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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtctctcaccgtttttgctatgttgagatgttaatgatatggagttaactacttattgaaaagtaagcgctcccatcacttagcacgtctccgtttgcagGGAGTGAGTCTCGCAAGGCGCTTTGCATTAGTCCCATTGGGGCCCCCACTTTTGGCCTATAAGAGTAACTGCAAAGCGATGTTGAAGGCGGTTGATGACA

Basic information

species Physcomitrella patens
transcript PP1S181_117V6.1
intron # 5
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|162162595|gb|FC338689.1|FC338689
EST:     TATTCAAGCAGGCTTTTGTGGCTGTGCAGTCCTGCGTTGTTCACCTCCAG                         GGAGTGAGTCTCGCAAGGCGCTTTGCATTAGTCCCATTGGGGCCCCCACTT
genomic: TATTCAAGCAGGCTTTTGTGGCTGTGCAGTCCTGCGTTGTTCACCTCCAGgtctgtcttc ... ccgtttgcagGGAGTGAGTCTCGCAAGGCGCTTTGCATTAGTCCCATTGGGGCCCCCACTT
EST: gi|162221408|gb|FC397217.1|FC397217
EST:     TATTCAAGCAGGCTTTTGTGGCTGTGCAGTCCTGCGTTGTTCACCTCCAG                         GGAGTGAGTCTCGCAAGGCGCTTTGCATTAGTCCCATTGGGGCCCCCACTT
genomic: TATTCAAGCAGGCTTTTGTGGCTGTGCAGTCCTGCGTTGTTCACCTCCAGgtctgtcttc ... ccgtttgcagGGAGTGAGTCTCGCAAGGCGCTTTGCATTAGTCCCATTGGGGCCCCCACTT
EST: gi|162258112|gb|FC433894.1|FC433894
EST:     AGTCCTGCGTTGTTCACCTCCAG                         GGAGTGAGTCTCGCAAGGCGCTTTGCATTAGTCCCATTGGGGCCCCCACTT
genomic: AGTCCTGCGTTGTTCACCTCCAGgtctgtcttc ... ccgtttgcagGGAGTGAGTCTCGCAAGGCGCTTTGCATTAGTCCCATTGGGGCCCCCACTT
EST: gi|162233878|gb|FC409728.1|FC409728
EST:     TATTCAAGCAGGCTTTTGTGGCTGTGCAGTCCTGCGTTGTTCACCTCCAG                         GGAGTGAGTCTCGCAAGGCGCTTTGCATTAGTCCCATTGGGGCCCCCACTT
genomic: TATTCAAGCAGGCTTTTGTGGCTGTGCAGTCCTGCGTTGTTCACCTCCAGgtctgtcttc ... ccgtttgcagGGAGTGAGTCTCGCAAGGCGCTTTGCATTAGTCCCATTGGGGCCCCCACTT
EST: gi|162198877|gb|FC372904.1|FC372904
EST:     TATTCAAGCAGGCTTTTGTGGCTGTGCAGTCCTGCGTTGTTCACCTCCAG                         GGAGTGAGTCTCGCAAGGCGCTTTGCATTAGTCCCATTGGGGCCCCCACTT
genomic: TATTCAAGCAGGCTTTTGTGGCTGTGCAGTCCTGCGTTGTTCACCTCCAGgtctgtcttc ... ccgtttgcagGGAGTGAGTCTCGCAAGGCGCTTTGCATTAGTCCCATTGGGGCCCCCACTT
EST: gi|162162497|gb|FC339215.1|FC339215
EST:     TATTCAAGCAGGCTTTTGTGGCTGTGCAGTCCTGCGTTGTTCACCTCCAG                         GGAGTGAGTCTCGCAAGGCGCTTTGCATTAGTCCCATTGGGGCCCCCACTT
genomic: TATTCAAGCAGGCTTTTGTGGCTGTGCAGTCCTGCGTTGTTCACCTCCAGgtctgtcttc ... ccgtttgcagGGAGTGAGTCTCGCAAGGCGCTTTGCATTAGTCCCATTGGGGCCCCCACTT
EST: gi|162152120|gb|FC328710.1|FC328710
EST:     TATTCAAGCAAGCTTTTGTGGCTGTGCAGTCCTGCGTTGTTCACCTCCAG                         GGAGTGAGTCTCGCAAGGCGCTTTGCATTAGTC
genomic: TATTCAAGCAGGCTTTTGTGGCTGTGCAGTCCTGCGTTGTTCACCTCCAGgtctgtcttc ... ccgtttgcagGGAGTGAGTCTCGCAAGGCGCTTTGCATTAGTC
EST: gi|162158626|gb|FC335526.1|FC335526
EST:     TATTCAAGCAGGCTTTTGTGGCTGTGCAGTCCTGCGTTGTTCACCTCCAG                         GGAGTGAGTCTCGCAAGGCGCTTTGCATTAGTCCCATTGGGGCCCCCACTT
genomic: TATTCAAGCAGGCTTTTGTGGCTGTGCAGTCCTGCGTTGTTCACCTCCAGgtctgtcttc ... ccgtttgcagGGAGTGAGTCTCGCAAGGCGCTTTGCATTAGTCCCATTGGGGCCCCCACTT

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), 35 (downstream exon)
Score: 10

CAATATCCCTTCGACCTACCTACGGAAGCTTTCTCATTTGAGATATTCAAGCAGGCTTTTGTGGCTGTGCAGTCCTGCGTTGTTCACCTCCAGgtctgtcttc ... ccgtttgcagGGAGTGAGTCTCGCAAGGCGCTTTGCATTAGTCCCATTGGGGCCCCCACTTTTGGCCTATAAGAGTAACTGCAAAGCGATGTTGAAGGCGGTTGATGACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taactacttattgaaaagtaagcgctcccatcacttagcacgtctccgtttgcagGGAGTGAGTCTCGCAAGGCGCTTTGCATTAGTCCCATTGGGGCCCCCACTTTTGGCCTATAAGAGTAACTGCAAAGCGATGTTGAAGGCGGTTGATGACA
 agttaac  putative branch site (score: 10)
                                          tctccgttt  putative PPT
       ttattgaaaagtaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctctcaccgtttttgctatgttgagatgttaatgatatggagttaactacttattgaaaagtaagcgctcccatcacttagcacgtctccgtttgcagGGAGTGAGTCTCGCAAGGCGCTTTGCATTAGTCCCATTGGGGCCCCCACTTTTGGCCTATAAGAGTAACTGCAAAGCGATGTTGAAGGCGGTTGATGACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG