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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attgacggcatttatactaatcatgcatgcttcaagtttttccgacggtgtcttgttaccctatttattttcagaaacatgacatgtggtttatgtgaagGCTACAGGCAGCGTGAATCTTTGGGATCATGATTGGCAAAGAGCGGCCCGCATGGCAAGTTATGGGTTTCTGATATATGGGCCATTATCACAGGTGTGGT

Basic information

species Physcomitrella patens
transcript PP1S94_157V6.1
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|208392132|gb|DC949564.1|DC949564
EST:     AGCAGAGAGTTGCGGAGGATGTGGCTGGCGGACTTACAATTGGAAATCAG                         GCTACAGGCAGCGTGAATCTTTGGGATCATGATTGGCAAAGAGCGGCCCGC
genomic: AGCAGAGAGTTGCGGAGGATGTGGCTGGCGGACTTACAATTGGAAATCAGgttattgggt ... ttatgtgaagGCTACAGGCAGCGTGAATCTTTGGGATCATGATTGGCAAAGAGCGGCCCGC
EST: gi|208389112|gb|DC945688.1|DC945688
EST:     AGCAGAGAGTTGCGGAGGATGTGGCTGGCGGACTTACAATTGGAAATCAG                         GCTACAGGCAGCGTGAATCTTTGGGATCATGATTGGCAAAGAGCGGCCCGC
genomic: AGCAGAGAGTTGCGGAGGATGTGGCTGGCGGACTTACAATTGGAAATCAGgttattgggt ... ttatgtgaagGCTACAGGCAGCGTGAATCTTTGGGATCATGATTGGCAAAGAGCGGCCCGC
EST: gi|208367534|gb|DC943937.1|DC943937
EST:     AGCAGAGAGTTGCGGAGGATGTGGCTGGCGGACTTACAATTGGAAATCAG                         GCTACAGGCAGCGTGAATCTTTGGGATCATGATTGGCAAAGAGCGGCCCGC
genomic: AGCAGAGAGTTGCGGAGGATGTGGCTGGCGGACTTACAATTGGAAATCAGgttattgggt ... ttatgtgaagGCTACAGGCAGCGTGAATCTTTGGGATCATGATTGGCAAAGAGCGGCCCGC
EST: gi|162250631|gb|FC428222.1|FC428222
EST:     AGCAGAGAGTTGCGGAGGATGTGGCTGGCGGACTTACAATTGGAAATCAG                         GCTACAGGCAGCGTGAATCTTTGGGATCATGATTGGCAAAGAGCGGCCCGC
genomic: AGCAGAGAGTTGCGGAGGATGTGGCTGGCGGACTTACAATTGGAAATCAGgttattgggt ... ttatgtgaagGCTACAGGCAGCGTGAATCTTTGGGATCATGATTGGCAAAGAGCGGCCCGC
EST: gi|208378723|gb|DC914697.1|DC914697
EST:     AGCAGAGAGTTGCGGAGGATGTGGCTGGCGGACTTACAATTGGAAATCAG                         GCTACAGGCAGCGTGAATCTTTGGGATCATGATTGGCAAAGAGCGGCCCGC
genomic: AGCAGAGAGTTGCGGAGGATGTGGCTGGCGGACTTACAATTGGAAATCAGgttattgggt ... ttatgtgaagGCTACAGGCAGCGTGAATCTTTGGGATCATGATTGGCAAAGAGCGGCCCGC
EST: gi|67695308|gb|BJ955541.1|BJ955541
EST:     AGCAGAGAGTTGCGGAGGATGTGGCTGGCGGACTTACAATTGGAAATCAG                         GCTACAGGCAGCGTGAATCTTTGGGATCATGATTGGCAAAGAGCGGCCCGC
genomic: AGCAGAGAGTTGCGGAGGATGTGGCTGGCGGACTTACAATTGGAAATCAGgttattgggt ... ttatgtgaagGCTACAGGCAGCGTGAATCTTTGGGATCATGATTGGCAAAGAGCGGCCCGC
EST: gi|208381786|gb|DC928449.1|DC928449
EST:     AGCAGAGAGTTGCGGAGGATGTGGCTGGCGGACTTACAATTGGAAATCAG                         GCTACAGGCAGCGTGAATCTTTGGGATCATGATTGGCAAAGAGCGGCCCGC
genomic: AGCAGAGAGTTGCGGAGGATGTGGCTGGCGGACTTACAATTGGAAATCAGgttattgggt ... ttatgtgaagGCTACAGGCAGCGTGAATCTTTGGGATCATGATTGGCAAAGAGCGGCCCGC
EST: gi|208394106|gb|DC957187.1|DC957187
EST:     AGCAGAGAGTTGCGGAGGATGTGGCTGGCGGACTTACAATTGGAAATCAG                         GCTACAGGCAGCGTGAATCTTTGGGATCATGATTGGCAAAGAGCGGCCCGC
genomic: AGCAGAGAGTTGCGGAGGATGTGGCTGGCGGACTTACAATTGGAAATCAGgttattgggt ... ttatgtgaagGCTACAGGCAGCGTGAATCTTTGGGATCATGATTGGCAAAGAGCGGCCCGC
EST: gi|162250632|gb|FC428223.1|FC428223
EST:     AGCAGAGAGTTGCGGAGGATGTGGCTGGCGGACTTACAATTGGAAATCAG                         GCTACAGGCAGCGTGAATCTTTGGGATCATGATTGGCAAAGAGCGGCCCGC
genomic: AGCAGAGAGTTGCGGAGGATGTGGCTGGCGGACTTACAATTGGAAATCAGgttattgggt ... ttatgtgaagGCTACAGGCAGCGTGAATCTTTGGGATCATGATTGGCAAAGAGCGGCCCGC
EST: gi|208365240|gb|DC931178.1|DC931178
EST:     AGCAGAGAGTTGCGGAGGATGTGGCTGGCGGACTTACAATTGGAAATCAG                         GCTACAGGCAGCGTGAATCTTTGGGATCATGATTGGCAAAGAGCGGCCCGC
genomic: AGCAGAGAGTTGCGGAGGATGTGGCTGGCGGACTTACAATTGGAAATCAGgttattgggt ... ttatgtgaagGCTACAGGCAGCGTGAATCTTTGGGATCATGATTGGCAAAGAGCGGCCCGC
EST: gi|208361882|gb|DC953932.1|DC953932
EST:     AGCAGAGAGTTGCGGAGGATGTGGCTGGCGGACTTACAATTGGAAATCAG                         GCTACAGGCAGCGTGAATCTTTGGGATCATGATTGGCAAAGAGCGGCCCGC
genomic: AGCAGAGAGTTGCGGAGGATGTGGCTGGCGGACTTACAATTGGAAATCAGgttattgggt ... ttatgtgaagGCTACAGGCAGCGTGAATCTTTGGGATCATGATTGGCAAAGAGCGGCCCGC
EST: gi|208377816|gb|DC940928.1|DC940928
EST:     AGCAGAGAGTTGCGGAGGATGTGGCTGGCGGACTTACAATTGGAAATCAG                         GCTACAGGCAGCGTGAATCTTTGGGATCATGATTGGCAAAGAGCGGCCCGC
genomic: AGCAGAGAGTTGCGGAGGATGTGGCTGGCGGACTTACAATTGGAAATCAGgttattgggt ... ttatgtgaagGCTACAGGCAGCGTGAATCTTTGGGATCATGATTGGCAAAGAGCGGCCCGC
EST: gi|67571942|gb|BJ944766.1|BJ944766
EST:     AGCAGAGAGTTGCGGAGGATGTGGCTGGCGGACTTACAATTGGAAATCAG                         GCTACAGGCAGCGTGAATCTTTGGGATCATGATTGGCAAAGAGCGGCCCGC
genomic: AGCAGAGAGTTGCGGAGGATGTGGCTGGCGGACTTACAATTGGAAATCAGgttattgggt ... ttatgtgaagGCTACAGGCAGCGTGAATCTTTGGGATCATGATTGGCAAAGAGCGGCCCGC
EST: gi|208365662|gb|DC935759.1|DC935759
EST:     AGCAGAGAGTTGCGGAGGATGTGGCTGGCGGACTTACAATTGGAAATCAG                         GCTACAGGCAGCGTGAATCTTTGGGATCATGATTGGCAAAGAGCGGCCCGC
genomic: AGCAGAGAGTTGCGGAGGATGTGGCTGGCGGACTTACAATTGGAAATCAGgttattgggt ... ttatgtgaagGCTACAGGCAGCGTGAATCTTTGGGATCATGATTGGCAAAGAGCGGCCCGC

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: 34 (upstream exon), 35 (downstream exon)
Score: 14

TATAGCGCAGCTCGTTGCTCGCTACAAGCGGCGCAAGGTGCTGGAGGAACAGCAGAGAGTTGCGGAGGATGTGGCTGGCGGACTTACAATTGGAAATCAGgttattgggt ... ttatgtgaagGCTACAGGCAGCGTGAATCTTTGGGATCATGATTGGCAAAGAGCGGCCCGCATGGCAAGTTATGGGTTTCTGATATATGGGCCATTATCACAGGTGTGGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cggtgtcttgttaccctatttattttcagaaacatgacatgtggtttatgtgaagGCTACAGGCAGCGTGAATCTTTGGGATCATGATTGGCAAAGAGCGGCCCGCATGGCAAGTTATGGGTTTCTGATATATGGGCCATTATCACAGGTGTGGT
                tatttattttcagaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attgacggcatttatactaatcatgcatgcttcaagtttttccgacggtgtcttgttaccctatttattttcagaaacatgacatgtggtttatgtgaagGCTACAGGCAGCGTGAATCTTTGGGATCATGATTGGCAAAGAGCGGCCCGCATGGCAAGTTATGGGTTTCTGATATATGGGCCATTATCACAGGTGTGGT

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