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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAAGCAGTGGAGCATCCTGGTTGGTGTCCAGATCCGCACAAGCCTCCCTGTGCAGGgtaataagtcaacctgtatttagttagtgattcgtgtcttaccttcctcctttggtcgttgaaatttactgtctgttagttgttgggtatttacttcttgtttaatactgcag

Basic information

species Physcomitrella patens
transcript PP1S129_53V6.1
intron # 10
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|162181747|gb|FC357346.1|FC357346
EST:     GTGGAGCATCCTGGTTGGTGTCCAGATCCGCACAAGCCTCCCTGTGCAGG                         ATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCAT
genomic: GTGGAGCATCCTGGTTGGTGTCCAGATCCGCACAAGCCTCCCTGTGCAGGgtaataagtc ... aatactgcagATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCAT
EST: gi|37844061|gb|BJ602069.1|BJ602069
EST:     GTGGAGCATCCTGGTTGGTGTCCAGATCCGCACAAGCCTCCCTGTGCAGG                         ATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCAT
genomic: GTGGAGCATCCTGGTTGGTGTCCAGATCCGCACAAGCCTCCCTGTGCAGGgtaataagtc ... aatactgcagATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCAT
EST: gi|162268144|gb|FC443822.1|FC443822
EST:     GTGGAGCATCCTGGTTGGTGTCCAGATCCGCACAAGCCTCCCTGTGCAGG                         ATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCAT
genomic: GTGGAGCATCCTGGTTGGTGTCCAGATCCGCACAAGCCTCCCTGTGCAGGgtaataagtc ... aatactgcagATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCAT
EST: gi|162268143|gb|FC443821.1|FC443821
EST:     GTGGAGCATCCTGGTTGGTGTCCAGATCCGCACAAGCCTCCCTGTGCAGG                         ATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCAT
genomic: GTGGAGCATCCTGGTTGGTGTCCAGATCCGCACAAGCCTCCCTGTGCAGGgtaataagtc ... aatactgcagATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCAT
EST: gi|37841807|gb|BJ599815.1|BJ599815
EST:     GTGGAGCATCCTGGTTGGTGTCCAGATCCGCACAAGCCTCCCTGTGCAGG                         ATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCAT
genomic: GTGGAGCATCCTGGTTGGTGTCCAGATCCGCACAAGCCTCCCTGTGCAGGgtaataagtc ... aatactgcagATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCAT
EST: gi|37849671|gb|BJ607679.1|BJ607679
EST:     GTGGAGCATCCTGGTTGGTGTCCAGATCCGCACAAGCCTCCCTGTGCAGG                         ATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCAT
genomic: GTGGAGCATCCTGGTTGGTGTCCAGATCCGCACAAGCCTCCCTGTGCAGGgtaataagtc ... aatactgcagATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCAT
EST: gi|162198683|gb|FC373464.1|FC373464
EST:     GTGGAGCATCCTGGTTGGTGTCCAGATCCGCACAAGCCTCCCTGTGCAGG                         ATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCAT
genomic: GTGGAGCATCCTGGTTGGTGTCCAGATCCGCACAAGCCTCCCTGTGCAGGgtaataagtc ... aatactgcagATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCAT
EST: gi|162165626|gb|FC341465.1|FC341465
EST:     GTGGAGCATCCTGGTTGGTGTCCAGATCCGCACAAGCCTCCCTGTGCAGG                         ATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCAT
genomic: GTGGAGCATCCTGGTTGGTGTCCAGATCCGCACAAGCCTCCCTGTGCAGGgtaataagtc ... aatactgcagATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCAT
EST: gi|208371453|gb|DC955789.1|DC955789
EST:     GTGGAGCATCCTGGTTGGTGTCCAGATCCGCACAAGCCTCCCTGTGCAGG                         ATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCAT
genomic: GTGGAGCATCCTGGTTGGTGTCCAGATCCGCACAAGCCTCCCTGTGCAGGgtaataagtc ... aatactgcagATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCAT
EST: gi|162165627|gb|FC341466.1|FC341466
EST:     GTGGAGCATCCTGGTTGGTGTCCAGATCCGCACAAGCCTCCCTGTGCAGG                         ATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCAT
genomic: GTGGAGCATCCTGGTTGGTGTCCAGATCCGCACAAGCCTCCCTGTGCAGGgtaataagtc ... aatactgcagATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCAT
EST: gi|37827443|gb|BJ585455.1|BJ585455
EST:     GTGGAGCATCCTGGTTGGTGTCCAGATCCGCACAAGCCTCCCTGTGCAGG                         ATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCAT
genomic: GTGGAGCATCCTGGTTGGTGTCCAGATCCGCACAAGCCTCCCTGTGCAGGgtaataagtc ... aatactgcagATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCAT
EST: gi|162198682|gb|FC373463.1|FC373463
EST:     GTGGAGCATCCTGGTTGGTGTCCAGATCCGCACAAGCCTCCCTGTGCAGG                         ATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCAT
genomic: GTGGAGCATCCTGGTTGGTGTCCAGATCCGCACAAGCCTCCCTGTGCAGGgtaataagtc ... aatactgcagATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCAT

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: 32 (upstream exon), 32 (downstream exon)
Score: 14

GGAAGCAGTGGAGCATCCTGGTTGGTGTCCAGATCCGCACAAGCCTCCCTGTGCAGGgtaataagtc ... aatactgcagATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCATCTGGTACATAATACAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAAGCAGTGGAGCATCCTGGTTGGTGTCCAGATCCGCACAAGCCTCCCTGTGCAGGgtaataagtcaacctgtatttagttagtgattcgtgtcttaccttcctcctttggtcgttgaaatttactgtctgttagttgttgggtatttacttcttgtttaatactgcag

- - -  GTGGAG
- - - -  GGAGCA