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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttttcaccagatttccattgttgtctaacccgaaattacagattcaactgtggaaggtgcccatgattcactgtcaatgttcaagacattgttcgcatttactaacttctatgccagacagcctttttacactagtactttttattgttttgcagGATGATTCAGCGAAACAGGCAGCCAAGCTTGTATTCGAGACGGCTTTGTTAGAGAGTGGGTTTGTCTTGGAGGACCCTAAAGACTTCGCCAACCGCATTT

Basic information

species Physcomitrella patens
transcript PP1S126_38V6.1
intron # 15
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|37841475|gb|BJ599483.1|BJ599483
EST:     AGCACCCAATTATCAAAGATTTGAAGGAGAAAATATCCTTGAGTTCTGAG                         GATGATTCAGCGAAACAGGCAGCCAAGCTTGTATTCGAGACGGCTTTGTTA
genomic: AGCACCCAATTATCAAAGATTTGAAGGAGAAAATATCCTTGAGTTCTGAGgtgagttttc ... tgttttgcagGATGATTCAGCGAAACAGGCAGCCAAGCTTGTATTCGAGACGGCTTTGTTA
EST: gi|162166690|gb|FC342659.1|FC342659
EST:     AGCACCCAATTATCAAAGATTTGAAGGAGAAAATATCCTTGAGTTCTGAG                         GATGATTCAGCGAAACAGGCAGCCAAGCTTGTATTCGAGACGGCTTTGTTA
genomic: AGCACCCAATTATCAAAGATTTGAAGGAGAAAATATCCTTGAGTTCTGAGgtgagttttc ... tgttttgcagGATGATTCAGCGAAACAGGCAGCCAAGCTTGTATTCGAGACGGCTTTGTTA
EST: gi|37838652|gb|BJ596660.1|BJ596660
EST:     AGCACCCAATTATCAAAGATTTGAAGGAGAAAATATCCTTGAGTTCTGAG                         GATGATTCAGCGAAACAGGCAGCCAAGCTTGTATTCGAGACGGCTTTGTTA
genomic: AGCACCCAATTATCAAAGATTTGAAGGAGAAAATATCCTTGAGTTCTGAGgtgagttttc ... tgttttgcagGATGATTCAGCGAAACAGGCAGCCAAGCTTGTATTCGAGACGGCTTTGTTA
EST: gi|18341140|gb|BJ173173.1|BJ173173
EST:     AGCACCCAATTATCAAAGATTTGAAGNAGAAAATATCCTTGAGTTNTGAG                         GATGATTCAGCGAAACAGGCAGCCAAGCTTGTATTCGAGACGGCTTTGTTA
genomic: AGCACCCAATTATCAAAGATTTGAAGGAGAAAATATCCTTGAGTTCTGAGgtgagttttc ... tgttttgcagGATGATTCAGCGAAACAGGCAGCCAAGCTTGTATTCGAGACGGCTTTGTTA
EST: gi|162240202|gb|FC418329.1|FC418329
EST:     AGCACCCAATTATCAAAGATTTGAAGGAGAAAATATCCTTGAGTTCTGAG                         GATGATTCAGCGAAACAGGCAGCCAAGCTTGTATTCGAGACGGCTTTGTTA
genomic: AGCACCCAATTATCAAAGATTTGAAGGAGAAAATATCCTTGAGTTCTGAGgtgagttttc ... tgttttgcagGATGATTCAGCGAAACAGGCAGCCAAGCTTGTATTCGAGACGGCTTTGTTA
EST: gi|37843903|gb|BJ601911.1|BJ601911
EST:     AGCACCCAATTATCAAAGATTTGAAGGAGAAAATATCCTTGAGTTCTGAG                         GATGATTCAGCGAAACAGGCAGCCAAGCTTGTATTCGAGACGGCTTTGTTA
genomic: AGCACCCAATTATCAAAGATTTGAAGGAGAAAATATCCTTGAGTTCTGAGgtgagttttc ... tgttttgcagGATGATTCAGCGAAACAGGCAGCCAAGCTTGTATTCGAGACGGCTTTGTTA
EST: gi|37836149|gb|BJ594157.1|BJ594157
EST:     AGCACCCAATTATCAAAGATTTGAAGGAGAAAATATCCTTGAGTTCTGAG                         GATGATTCAGCGAAACAGGCAGCCAAGCTTGTATTCGAGACGGCTTTGTTA
genomic: AGCACCCAATTATCAAAGATTTGAAGGAGAAAATATCCTTGAGTTCTGAGgtgagttttc ... tgttttgcagGATGATTCAGCGAAACAGGCAGCCAAGCTTGTATTCGAGACGGCTTTGTTA
EST: gi|18332522|gb|BJ164535.1|BJ164535
EST:     GCACCCAATTATCAAAGATTTGAAGGAGAAAATATCCTTGAGTTCTGAG                         GATGATTCAGCGAAACAGGCAGCCAAGCTTGTATTCGAGACGGCTTTGTTA
genomic: GCACCCAATTATCAAAGATTTGAAGGAGAAAATATCCTTGAGTTCTGAGgtgagttttc ... tgttttgcagGATGATTCAGCGAAACAGGCAGCCAAGCTTGTATTCGAGACGGCTTTGTTA
EST: gi|37826825|gb|BJ584837.1|BJ584837
EST:     AGCACCCAATTATCAAAGATTTGAAGGAGAAAATATCCTTGAGTTCTGAG                         GATGATTCAGCGAAACAGGCAGCCAAGCTTGTATTCGAGACGGCTTTGTTA
genomic: AGCACCCAATTATCAAAGATTTGAAGGAGAAAATATCCTTGAGTTCTGAGgtgagttttc ... tgttttgcagGATGATTCAGCGAAACAGGCAGCCAAGCTTGTATTCGAGACGGCTTTGTTA
EST: gi|37825141|gb|BJ583207.1|BJ583207
EST:     AGCACCCAATTATCAAAGATTTGAAGGAGAAAATATCCTTGAGTTCTGAG                         GATGATTCAGCGAAACAGGCAGCCAAGCTTGTATTCGAGACGGCTTTGTTA
genomic: AGCACCCAATTATCAAAGATTTGAAGGAGAAAATATCCTTGAGTTCTGAGgtgagttttc ... tgttttgcagGATGATTCAGCGAAACAGGCAGCCAAGCTTGTATTCGAGACGGCTTTGTTA
EST: gi|37826145|gb|BJ584157.1|BJ584157
EST:     AGCACCCAATTATCAAAGATTTGAAGGAGAAAATATCCTTGAGTTCTGAG                         GATGATTCAGCGAAACAGGCAGCCAAGCTTGTATTCGAGACGGCTTTGTTA
genomic: AGCACCCAATTATCAAAGATTTGAAGGAGAAAATATCCTTGAGTTCTGAGgtgagttttc ... tgttttgcagGATGATTCAGCGAAACAGGCAGCCAAGCTTGTATTCGAGACGGCTTTGTTA
EST: gi|162260418|gb|FC435044.1|FC435044
EST:     AGCACCCAATTATCAAAGATTTGAAGGAGAAAATATCCTTGAGTTCTGAG                         GATGATTCAGCGAAACAGGCAGCCAAGCTTGTATTCGAGACGGCTTTGTTA
genomic: AGCACCCAATTATCAAAGATTTGAAGGAGAAAATATCCTTGAGTTCTGAGgtgagttttc ... tgttttgcagGATGATTCAGCGAAACAGGCAGCCAAGCTTGTATTCGAGACGGCTTTGTTA
EST: gi|162240201|gb|FC418328.1|FC418328
EST:     AGCACCCAATTATCAAAGATTTGAAGGAGAAAATATCCTTGAGTTCTGAG                         GATGATTCAGCGAAACAGGCAGCCAAGCTTGTATTCGAGACGGCTTTGTTA
genomic: AGCACCCAATTATCAAAGATTTGAAGGAGAAAATATCCTTGAGTTCTGAGgtgagttttc ... tgttttgcagGATGATTCAGCGAAACAGGCAGCCAAGCTTGTATTCGAGACGGCTTTGTTA
EST: gi|162168869|gb|FC345343.1|FC345343
EST:     AAAGATTTGAAGGAGAAAATATCCTTGAGTTCTGAG                         GATGATTCAGCGAAACAGGCAGCCAAGCTTGTATTCGAGACGGCTTTGTTA
genomic: AAAGATTTGAAGGAGAAAATATCCTTGAGTTCTGAGgtgagttttc ... tgttttgcagGATGATTCAGCGAAACAGGCAGCCAAGCTTGTATTCGAGACGGCTTTGTTA
EST: gi|37841177|gb|BJ599185.1|BJ599185
EST:     AGCACCCAATTATCAAAGATTTGAAGGAGAAAATATCCTTGAGTTCTGAG                         GATGATTCAGCGAAACAGGCAGCCAAGCTTGTATTCGAGACGGCTTTGTTA
genomic: AGCACCCAATTATCAAAGATTTGAAGGAGAAAATATCCTTGAGTTCTGAGgtgagttttc ... tgttttgcagGATGATTCAGCGAAACAGGCAGCCAAGCTTGTATTCGAGACGGCTTTGTTA
EST: gi|37834239|gb|BJ592251.1|BJ592251
EST:     AGCACCCAATTATCAAAGATTTGAAGGAGAAAATATCCTTGAGTTCTGAG                         GATGATTCAGCGAAACAGGCAGCCAAGCTTGTATTCGAGACGGCTTTGTTA
genomic: AGCACCCAATTATCAAAGATTTGAAGGAGAAAATATCCTTGAGTTCTGAGgtgagttttc ... tgttttgcagGATGATTCAGCGAAACAGGCAGCCAAGCTTGTATTCGAGACGGCTTTGTTA
EST: gi|37831437|gb|BJ589449.1|BJ589449
EST:     AGCACCCAATTATCAAAGATTTGAAGGAGAAAATATCCTTGAGTTCTGAG                         GATGATTCAGCGAAACAGGCAGCCAAGCTTGTATTCGAGACGGCTTTGTTA
genomic: AGCACCCAATTATCAAAGATTTGAAGGAGAAAATATCCTTGAGTTCTGAGgtgagttttc ... tgttttgcagGATGATTCAGCGAAACAGGCAGCCAAGCTTGTATTCGAGACGGCTTTGTTA
EST: gi|37843052|gb|BJ601060.1|BJ601060
EST:     AGCACCCAATTATCAAAGATTTGAAGGAGAAAATATCCTTGAGTTCTGAG                         GATGATTCAGCGAAACAGGCAGCCAAGCTTGTATTCGAGACGGCTTTGTTA
genomic: AGCACCCAATTATCAAAGATTTGAAGGAGAAAATATCCTTGAGTTCTGAGgtgagttttc ... tgttttgcagGATGATTCAGCGAAACAGGCAGCCAAGCTTGTATTCGAGACGGCTTTGTTA
EST: gi|67727873|gb|BJ978132.1|BJ978132
EST:     AGCACCCAATTATCAAAGATTTGAAGGAGAAAATATCCTTGAGTTCTGAG                         GATGATTCAGCGAAACAGGCAGCCAAGCTTGTATTCGAGACGGCTTTGTTA
genomic: AGCACCCAATTATCAAAGATTTGAAGGAGAAAATATCCTTGAGTTCTGAGgtgagttttc ... tgttttgcagGATGATTCAGCGAAACAGGCAGCCAAGCTTGTATTCGAGACGGCTTTGTTA
EST: gi|162196000|gb|FC372691.1|FC372691
EST:     AGCACCCAATTATCAAAGATTTGAAGGAGAAAATATCCTTGAGTTCTGAG                         GATGATTCAGCGAAACAGGCAGCCAAGCTTGTATTCGAGACGGCTTTGTTA
genomic: AGCACCCAATTATCAAAGATTTGAAGGAGAAAATATCCTTGAGTTCTGAGgtgagttttc ... tgttttgcagGATGATTCAGCGAAACAGGCAGCCAAGCTTGTATTCGAGACGGCTTTGTTA
EST: gi|37847752|gb|BJ605760.1|BJ605760
EST:     AGCACCCAATTATCAAAGATTTGAAGGAGAAAATATCCTTGAGTTCTGAG                         GATGATTCAGCGAAACAGGCAGCCAAGCTTGTATTCGAGACGGCTTTGTTA
genomic: AGCACCCAATTATCAAAGATTTGAAGGAGAAAATATCCTTGAGTTCTGAGgtgagttttc ... tgttttgcagGATGATTCAGCGAAACAGGCAGCCAAGCTTGTATTCGAGACGGCTTTGTTA
EST: gi|18334981|gb|BJ166999.1|BJ166999
EST:     AGCACCCAATTATCAAAGATTTGAAGGAGAAAATATCCTTGAGTTCTGAG                         GATGATTCAGCGAAACAGGCAGCCAAGCTTGTATTCGAGACGGCTTTGTTA
genomic: AGCACCCAATTATCAAAGATTTGAAGGAGAAAATATCCTTGAGTTCTGAGgtgagttttc ... tgttttgcagGATGATTCAGCGAAACAGGCAGCCAAGCTTGTATTCGAGACGGCTTTGTTA
EST: gi|37826629|gb|BJ584641.1|BJ584641
EST:     CCCAATTATCAAAGATTTGAAGGAGAAAATATCCTTGAGTTCTGAG                         GATGATTCAGCGAAACAGGCAGCCAAGCTTGTATTCGAGACGGCTTTGTTA
genomic: CCCAATTATCAAAGATTTGAAGGAGAAAATATCCTTGAGTTCTGAGgtgagttttc ... tgttttgcagGATGATTCAGCGAAACAGGCAGCCAAGCTTGTATTCGAGACGGCTTTGTTA
EST: gi|37824151|gb|BJ582217.1|BJ582217
EST:     AGCACCCAATTATCAAAGATTTGAAGGAGAAAATATCCTTGAGTTCTGAG                         GATGATTCAGCGAAACAGGCAGCCAAGCTTGTATTCGAGACGGCTTTGTTA
genomic: AGCACCCAATTATCAAAGATTTGAAGGAGAAAATATCCTTGAGTTCTGAGgtgagttttc ... tgttttgcagGATGATTCAGCGAAACAGGCAGCCAAGCTTGTATTCGAGACGGCTTTGTTA

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: 33 (upstream exon), 35 (downstream exon)
Score: 19

CAGCAAGCAGTCCTATATGCGTGGTAAAAGGATTCTGGAAATCAACCCCAAGCACCCAATTATCAAAGATTTGAAGGAGAAAATATCCTTGAGTTCTGAGgtgagttttc ... tgttttgcagGATGATTCAGCGAAACAGGCAGCCAAGCTTGTATTCGAGACGGCTTTGTTAGAGAGTGGGTTTGTCTTGGAGGACCCTAAAGACTTCGCCAACCGCATTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actaacttctatgccagacagcctttttacactagtactttttattgttttgcagGATGATTCAGCGAAACAGGCAGCCAAGCTTGTATTCGAGACGGCTTTGTTAGAGAGTGGGTTTGTCTTGGAGGACCCTAAAGACTTCGCCAACCGCATTT
 tactaac  putative branch site (score: 19)
                                     ctttttattgtttt  putative PPT
                                   tactttttattgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttttcaccagatttccattgttgtctaacccgaaattacagattcaactgtggaaggtgcccatgattcactgtcaatgttcaagacattgttcgcatttactaacttctatgccagacagcctttttacactagtactttttattgttttgcagGATGATTCAGCGAAACAGGCAGCCAAGCTTGTATTCGAGACGGCTTTGTTAGAGAGTGGGTTTGTCTTGGAGGACCCTAAAGACTTCGCCAACCGCATTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA