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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttacgcaccatcatcacttgaggtatgttttttcttttcttttttcttttcttttcctgtaacactttgtaacgtttctggttccaacctcttatgacagTGGGCGCAAGAGGATGAGTGTCATTTACTGTATTACATACATGCTGAGTTGCTTTACGAAGCATTCTCCAGAGTACAGGGTGTTGATGTTGGGACGTGTA

Basic information

species Physcomitrella patens
transcript PP1S18_8V6.2
intron # 2
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|162188274|gb|FC364768.1|FC364768
EST:     GGATCATCCATGCTTTTCGGGACTATTGTTGGATCTCTTGCCGATCGATA                         TGGGCGCAAGAGGATGAGTGTCATTTACTGTATTACATACATGCTGAGTTG
genomic: GGATCATCCATGCTTTTCGGGACTATTGTTGGATCTCTTGCCGATCGATAgtaagtgttc ... cttatgacagTGGGCGCAAGAGGATGAGTGTCATTTACTGTATTACATACATGCTGAGTTG
EST: gi|100356422|gb|BY946357.1|BY946357
EST:     GGATCATCCATGCTTTTCGGGACTATTGTTGGATCTCTTGCCGATCGATA                         TGGGCGCAAGAGGATGAGTGTCATTTACTGTATTACATACATGCTGAGTTG
genomic: GGATCATCCATGCTTTTCGGGACTATTGTTGGATCTCTTGCCGATCGATAgtaagtgttc ... cttatgacagTGGGCGCAAGAGGATGAGTGTCATTTACTGTATTACATACATGCTGAGTTG
EST: gi|208362207|gb|DC939631.1|DC939631
EST:     GGATCATCCATGCTTTTCGGGACTATTGTTGGATCTCTTGCCGATCGATA                         TGGGCGCAAGAGGATGAGTGTCATTTACTGTATTACATACATGCTGAGTTG
genomic: GGATCATCCATGCTTTTCGGGACTATTGTTGGATCTCTTGCCGATCGATAgtaagtgttc ... cttatgacagTGGGCGCAAGAGGATGAGTGTCATTTACTGTATTACATACATGCTGAGTTG

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), 29 (downstream exon)
Score: 7

TTTACGGGTACAATAAAGGTGATATCGGAAAGCTTTTCATAGCTGGATTTGGATCATCCATGCTTTTCGGGACTATTGTTGGATCTCTTGCCGATCGATAgtaagtgttc ... cttatgacagTGGGCGCAAGAGGATGAGTGTCATTTACTGTATTACATACATGCTGAGTTGCTTTACGAAGCATTCTCCAGAGTACAGGGTGTTGATGTTGGGACGTGTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttcttttcctgtaacactttgtaacgtttctggttccaacctcttatgacagTGGGCGCAAGAGGATGAGTGTCATTTACTGTATTACATACATGCTGAGTTGCTTTACGAAGCATTCTCCAGAGTACAGGGTGTTGATGTTGGGACGTGTA
                     ttgtaac  putative branch site (score: 7)
                                          cctcttat  putative PPT
                    tttgtaa  TA-rich tract