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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGAGCAAGTTTTAAAAACACAAGTGACAAAGACTCGGCAAGCGATGAAGAGGCTGTGGACGAGAAGTCCCAGGTTCTCCGTGCGGCCATGTCTCACGTGgtatgtgcatagatcttactctactgcaaaagcatccatagtcctgtccctcaccaattgcaattgaccagattcgtctctgatctgtgtttggaaagttttactgcag

Basic information

species Physcomitrella patens
transcript PP1S6_148V6.1
intron # 2
splice site 5'
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|100429193|gb|BY977987.1|BY977987
EST:     AGGCTGTGGACGAGAAGTCCCAGGTTCTCCGTGCGGCCATGTCTCACGTG                         TCAAGGCTAGGGTGGACAGAATCTGCTCTTGTGCAAGGTGCGAAGGACGCC
genomic: AGGCTGTGGACGAGAAGTCCCAGGTTCTCCGTGCGGCCATGTCTCACGTGgtatgtgcat ... tttactgcagTCAAGGCTAGGGTGGACAGAATCTGCTCTTGTGCAAGGTGCGAAGGACGCC
EST: gi|162220971|gb|FC396156.1|FC396156
EST:     AGGCTGTGGACGAGAAGTCCCAGGTTCTCCGTGCGGCCATGTCTCACGTG                         TCAAGGCTAGGGTGGACAGAATCTGCTCTTGTGCAAGGTGCGAAGGACGCC
genomic: AGGCTGTGGACGAGAAGTCCCAGGTTCTCCGTGCGGCCATGTCTCACGTGgtatgtgcat ... tttactgcagTCAAGGCTAGGGTGGACAGAATCTGCTCTTGTGCAAGGTGCGAAGGACGCC
EST: gi|100444940|gb|BY982768.1|BY982768
EST:     AAGCTGTGGACGAGAAGTCCCAGGTTCTCCGTGCGGCCATGTCTCACGTG                         TCAAGGCTAGGGTGGACAGAATCTGCTCTTG
genomic: AGGCTGTGGACGAGAAGTCCCAGGTTCTCCGTGCGGCCATGTCTCACGTGgtatgtgcat ... tttactgcagTCAAGGCTAGGGTGGACAGAATCTGCTCTTG
EST: gi|162273082|gb|FC447776.1|FC447776
EST:     AGGCTGTGGACGAGAAGTCCCAGGTTCTCCGTGCGGCCATGTCTCACGTG                         TCAAGGCTAGGGTGGACAGAATCTGCTCTTGTGCAAGGTGCGAAGGACGCC
genomic: AGGCTGTGGACGAGAAGTCCCAGGTTCTCCGTGCGGCCATGTCTCACGTGgtatgtgcat ... tttactgcagTCAAGGCTAGGGTGGACAGAATCTGCTCTTGTGCAAGGTGCGAAGGACGCC
EST: gi|162190184|gb|FC365926.1|FC365926
EST:     AGGCTGTGGACGAGAAGTCCCAGGTTCTCCGTGCGGCCATGTCTCACGTG                         TCAAGGCTAGGGTGGACAGAATCTGCTCTTGTGCAAGGTGCGAAGGACGCC
genomic: AGGCTGTGGACGAGAAGTCCCAGGTTCTCCGTGCGGCCATGTCTCACGTGgtatgtgcat ... tttactgcagTCAAGGCTAGGGTGGACAGAATCTGCTCTTGTGCAAGGTGCGAAGGACGCC
EST: gi|162161863|gb|FC337952.1|FC337952
EST:     AGGCTGTGGACGAGAAGTCCCAGGTTCTCCGTGCGGCCATGTCTCACGTG                         TCAAGGCTAGGGTGGACAGAATCTGCTCTTGTGCAAGGTGCGAAGGACGCC
genomic: AGGCTGTGGACGAGAAGTCCCAGGTTCTCCGTGCGGCCATGTCTCACGTGgtatgtgcat ... tttactgcagTCAAGGCTAGGGTGGACAGAATCTGCTCTTGTGCAAGGTGCGAAGGACGCC
EST: gi|37826992|gb|BJ585004.1|BJ585004
EST:     CTCCGTGCGGCCATGTCTCACGTG                         TCAAGGCTAGGGTGGACAGAATCTGCTCTTGTGCAAGGTGCGAAGGACGCC
genomic: CTCCGTGCGGCCATGTCTCACGTGgtatgtgcat ... tttactgcagTCAAGGCTAGGGTGGACAGAATCTGCTCTTGTGCAAGGTGCGAAGGACGCC
EST: gi|208370955|gb|DC944330.1|DC944330
EST:     AGGCTGTGGACGAGAAGTCCCAGGTTCTCCGTGCGGCCATGTCTCACGTG                         TCAAGGCTAGGGTGGACAGAATCTGCTCTTGTGCAAGGTGCGAAGGACGCC
genomic: AGGCTGTGGACGAGAAGTCCCAGGTTCTCCGTGCGGCCATGTCTCACGTGgtatgtgcat ... tttactgcagTCAAGGCTAGGGTGGACAGAATCTGCTCTTGTGCAAGGTGCGAAGGACGCC
EST: gi|208377435|gb|DC927081.1|DC927081
EST:     AGGCTGTGGACGAGAAGTCCCAGGTTCTCCGTGCGGCCATGTCTCACGTG                         TCAAGGCTAGGGTGGACAGAATCTGCTCTTGTGCAAGGTGCGAAGGACGCC
genomic: AGGCTGTGGACGAGAAGTCCCAGGTTCTCCGTGCGGCCATGTCTCACGTGgtatgtgcat ... tttactgcagTCAAGGCTAGGGTGGACAGAATCTGCTCTTGTGCAAGGTGCGAAGGACGCC
EST: gi|100441361|gb|BY962650.1|BY962650
EST:     AGGCTGTGGACGAGAAGTCCCAGGTTCTCCGTGCGGGCATGTCTCACGTG                         TCAAGGCTAGGGTGGACAGAATCTGCTCTTGTGGCA-GGTGCGAAGGACGC
genomic: AGGCTGTGGACGAGAAGTCCCAGGTTCTCCGTGCGGCCATGTCTCACGTGgtatgtgcat ... tttactgcagTCAAGGCTAGGGTGGACAGAATCTGCTCTTGTG-CAAGGTGCGAAGGACGC
EST: gi|162190183|gb|FC365925.1|FC365925
EST:     GCGGCCATGTCTCACGTG                         TCAAGGCTAGGGTGGACAGAATCTGCTCTTGTGCAAGGTGCGAAGGACGCC
genomic: GCGGCCATGTCTCACGTGgtatgtgcat ... tttactgcagTCAAGGCTAGGGTGGACAGAATCTGCTCTTGTGCAAGGTGCGAAGGACGCC
EST: gi|162211282|gb|FC387512.1|FC387512
EST:     AGGCTGTGGACGAGAAGTCCCAGGTTCTCCGTGCGGCCATGTCTCACGTG                         TCAAGGCTAGGGTGGACAGAATCTGCTCTTGTGCAAGGTGCGAAGGACGCC
genomic: AGGCTGTGGACGAGAAGTCCCAGGTTCTCCGTGCGGCCATGTCTCACGTGgtatgtgcat ... tttactgcagTCAAGGCTAGGGTGGACAGAATCTGCTCTTGTGCAAGGTGCGAAGGACGCC
EST: gi|100376216|gb|BY986078.1|BY986078
EST:     AGGCTGTGGACGAGAAGTCCCAGGGTCTCCGTGCGGCCATGTCTCACGTG                         TCAAGGCTAGGGTGGACA
genomic: AGGCTGTGGACGAGAAGTCCCAGGTTCTCCGTGCGGCCATGTCTCACGTGgtatgtgcat ... tttactgcagTCAAGGCTAGGGTGGACA
EST: gi|162220972|gb|FC396157.1|FC396157
EST:     AGGCTGTGGACGAGAAGTCCCAGGTTCTCCGTGCGGCCATGTCTCACGTG                         TCAAGGCTAGGGTGGACAGAATCTGCTCTTGTGCAAGGTGCGAAGGACGCC
genomic: AGGCTGTGGACGAGAAGTCCCAGGTTCTCCGTGCGGCCATGTCTCACGTGgtatgtgcat ... tttactgcagTCAAGGCTAGGGTGGACAGAATCTGCTCTTGTGCAAGGTGCGAAGGACGCC
EST: gi|208351093|gb|DC921339.1|DC921339
EST:     AGGCTGTGGACGAGAAGTCCCAGGTTCTCCGTGCGGCCATGTCTCACGTG                         TCAAGGCTAGGGTGGACAGAATCTGCTCTTGTGCAAGGTGCGAAGGACGCC
genomic: AGGCTGTGGACGAGAAGTCCCAGGTTCTCCGTGCGGCCATGTCTCACGTGgtatgtgcat ... tttactgcagTCAAGGCTAGGGTGGACAGAATCTGCTCTTGTGCAAGGTGCGAAGGACGCC
EST: gi|100363494|gb|BY966417.1|BY966417
EST:     AGGCTGTGGACGAGAAGTCCCAGGTTCTCCGTGCGGCCATGTCTCACGTG                         TCAAGGCTAGGGTGGACAGAATCTGCTCTTGTGCAAGGTGCGAAGGACGCC
genomic: AGGCTGTGGACGAGAAGTCCCAGGTTCTCCGTGCGGCCATGTCTCACGTGgtatgtgcat ... tttactgcagTCAAGGCTAGGGTGGACAGAATCTGCTCTTGTGCAAGGTGCGAAGGACGCC
EST: gi|208346672|gb|DC913318.1|DC913318
EST:     AGGCTGTGGACGAGAAGTCCCAGGTTCTCCGTGCGGCCATGTCTCACGTG                         TCAAGGCTAGGGTGGACAGAATCTGCTCTTGTGCAAGGTGCGAANGACNCC
genomic: AGGCTGTGGACGAGAAGTCCCAGGTTCTCCGTGCGGCCATGTCTCACGTGgtatgtgcat ... tttactgcagTCAAGGCTAGGGTGGACAGAATCTGCTCTTGTGCAAGGTGCGAAGGACGCC
EST: gi|208384841|gb|DC907454.1|DC907454
EST:     AGGCTGTGGACGAGAAGTCCCAGGTTCTCCGTGCGGCCATGTCTCACGTG                         TCAAGGCTAGGGTGGACAGAATCTGCTCTTGTGCAAGGTGCGAAGGACGCC
genomic: AGGCTGTGGACGAGAAGTCCCAGGTTCTCCGTGCGGCCATGTCTCACGTGgtatgtgcat ... tttactgcagTCAAGGCTAGGGTGGACAGAATCTGCTCTTGTGCAAGGTGCGAAGGACGCC
EST: gi|208363381|gb|DC946979.1|DC946979
EST:     AGGCTGTGGACGAGAAGTCCCAGGTTCTCCGTGCGGCCATGTCTCACGTG                         TCAAGGCTAGGGTGGACAGAATCTGCTCTTGTGCAAGGTGCGAAGGACGCC
genomic: AGGCTGTGGACGAGAAGTCCCAGGTTCTCCGTGCGGCCATGTCTCACGTGgtatgtgcat ... tttactgcagTCAAGGCTAGGGTGGACAGAATCTGCTCTTGTGCAAGGTGCGAAGGACGCC
EST: gi|162274452|gb|FC450687.1|FC450687
EST:     AGGCTGTGGACGAGAAGTCCCAGGTTCTCCGTGCGGCCATGTCTCACGTG                         TCAAGGCTAGGGTGGACAGAATCTGCTCTTGTGCAAGGTGCGAAGGACGCC
genomic: AGGCTGTGGACGAGAAGTCCCAGGTTCTCCGTGCGGCCATGTCTCACGTGgtatgtgcat ... tttactgcagTCAAGGCTAGGGTGGACAGAATCTGCTCTTGTGCAAGGTGCGAAGGACGCC
EST: gi|208382343|gb|DC919331.1|DC919331
EST:     AGGCTGTGGACGAGNAGTCCCAGGTTCTCCGTGCGGCCATGTCTCACGTG                         TCAAGGCTAGGGTGGACAGAATCTGCTCTTGTGCAAGGTGCGAAGGACGCC
genomic: AGGCTGTGGACGAGAAGTCCCAGGTTCTCCGTGCGGCCATGTCTCACGTGgtatgtgcat ... tttactgcagTCAAGGCTAGGGTGGACAGAATCTGCTCTTGTGCAAGGTGCGAAGGACGCC
EST: gi|100447936|gb|CJ972235.1|CJ972235
EST:     AGGCTGTGGACGAGAAGTCCCAGGTTCTCCGTGCGGCCATGTCTCACGTG                         TCAAGGCTAGGGTGGACAGAATCTGCTCTTGTGCAAGGTGCGAAGGACGCC
genomic: AGGCTGTGGACGAGAAGTCCCAGGTTCTCCGTGCGGCCATGTCTCACGTGgtatgtgcat ... tttactgcagTCAAGGCTAGGGTGGACAGAATCTGCTCTTGTGCAAGGTGCGAAGGACGCC
EST: gi|208346915|gb|DC905445.1|DC905445
EST:     AGGCTGTGGACGAGAAGTCCCAGGTTCTCCGTGCGGCCATGTCTCACGTG                         TCAAGGCTAGGGTGGACAGAATCTGCTCTTGTGCAAGGTGCGAAGGACGCC
genomic: AGGCTGTGGACGAGAAGTCCCAGGTTCTCCGTGCGGCCATGTCTCACGTGgtatgtgcat ... tttactgcagTCAAGGCTAGGGTGGACAGAATCTGCTCTTGTGCAAGGTGCGAAGGACGCC
EST: gi|100451262|gb|CJ974677.1|CJ974677
EST:     AAGCTGTGGACGAGAAGTCCCAGGTTCTCCGTGCGGCCATGTCTCACGTG                         TCAAGGCTAGGGTGGACAGAATCTGCTCTNGTGCA
genomic: AGGCTGTGGACGAGAAGTCCCAGGTTCTCCGTGCGGCCATGTCTCACGTGgtatgtgcat ... tttactgcagTCAAGGCTAGGGTGGACAGAATCTGCTCTTGTGCA

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: 34 (upstream exon), 33 (downstream exon)
Score: 12

TGGAGCAAGTTTTAAAAACACAAGTGACAAAGACTCGGCAAGCGATGAAGAGGCTGTGGACGAGAAGTCCCAGGTTCTCCGTGCGGCCATGTCTCACGTGgtatgtgcat ... tttactgcagTCAAGGCTAGGGTGGACAGAATCTGCTCTTGTGCAAGGTGCGAAGGACGCCGGGTTGTCGCCTGCCATCGTGGGCTCTTTCCCACGCAAAGACGCCGCTC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGAGCAAGTTTTAAAAACACAAGTGACAAAGACTCGGCAAGCGATGAAGAGGCTGTGGACGAGAAGTCCCAGGTTCTCCGTGCGGCCATGTCTCACGTGgtatgtgcatagatcttactctactgcaaaagcatccatagtcctgtccctcaccaattgcaattgaccagattcgtctctgatctgtgtttggaaagttttactgcag

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