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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTCAAGTAATCAAGAAGGGACAAGTGGTGTGCTACTTAGAGCAGCTTGGCACACAACAACCTGTAGAGgtatgttataaattttagcagttactacaaagttcttatttgtgaattccaattaggtttttttctggttttcttttattgtttatagagttctgtctgc...

Basic information

species Physcomitrella patens
transcript PP1S45_62V6.1
intron # 5
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:     GACAAGTGGTGTGCTACTTAGAGCAGCTTGGCACACAACAACCTGTAGAG                         GCTGAGGTTACTGGTGAAGTCGAGAAAGTTCTGTGGGAAGATGGAG
genomic: GACAAGTGGTGTGCTACTTAGAGCAGCTTGGCACACAACAACCTGTAGAGgtatgttata ... gcttctgcagGCTGAGGTTACTGGTGAAGTCGAGAAAGTTCTGTGGGAAGATGGAG
EST: gi|67569095|gb|BJ941919.1|BJ941919
EST:     GACAAGTGGTGTGCTACTTAGAGCAGCTTGGCACACAACAACCTGTAGAG                         GCTGAGGTTACTGGTGAAGT
genomic: GACAAGTGGTGTGCTACTTAGAGCAGCTTGGCACACAACAACCTGTAGAGgtatgttata ... gcttctgcagGCTGAGGTTACTGGTGAAGT
EST: gi|67692331|gb|BJ952564.1|BJ952564
EST:     GACAAGTGGTGTGCTACTTAGAGCAGCTTGGCACACAACAACCTGTAGAG                         GCTGAGGTTACTGGTGAAGTCGAGAAAGTTCTGTGGGAAGATGGAG
genomic: GACAAGTGGTGTGCTACTTAGAGCAGCTTGGCACACAACAACCTGTAGAGgtatgttata ... gcttctgcagGCTGAGGTTACTGGTGAAGTCGAGAAAGTTCTGTGGGAAGATGGAG
EST: gi|208366599|gb|DC954879.1|DC954879
EST:     GACAAGTGGTGTGCTACTTAGAGCAGCTTGGCACACAACAACCTGTAGAG                         GCTGAGGTTACTGGTGAAGTCGAGAAAGTTCTGTGGGAAGATGGAG
genomic: GACAAGTGGTGTGCTACTTAGAGCAGCTTGGCACACAACAACCTGTAGAGgtatgttata ... gcttctgcagGCTGAGGTTACTGGTGAAGTCGAGAAAGTTCTGTGGGAAGATGGAG
EST: gi|7047215|gb|AW477109.1|AW477109
EST:     GACAAGTGGTGTGCTACTTAGAGCAGCTTGGCACACAACAACCTGTAGAG                         GCTGAGGTTACTGGTGAAGTCGAGAAAGTTCTGTGGGAAGATGGAG
genomic: GACAAGTGGTGTGCTACTTAGAGCAGCTTGGCACACAACAACCTGTAGAGgtatgttata ... gcttctgcagGCTGAGGTTACTGGTGAAGTCGAGAAAGTTCTGTGGGAAGATGGAG
EST: gi|18333853|gb|BJ165869.1|BJ165869
EST:     GACAAGTGGTGTGCTACTTAGAGCAGCTTGGCACACAACAACCTGTAGAG                         GCTGAGGTTACTGGTGAAGTCGAGAAAGTTCTGTGGGAAGATGGAG
genomic: GACAAGTGGTGTGCTACTTAGAGCAGCTTGGCACACAACAACCTGTAGAGgtatgttata ... gcttctgcagGCTGAGGTTACTGGTGAAGTCGAGAAAGTTCTGTGGGAAGATGGAG
EST: gi|67692450|gb|BJ952683.1|BJ952683
EST:     GACAAGTGGTGTGCTACTTAGAGCAGCTTGGCACACAACAACCTGTAGAG                         GCTGAGGTTACTGGTGAAGTCGAGAAAGTTCTGTGGGAAGATGGAG
genomic: GACAAGTGGTGTGCTACTTAGAGCAGCTTGGCACACAACAACCTGTAGAGgtatgttata ... gcttctgcagGCTGAGGTTACTGGTGAAGTCGAGAAAGTTCTGTGGGAAGATGGAG
EST: gi|37836220|gb|BJ594228.1|BJ594228
EST:     GACAAGTGGTGTGCTACTTAGAGCAGCTTGGCACACAACAACCTGTAGAG                         GCTGAGGTTACTGGTGAAGTCGAGAAAGTTCTGTGGGAAGATGGAG
genomic: GACAAGTGGTGTGCTACTTAGAGCAGCTTGGCACACAACAACCTGTAGAGgtatgttata ... gcttctgcagGCTGAGGTTACTGGTGAAGTCGAGAAAGTTCTGTGGGAAGATGGAG
EST: gi|208353220|gb|DC921880.1|DC921880
EST:     GACAAGTGGTGTGCTACTTAGAGCAGCTTGGCACACAACAACCTGTAGAG                         GCTGAGGTTACTGGTGAAGTCGAGAAAGTTCTGTGGGAAGATGGAG
genomic: GACAAGTGGTGTGCTACTTAGAGCAGCTTGGCACACAACAACCTGTAGAGgtatgttata ... gcttctgcagGCTGAGGTTACTGGTGAAGTCGAGAAAGTTCTGTGGGAAGATGGAG
EST: gi|67695352|gb|BJ955585.1|BJ955585
EST:     GACAAGTGGTGTGCTACTTAGAGCAGCTTGGCACACAACAACCTGTAGAG                         GCTGAGGTTACTGGTGAAGTCGAGAAAGTTCTGTGGGAAGATGGAG
genomic: GACAAGTGGTGTGCTACTTAGAGCAGCTTGGCACACAACAACCTGTAGAGgtatgttata ... gcttctgcagGCTGAGGTTACTGGTGAAGTCGAGAAAGTTCTGTGGGAAGATGGAG
EST: gi|162210193|gb|FC386704.1|FC386704
EST:     GACAAGTGGTGTGCTACTTAGAGCAGCTTGGCACACAACAACCTGTAGAG                         GCTGAGGTTACTGGTGAAGTCGAGAAAGTTCTGTGGGAAGATGGAG
genomic: GACAAGTGGTGTGCTACTTAGAGCAGCTTGGCACACAACAACCTGTAGAGgtatgttata ... gcttctgcagGCTGAGGTTACTGGTGAAGTCGAGAAAGTTCTGTGGGAAGATGGAG

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: 31 (upstream exon), 33 (downstream exon)
Score: 2

GGTCAAGTAATCAAGAAGGGACAAGTGGTGTGCTACTTAGAGCAGCTTGGCACACAACAACCTGTAGAGgtatgttata ... gcttctgcagGCTGAGGTTACTGGTGAAGTCGAGAAAGTTCTGTGGGAAGATGGAG





























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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTCAAGTAATCAAGAAGGGACAAGTGGTGTGCTACTTAGAGCAGCTTGGCACACAACAACCTGTAGAGgtatgttataaattttagcagttactacaaagttcttatttgtgaattccaattaggtttttttctggttttcttttattgtttatagagttctgtctgc

- - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - -  GCAGCT