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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgtgtgtgtttctactcagtctacagtttttcttattatatcgttagtcatgaattgtaactcactcgatctcgtgccttttgattcggatctctggcagCGCATCAATGGGCTAGCTCAAGTGCGCAAGGCGAAGAAGGCTGAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAG

Basic information

species Physcomitrella patens
transcript PP1S31_130V6.1
intron # 5
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|162157523|gb|FC333781.1|FC333781
EST:     AAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAG                         CGCATCAATGGGCTAGCTCAAGTGCGCAAGGCGAAGAAGGCTGAGGTGGAC
genomic: AAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAGgttagtaggt ... tctctggcagCGCATCAATGGGCTAGCTCAAGTGCGCAAGGCGAAGAAGGCTGAGGTGGAC
EST: gi|162253296|gb|FC428890.1|FC428890
EST:     TCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAG                         CGCATCAATGGGCTAGCTCAAGTGCGCAAGGCGAAGAAGGCTGAGGTGGAC
genomic: TCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAGgttagtaggt ... tctctggcagCGCATCAATGGGCTAGCTCAAGTGCGCAAGGCGAAGAAGGCTGAGGTGGAC
EST: gi|208374619|gb|DC948619.1|DC948619
EST:     TCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAG                         CGCATCAATGGGCTAGCTCAAGTGCGCAAGGCGAAGAAGGCTGAGGTGGAC
genomic: TCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAGgttagtaggt ... tctctggcagCGCATCAATGGGCTAGCTCAAGTGCGCAAGGCGAAGAAGGCTGAGGTGGAC
EST: gi|208351971|gb|DC925780.1|DC925780
EST:     TCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAG                         CGCATCAATGGGCTAGCTCAAGTGCGCAAGGCGAAGAAGGCTGAGGTGGAC
genomic: TCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAGgttagtaggt ... tctctggcagCGCATCAATGGGCTAGCTCAAGTGCGCAAGGCGAAGAAGGCTGAGGTGGAC
EST: gi|162184555|gb|FC360029.1|FC360029
EST:     TCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAG                         CGCATCAATGGGCTAGCTCAAGTGCGCAAGGCGAAGAAGGCTGAGGTGGAC
genomic: TCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAGgttagtaggt ... tctctggcagCGCATCAATGGGCTAGCTCAAGTGCGCAAGGCGAAGAAGGCTGAGGTGGAC
EST: gi|162151813|gb|FC328059.1|FC328059
EST:     GAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAG                         CGCATCAATGGGCTAGCTCAAGTGCGCAAGGCGAAGAAGGCTGAGGTGGAC
genomic: GAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAGgttagtaggt ... tctctggcagCGCATCAATGGGCTAGCTCAAGTGCGCAAGGCGAAGAAGGCTGAGGTGGAC
EST: gi|162156787|gb|FC333599.1|FC333599
EST:     CGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAAATAA-G                         CGCATCAATGGGCTAGCTCAAGTG
genomic: CGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAA-TAAAGgttagtaggt ... tctctggcagCGCATCAATGGGCTAGCTCAAGTG
EST: gi|18338140|gb|BJ170164.1|BJ170164
EST:     GTGGAGTCGATGATGCGGCGAATAAAG                         CGCATCAATGGGCTAGCTCAAGTGCGCAAGGCGAAGAAGGCTGAGGTGGAC
genomic: GTGGAGTCGATGATGCGGCGAATAAAGgttagtaggt ... tctctggcagCGCATCAATGGGCTAGCTCAAGTGCGCAAGGCGAAGAAGGCTGAGGTGGAC
EST: gi|67725452|gb|BJ975711.1|BJ975711
EST:     TCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAG                         CGCATCAATGGGCTAGCTCAAGTGCGCAAGGCGAAGAAGGCTGAGGTGGAC
genomic: TCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAGgttagtaggt ... tctctggcagCGCATCAATGGGCTAGCTCAAGTGCGCAAGGCGAAGAAGGCTGAGGTGGAC
EST: gi|162184554|gb|FC360028.1|FC360028
EST:     TCTGAGGTGGAGTCGATGATGCGGCGAATAAAG                         CGCATCAATGGGCTAGCTCAAGTGCGCAAGGCGAAGAAGGCTGAGGTGGAC
genomic: TCTGAGGTGGAGTCGATGATGCGGCGAATAAAGgttagtaggt ... tctctggcagCGCATCAATGGGCTAGCTCAAGTGCGCAAGGCGAAGAAGGCTGAGGTGGAC
EST: gi|162195572|gb|FC371873.1|FC371873
EST:     GAGGTGGAGTCGATGATGCGGCGAATAAAG                         CGCATCAATGGGCTAGCTCAAGTGCGCAAGGCGAAGAAGGCTGAGGTGGAC
genomic: GAGGTGGAGTCGATGATGCGGCGAATAAAGgttagtaggt ... tctctggcagCGCATCAATGGGCTAGCTCAAGTGCGCAAGGCGAAGAAGGCTGAGGTGGAC
EST: gi|37831922|gb|BJ589934.1|BJ589934
EST:     GTCGATGATGCGGCGAATAAAG                         CGCATCAATGGGCTAGCTCAAGTGCGCAAGGCGAAGAAGGCTGAGGTGGAC
genomic: GTCGATGATGCGGCGAATAAAGgttagtaggt ... tctctggcagCGCATCAATGGGCTAGCTCAAGTGCGCAAGGCGAAGAAGGCTGAGGTGGAC
EST: gi|162162261|gb|FC338043.1|FC338043
EST:     TCGATGATGCGGCG-ATAAAAG                         CGCATCAATGGGCTAGCTCAAGTGCGCAAGGCGAAGAAGGCTGAGGTGGA
genomic: TCGATGATGCGGCGAAT-AAAGgttagtaggt ... tctctggcagCGCATCAATGGGCTAGCTCAAGTGCGCAAGGCGAAGAAGGCTGAGGTGGA
EST: gi|162161773|gb|FC338213.1|FC338213
EST:     GTCGATGATGCGGCGAATAAAG                         CGCATCAATGGGCTAGCTCAAGTGCGCAAGGCGAAGAAGGCTGAGGTGGAC
genomic: GTCGATGATGCGGCGAATAAAGgttagtaggt ... tctctggcagCGCATCAATGGGCTAGCTCAAGTGCGCAAGGCGAAGAAGGCTGAGGTGGAC
EST: gi|162178673|gb|FC354462.1|FC354462
EST:     TCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAG                         CGCATCAATGGGCTAGCTCAAGTGCGCAAGGCGAAGAAGGCTGAGGTGGAC
genomic: TCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAGgttagtaggt ... tctctggcagCGCATCAATGGGCTAGCTCAAGTGCGCAAGGCGAAGAAGGCTGAGGTGGAC
EST: gi|162155636|gb|FC331561.1|FC331561
EST:     TCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAG                         CGCATCAATGGGCTAGCTCAAGTGCGCAAGGCGAAGAAGGCTGAGGTGGAC
genomic: TCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAGgttagtaggt ... tctctggcagCGCATCAATGGGCTAGCTCAAGTGCGCAAGGCGAAGAAGGCTGAGGTGGAC
EST: gi|162176070|gb|FC351864.1|FC351864
EST:     TCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAG                         CGCATCAATGGGCTAGCTCAAGTGCGCAAGGCGAAGAAGGCTGAGGTGGAC
genomic: TCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAGgttagtaggt ... tctctggcagCGCATCAATGGGCTAGCTCAAGTGCGCAAGGCGAAGAAGGCTGAGGTGGAC
EST: gi|208373025|gb|DC948790.1|DC948790
EST:     TCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAG                         CGCATCNATGGGCTAGCTCAAGTGCGCAAGGCGAAGAAGGCTGAGGTGGAC
genomic: TCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAGgttagtaggt ... tctctggcagCGCATCAATGGGCTAGCTCAAGTGCGCAAGGCGAAGAAGGCTGAGGTGGAC
EST: gi|162187276|gb|FC363226.1|FC363226
EST:     GTCGATGATGCGGCGAATAAAG                         CGCATC-ATGGGGCTAGCTCAAGTGCGCAAGGCGAAGAAGGCTGAGGTGGA
genomic: GTCGATGATGCGGCGAATAAAGgttagtaggt ... tctctggcagCGCATCAAT-GGGCTAGCTCAAGTGCGCAAGGCGAAGAAGGCTGAGGTGGA
EST: gi|162155637|gb|FC331562.1|FC331562
EST:     TCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAG                         CGCATCAATGGGCTAGCTCAAGTGCGCAAGGCGAAGAAGGCTGAGGTGGAC
genomic: TCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAGgttagtaggt ... tctctggcagCGCATCAATGGGCTAGCTCAAGTGCGCAAGGCGAAGAAGGCTGAGGTGGAC
EST: gi|37827407|gb|BJ585419.1|BJ585419
EST:     TCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAG                         CGCATCAATGGGCTAGCTCAAGTGCGCAAGGCGAAGAAGGCTGAGGTGGAC
genomic: TCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAGgttagtaggt ... tctctggcagCGCATCAATGGGCTAGCTCAAGTGCGCAAGGCGAAGAAGGCTGAGGTGGAC
EST: gi|162162411|gb|FC339168.1|FC339168
EST:     TCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAG                         CGCATCAATGGGCTAGCTCAAGTGCGCAAGGCGAAGAAGGCTGAGGTGGAC
genomic: TCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAGgttagtaggt ... tctctggcagCGCATCAATGGGCTAGCTCAAGTGCGCAAGGCGAAGAAGGCTGAGGTGGAC
EST: gi|162162262|gb|FC338044.1|FC338044
EST:     TCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAG                         CGCATCAATGGGCTAGCTCAAGTGCGCAAGGCGAAGAAGGCTGAGGTGGAC
genomic: TCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAGgttagtaggt ... tctctggcagCGCATCAATGGGCTAGCTCAAGTGCGCAAGGCGAAGAAGGCTGAGGTGGAC
EST: gi|162178674|gb|FC354463.1|FC354463
EST:     TCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAG                         CGCATCAATGGGCTAGCTCAAGTGCGCAAGGCGAAGAAGGCTGAGGTGGAC
genomic: TCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAGgttagtaggt ... tctctggcagCGCATCAATGGGCTAGCTCAAGTGCGCAAGGCGAAGAAGGCTGAGGTGGAC
EST: gi|208356256|gb|DC946262.1|DC946262
EST:     TCGATCTTGTTAAAGAATTTGAGGTGGAGTCGATGATGCGGCGAATAAAG                         CGCATCAATGGGCTAGCTCAAGTGCGCAAGGCGAAGAAGGCTGAGGTGGAC
genomic: TCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAGgttagtaggt ... tctctggcagCGCATCAATGGGCTAGCTCAAGTGCGCAAGGCGAAGAAGGCTGAGGTGGAC
EST: gi|162157524|gb|FC333782.1|FC333782
EST:     TCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAG                         CGCATCAATGGGCTAGCTCAAGTGCGCAAGGCGAAGAAGGCTGAGGTGGAC
genomic: TCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAGgttagtaggt ... tctctggcagCGCATCAATGGGCTAGCTCAAGTGCGCAAGGCGAAGAAGGCTGAGGTGGAC
EST: gi|208364862|gb|DC943680.1|DC943680
EST:     TGAGGTGGAGTCGATGATGCGGCGAATAAAG                         CGCATCAATGGGCTAGCTCAAGTGCGCAAGGCGAAGAAGGCTGAGGTGGAC
genomic: TGAGGTGGAGTCGATGATGCGGCGAATAAAGgttagtaggt ... tctctggcagCGCATCAATGGGCTAGCTCAAGTGCGCAAGGCGAAGAAGGCTGAGGTGGAC
EST: gi|162269789|gb|FC445657.1|FC445657
EST:     TCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAG                         CGCATCAATGGGCTAGCTCAAGTGCGCAAGGCGAAGAAGGCTGAGGTGGAC
genomic: TCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAGgttagtaggt ... tctctggcagCGCATCAATGGGCTAGCTCAAGTGCGCAAGGCGAAGAAGGCTGAGGTGGAC
EST: gi|162269788|gb|FC445656.1|FC445656
EST:     TCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAG                         CGCATCAATGGGCTAGCTCAAGTGCGCAAGGCGAAGAAGGCTGAGGTGGAC
genomic: TCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAGgttagtaggt ... tctctggcagCGCATCAATGGGCTAGCTCAAGTGCGCAAGGCGAAGAAGGCTGAGGTGGAC

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), 32 (downstream exon)
Score: 14

ATCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAGgttagtaggt ... tctctggcagCGCATCAATGGGCTAGCTCAAGTGCGCAAGGCGAAGAAGGCTGAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtcatgaattgtaactcactcgatctcgtgccttttgattcggatctctggcagCGCATCAATGGGCTAGCTCAAGTGCGCAAGGCGAAGAAGGCTGAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAG
                                             tctct  CT-rich tract
       aattgtaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgtgtgtgtttctactcagtctacagtttttcttattatatcgttagtcatgaattgtaactcactcgatctcgtgccttttgattcggatctctggcagCGCATCAATGGGCTAGCTCAAGTGCGCAAGGCGAAGAAGGCTGAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA