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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACATTGGTGTGGGGTTGAGTTCACCTCAAGCTTCGCTCAGCAGATTACCTGgtttggtttgcatcctttctacccttccctctcttcatctctctctctctcgctctcgctcgctcgactttctgaaaactgttttgcctctcaagaatcagttattttcacgcttcaagtgagtgaatatatgcacaattattgtctgtatttaaatttgatgatgcgttgtgtttaacag

Basic information

species Physcomitrella patens
transcript PP1S208_168V6.2
intron # 3
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|18366432|gb|BJ198511.1|BJ198511
EST:     CATTGGTGTGGGGTTGAGTTCACCTCAAGCTTCGCTCAGCAGATTACCTG                         GGTTAGAAAGAAATAGCTTCGGTTATCATGCCGACGATGGCAACGCATTTA
genomic: CATTGGTGTGGGGTTGAGTTCACCTCAAGCTTCGCTCAGCAGATTACCTGgtttggtttg ... tgtttaacagGGTTAGAAAGAAATAGCTTCGGTTATCATGCCGACGATGGCAACGCATTTA
EST: gi|208344499|gb|DC905060.1|DC905060
EST:     CATTGGTGTGGGGTTGAGTTCACCTCAAGCTTCGCTCAGCAGATTACCTG                         GGTTAGAAAGAAATAGCTTCGGTTATCATGCCGACGATGGCAACGCATTTA
genomic: CATTGGTGTGGGGTTGAGTTCACCTCAAGCTTCGCTCAGCAGATTACCTGgtttggtttg ... tgtttaacagGGTTAGAAAGAAATAGCTTCGGTTATCATGCCGACGATGGCAACGCATTTA
EST: gi|18361861|gb|BJ193928.1|BJ193928
EST:     CATTGGTGTGGGGTTGAGTTCACCTCAAGCTTCGCTCAGCAGATTACCTG                         GGTTAGAAAGAAATAGCTTCGGTTATCATGCCGACGATGGCAACGCATTTA
genomic: CATTGGTGTGGGGTTGAGTTCACCTCAAGCTTCGCTCAGCAGATTACCTGgtttggtttg ... tgtttaacagGGTTAGAAAGAAATAGCTTCGGTTATCATGCCGACGATGGCAACGCATTTA
EST: gi|100400993|gb|BY973046.1|BY973046
EST:     CATTGGTGTGGGGTTGAGTTCACCTCAAGCTTCGCTCAGCAGATTACCTG                         GGTTAGAAAGAAATAGCTTCGGTTATCATGCCGACGATGGCAACGCATTTA
genomic: CATTGGTGTGGGGTTGAGTTCACCTCAAGCTTCGCTCAGCAGATTACCTGgtttggtttg ... tgtttaacagGGTTAGAAAGAAATAGCTTCGGTTATCATGCCGACGATGGCAACGCATTTA
EST: gi|100390547|gb|BY952955.1|BY952955
EST:     CATTGGTGTGGGGTTGAGTTCACCTCAAGCTTCGCTCAGCAGATTACCTGGTTTG                     
genomic: CATTGGTGTGGGGTTGAGTTCACCTCAAGCTTCGCTCAGCAGATTACC-----TGgtttggtttg ... tgttta
EST: gi|208390623|gb|DC937555.1|DC937555
EST:     CATTGGTGTGGGGTTGAGTTCACCTCAAGCTTCGCTCAGCAGATTACCTG                         GGTTAGAAAGAAATAGCTTCGGTTATCATGCCGACGATGGCAACGCATTTA
genomic: CATTGGTGTGGGGTTGAGTTCACCTCAAGCTTCGCTCAGCAGATTACCTGgtttggtttg ... tgtttaacagGGTTAGAAAGAAATAGCTTCGGTTATCATGCCGACGATGGCAACGCATTTA

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: 21 (upstream exon), 21 (downstream exon)
Score: 2

GTACATTGGTGTGGGGTTGAGTTCACCTCAAGCTTCGCTCAGCAGATTACCTGgtttggtttg ... tgtttaacagGGTTAGAAAGAAATAGCTTCGGTTATCATGCCGACGATGGCAACGCATTTACTGGTTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTACATTGGTGTGGGGTTGAGTTCACCTCAAGCTTCGCTCAGCAGATTACCTGgtttggtttgcatcctttctacccttccctctcttcatctctctctctctcgctctcgctcgctcgactttctgaaaactgttttgcctctcaagaatcagttattttcacgcttcaagtgagtgaatatatgcacaattattgtctgtatttaaatttgatgatgcgttgtgtttaacag

- - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - -  GCAGAT