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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtttgcccttcaatttgaacttgatgctctaatagcgatccttcaatttgaaatgatcttgaacaatctgtaaatagttgtatgctagtattcagaaacttgactgcacgatttttctgcgcagATTTTTTATGTGTTGGGTTGCGTCTTTTTCTCACTTGAGTTGTTGTTGAGTATCTGGGTTATTAAG

Basic information

species Physcomitrella patens
transcript PP1S50_114V6.4
intron # 11
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|208349681|gb|DC917859.1|DC917859
EST:     GGGACTGTGGCCTGCCATCGGCTTATTTGGAGATAACGTTCTAGTTGCT                         ATTTTTTATGTGTTGGGTTGCGTCTTTTTCTCACTTGAGTTGTTGTTGAGT
genomic: GGGACTGTGGCCTGCCATCGGCTTATTTGGAGATAACGTTCTAGTTGCTgtgagtttgc ... ttctgcgcagATTTTTTATGTGTTGGGTTGCGTCTTTTTCTCACTTGAGTTGTTGTTGAGT
EST: gi|67701518|gb|BJ961751.1|BJ961751
EST:     GGGACTGTGGCCTGCCATCGGCTTATTTGGAGATAACGTTCTAGTTGCT                         ATTTTTTATGTGTTGGGTTGCGTCTTTTTCTCACTTGAGTTGTTGTTGAGT
genomic: GGGACTGTGGCCTGCCATCGGCTTATTTGGAGATAACGTTCTAGTTGCTgtgagtttgc ... ttctgcgcagATTTTTTATGTGTTGGGTTGCGTCTTTTTCTCACTTGAGTTGTTGTTGAGT
EST: gi|208394706|gb|DC903962.1|DC903962
EST:     GGGACTGTGGCCTGCCATCGGCTTATTTGGAGATAACGTTCTAGTTGCT                         ATTTTTTATGTGTTGGGTTGCGTCTTTTTCTCACTTGAGTTGTTGTTGAGT
genomic: GGGACTGTGGCCTGCCATCGGCTTATTTGGAGATAACGTTCTAGTTGCTgtgagtttgc ... ttctgcgcagATTTTTTATGTGTTGGGTTGCGTCTTTTTCTCACTTGAGTTGTTGTTGAGT
EST: gi|67695428|gb|BJ955661.1|BJ955661
EST:     GGGACTGTGGCCTGCCATCGGCTTATTTGGAGATAACGTTCTAGTTGCT                         ATTTTTTATGTGTTGGGTTGCGTCTTTTTCTCACTTGAGTTGTTGTTGAGT
genomic: GGGACTGTGGCCTGCCATCGGCTTATTTGGAGATAACGTTCTAGTTGCTgtgagtttgc ... ttctgcgcagATTTTTTATGTGTTGGGTTGCGTCTTTTTCTCACTTGAGTTGTTGTTGAGT
EST: gi|208380999|gb|DC919881.1|DC919881
EST:     GGGACTGTGGCCTGCCATCGGCTTATTTGGAGATAACGTTCTAGTTGCT                         ATTTTTTATGTGTTGGGTTGCGTCTTTTTCTCACTTGAGTTGTTGTTGAGT
genomic: GGGACTGTGGCCTGCCATCGGCTTATTTGGAGATAACGTTCTAGTTGCTgtgagtttgc ... ttctgcgcagATTTTTTATGTGTTGGGTTGCGTCTTTTTCTCACTTGAGTTGTTGTTGAGT
EST: gi|208375107|gb|DC944846.1|DC944846
EST:     GGGACTGTGGCCTGCCATCGGCTTATTTGGAGATAACGTTCTAGTTGCT                         ATTTTTTATGTGTTGGGTTGCGTCTTTTTCTCACTTGAGTTGTTGTTGAGT
genomic: GGGACTGTGGCCTGCCATCGGCTTATTTGGAGATAACGTTCTAGTTGCTgtgagtttgc ... ttctgcgcagATTTTTTATGTGTTGGGTTGCGTCTTTTTCTCACTTGAGTTGTTGTTGAGT
EST: gi|162258284|gb|FC434683.1|FC434683
EST:     GGGACTGTGGCCTGCCATCGGCTTATTTGGAGATAACGTTCTAGTTGCT                         ATTTTTTATGTGTTGGGTTGCGTCTTTTTCTCACTTGAGTTGTTGTTGAGT
genomic: GGGACTGTGGCCTGCCATCGGCTTATTTGGAGATAACGTTCTAGTTGCTgtgagtttgc ... ttctgcgcagATTTTTTATGTGTTGGGTTGCGTCTTTTTCTCACTTGAGTTGTTGTTGAGT

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: 30 (upstream exon), 30 (downstream exon)
Score: 10

GGGACTGTGGCCTGCCATCGGCTTATTTGGAGATAACGTTCTAGTTGCTgtgagtttgc ... ttctgcgcagATTTTTTATGTGTTGGGTTGCGTCTTTTTCTCACTTGAGTTGTTGTTGAGTATCTGGGTTATTAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaaatagttgtatgctagtattcagaaacttgactgcacgatttttctgcgcagATTTTTTATGTGTTGGGTTGCGTCTTTTTCTCACTTGAGTTGTTGTTGAGTATCTGGGTTATTAAG
                            acttgac  putative branch site (score: 10)
                                          tttttctgc  putative PPT
                                         atttttct  TA-rich tract