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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcatgtaattgaattcgtcgtaatatttttacaactctggagagtattaattagactttgaacattcttctggtcaactcatttttagttggcatgcagGTTTTGAGTATTGGGCGTGTGTTCGAAGTGAAAGGAGACGAGTTGATGTACACAGTGGAGATGGGCATTCATGGTCATGACCAGCAACCCCATCTTCGAG

Basic information

species Physcomitrella patens
transcript PP1S177_18V6.1
intron # 3
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|162238254|gb|FC414522.1|FC414522
EST:     AGAGGAAGATGGTGCAACTACAGAGTGATGCAGTGTGTAATGCTTCGAAG                         GTTTTGAGTATTGGGCGTGTGTTCGAAGTGAAAGGAGACGAGTTGATGTAC
genomic: AGAGGAAGATGGTGCAACTACAGAGTGATGCAGTGTGTAATGCTTCGAAGgttagttcct ... tggcatgcagGTTTTGAGTATTGGGCGTGTGTTCGAAGTGAAAGGAGACGAGTTGATGTAC
EST: gi|162159609|gb|FC335787.1|FC335787
EST:     AGAGGAAGATGGTGCAACTACAGAGTGATGCAGTGTGTAATGCTTCGAAGTTGGCATGCAG               
genomic: AGAGGAAGATGGTGCAACTACAGAGTGATGCAGTGTGTAATGCTTC-------G-A---AGgttagttcct ...
EST: gi|162233422|gb|FC410219.1|FC410219
EST:     AGAGGAAGATGGTGCAACTACAGAGTGATGCAGTGTGTAATGCTTCGAAG                         GTTTTGAGTATTGGGCGTGTGTTCGAAGTGAAAGGAGACGAGTTGATGTAC
genomic: AGAGGAAGATGGTGCAACTACAGAGTGATGCAGTGTGTAATGCTTCGAAGgttagttcct ... tggcatgcagGTTTTGAGTATTGGGCGTGTGTTCGAAGTGAAAGGAGACGAGTTGATGTAC
EST: gi|15320159|gb|BI487812.1|BI487812
EST:     AGAGGAAGATGGTGCAACTACAGAGTGATGCAGTGTGTAATGCTTCGAAG                         GTTTTGAGTATTGGGCGTGTGTTCGAAGTGAAAGGAGACGAGTTGATGTAC
genomic: AGAGGAAGATGGTGCAACTACAGAGTGATGCAGTGTGTAATGCTTCGAAGgttagttcct ... tggcatgcagGTTTTGAGTATTGGGCGTGTGTTCGAAGTGAAAGGAGACGAGTTGATGTAC
EST: gi|67574657|gb|BJ947481.1|BJ947481
EST:     AGAGGAAGATGGTGCAACTACAGAGTGATGCAGTGTGTAATGCTTCGAAG                         GTTTTGAGTATTGGGCGTGTGTTCGAAGTGAAAGGAGACGAGTTGATGTAC
genomic: AGAGGAAGATGGTGCAACTACAGAGTGATGCAGTGTGTAATGCTTCGAAGgttagttcct ... tggcatgcagGTTTTGAGTATTGGGCGTGTGTTCGAAGTGAAAGGAGACGAGTTGATGTAC
EST: gi|67698071|gb|BJ958304.1|BJ958304
EST:     AGAGGAAGATGGTGCAACTACAGAGTGATGCAGTGTGTAATGCTTCGAAG                         GTTTTGAGTATTGGGCGTGTGTTCGAAGTGAAAGGAGACGAGTTGATGTAC
genomic: AGAGGAAGATGGTGCAACTACAGAGTGATGCAGTGTGTAATGCTTCGAAGgttagttcct ... tggcatgcagGTTTTGAGTATTGGGCGTGTGTTCGAAGTGAAAGGAGACGAGTTGATGTAC
EST: gi|162251279|gb|FC428558.1|FC428558
EST:     AGAGGAAGATGGTGCAACTACAGAGTGATGCAGTGTGTAATGCTTCGAAG                         GTTTTGAGTATTGGGCGTGTGTTCGAAGTGAAAGGAGACGAGTTGATGTAC
genomic: AGAGGAAGATGGTGCAACTACAGAGTGATGCAGTGTGTAATGCTTCGAAGgttagttcct ... tggcatgcagGTTTTGAGTATTGGGCGTGTGTTCGAAGTGAAAGGAGACGAGTTGATGTAC
EST: gi|162238255|gb|FC414523.1|FC414523
EST:     AGAGGAAGATGGTGCAACTACAGAGTGATGCAGTGTGTAATGCTTCGAAG                         GTTTTGAGTATTGGGCGTGTGTTCGAAGTGAAAGGAGACGAGTTGATGTAC
genomic: AGAGGAAGATGGTGCAACTACAGAGTGATGCAGTGTGTAATGCTTCGAAGgttagttcct ... tggcatgcagGTTTTGAGTATTGGGCGTGTGTTCGAAGTGAAAGGAGACGAGTTGATGTAC

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), 34 (downstream exon)
Score: 14

AAAGGAATCTACGATGCGGAGAGGAAGATGGTGCAACTACAGAGTGATGCAGTGTGTAATGCTTCGAAGgttagttcct ... tggcatgcagGTTTTGAGTATTGGGCGTGTGTTCGAAGTGAAAGGAGACGAGTTGATGTACACAGTGGAGATGGGCATTCATGGTCATGACCAGCAACCCCATCTTCGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattaattagactttgaacattcttctggtcaactcatttttagttggcatgcagGTTTTGAGTATTGGGCGTGTGTTCGAAGTGAAAGGAGACGAGTTGATGTACACAGTGGAGATGGGCATTCATGGTCATGACCAGCAACCCCATCTTCGAG
 tattaat  putative branch site (score: 14)
                                    atttttagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcatgtaattgaattcgtcgtaatatttttacaactctggagagtattaattagactttgaacattcttctggtcaactcatttttagttggcatgcagGTTTTGAGTATTGGGCGTGTGTTCGAAGTGAAAGGAGACGAGTTGATGTACACAGTGGAGATGGGCATTCATGGTCATGACCAGCAACCCCATCTTCGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG