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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAATTTGCAATCCTAGTTACGGTAGTGTGAATGCAATCGGGACGTTGAATTCAGGACAGCAGCTGGTTGTGGAAAGCGAAGATGTGGACAATAAACGAGgtattaactgtgttcagaacgtccactgtattttgcagtcggattcctcgccctgtcttgtgtgtgcctaatttgagaacacccaggactcaaattatcataaatcctttcattaaactgatgtttccagtaggcggcattctctgttctatgtgattgtcatccatgaccctgttggcgatgtgtcttgtag

Basic information

species Physcomitrella patens
transcript PP1S486_3V6.1
intron # 1
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|18341981|gb|BJ174016.1|BJ174016
EST:     TTCAGGACAGCAGCTGGTTGTGGAAAGCGAAGATGTGGACAATAAACGAG                         CTCTTCTACGGGCCGGAGCCTGCACTCACGTACATATATGAGTATCCTAAG
genomic: TTCAGGACAGCAGCTGGTTGTGGAAAGCGAAGATGTGGACAATAAACGAGgtattaactg ... tgtcttgtagCTCTTCTACGGGCCGGAGCCTGCACTCACGTACATATATGAGTATCCTAAG
EST: gi|18345652|gb|BJ177695.1|BJ177695
EST:     TTCAGGACAGCAGCTGGTTGTGGAAAGCGAAGATGTGGACAATAAACGAG                         CTCTTCTACGGGCCGGAGCCTGCACTCACGTACATATATGAGTATCCTAAG
genomic: TTCAGGACAGCAGCTGGTTGTGGAAAGCGAAGATGTGGACAATAAACGAGgtattaactg ... tgtcttgtagCTCTTCTACGGGCCGGAGCCTGCACTCACGTACATATATGAGTATCCTAAG
EST: gi|18354050|gb|BJ186105.1|BJ186105
EST:     TTCAGGACAGCAGCTGGTTGTGGAAAGCGAAGATGTGGACAATAAACGAG                         CTCTTCTACGGGCCGGAGCCTGCACTCACGTACATATATGAGTATCCTAAG
genomic: TTCAGGACAGCAGCTGGTTGTGGAAAGCGAAGATGTGGACAATAAACGAGgtattaactg ... tgtcttgtagCTCTTCTACGGGCCGGAGCCTGCACTCACGTACATATATGAGTATCCTAAG
EST: gi|18342525|gb|BJ174560.1|BJ174560
EST:     TTCAGGACAGCAGCTGGTTGTGGAAAGCGAAGATGTGGACAATAAACGAG                         CTCTTCTACGGGCCGGAGCCTGCACTCACGTACATATATGAGTATCCTAAG
genomic: TTCAGGACAGCAGCTGGTTGTGGAAAGCGAAGATGTGGACAATAAACGAGgtattaactg ... tgtcttgtagCTCTTCTACGGGCCGGAGCCTGCACTCACGTACATATATGAGTATCCTAAG
EST: gi|100393250|gb|BY989796.1|BY989796
EST:     TTCAGGACAGCAGCTGGTTGTGGAAAGCGAAGATGTGGACAATAAACGAG                         CTCTTCTACGGGCCGGAGCCTGCACTCACGTACATATATGAGTATCCTAAG
genomic: TTCAGGACAGCAGCTGGTTGTGGAAAGCGAAGATGTGGACAATAAACGAGgtattaactg ... tgtcttgtagCTCTTCTACGGGCCGGAGCCTGCACTCACGTACATATATGAGTATCCTAAG
EST: gi|18343011|gb|BJ175048.1|BJ175048
EST:     TTCAGGACAGCAGCTGGTTGTGGAAAGCGAAGATGTGGACAATAAACGAG                         CTCTTCTACGGGCCGGAGCCTGCACTCACGTACATATATGAGTATCCTAAG
genomic: TTCAGGACAGCAGCTGGTTGTGGAAAGCGAAGATGTGGACAATAAACGAGgtattaactg ... tgtcttgtagCTCTTCTACGGGCCGGAGCCTGCACTCACGTACATATATGAGTATCCTAAG
EST: gi|18347187|gb|BJ179233.1|BJ179233
EST:     TTCAGGACAGCAGCTGGTTGTGGAAAGCGAAGATGTGGACAATAAACGAG                         CTCTTCTACGGGCCGGAGCCTGCACTCACGTACATATATGAGTATCCTAAG
genomic: TTCAGGACAGCAGCTGGTTGTGGAAAGCGAAGATGTGGACAATAAACGAGgtattaactg ... tgtcttgtagCTCTTCTACGGGCCGGAGCCTGCACTCACGTACATATATGAGTATCCTAAG
EST: gi|208381045|gb|DC903901.1|DC903901
EST:     TTCAGGACAGCAGCTGGTTGTGGAAAGCGAAGATGTGGACAATAAACGAG                         CTCTTCTACGGGCCGGAGCCTGCACTCACGTACATATATGAGTATCCTAAG
genomic: TTCAGGACAGCAGCTGGTTGTGGAAAGCGAAGATGTGGACAATAAACGAGgtattaactg ... tgtcttgtagCTCTTCTACGGGCCGGAGCCTGCACTCACGTACATATATGAGTATCCTAAG

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), 28 (downstream exon)
Score: 4

CCAATTTGCAATCCTAGTTACGGTAGTGTGAATGCAATCGGGACGTTGAATTCAGGACAGCAGCTGGTTGTGGAAAGCGAAGATGTGGACAATAAACGAGgtattaactg ... tgtcttgtagCTCTTCTACGGGCCGGAGCCTGCACTCACGTACATATATGAGTATCCTAAGTTGAAGCCTGTAGAGGATGTTGTTGTGAAGGAACTGAACCATGCAAAGG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCAATTTGCAATCCTAGTTACGGTAGTGTGAATGCAATCGGGACGTTGAATTCAGGACAGCAGCTGGTTGTGGAAAGCGAAGATGTGGACAATAAACGAGgtattaactgtgttcagaacgtccactgtattttgcagtcggattcctcgccctgtcttgtgtgtgcctaatttgagaacacccaggactcaaattatcataaatcctttcattaaactgatgtttccagtaggcggcattctctgttctatgtgattgtcatccatgaccctgttggcgatgtgtcttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG