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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGTTATGGCCCGCTTGTCACTGTGTGAGCGAGTCGCTGCTTGTGTTTTCGTTCCGgtaattttggacctcgctcgtgaattcttcgctctcttgtttttattttattgctagggtgtgtctggtttcgtttttgtattgcgaagtggaataattg...

Basic information

species Physcomitrella patens
transcript PP1S13_127V6.2
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|100407241|gb|BY974073.1|BY974073
EST:     GTGTGAGCGAGTCGCTGCTTGTGTTTTCGTTCCG                         AGGACTGGCGGACAAAATGGCAATTACAGCCGGAATGAGTAAATGCGTGGG
genomic: GTGTGAGCGAGTCGCTGCTTGTGTTTTCGTTCCGgtaattttgg ... tgtggtgcagAGGACTGGCGGACAAAATGGCAATTACAGCCGGAATGAGTAAATGCGTGGG
EST: gi|18351331|gb|BJ183383.1|BJ183383
EST:     ACTGTGTGAGCGAGTCGCTGCTTGTGTTTTCGTTCCG                         AGGACTGGCGGACAAAATGGCAATTACAGCCGGAATGAGTAAATGCGTGGG
genomic: ACTGTGTGAGCGAGTCGCTGCTTGTGTTTTCGTTCCGgtaattttgg ... tgtggtgcagAGGACTGGCGGACAAAATGGCAATTACAGCCGGAATGAGTAAATGCGTGGG
EST: gi|100366004|gb|BY967247.1|BY967247
EST:     GTGAGCGAGTCGCTGCTTGTGTTTTCGTTCCG                         AGGACTGGCGGACAAAATGGCAATTACAGCCGGAATGAGTAAATGCGTGGG
genomic: GTGAGCGAGTCGCTGCTTGTGTTTTCGTTCCGgtaattttgg ... tgtggtgcagAGGACTGGCGGACAAAATGGCAATTACAGCCGGAATGAGTAAATGCGTGGG
EST: gi|18355834|gb|BJ187893.1|BJ187893
EST:     GTCACTGTGTGAGCGAGTCGCTGCTTGTGTTTTCGTTCCG                         AGGACTGGCGGACAAAATGGCAATTACAGCCGGAATGAGTAAATGCGTGGG
genomic: GTCACTGTGTGAGCGAGTCGCTGCTTGTGTTTTCGTTCCGgtaattttgg ... tgtggtgcagAGGACTGGCGGACAAAATGGCAATTACAGCCGGAATGAGTAAATGCGTGGG
EST: gi|18328557|gb|BJ160562.1|BJ160562
EST:     GTGTGAGCGAGTCGCTGCTTGTGTTTTCGTTCCG                         AGGACTGGCGGACAAAATGGCAATTACAGCCGGAATGAGTAAATGCGTGGG
genomic: GTGTGAGCGAGTCGCTGCTTGTGTTTTCGTTCCGgtaattttgg ... tgtggtgcagAGGACTGGCGGACAAAATGGCAATTACAGCCGGAATGAGTAAATGCGTGGG
EST: gi|208367054|gb|DC935910.1|DC935910
EST:     GTTTTCGTTCCG                         AGGACTGGCGGACAAAATGGCAATTACAGCCGGAATGAGTAAATGCGTGGG
genomic: GTTTTCGTTCCGgtaattttgg ... tgtggtgcagAGGACTGGCGGACAAAATGGCAATTACAGCCGGAATGAGTAAATGCGTGGG
EST: gi|67575873|gb|BJ948697.1|BJ948697
EST:     GTTTTCGTTCCG                         AGGACTGGCGGACAAAATGGCAATTACAGCCGGAATGAGTAAATGCGTGGG
genomic: GTTTTCGTTCCGgtaattttgg ... tgtggtgcagAGGACTGGCGGACAAAATGGCAATTACAGCCGGAATGAGTAAATGCGTGGG
EST: gi|208382201|gb|DC914834.1|DC914834
EST:     GTGTGAGCGAGTCGCTGCTTGTGTTTTCGTTCCG                         AGGACTGGCGGACAAAATGGCAATTACAGCCGGAATGAGTAAATGCGTGGG
genomic: GTGTGAGCGAGTCGCTGCTTGTGTTTTCGTTCCGgtaattttgg ... tgtggtgcagAGGACTGGCGGACAAAATGGCAATTACAGCCGGAATGAGTAAATGCGTGGG
EST: gi|67573975|gb|BJ946799.1|BJ946799
EST:     GCCCGCTTGTCACTGTGTGAGCGAGTCGCTGCTTGTGTTTTCGTTCCG                         AGGACTGGCGGACAAAATGGCAATTACAGCCGGAATGAGTAAATGCGTGGG
genomic: GCCCGCTTGTCACTGTGTGAGCGAGTCGCTGCTTGTGTTTTCGTTCCGgtaattttgg ... tgtggtgcagAGGACTGGCGGACAAAATGGCAATTACAGCCGGAATGAGTAAATGCGTGGG
EST: gi|18372687|gb|BJ204289.1|BJ204289
EST:     GTCACTGTGTGAGCGAGTCGCTGCTTGTGTTTTCGTTCCG                         AGGACTGGCGGACAAAATGGCAATTACAGCCGGAATGAGTAAATGCGTGGG
genomic: GTCACTGTGTGAGCGAGTCGCTGCTTGTGTTTTCGTTCCGgtaattttgg ... tgtggtgcagAGGACTGGCGGACAAAATGGCAATTACAGCCGGAATGAGTAAATGCGTGGG
EST: gi|18347787|gb|BJ179834.1|BJ179834
EST:     GTCACTGTGTGAGCGAGTCGCTGCTTGTGTTTTCGTTCCG                         AGGACTGGCGGACAAAATGGCAATTACAGCCGGAATGAGTAAATGCGTGGG
genomic: GTCACTGTGTGAGCGAGTCGCTGCTTGTGTTTTCGTTCCGgtaattttgg ... tgtggtgcagAGGACTGGCGGACAAAATGGCAATTACAGCCGGAATGAGTAAATGCGTGGG
EST: gi|100415484|gb|BY992866.1|BY992866
EST:     AGTCGCTGCTTGTGTTTTCGTTCCG                         AGGACTGGCGGACAAAATGGCAATTACAGCCGGAATGAGTAAATGCGTGGG
genomic: AGTCGCTGCTTGTGTTTTCGTTCCGgtaattttgg ... tgtggtgcagAGGACTGGCGGACAAAATGGCAATTACAGCCGGAATGAGTAAATGCGTGGG
EST: gi|18330436|gb|BJ162442.1|BJ162442
EST:     GTGAGCGAGTCGCTGCTTGTGTTTTCGTTCCG                         AGGACTGGCGGACAAAATGGCAATTACAGCCGGAATGAGTAAATGCGTGGG
genomic: GTGAGCGAGTCGCTGCTTGTGTTTTCGTTCCGgtaattttgg ... tgtggtgcagAGGACTGGCGGACAAAATGGCAATTACAGCCGGAATGAGTAAATGCGTGGG
EST: gi|18348525|gb|BJ180574.1|BJ180574
EST:     GTCACTGTGTGAGCGAGTCGCTGCTTGTGTTTTCGTTCCG                         AGGACTGGCGGACAAAATGGCAATTACAGCCGGAATGAGTAAATGCGTGGG
genomic: GTCACTGTGTGAGCGAGTCGCTGCTTGTGTTTTCGTTCCGgtaattttgg ... tgtggtgcagAGGACTGGCGGACAAAATGGCAATTACAGCCGGAATGAGTAAATGCGTGGG
EST: gi|100389613|gb|BY952419.1|BY952419
EST:     GTGTGAGCGAGTCGCTGCTTGTGTTTTCGTTCCG                         AGGACTGGCGGACAAAATGGCAATTACAGCCGGAATGAGTAAATGCGTGGG
genomic: GTGTGAGCGAGTCGCTGCTTGTGTTTTCGTTCCGgtaattttgg ... tgtggtgcagAGGACTGGCGGACAAAATGGCAATTACAGCCGGAATGAGTAAATGCGTGGG
EST: gi|100443450|gb|BY981877.1|BY981877
EST:     GTCACTGTGTGAGCGAGTCGCTGCTTGTGTTTTCGTTCCG                         AGGACTGGCGGACAAAATGGCAATTACAGCCGGAATGAGTAAATGCGTGGG
genomic: GTCACTGTGTGAGCGAGTCGCTGCTTGTGTTTTCGTTCCGgtaattttgg ... tgtggtgcagAGGACTGGCGGACAAAATGGCAATTACAGCCGGAATGAGTAAATGCGTGGG
EST: gi|18373476|gb|BJ205054.1|BJ205054
EST:     GTCACTGTGTGAGCGAGTCGCTGCTTGTGTTTTCGTTCCG                         AGGACTGGCGGACAAAATGGCAATTACAGCCGGAATGAGTAAATGCGTGGG
genomic: GTCACTGTGTGAGCGAGTCGCTGCTTGTGTTTTCGTTCCGgtaattttgg ... tgtggtgcagAGGACTGGCGGACAAAATGGCAATTACAGCCGGAATGAGTAAATGCGTGGG

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: 27 (upstream exon), 26 (downstream exon)
Score: 14

CGTTATGGCCCGCTTGTCACTGTGTGAGCGAGTCGCTGCTTGTGTTTTCGTTCCGgtaattttgg ... tgtggtgcagAGGACTGGCGGACAAAATGGCAATTACAGCCGGAATGAGTAAATGCGTGGGGGCAGCGTGCGTCCGTGGTATAGTTGTGAAGGAGGTTATCTTGGGGCGT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGTTATGGCCCGCTTGTCACTGTGTGAGCGAGTCGCTGCTTGTGTTTTCGTTCCGgtaattttggacctcgctcgtgaattcttcgctctcttgtttttattttattgctagggtgtgtctggtttcgtttttgtattgcgaagtggaataattg

- - - - - - - - - - - - - - - - - GCTGCT