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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtagagtctgttcagattgagttatacgtatcaaatgtcatgttaaactcccttagtgatgcgtaattttggacaatgtagtgacatgatctgcttcagGCTCCGTCTTGTTGGACTGAATATGTATCAGACTCCTCAGAAGAACCCTTCGAGGTCAAGCCGATCTGTAAAGCTGTCTCAGAGCTTTTGAAGATTTTTC

Basic information

species Physcomitrella patens
transcript PP1S92_44V6.2
intron # 8
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|162268964|gb|FC445456.1|FC445456
EST:     AGGGATGCCACAGGTGCTGTAGGCTACTTGGAAACATGATCATGCAATCA                         GCTCCGTCTTGTTGGACTGAATATGTATCAGACTCCTCAGAAGAACCCTTC
genomic: AGGGATGCCACAGGTGCTGTAGGCTACTTGGAAACATGATCATGCAATCAgtaagtagcg ... tctgcttcagGCTCCGTCTTGTTGGACTGAATATGTATCAGACTCCTCAGAAGAACCCTTC
EST: gi|162273206|gb|FC449213.1|FC449213
EST:     AGGGATGCCACAGGTGCTGTAGGCTACTTGGAAACATGATCATGCAATCA                         GCTCCGTCTTGTTGGACTGAATATGTATCAGACTCCTCAGAAGAACCCTTC
genomic: AGGGATGCCACAGGTGCTGTAGGCTACTTGGAAACATGATCATGCAATCAgtaagtagcg ... tctgcttcagGCTCCGTCTTGTTGGACTGAATATGTATCAGACTCCTCAGAAGAACCCTTC
EST: gi|162271606|gb|FC447491.1|FC447491
EST:     AGGGATGCCACAGGTGCTGTAGGCTACTTGGAAACATGATCATGCAATCA                         GCTCCGTCTTGTTGGACTGAATATGTATCAGACTCCTCAGAAGAACCCTTC
genomic: AGGGATGCCACAGGTGCTGTAGGCTACTTGGAAACATGATCATGCAATCAgtaagtagcg ... tctgcttcagGCTCCGTCTTGTTGGACTGAATATGTATCAGACTCCTCAGAAGAACCCTTC
EST: gi|162271607|gb|FC447492.1|FC447492
EST:     AGGGATGCCACAGGTGCTGTAGGCTACTTGGAAACATGATCATGCAATCA                         GCTCCGTCTTGTTGGACTGAATATGTATCAGACTCCTC
genomic: AGGGATGCCACAGGTGCTGTAGGCTACTTGGAAACATGATCATGCAATCAgtaagtagcg ... tctgcttcagGCTCCGTCTTGTTGGACTGAATATGTATCAGACTCCTC
EST: gi|162273207|gb|FC449214.1|FC449214
EST:     AGGGATGCCACAGGTGCTGTAGGCTACTTGGAAACATGATCATGCAATCA                         GCTCCGTCTTGTTGGACTGAATATGTATCAGACTCCTCAGAAGAACCCTTC
genomic: AGGGATGCCACAGGTGCTGTAGGCTACTTGGAAACATGATCATGCAATCAgtaagtagcg ... tctgcttcagGCTCCGTCTTGTTGGACTGAATATGTATCAGACTCCTCAGAAGAACCCTTC
EST: gi|162269990|gb|FC445455.1|FC445455
EST:     AGGGATGCCACAGGTGCTGTAGGCTACTTGGAAACATGATCATGCAATCA                         GCTCCGTCTTGTTGGACTGAATATGTATCAGACTCCTCAGAAGAACCCTTC
genomic: AGGGATGCCACAGGTGCTGTAGGCTACTTGGAAACATGATCATGCAATCAgtaagtagcg ... tctgcttcagGCTCCGTCTTGTTGGACTGAATATGTATCAGACTCCTCAGAAGAACCCTTC
EST: gi|162277386|gb|FC453192.1|FC453192
EST:     AGGGATGCCACAGGTGCTGTAGGCTACTTGGAAACATGATCATGCAATCA                         GCTCCGTCTTGTTGGACTGAATATGTATCAGACTCCTCAGAAGAACCCTTC
genomic: AGGGATGCCACAGGTGCTGTAGGCTACTTGGAAACATGATCATGCAATCAgtaagtagcg ... tctgcttcagGCTCCGTCTTGTTGGACTGAATATGTATCAGACTCCTCAGAAGAACCCTTC
EST: gi|67701058|gb|BJ961291.1|BJ961291
EST:     AGGGATGCCACAGGTGCTGTAGGCTACTTGGAAACATGATCATGCAATCA                         GCTCCGTCTTGTTGGACTGAATATGTATCAGACTCCTCAGAAGAACCCTTC
genomic: AGGGATGCCACAGGTGCTGTAGGCTACTTGGAAACATGATCATGCAATCAgtaagtagcg ... tctgcttcagGCTCCGTCTTGTTGGACTGAATATGTATCAGACTCCTCAGAAGAACCCTTC
EST: gi|162264663|gb|FC441661.1|FC441661
EST:     AGGGATGCCACAGGTGCTGTAGGCTACTTGGAAACATGATCATGCAATCA                         GCTCCGTCTTGTTGGACTGAATATGTATCAGACTCCTCAGAAGAACCCTTC
genomic: AGGGATGCCACAGGTGCTGTAGGCTACTTGGAAACATGATCATGCAATCAgtaagtagcg ... tctgcttcagGCTCCGTCTTGTTGGACTGAATATGTATCAGACTCCTCAGAAGAACCCTTC

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), 33 (downstream exon)
Score: 11

GATTTCACAAGAACAAGGGATGCCACAGGTGCTGTAGGCTACTTGGAAACATGATCATGCAATCAgtaagtagcg ... tctgcttcagGCTCCGTCTTGTTGGACTGAATATGTATCAGACTCCTCAGAAGAACCCTTCGAGGTCAAGCCGATCTGTAAAGCTGTCTCAGAGCTTTTGAAGATTTTTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaactcccttagtgatgcgtaattttggacaatgtagtgacatgatctgcttcagGCTCCGTCTTGTTGGACTGAATATGTATCAGACTCCTCAGAAGAACCCTTCGAGGTCAAGCCGATCTGTAAAGCTGTCTCAGAGCTTTTGAAGATTTTTC
                                             tctgcttc  CT-rich tract
                   taatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtagagtctgttcagattgagttatacgtatcaaatgtcatgttaaactcccttagtgatgcgtaattttggacaatgtagtgacatgatctgcttcagGCTCCGTCTTGTTGGACTGAATATGTATCAGACTCCTCAGAAGAACCCTTCGAGGTCAAGCCGATCTGTAAAGCTGTCTCAGAGCTTTTGAAGATTTTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA