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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCTATTCTTAAGAATAATGAAGGTCTTGTTTTGAAGTATAAGGCTGTCATCAATGACGGCTTTAAGCTCCCCCTTGGCGAGGCATTGAAGCTTGAGCAGgtatcctaatgtagctgccaagcgctactctgtttgcacgttaagacacacctattcggttagtttttgaatttcgggggctaactttcagtgcaaatcactggacagcctgcctgatgatgtttattttattttattttgtaccttactttctatttgatgctgtgatgtag

Basic information

species Physcomitrella patens
transcript PP1S62_178V6.1
intron # 4
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|37831578|gb|BJ589590.1|BJ589590
EST:     TCAATGACGGCTTTAAGCTCCCCCTTGGCGAGGCATTGAAGCTTGAGCAG                         GAGAGGGGGCATGAATATTATGCCAATATGAAGCCGGAGGAGTTTGCTGCA
genomic: TCAATGACGGCTTTAAGCTCCCCCTTGGCGAGGCATTGAAGCTTGAGCAGgtatcctaat ... tgtgatgtagGAGAGGGGGCATGAATATTATGCCAATATGAAGCCGGAGGAGTTTGCTGCA
EST: gi|162257573|gb|FC433707.1|FC433707
EST:     TCAATGACGGCTTTAAGCTCCCCCTTGGCGAGGCATTGAAGCTTGAGCAG                         GAGAGGGGGCATGAATATTATGCCAATATGAAGCCGGAGGAGTTTGCTGCA
genomic: TCAATGACGGCTTTAAGCTCCCCCTTGGCGAGGCATTGAAGCTTGAGCAGgtatcctaat ... tgtgatgtagGAGAGGGGGCATGAATATTATGCCAATATGAAGCCGGAGGAGTTTGCTGCA
EST: gi|162267394|gb|FC443937.1|FC443937
EST:     TCAATGACGGCTTTAAGCTCCCCCTTGGCGAGGCATTGAAGCTTGAGCAG                         GAGAGGGGGCATGAATATTATGCCAATATGAAGCC
genomic: TCAATGACGGCTTTAAGCTCCCCCTTGGCGAGGCATTGAAGCTTGAGCAGgtatcctaat ... tgtgatgtagGAGAGGGGGCATGAATATTATGCCAATATGAAGCC
EST: gi|162262355|gb|FC437682.1|FC437682
EST:     TCAATGACGGCTTTAAGCTCCCCCTTGGCGAGGCATTGAAGCTTGAGCAG                         GAGAGGGGGCATGAATATTATGCCAATATGAAGCCGGAGGAGTTTGCTGCA
genomic: TCAATGACGGCTTTAAGCTCCCCCTTGGCGAGGCATTGAAGCTTGAGCAGgtatcctaat ... tgtgatgtagGAGAGGGGGCATGAATATTATGCCAATATGAAGCCGGAGGAGTTTGCTGCA
EST: gi|162257574|gb|FC433708.1|FC433708
EST:     TCAATGACGGCTTTAAGCTCCCCCTTGGCGAGGCATTGAAGCTTGAGCAG                         GAGAGGGGGCATGAATATTATGCCAATATGAAGCCGGAGGAGTTTGCTGCA
genomic: TCAATGACGGCTTTAAGCTCCCCCTTGGCGAGGCATTGAAGCTTGAGCAGgtatcctaat ... tgtgatgtagGAGAGGGGGCATGAATATTATGCCAATATGAAGCCGGAGGAGTTTGCTGCA
EST: gi|37830630|gb|BJ588642.1|BJ588642
EST:     TCAATGACGGCTTTAAGCTCCCCCTTGGCGAGGCATTGAAGCTTGAGCAG                         GAGAGGGGGCATGAATATTATGCCAATATGAAGCCGGAGGAGTTTGCTGCA
genomic: TCAATGACGGCTTTAAGCTCCCCCTTGGCGAGGCATTGAAGCTTGAGCAGgtatcctaat ... tgtgatgtagGAGAGGGGGCATGAATATTATGCCAATATGAAGCCGGAGGAGTTTGCTGCA
EST: gi|37844478|gb|BJ602486.1|BJ602486
EST:     TCAATGACGGCTTTAAGCTCCCCCTTGGCGAGGCATTGAAGCTTGAGCAG                         GAGAGGGGGCATGAATATTATGCCAATATGAAGCCGGAGGAGTTTGCTGCA
genomic: TCAATGACGGCTTTAAGCTCCCCCTTGGCGAGGCATTGAAGCTTGAGCAGgtatcctaat ... tgtgatgtagGAGAGGGGGCATGAATATTATGCCAATATGAAGCCGGAGGAGTTTGCTGCA
EST: gi|162267393|gb|FC443936.1|FC443936
EST:     TCAATGACGGCTTTAAGCTCCCCCTTGGCGAGGCATTGAAGCTTGAGCAG                         GAGAGGGGGCATGAATATTATGCCAATATGAAGCCGGAGGAGTTTGCTGCA
genomic: TCAATGACGGCTTTAAGCTCCCCCTTGGCGAGGCATTGAAGCTTGAGCAGgtatcctaat ... tgtgatgtagGAGAGGGGGCATGAATATTATGCCAATATGAAGCCGGAGGAGTTTGCTGCA
EST: gi|162262356|gb|FC437683.1|FC437683
EST:     TCAATGACGGCTTTAAGCTCCCCCTTGGCGAGGCATTGAAGCTTGAGCAG                         GAGAGGGGGCATGAATATTATGCCAATATGAAGCC
genomic: TCAATGACGGCTTTAAGCTCCCCCTTGGCGAGGCATTGAAGCTTGAGCAGgtatcctaat ... tgtgatgtagGAGAGGGGGCATGAATATTATGCCAATATGAAGCC
EST: gi|37834764|gb|BJ592776.1|BJ592776
EST:     TCAATGACGGCTTTAAGCTCCCCCTTGGCGAGGCATTGAAGCTTGAGCAG                         GAGAGGGGGCATGAATATTATGCCAATATGAAGCCGGAGGAGTTTGCTGCA
genomic: TCAATGACGGCTTTAAGCTCCCCCTTGGCGAGGCATTGAAGCTTGAGCAGgtatcctaat ... tgtgatgtagGAGAGGGGGCATGAATATTATGCCAATATGAAGCCGGAGGAGTTTGCTGCA

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), 34 (downstream exon)
Score: 9

GGCTATTCTTAAGAATAATGAAGGTCTTGTTTTGAAGTATAAGGCTGTCATCAATGACGGCTTTAAGCTCCCCCTTGGCGAGGCATTGAAGCTTGAGCAGgtatcctaat ... tgtgatgtagGAGAGGGGGCATGAATATTATGCCAATATGAAGCCGGAGGAGTTTGCTGCAATGCAGGAGTTTATCGCCGGGCGATCTTCAAAGCAGTCGAAACCTAAGT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCTATTCTTAAGAATAATGAAGGTCTTGTTTTGAAGTATAAGGCTGTCATCAATGACGGCTTTAAGCTCCCCCTTGGCGAGGCATTGAAGCTTGAGCAGgtatcctaatgtagctgccaagcgctactctgtttgcacgttaagacacacctattcggttagtttttgaatttcgggggctaactttcagtgcaaatcactggacagcctgcctgatgatgtttattttattttattttgtaccttactttctatttgatgctgtgatgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG