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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttatttagattgtctgcttactattacgcagagcattctactctttattcctattggagtaaggggcagttaagattccaagtgacgtggatgtgtatacgtactagtcgtagaacatgcggtcccgaacctcttattgtgtgcatttcttaatgaggatattttccagCCTTGGAGCGTGCCAGAGGTACTACGCCCTCTGTATGAATCGCCGGCTGTACTTGCGCAGCGGTCTACTATTGCG

Basic information

species Physcomitrella patens
transcript PP1S67_107V6.1
intron # 10
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|100404741|gb|BY991260.1|BY991260
EST:     GCGATGGAGGGGGCTGTATCATTCACGTCGTAGATCATTATGACAACGGG                         CCTTGGAGCGTGCCAGAGGTACTACGCCCTCTGTATGAATCGCCGGCTGTA
genomic: GCGATGGAGGGGGCTGTATCATTCACGTCGTAGATCATTATGACAACGGGgtaagttatt ... tattttccagCCTTGGAGCGTGCCAGAGGTACTACGCCCTCTGTATGAATCGCCGGCTGTA
EST: gi|162184099|gb|FC358845.1|FC358845
EST:     GCGATGGAGGGGGCTGTATCATTCACGTCGTAGATCATTATGACAACGGG                         CCTTGGAGCGTGCCAGAGGTACTACGCCCTCTGTATGAATCGCCGGCTGTA
genomic: GCGATGGAGGGGGCTGTATCATTCACGTCGTAGATCATTATGACAACGGGgtaagttatt ... tattttccagCCTTGGAGCGTGCCAGAGGTACTACGCCCTCTGTATGAATCGCCGGCTGTA
EST: gi|100450755|gb|CJ974423.1|CJ974423
EST:     GCGATGGAGGGGGCTGTATCATTCACGTCGTAGATCATTATGACAACGGG                         CCTTGGAGCGTGCCAGAGGTACTACGCCCTCTGTATGAATCGCCGGCTGTA
genomic: GCGATGGAGGGGGCTGTATCATTCACGTCGTAGATCATTATGACAACGGGgtaagttatt ... tattttccagCCTTGGAGCGTGCCAGAGGTACTACGCCCTCTGTATGAATCGCCGGCTGTA

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: 35 (upstream exon), 26 (downstream exon)
Score: 5

GTCCTTTGTGAGAGGAGAAATGTTCCCAAGCGGCTATCTGATTCGCCCATGCGATGGAGGGGGCTGTATCATTCACGTCGTAGATCATTATGACAACGGGgtaagttatt ... tattttccagCCTTGGAGCGTGCCAGAGGTACTACGCCCTCTGTATGAATCGCCGGCTGTACTTGCGCAGCGGTCTACTATTGCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatgcggtcccgaacctcttattgtgtgcatttcttaatgaggatattttccagCCTTGGAGCGTGCCAGAGGTACTACGCCCTCTGTATGAATCGCCGGCTGTACTTGCGCAGCGGTCTACTATTGCG
                                 tcttaat  putative branch site (score: 5)
                                             tattttcc  putative PPT
                              atttcttaat  TA-rich tract