATTGACGAAGTTAGGTGTGGCTCGAGAA
genomic: TCCCTGGTGTGAAAAAGGAGGAATTATTACGAGTTGTCAGTCATCCACAGgtacatgata ... cgaatcttagGCTCTAGCTCAGTGTGAGCAAGGATTGACGAAGTTAGGTGTGGCTCGAGAA
EST: gi|37847781|gb|BJ605789.1|BJ605789
EST:     TCCCTGGTGTGAAAAAGGAGGAATTATTACGAGTTGTCAGTCATCCACAG                         GCTCTAGCTCAGTGTGAGCAAGGATTGACGAAGTTAGGTGTGGCTCGAGAA
genomic: TCCCTGGTGTGAAAAAGGAGGAATTATTACGAGTTGTCAGTCATCCACAGgtacatgata ... cgaatcttagGCTCTAGCTCAGTGTGAGCAAGGATTGACGAAGTTAGGTGTGGCTCGAGAA
EST: gi|208375291|gb|DC945018.1|DC945018
EST:     TCCCTGGTGTGAAAAAGGAGGAATTATTACGAGTTGTCAGTCATCCACAG                         GCTCTAGCTCAGTGTGAGCAAGGATTGACGAAGTTAGGTGTGGCTCGAGAA
genomic: TCCCTGGTGTGAAAAAGGAGGAATTATTACGAGTTGTCAGTCATCCACAGgtacatgata ... cgaatcttagGCTCTAGCTCAGTGTGAGCAAGGATTGACGAAGTTAGGTGTGGCTCGAGAA
EST: gi|18334585|gb|BJ166602.1|BJ166602
EST:     TCCCTGGTGTGAAAAAGGAGGAATTATTACGAGTTGTCAGTCATCCACAG                         GCTCTAGCTCAGTGTGAGCAAGGATTGACGAAGTTAGGTGTGGCTCGAGAA
genomic: TCCCTGGTGTGAAAAAGGAGGAATTATTACGAGTTGTCAGTCATCCACAGgtacatgata ... cgaatcttagGCTCTAGCTCAGTGTGAGCAAGGATTGACGAAGTTAGGTGTGGCTCGAGAA
EST: gi|208365784|gb|DC951047.1|DC951047
EST:     TCCCTGGTGTGAAAAAGGAGGAATTATTACGAGTTGTCAGTCATCCACAG                         GCTCTAGCTCAGTGTGAGCAAGGATTGACGAAGTTAGGTGTGGCTCGAGAA
genomic: TCCCTGGTGTGAAAAAGGAGGAATTATTACGAGTTGTCAGTCATCCACAGgtacatgata ... cgaatcttagGCTCTAGCTCAGTGTGAGCAAGGATTGACGAAGTTAGGTGTGGCTCGAGAA
EST: gi|100407545|gb|BY991747.1|BY991747
EST:     TCCCTGGTGTGAAAAAGGAGGAATTATTACGAGTTGTCAGTCATCCACAA                         GCTCTAGCTCAGTGTGAGCAAGGATTGANAAATTTAGGTGTGGCTCGAGA
genomic: TCCCTGGTGTGAAAAAGGAGGAATTATTACGAGTTGTCAGTCATCCACAGgtacatgata ... cgaatcttagGCTCTAGCTCAGTGTGAGCAAGGATTGACGAAGTTAGGTGTGGCTCGAGA
EST: gi|18334591|gb|BJ166608.1|BJ166608
EST:     TCCCTGGTGTGAAAAAGGAGGAATTATTACGAGTTGTCAGTCATCCACAG                         GCTCTAGCTCAGTGTGAGCAAGGATTGACGAAGTTAGGTGTGGCTCGAGAA
genomic: TCCCTGGTGTGAAAAAGGAGGAATTATTACGAGTTGTCAGTCATCCACAGgtacatgata ... cgaatcttagGCTCTAGCTCAGTGTGAGCAAGGATTGACGAAGTTAGGTGTGGCTCGAGAA
EST: gi|18340558|gb|BJ172586.1|BJ172586
EST:     CCCNTGGTGTGAAAAAGGAGGAATTATTACGAGTTGTCAGTCATCCACAG                         GCTCTAGCTCAGTGTGAGCAAGGATTGACGAAGTTAGGTGTGGCTCGAGAA
genomic: CCC-TGGTGTGAAAAAGGAGGAATTATTACGAGTTGTCAGTCATCCACAGgtacatgata ... cgaatcttagGCTCTAGCTCAGTGTGAGCAAGGATTGACGAAGTTAGGTGTGGCTCGAGAA
EST: gi|162196646|gb|FC374936.1|FC374936
EST:     TCCCTGGTGTGAAAAAGGAGGAATTATTACGAGTTGTCAGTCATCCACAG                         GCTCTAGCTCAGTGTGAGCAAGGATTGACGAAGTTAGGTGTGGCTCGAGAA
genomic: TCCCTGGTGTGAAAAAGGAGGAATTATTACGAGTTGTCAGTCATCCACAGgtacatgata ... cgaatcttagGCTCTAGCTCAGTGTGAGCAAGGATTGACGAAGTTAGGTGTGGCTCGAGAA
EST: gi|208367467|gb|DC955675.1|DC955675
EST:     TCCCTGGTGTGAAAAAGGAGGAATTATTACGAGTTGTCAGTCATCCACAG                         GCTCTAGCTCAGTGTGAGCAAGGATTGACGAAGTTAGGTGTGGCTCGAGAA
genomic: TCCCTGGTGTGAAAAAGGAGGAATTATTACGAGTTGTCAGTCATCCACAGgtacatgata ... cgaatcttagGCTCTAGCTCAGTGTGAGCAAGGATTGACGAAGTTAGGTGTGGCTCGAGAA
EST: gi|37842276|gb|BJ600284.1|BJ600284
EST:     TCAGTCATCCACAG                         GCTCTAGCTCAGTGTGAGCAAGGATTGACGAAGTTAGGTGTGGCTCGAGAA
genomic: TCAGTCATCCACAGgtacatgata ... cgaatcttagGCTCTAGCTCAGTGTGAGCAAGGATTGACGAAGTTAGGTGTGGCTCGAGAA

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: 33 (upstream exon), 33 (downstream exon)
Score: 6

TCATATAGTTGGTGAAGTTCAACTTGCAATTCATCATTGCCTCTTAGCACTCCCTGGTGTGAAAAAGGAGGAATTATTACGAGTTGTCAGTCATCCACAGgtacatgata ... cgaatcttagGCTCTAGCTCAGTGTGAGCAAGGATTGACGAAGTTAGGTGTGGCTCGAGAAGCTGTAGATGATACTGCCGGAGCTGCACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcacaaatgttggatctcttgttctcatgatttagactttttttacgaatcttagGCTCTAGCTCAGTGTGAGCAAGGATTGACGAAGTTAGGTGTGGCTCGAGAAGCTGTAGATGATACTGCCGGAGCTGCACAG
                                    ctttttttac  CT-rich tract
                             atttagacttttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttagttctctaattcttgttttggaacgtaatggatgtcttgtctgcacaaatgttggatctcttgttctcatgatttagactttttttacgaatcttagGCTCTAGCTCAGTGTGAGCAAGGATTGACGAAGTTAGGTGTGGCTCGAGAAGCTGTAGATGATACTGCCGGAGCTGCACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - -ctgcaca