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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGGATACCGCTGGTCAAGAAAGATTCAGGACAATCACGAGCAGCTATTACCGTGGTGCCCATGGGATAATTgtaagtggatttttgcattactgttgaggaaaatttctgttaattgattcctgttacgtaggcttgtgtaacttgtgattaggttgaatttttaatgtcttggaatatgagtgtcttcgttgttttcttgcag

Basic information

species Physcomitrella patens
transcript PP1S95_20V6.1
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|37843982|gb|BJ601990.1|BJ601990
EST:     GATTCAGGACAATCACGAGCAGCTATTACCGTGGTGCCCATGGGATAATT                         ATTGTGTACGATGTTACGGATCAGGAAAGTTTTAACAATGTAAAGCAATGG
genomic: GATTCAGGACAATCACGAGCAGCTATTACCGTGGTGCCCATGGGATAATTgtaagtggat ... tttcttgcagATTGTGTACGATGTTACGGATCAGGAAAGTTTTAACAATGTAAAGCAATGG
EST: gi|18325475|gb|BJ157472.1|BJ157472
EST:     GATTCAGGACAATCACGAGCAGCTATTACCGTGGTGCCCATGGGATAATT                         ATTGTGTACGATGTTACGGATCAGGAAAGTTTTAACAGTGTAAAGCAATGG
genomic: GATTCAGGACAATCACGAGCAGCTATTACCGTGGTGCCCATGGGATAATTgtaagtggat ... tttcttgcagATTGTGTACGATGTTACGGATCAGGAAAGTTTTAACAATGTAAAGCAATGG
EST: gi|208352608|gb|DC918317.1|DC918317
EST:     GATTCAGGACAATCACGAGCAGCTATTACCGTGGTGCCCATGGGATAATT                         ATTGTGTACGATGTTACGGATCAGGAAAGTTTTAACAATGTAAAGCAATGG
genomic: GATTCAGGACAATCACGAGCAGCTATTACCGTGGTGCCCATGGGATAATTgtaagtggat ... tttcttgcagATTGTGTACGATGTTACGGATCAGGAAAGTTTTAACAATGTAAAGCAATGG
EST: gi|100448519|gb|CJ972818.1|CJ972818
EST:     GATTCAGGACAATCACGAGCAGCTATTACCGTGGTGCCCATGGGATAATT                         ATTGTGTACGATGTTACGGATCAGGAAAGTTTTAACAATGTAAAGCAATGG
genomic: GATTCAGGACAATCACGAGCAGCTATTACCGTGGTGCCCATGGGATAATTgtaagtggat ... tttcttgcagATTGTGTACGATGTTACGGATCAGGAAAGTTTTAACAATGTAAAGCAATGG
EST: gi|208393356|gb|DC904016.1|DC904016
EST:     GATTCAGGACAATCACGAGCAGCTATTACCGTGGTGCCCATGGGATAATT                         ATTGTGTACGATGTTACGGATCAGGAAAGTTTTAACAATGTAAAGCAATGG
genomic: GATTCAGGACAATCACGAGCAGCTATTACCGTGGTGCCCATGGGATAATTgtaagtggat ... tttcttgcagATTGTGTACGATGTTACGGATCAGGAAAGTTTTAACAATGTAAAGCAATGG
EST: gi|37846790|gb|BJ604798.1|BJ604798
EST:     GATTCAGGACAATCACGAGCAGCTATTACCGTGGTGCCCATGGGATAATT                         ATTGTGTACGATGTTACGGATCAGGAAAGTTTTAACAATGTAAAGCAATGG
genomic: GATTCAGGACAATCACGAGCAGCTATTACCGTGGTGCCCATGGGATAATTgtaagtggat ... tttcttgcagATTGTGTACGATGTTACGGATCAGGAAAGTTTTAACAATGTAAAGCAATGG
EST: gi|208365886|gb|DC955461.1|DC955461
EST:     CCATGGGATAATT                         ATTGTGTACGATGTTACGGATCAGGAAAGTTTTANCAATGTAAAGCAATGG
genomic: CCATGGGATAATTgtaagtggat ... tttcttgcagATTGTGTACGATGTTACGGATCAGGAAAGTTTTAACAATGTAAAGCAATGG
EST: gi|37845387|gb|BJ603395.1|BJ603395
EST:     GATTCAGGACAATCACGAGCAGCTATTACCGTGGTGCCCATGGGATAATT                         ATTGTGTACGATGTTACGGATCAGGAAAGTTTTAACAATGTAAAGCAATGG
genomic: GATTCAGGACAATCACGAGCAGCTATTACCGTGGTGCCCATGGGATAATTgtaagtggat ... tttcttgcagATTGTGTACGATGTTACGGATCAGGAAAGTTTTAACAATGTAAAGCAATGG
EST: gi|37851673|gb|BJ609681.1|BJ609681
EST:     GATTCAGGACAATCACGAGCAGCTATTACCGTGGTGCCCATGGGATAATT                         ATTGTGTACGATGTTACGGATCAGGAAAGTTTTAACAATGTAAAGCAATGG
genomic: GATTCAGGACAATCACGAGCAGCTATTACCGTGGTGCCCATGGGATAATTgtaagtggat ... tttcttgcagATTGTGTACGATGTTACGGATCAGGAAAGTTTTAACAATGTAAAGCAATGG

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: 29 (upstream exon), 9 (downstream exon)
Score: 3

TGGGATACCGCTGGTCAAGAAAGATTCAGGACAATCACGAGCAGCTATTACCGTGGTGCCCATGGGATAATTgtaagtggat ... tttcttgcagATTGTGTACGATGTTACGGATCAGGAAAGTTTTAACAATGTAAAGCAATGGTTGAATGAAATCGATCGTTATGCAAGTGAGAACGTGAATAAGCTGCTTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGGATACCGCTGGTCAAGAAAGATTCAGGACAATCACGAGCAGCTATTACCGTGGTGCCCATGGGATAATTgtaagtggatttttgcattactgttgaggaaaatttctgttaattgattcctgttacgtaggcttgtgtaacttgtgattaggttgaatttttaatgtcttggaatatgagtgtcttcgttgttttcttgcag

- - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - GCAGCT