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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggtcttccattgtagagaaaaattgtcaaacctgcacactaacagccggggtgtaatctacattctctgtactcatatgtgtacactctattttgaccagGAGTACTACGACCCAGACAAATCCATGTTGGAGCTTGTGTTCGCCCCTGCCGACAAATGGATCAGCAAAAGTGACCAGGAGATTGTCGATGCAACAATGG

Basic information

species Physcomitrella patens
transcript PP1S369_27V6.1
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|162192388|gb|FC371657.1|FC371657
EST:     GCAGGAGTCCACTCTTGAGTGTGTACGCCGATATGTCCACTACGTGTAAG                         GAGTACTACGACCCAGACAAATCCATGTTGGAGCTTGTGTTCGCCCCTGCC
genomic: GCAGGAGTCCACTCTTGAGTGTGTACGCCGATATGTCCACTACGTGTAAGgtgagattat ... ttttgaccagGAGTACTACGACCCAGACAAATCCATGTTGGAGCTTGTGTTCGCCCCTGCC
EST: gi|162267103|gb|FC443334.1|FC443334
EST:     GAGTGTGTACGCCGATATGTCCACTACGTGTAAG                         GAGTACTACGACCCAGACAAATCCATGTTGGAGCTTGTGTTCGCCCCTGCC
genomic: GAGTGTGTACGCCGATATGTCCACTACGTGTAAGgtgagattat ... ttttgaccagGAGTACTACGACCCAGACAAATCCATGTTGGAGCTTGTGTTCGCCCCTGCC
EST: gi|208391107|gb|DC938137.1|DC938137
EST:     GCAGGAGTCCACTCTTGAGTGTGTACGCCGATATGTCCACTACGTGTAAG                         GAGTACTACGACC
genomic: GCAGGAGTCCACTCTTGAGTGTGTACGCCGATATGTCCACTACGTGTAAGgtgagattat ... ttttgaccagGAGTACTACGACC
EST: gi|162187988|gb|FC364978.1|FC364978
EST:     GCAGGAGTCCACTCTTGAGTGTGTACGCCGATATGTCCACTACGTGTAAG                         GAGTACTACGACCCAGACAAATCCATGTTGGAGCTTGTGTTCGCCCCTGCC
genomic: GCAGGAGTCCACTCTTGAGTGTGTACGCCGATATGTCCACTACGTGTAAGgtgagattat ... ttttgaccagGAGTACTACGACCCAGACAAATCCATGTTGGAGCTTGTGTTCGCCCCTGCC
EST: gi|18334431|gb|BJ166448.1|BJ166448
EST:     TCCACTACGTGTAAG                         GAGTACTACGACCCAGACAAATCCATGTTGGAGCTTGTGTTCGCCCCTGCC
genomic: TCCACTACGTGTAAGgtgagattat ... ttttgaccagGAGTACTACGACCCAGACAAATCCATGTTGGAGCTTGTGTTCGCCCCTGCC
EST: gi|208366040|gb|DC951185.1|DC951185
EST:     GCAGGAGTCCACTCTTGAGTGTGTACGCCGATATGTCCACTACGTGTAAG                         GAGTACTACGACCCAGACAAATCCATGTTGGAGCTTGTGTTCGCCCCTGCC
genomic: GCAGGAGTCCACTCTTGAGTGTGTACGCCGATATGTCCACTACGTGTAAGgtgagattat ... ttttgaccagGAGTACTACGACCCAGACAAATCCATGTTGGAGCTTGTGTTCGCCCCTGCC
EST: gi|162202823|gb|FC379805.1|FC379805
EST:     GCAGGAGTCCACTCTTGAGTGTGTACGCCGATATGTCCACTACGTGTAAG                         GAGTACTACGACCCAGACAAATCCATGTTGGAGCTTGTGTTCGCCCCTGCC
genomic: GCAGGAGTCCACTCTTGAGTGTGTACGCCGATATGTCCACTACGTGTAAGgtgagattat ... ttttgaccagGAGTACTACGACCCAGACAAATCCATGTTGGAGCTTGTGTTCGCCCCTGCC
EST: gi|162192389|gb|FC371658.1|FC371658
EST:     GCAGGAGTCCACTCTTGAGTGTGTACGCCGATATGTCCACTACGTGTAAG                         GAGTACTACGACCCAGACAAATCCATGTTGGAGCTTGTGTTCGCCCCTGCC
genomic: GCAGGAGTCCACTCTTGAGTGTGTACGCCGATATGTCCACTACGTGTAAGgtgagattat ... ttttgaccagGAGTACTACGACCCAGACAAATCCATGTTGGAGCTTGTGTTCGCCCCTGCC

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: 32 (upstream exon), 34 (downstream exon)
Score: 14

GTTTGACCGGAAGTTGAAAGCTACGTATGATCACTTGCTATTTAGCAGGAGTCCACTCTTGAGTGTGTACGCCGATATGTCCACTACGTGTAAGgtgagattat ... ttttgaccagGAGTACTACGACCCAGACAAATCCATGTTGGAGCTTGTGTTCGCCCCTGCCGACAAATGGATCAGCAAAAGTGACCAGGAGATTGTCGATGCAACAATGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccggggtgtaatctacattctctgtactcatatgtgtacactctattttgaccagGAGTACTACGACCCAGACAAATCCATGTTGGAGCTTGTGTTCGCCCCTGCCGACAAATGGATCAGCAAAAGTGACCAGGAGATTGTCGATGCAACAATGG
                                        ctctatttt  CT-rich tract
                                         tctatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtcttccattgtagagaaaaattgtcaaacctgcacactaacagccggggtgtaatctacattctctgtactcatatgtgtacactctattttgaccagGAGTACTACGACCCAGACAAATCCATGTTGGAGCTTGTGTTCGCCCCTGCCGACAAATGGATCAGCAAAAGTGACCAGGAGATTGTCGATGCAACAATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - -ctgcaca