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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcttttgccgcgatagatgcacgagttccacatttgaaatgcatcacgaagtcgctgttccattgaattaacttgttcgtgttgtattatcttttaatagGGGCGGAGCAGCTTTGATCATGGTATCACTTGCAGTAATTGCAGGCTCCCTTGCGCCTAAAGTGAACGAACTACTGAAGCGTGAATTGGAAATGCCTGTG

Basic information

species Physcomitrella patens
transcript PP1S77_163V6.1
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|162252026|gb|FC426731.1|FC426731
EST:     ACTGTTGAAATTGAGTCAGGATGCACTGTATGGCAACAGCTGAGTGTCAG                         GGGCGGAGCAGCTTTGATCATGGTATCACTTGCAGTAATTGCAGGCTCCCT
genomic: ACTGTTGAAATTGAGTCAGGATGCACTGTATGGCAACAGCTGAGTGTCAGgtacaacatc ... cttttaatagGGGCGGAGCAGCTTTGATCATGGTATCACTTGCAGTAATTGCAGGCTCCCT
EST: gi|162251970|gb|FC426675.1|FC426675
EST:     ACTGTTGAAATTGAGTCAGGATGCACTGTATGGCAACAGCTGAGTGTCAG                         GGGCGGAGCAGCTTTGATCATGGTATCACTTGCAGTAATTGCAGGCTCCCT
genomic: ACTGTTGAAATTGAGTCAGGATGCACTGTATGGCAACAGCTGAGTGTCAGgtacaacatc ... cttttaatagGGGCGGAGCAGCTTTGATCATGGTATCACTTGCAGTAATTGCAGGCTCCCT
EST: gi|162214634|gb|FC390665.1|FC390665
EST:     ACTGTTGAAATTGAGTCAGGATGCACTGTATGGCAACAGCTGAGTGTCAG                         GGGCGGAGCAGCTTTGATCATGGTATCACTTGCAGTAATTGCAGGCTCCCT
genomic: ACTGTTGAAATTGAGTCAGGATGCACTGTATGGCAACAGCTGAGTGTCAGgtacaacatc ... cttttaatagGGGCGGAGCAGCTTTGATCATGGTATCACTTGCAGTAATTGCAGGCTCCCT
EST: gi|162239911|gb|FC415750.1|FC415750
EST:     ACTGTTGAAATTGAGTCAGGATGCACTGTATGGCAACAGCTGAGTGTCAG                         GGGCGGAGCAGCTTTGATCATGGTATCACTTGCAGTAATTGCAGGCTCCCT
genomic: ACTGTTGAAATTGAGTCAGGATGCACTGTATGGCAACAGCTGAGTGTCAGgtacaacatc ... cttttaatagGGGCGGAGCAGCTTTGATCATGGTATCACTTGCAGTAATTGCAGGCTCCCT
EST: gi|162233211|gb|FC409553.1|FC409553
EST:     ACTGTTGAAATTGAGTCAGGATGCACTGTATGGCAACAGCTGAGTGTCAG                         GGGCGGAGCAGCTTTGATCATGGTATCACTTGCAGTAATTGCAGGCTCCCT
genomic: ACTGTTGAAATTGAGTCAGGATGCACTGTATGGCAACAGCTGAGTGTCAGgtacaacatc ... cttttaatagGGGCGGAGCAGCTTTGATCATGGTATCACTTGCAGTAATTGCAGGCTCCCT
EST: gi|37838337|gb|BJ596345.1|BJ596345
EST:     ACTGTTGAAATTGAGTCAGGATGCACTGTATGGCAACAGCTGAGTGTCAG                         GGGCGGAGCAGCTTTGATCATGGTATCACTTGCAGTAATTGCAGGCTCCCT
genomic: ACTGTTGAAATTGAGTCAGGATGCACTGTATGGCAACAGCTGAGTGTCAGgtacaacatc ... cttttaatagGGGCGGAGCAGCTTTGATCATGGTATCACTTGCAGTAATTGCAGGCTCCCT
EST: gi|162239910|gb|FC415749.1|FC415749
EST:     ACTGTTGAAATTGAGTCAGGATGCACTGTATGGCAACAGCTGAGTGTCAG                         GGGCGGAGCAGCTTTGATCATGGTATCACTTGCAGTAATTGCAGGCTCCCT
genomic: ACTGTTGAAATTGAGTCAGGATGCACTGTATGGCAACAGCTGAGTGTCAGgtacaacatc ... cttttaatagGGGCGGAGCAGCTTTGATCATGGTATCACTTGCAGTAATTGCAGGCTCCCT
EST: gi|100396568|gb|BY990190.1|BY990190
EST:     ACTGTTGAAATTGAGTCAGGATGCACTGTATGGCAACAGCTGAGTGTCAG                         GGGCGGAGCAGCTTTGATCATGGTATCACTTGCAGTAATTGCAGGCTCCCT
genomic: ACTGTTGAAATTGAGTCAGGATGCACTGTATGGCAACAGCTGAGTGTCAGgtacaacatc ... cttttaatagGGGCGGAGCAGCTTTGATCATGGTATCACTTGCAGTAATTGCAGGCTCCCT
EST: gi|67692379|gb|BJ952612.1|BJ952612
EST:     ACTGTTGAAATTGAGTCAGGATGCACTGTATGGCAACAGCTGAGTGTCAG                         GGGCGGAGCAGCTTTGATCATGGTATCACTTGCAGTAATTGCAGGCTCCCT
genomic: ACTGTTGAAATTGAGTCAGGATGCACTGTATGGCAACAGCTGAGTGTCAGgtacaacatc ... cttttaatagGGGCGGAGCAGCTTTGATCATGGTATCACTTGCAGTAATTGCAGGCTCCCT
EST: gi|162251969|gb|FC426674.1|FC426674
EST:     ACTGTTGAAATTGAGTCAGGATGCACTGTATGGCAACAGCTGAGTGTCAG                         GGGCGGAGCAGCTTTGATCATGGTATCACTTGCAGTAATTGCAGGCTCCCT
genomic: ACTGTTGAAATTGAGTCAGGATGCACTGTATGGCAACAGCTGAGTGTCAGgtacaacatc ... cttttaatagGGGCGGAGCAGCTTTGATCATGGTATCACTTGCAGTAATTGCAGGCTCCCT
EST: gi|162214635|gb|FC390666.1|FC390666
EST:     ACTGTTGAAATTGAGTCAGGATGCACTGTATGGCAACAGCTGAGTGTCAG                         GGGCGGAGCAGCTTTGATCATGGTATCACTTGCAGTAATTGCAGGCTCCCT
genomic: ACTGTTGAAATTGAGTCAGGATGCACTGTATGGCAACAGCTGAGTGTCAGgtacaacatc ... cttttaatagGGGCGGAGCAGCTTTGATCATGGTATCACTTGCAGTAATTGCAGGCTCCCT
EST: gi|18335032|gb|BJ167050.1|BJ167050
EST:     ACTGTTGAAATTGAGTCAGGATGCACTGTATGGCAACAGCTGAGTGTCAG                         GGGCGGAGCAGCTTTGATCATGGTATCACTTGCAGTAATTGCAGGCTCCCT
genomic: ACTGTTGAAATTGAGTCAGGATGCACTGTATGGCAACAGCTGAGTGTCAGgtacaacatc ... cttttaatagGGGCGGAGCAGCTTTGATCATGGTATCACTTGCAGTAATTGCAGGCTCCCT
EST: gi|162253434|gb|FC430068.1|FC430068
EST:     ACTGTTGAAATTGAGTCAGGATGCACTGTATGGCAACAGCTGAGTGTCAG                         GGGCGGAGCAGCTTTGATCATGGTATCACTTGCAGTAATTGCAGGCTCCCT
genomic: ACTGTTGAAATTGAGTCAGGATGCACTGTATGGCAACAGCTGAGTGTCAGgtacaacatc ... cttttaatagGGGCGGAGCAGCTTTGATCATGGTATCACTTGCAGTAATTGCAGGCTCCCT
EST: gi|208392848|gb|DC928534.1|DC928534
EST:     ACTGTTGAAATTGAGTCAGGATGCACTGTATGGCAACAGCTGAGTGTCAG                         GGGCGGAGCAGCTTTGATCATGGTATCACTTGCAGTAATTGCAGGCTCCCT
genomic: ACTGTTGAAATTGAGTCAGGATGCACTGTATGGCAACAGCTGAGTGTCAGgtacaacatc ... cttttaatagGGGCGGAGCAGCTTTGATCATGGTATCACTTGCAGTAATTGCAGGCTCCCT
EST: gi|162264402|gb|FC440568.1|FC440568
EST:     ACTGTTGAAATTGAGTCAGGATGCACTGTATGGCAACAGCTGAGTGTCAG                         GGGCGGAGCAGCTTTGATCATGGTATCACTTGCAGTAATTGCAGGCTCCCT
genomic: ACTGTTGAAATTGAGTCAGGATGCACTGTATGGCAACAGCTGAGTGTCAGgtacaacatc ... cttttaatagGGGCGGAGCAGCTTTGATCATGGTATCACTTGCAGTAATTGCAGGCTCCCT
EST: gi|162253435|gb|FC430069.1|FC430069
EST:     ACTGTTGAAATTGAGTCAGGATGCACTGTATGGCAACAGCTGAGTGTCAG                         GGGCGGAGCAGCTTTGATCATGGTATCACTTGCAGTAATTGCAGGCTCCCT
genomic: ACTGTTGAAATTGAGTCAGGATGCACTGTATGGCAACAGCTGAGTGTCAGgtacaacatc ... cttttaatagGGGCGGAGCAGCTTTGATCATGGTATCACTTGCAGTAATTGCAGGCTCCCT

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), 35 (downstream exon)
Score: 57

AAGAGATGATTATTGGAAGAACTGCGATGTTGGGATTTTTCGCTGCTATGACTGTTGAAATTGAGTCAGGATGCACTGTATGGCAACAGCTGAGTGTCAGgtacaacatc ... cttttaatagGGGCGGAGCAGCTTTGATCATGGTATCACTTGCAGTAATTGCAGGCTCCCTTGCGCCTAAAGTGAACGAACTACTGAAGCGTGAATTGGAAATGCCTGTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acgaagtcgctgttccattgaattaacttgttcgtgttgtattatcttttaatagGGGCGGAGCAGCTTTGATCATGGTATCACTTGCAGTAATTGCAGGCTCCCTTGCGCCTAAAGTGAACGAACTACTGAAGCGTGAATTGGAAATGCCTGTG
                    aattaac  putative branch site (score: 57)
                                         ttatctttt  putative PPT
                                    ttgtattatcttttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcttttgccgcgatagatgcacgagttccacatttgaaatgcatcacgaagtcgctgttccattgaattaacttgttcgtgttgtattatcttttaatagGGGCGGAGCAGCTTTGATCATGGTATCACTTGCAGTAATTGCAGGCTCCCTTGCGCCTAAAGTGAACGAACTACTGAAGCGTGAATTGGAAATGCCTGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC