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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgactcccaaccaatggagctgtagcaagcagatggctatatgccaaatactcatcaaattgtcttcaatgcacaattctcgatgcatcctcaagtttttgataagcttttctttttgccatttaactttcattgtatctctatctagGTTCCGGAGGCCCTTGTCCCTGAGACGTGTGCTAGGGTTATGTCGCTGACAGACGGCACTGCAAAA

Basic information

species Physcomitrella patens
transcript PP1S5_195V6.1
intron # 9
splice site 3'
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|162232153|gb|FC407729.1|FC407729
EST:     CGGACGAGGTGGGAAAATTTTCAAG                         GTTCCGGAGGCCCTTGTCCCTGAGACGTGTGCTAGGGTTATGTCGCTGACA
genomic: CGGACGAGGTGGGAAAATTTTCAAGgtttgactcc ... ctctatctagGTTCCGGAGGCCCTTGTCCCTGAGACGTGTGCTAGGGTTATGTCGCTGACA
EST: gi|67571511|gb|BJ944335.1|BJ944335
EST:     CGGACGAGGTGGGAAAATTTTCAAG                         GTTCCGGAGGCCCTTGTCCCTGAGACGTGTGCTAGGGTTATGTCGCTGACA
genomic: CGGACGAGGTGGGAAAATTTTCAAGgtttgactcc ... ctctatctagGTTCCGGAGGCCCTTGTCCCTGAGACGTGTGCTAGGGTTATGTCGCTGACA
EST: gi|162232167|gb|FC407730.1|FC407730
EST:     CGGACGAGGTGGGAAAATTTTCAAG                         GTTCCGGAGGCCCTTGTCCCTGAGACGTGTGCTAGGGTTATGTCGCTGACA
genomic: CGGACGAGGTGGGAAAATTTTCAAGgtttgactcc ... ctctatctagGTTCCGGAGGCCCTTGTCCCTGAGACGTGTGCTAGGGTTATGTCGCTGACA
EST: gi|162159330|gb|FC335144.1|FC335144
EST:     CGGACGAGGTGGGAAAATTTTCAAG                         GTTCCGGAGGCCCTTGTCCCTGAGACGTGTGCTAGGGTTATGTCGCTGACA
genomic: CGGACGAGGTGGGAAAATTTTCAAGgtttgactcc ... ctctatctagGTTCCGGAGGCCCTTGTCCCTGAGACGTGTGCTAGGGTTATGTCGCTGACA

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: 22 (upstream exon), 25 (downstream exon)
Score: 10

ACGAGGTGGGAAAATTTTCAAGgtttgactcc ... ctctatctagGTTCCGGAGGCCCTTGTCCCTGAGACGTGTGCTAGGGTTATGTCGCTGACAGACGGCACTGCAAAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtttttgataagcttttctttttgccatttaactttcattgtatctctatctagGTTCCGGAGGCCCTTGTCCCTGAGACGTGTGCTAGGGTTATGTCGCTGACAGACGGCACTGCAAAA
                           atttaac  putative branch site (score: 10)
                                            tctctatct  putative PPT
                           atttaactttcatt  TA-rich tract