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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acctcatgttaagttctgatcccgtaacgtgctccaaaggttgtgtttgtcagtcttaattatttgaattattttgaagttttcgtgcactctattgcagGTGAGAGAACTAGGCGTCCGAAGGTGCAAGATACCTTGACAATACCAATTTGTCAGACATCCACTTATACGTTTAAAGATACAGCTGAGTTGATTGCATT

Basic information

species Physcomitrella patens
transcript PP1S49_246V6.1
intron # 1
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|162153103|gb|FC329509.1|FC329509
EST:     GACTGAGAAGCCCAGGCGGAGCAAATCAAGCACGCTGGCTGTTCATGGTG                         GTGAGAGAACTAGGCGTCCGAAGGTGCAAGATACCTTGACAATACCAATTT
genomic: GACTGAGAAGCCCAGGCGGAGCAAATCAAGCACGCTGGCTGTTCATGGTGgtgagtggct ... tctattgcagGTGAGAGAACTAGGCGTCCGAAGGTGCAAGATACCTTGACAATACCAATTT
EST: gi|162159189|gb|FC334360.1|FC334360
EST:     GACTGAGAAGCCCAGGCGGAGCAAATCAAGCACGCTGGCTGTTCATGGTG                         GTGAGAGAACTAGGCGTCCGAAGGTGCAAGATACCTTGACAATACCAATTT
genomic: GACTGAGAAGCCCAGGCGGAGCAAATCAAGCACGCTGGCTGTTCATGGTGgtgagtggct ... tctattgcagGTGAGAGAACTAGGCGTCCGAAGGTGCAAGATACCTTGACAATACCAATTT
EST: gi|162165502|gb|FC340613.1|FC340613
EST:     GACTGAGAAGCCCAGGCGGAGCAAATCAAGCACGCTGGCTGTTCATGGTG                         GTGAGAGAACTAGGCGTCCGAAGGTGCAAGATACCTTGACAATACCAATTT
genomic: GACTGAGAAGCCCAGGCGGAGCAAATCAAGCACGCTGGCTGTTCATGGTGgtgagtggct ... tctattgcagGTGAGAGAACTAGGCGTCCGAAGGTGCAAGATACCTTGACAATACCAATTT
EST: gi|100369986|gb|BY967471.1|BY967471
EST:     GACTGAGAAGCCCAGGCGGAGCAAATCAAGCACGCTGGCTGTTCATGGTG                         GTGAGAGAACTANGCGTCCGAAGGTGCAAGATACCTTGANCA-TACCAATT
genomic: GACTGAGAAGCCCAGGCGGAGCAAATCAAGCACGCTGGCTGTTCATGGTGgtgagtggct ... tctattgcagGTGAGAGAACTAGGCGTCCGAAGGTGCAAGATACCTTGA-CAATACCAATT
EST: gi|100405639|gb|BY973778.1|BY973778
EST:     GACTGAGAAGCCCAGGCGGAGCAAATCAAGCACGCTGGCTGTTCATGGTG                         GTGAGAGAACTAGGCGTCCGAAGGTGCAAGATACCTTGACAATACCAATTT
genomic: GACTGAGAAGCCCAGGCGGAGCAAATCAAGCACGCTGGCTGTTCATGGTGgtgagtggct ... tctattgcagGTGAGAGAACTAGGCGTCCGAAGGTGCAAGATACCTTGACAATACCAATTT
EST: gi|162165090|gb|FC341631.1|FC341631
EST:     GACTGAGAAGCCCAGGCGGAGCAAATCAAGCACGCTGGCTGTTCATGGTG                         GTGAGAGAACTAGGCGTCCGAAGGTGCAAGATACCTTGACAATACCAATTT
genomic: GACTGAGAAGCCCAGGCGGAGCAAATCAAGCACGCTGGCTGTTCATGGTGgtgagtggct ... tctattgcagGTGAGAGAACTAGGCGTCCGAAGGTGCAAGATACCTTGACAATACCAATTT
EST: gi|162164566|gb|FC341861.1|FC341861
EST:     GACTGAGAAGCCCAGGCGGAGCAAATCAAGCACGCTGGCTGTTCATGGTG                         GTGAGAGAACTAGGCGTCCGAAGGTGCAAGATACCTTGACAATACCAATTT
genomic: GACTGAGAAGCCCAGGCGGAGCAAATCAAGCACGCTGGCTGTTCATGGTGgtgagtggct ... tctattgcagGTGAGAGAACTAGGCGTCCGAAGGTGCAAGATACCTTGACAATACCAATTT

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: 10 (upstream exon), 26 (downstream exon)
Score: 1

GAGGCTCTTCTTGAGTCTGGCACCTCTCTTGCTAGTGCAGGAGCTTCAGAGACTGAGAAGCCCAGGCGGAGCAAATCAAGCACGCTGGCTGTTCATGGTGgtgagtggct ... tctattgcagGTGAGAGAACTAGGCGTCCGAAGGTGCAAGATACCTTGACAATACCAATTTGTCAGACATCCACTTATACGTTTAAAGATACAGCTGAGTTGATTGCATT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtcagtcttaattatttgaattattttgaagttttcgtgcactctattgcagGTGAGAGAACTAGGCGTCCGAAGGTGCAAGATACCTTGACAATACCAATTTGTCAGACATCCACTTATACGTTTAAAGATACAGCTGAGTTGATTGCATT
        tcttaat  putative branch site (score: 1)
                                            ctctatt  putative PPT
        tcttaattatttgaat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acctcatgttaagttctgatcccgtaacgtgctccaaaggttgtgtttgtcagtcttaattatttgaattattttgaagttttcgtgcactctattgcagGTGAGAGAACTAGGCGTCCGAAGGTGCAAGATACCTTGACAATACCAATTTGTCAGACATCCACTTATACGTTTAAAGATACAGCTGAGTTGATTGCATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - -tgctcca