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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAACACCGCCCTCTCTGCAGCGTCGCTGAAGCCCGTCTCAAATTTTGGTCTCATGGAAGCAGCTGCTGATGCTGGGATAGTTTTCGTCACCTCCCCAAAGgtgatacatgcttttgcttgctttctttaaaagggttacacttacttggtcgtagccctcgatttactgcttcaggactcttccctgcggatatgatcct...

Basic information

species Physcomitrella patens
transcript PP1S45_62V6.1
intron # 3
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|208393703|gb|DC946053.1|DC946053
EST:     TCATGGAAGCAGCTGCTGATGCTGGGATAGTTTTCGTCACCTCCCCAAAG                         GTTGGGCTCTTCAGAAAAGGAAGAACTGTGAAGGGAAGAAGTGGTCCTCCA
genomic: TCATGGAAGCAGCTGCTGATGCTGGGATAGTTTTCGTCACCTCCCCAAAGgtgatacatg ... gggtgatcagGTTGGGCTCTTCAGAAAAGGAAGAACTGTGAAGGGAAGAAGTGGTCCTCCA
EST: gi|67569095|gb|BJ941919.1|BJ941919
EST:     TCATGGAAGCAGCTGCTGATGCTGGGATAGTTTTCGTCACCTCCCCAAAG                         GTTGGGCTCTTCAGAAAAGGAAGAACTGTGAAGGGAAGAAGTGGTCCTCCA
genomic: TCATGGAAGCAGCTGCTGATGCTGGGATAGTTTTCGTCACCTCCCCAAAGgtgatacatg ... gggtgatcagGTTGGGCTCTTCAGAAAAGGAAGAACTGTGAAGGGAAGAAGTGGTCCTCCA
EST: gi|67692331|gb|BJ952564.1|BJ952564
EST:     TCATGGAAGCAGCTGCTGATGCTGGGATAGTTTTCGTCACCTCCCCAAAG                         GTTGGGCTCTTCAGAAAAGGAAGAACTGTGAAGGGAAGAAGTGGTCCTCCA
genomic: TCATGGAAGCAGCTGCTGATGCTGGGATAGTTTTCGTCACCTCCCCAAAGgtgatacatg ... gggtgatcagGTTGGGCTCTTCAGAAAAGGAAGAACTGTGAAGGGAAGAAGTGGTCCTCCA
EST: gi|208366599|gb|DC954879.1|DC954879
EST:     TCATGGAAGCAGCTGCTGATGCTGGGATAGTTTTCGTCACCTCCCCAAAG                         GTTGGGCTCTTCAGAAAAGGAAGAACTGTGAAGGGAAGAAGTGGTCCTCCA
genomic: TCATGGAAGCAGCTGCTGATGCTGGGATAGTTTTCGTCACCTCCCCAAAGgtgatacatg ... gggtgatcagGTTGGGCTCTTCAGAAAAGGAAGAACTGTGAAGGGAAGAAGTGGTCCTCCA
EST: gi|18333853|gb|BJ165869.1|BJ165869
EST:     TCATGGAAGCAGCTGCTGATGCTGGGATAGTTTTCGTCACCTCCCCAAAG                         GTTGGGCTCTTCAGAAAAGGAAGAACTGTGAAGGGAAGAAGTGGTCCTCCA
genomic: TCATGGAAGCAGCTGCTGATGCTGGGATAGTTTTCGTCACCTCCCCAAAGgtgatacatg ... gggtgatcagGTTGGGCTCTTCAGAAAAGGAAGAACTGTGAAGGGAAGAAGTGGTCCTCCA
EST: gi|67692450|gb|BJ952683.1|BJ952683
EST:     TCATGGAAGCAGCTGCTGATGCTGGGATAGTTTTCGTCACCTCCCCAAAG                         GTTGGGCTCTTCAGAAAAGGAAGAACTGTGAAGGGAAGAAGTGGTCCTCCA
genomic: TCATGGAAGCAGCTGCTGATGCTGGGATAGTTTTCGTCACCTCCCCAAAGgtgatacatg ... gggtgatcagGTTGGGCTCTTCAGAAAAGGAAGAACTGTGAAGGGAAGAAGTGGTCCTCCA
EST: gi|37836220|gb|BJ594228.1|BJ594228
EST:     TCATGGAAGCAGCTGCTGATGCTGGGATAGTTTTCGTCACCTCCCCAAAG                         GTTGGGCTCTTCAGAAAAGGAAGAACTGTGAAGGGAAGAAGTGGTCCTCCA
genomic: TCATGGAAGCAGCTGCTGATGCTGGGATAGTTTTCGTCACCTCCCCAAAGgtgatacatg ... gggtgatcagGTTGGGCTCTTCAGAAAAGGAAGAACTGTGAAGGGAAGAAGTGGTCCTCCA
EST: gi|208353220|gb|DC921880.1|DC921880
EST:     TCATGGAAGCAGCTGCTGATGCTGGGATAGTTTTCGTCACCTCCCCAAAG                         GTTGGGCTCTTCAGAAAAGGAAGAACTGTGAAGGGAAGAAGTGGTCCTCCA
genomic: TCATGGAAGCAGCTGCTGATGCTGGGATAGTTTTCGTCACCTCCCCAAAGgtgatacatg ... gggtgatcagGTTGGGCTCTTCAGAAAAGGAAGAACTGTGAAGGGAAGAAGTGGTCCTCCA
EST: gi|67695352|gb|BJ955585.1|BJ955585
EST:     TCATGGAAGCAGCTGCTGATGCTGGGATAGTTTTCGTCACCTCCCCAAAG                         GTTGGGCTCTTCAGAAAAGGAAGAACTGTGAAGGGAAGAAGTGGTCCTCCA
genomic: TCATGGAAGCAGCTGCTGATGCTGGGATAGTTTTCGTCACCTCCCCAAAGgtgatacatg ... gggtgatcagGTTGGGCTCTTCAGAAAAGGAAGAACTGTGAAGGGAAGAAGTGGTCCTCCA
EST: gi|208392034|gb|DC941882.1|DC941882
EST:     TCATGGAAGCAGCTGCTGATGCTGGGATAGTTTTCGTCACCTCCCCAA-G                         GTTGGGCTCTTCANAAA-GGAA-AACTGTGAAGGNAA-AANTGGTCCTCC-
genomic: TCATGGAAGCAGCTGCTGATGCTGGGATAGTTTTCGTCACCTCCCCAAAGgtgatacatg ... gggtgatcagGTTGGGCTCTTCAGAAAAGGAAGAACTGTGAAGGGAAGAAGTGGTCCTCCA
EST: gi|208371076|gb|DC931550.1|DC931550
EST:     TCATGGAAGCAGCTGCTGATGCTGGGATAGTTTTCGTCACCTCCCCAANG                         -TTGGGCTCTTCA
genomic: TCATGGAAGCAGCTGCTGATGCTGGGATAGTTTTCGTCACCTCCCCAAAGgtgatacatg ... gggtgatcagGTTGGGCTCTTCA
EST: gi|162210193|gb|FC386704.1|FC386704
EST:     CCTCCCCAAAG                         GTTGGGCTCTTCAGAAAAGGAAGAACTGTGAAGGGAAGAAGTGGTCCTCCA
genomic: CCTCCCCAAAGgtgatacatg ... gggtgatcagGTTGGGCTCTTCAGAAAAGGAAGAACTGTGAAGGGAAGAAGTGGTCCTCCA

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-Seq library.


Block sizes: 33 (upstream exon), 30 (downstream exon)
Score: 18

GAACACCGCCCTCTCTGCAGCGTCGCTGAAGCCCGTCTCAAATTTTGGTCTCATGGAAGCAGCTGCTGATGCTGGGATAGTTTTCGTCACCTCCCCAAAGgtgatacatg ... gggtgatcagGTTGGGCTCTTCAGAAAAGGAAGAACTGTGAAGGGAAGAAGTGGTCCTCCACTGTGCGAGGAG





























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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAACACCGCCCTCTCTGCAGCGTCGCTGAAGCCCGTCTCAAATTTTGGTCTCATGGAAGCAGCTGCTGATGCTGGGATAGTTTTCGTCACCTCCCCAAAGgtgatacatgcttttgcttgctttctttaaaagggttacacttacttggtcgtagccctcgatttactgcttcaggactcttccctgcggatatgatcct

- - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG