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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgttactatcaatcattttcatttctaagttacacatcaggcgatcatctaatttcaattccctattattaggagcacgtactacatctgattaatcatgccaatttttcgcaagtcttcacgatgttttcatgttgacacctttcctcactatttgtacacgtgggttccccagGAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAG

Basic information

species Physcomitrella patens
transcript PP1S61_17V6.2
intron # 3
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|208364085|gb|DC943397.1|DC943397
EST:     AGCAGCAGCTGCTCACGGCCTCGCGCTAGTTGCTATGGATACCTCCCCAC                         GAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAG
genomic: AGCAGCAGCTGCTCACGGCCTCGCGCTAGTTGCTATGGATACCTCCCCACgtacgttact ... ggttccccagGAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAG
EST: gi|18343395|gb|BJ175433.1|BJ175433
EST:     AGCAGCAGCTGCTCACGGCCTCGCGCTAGTTGCTATGGATACCTCCCCAC                         GAGGGNTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAG
genomic: AGCAGCAGCTGCTCACGGCCTCGCGCTAGTTGCTATGGATACCTCCCCACgtacgttact ... ggttccccagGAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAG
EST: gi|67719202|gb|BJ969461.1|BJ969461
EST:     AGCAGCAGCTGCTCACGGCCTCGCGCTAGTTGCTATGGATACCTCCCCAC                         GAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAG
genomic: AGCAGCAGCTGCTCACGGCCTCGCGCTAGTTGCTATGGATACCTCCCCACgtacgttact ... ggttccccagGAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAG
EST: gi|208381483|gb|DC919485.1|DC919485
EST:     AGCAGCAGCTGCTCACGGCCTCGCGNTAGTTGCTATGGATACCTCCCCAC                         GAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAG
genomic: AGCAGCAGCTGCTCACGGCCTCGCGCTAGTTGCTATGGATACCTCCCCACgtacgttact ... ggttccccagGAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAG
EST: gi|162192829|gb|FC370161.1|FC370161
EST:     AGCAGCAGCTGCTCACGGCCTCGCGCTAGTTGCTATGGATACCTCCCCAC                         GAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAG
genomic: AGCAGCAGCTGCTCACGGCCTCGCGCTAGTTGCTATGGATACCTCCCCACgtacgttact ... ggttccccagGAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAG
EST: gi|67727505|gb|BJ977764.1|BJ977764
EST:     TGGATACCTCCCCAC                         GAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAG
genomic: TGGATACCTCCCCACgtacgttact ... ggttccccagGAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAG
EST: gi|208350927|gb|DC910474.1|DC910474
EST:     AGCAGCAGCTGCTCACGGCCTCGCGCTAGTTGCTATGGATACCTCCCCAC                         GANGGCTGAATGTGGAAGGGGAGTCNGATAGCTGGGATT-CGGCACAG
genomic: AGCAGCAGCTGCTCACGGCCTCGCGCTAGTTGCTATGGATACCTCCCCACgtacgttact ... ggttccccagGAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAG
EST: gi|208348165|gb|DC920956.1|DC920956
EST:     AGCAGCAGCTGCTCACGGCCTCGCGCTAGTTGCTATGGATACCTCCCCAC                         GAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAG
genomic: AGCAGCAGCTGCTCACGGCCTCGCGCTAGTTGCTATGGATACCTCCCCACgtacgttact ... ggttccccagGAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAG
EST: gi|100394127|gb|BY971952.1|BY971952
EST:     AGCAGCAGCTGCTCACGGCCTCGCGCTAGTTGCTATGGATACCTCCCCAC                         GAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAG
genomic: AGCAGCAGCTGCTCACGGCCTCGCGCTAGTTGCTATGGATACCTCCCCACgtacgttact ... ggttccccagGAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAG
EST: gi|208396633|gb|DC924301.1|DC924301
EST:     AGCAGCAGNTGCTCACGGCCTCGCGNTAGGTGNTATGGATACCTCCCCAC                         GAGGGCTGAATGTGGNAGGGGAGTCGGATAGCTGGGATTTCGGCACAG
genomic: AGCAGCAGCTGCTCACGGCCTCGCGCTAGTTGCTATGGATACCTCCCCACgtacgttact ... ggttccccagGAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAG
EST: gi|100421061|gb|BY993592.1|BY993592
EST:     AGCAGCAGCTGCTCACGGCCTCGCGCTAGTTGCTATGGATACCTCCCCAC                         GAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAG
genomic: AGCAGCAGCTGCTCACGGCCTCGCGCTAGTTGCTATGGATACCTCCCCACgtacgttact ... ggttccccagGAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAG
EST: gi|100383603|gb|BY950387.1|BY950387
EST:     AGCAGCAGCTGCTCACGGCCTCGCGCTAGTTGCTATGGATACCTCCCCAC                         GAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAG
genomic: AGCAGCAGCTGCTCACGGCCTCGCGCTAGTTGCTATGGATACCTCCCCACgtacgttact ... ggttccccagGAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAG
EST: gi|208345645|gb|DC905603.1|DC905603
EST:     AGCAGCAGCTGCTCACGGCCTCGCGCTAGTTGCTATGGATACCTCCCCAC                         GAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAG
genomic: AGCAGCAGCTGCTCACGGCCTCGCGCTAGTTGCTATGGATACCTCCCCACgtacgttact ... ggttccccagGAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAG
EST: gi|162267025|gb|FC443074.1|FC443074
EST:     AGCAGCAGCTGCTCACGGCCTCGCGCTAGTTGCTATGGATACCTCCCCAC                         GAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAG
genomic: AGCAGCAGCTGCTCACGGCCTCGCGCTAGTTGCTATGGATACCTCCCCACgtacgttact ... ggttccccagGAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAG
EST: gi|162267024|gb|FC443073.1|FC443073
EST:     CTAGTTGCTATGGATACCTCCCCAC                         GAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAG
genomic: CTAGTTGCTATGGATACCTCCCCACgtacgttact ... ggttccccagGAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAG
EST: gi|67694518|gb|BJ954751.1|BJ954751
EST:     AGCAGCAGCTGCTCACGGCCTCGCGCTAGTTGCTATGGATACCTCCCCAC                         GAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAG
genomic: AGCAGCAGCTGCTCACGGCCTCGCGCTAGTTGCTATGGATACCTCCCCACgtacgttact ... ggttccccagGAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAG
EST: gi|208384596|gb|DC907083.1|DC907083
EST:     AGCAGCAGCTGCTCACGGCCTCGCGCTAGTTGCTATGGATACCTCCCCAC                         GAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAG
genomic: AGCAGCAGCTGCTCACGGCCTCGCGCTAGTTGCTATGGATACCTCCCCACgtacgttact ... ggttccccagGAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAG
EST: gi|208344728|gb|DC905177.1|DC905177
EST:     AGCAGCAGCTGCTCACGGCCTCGCGCTAGTTGCTATGGATACCTCCCCAC                         GAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAG
genomic: AGCAGCAGCTGCTCACGGCCTCGCGCTAGTTGCTATGGATACCTCCCCACgtacgttact ... ggttccccagGAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAG
EST: gi|208371948|gb|DC948351.1|DC948351
EST:     AGCAGCAGCTGCTCACGGCCTCGCGNTAGTTGCTATGGATACCTCCCCAC                         GAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAG
genomic: AGCAGCAGCTGCTCACGGCCTCGCGCTAGTTGCTATGGATACCTCCCCACgtacgttact ... ggttccccagGAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAG

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: 31 (upstream exon), 35 (downstream exon)
Score: 16

GGGTTGACGTGCAACGACGAAAACTTCATCCAAAAATCTGGTGCACAACGAGCAGCAGCTGCTCACGGCCTCGCGCTAGTTGCTATGGATACCTCCCCACgtacgttact ... ggttccccagGAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acgatgttttcatgttgacacctttcctcactatttgtacacgtgggttccccagGAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAG
                        tcctcac  putative branch site (score: 16)
                                               ttcccc  putative PPT
                               tatttgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgttactatcaatcattttcatttctaagttacacatcaggcgatcatctaatttcaattccctattattaggagcacgtactacatctgattaatcatgccaatttttcgcaagtcttcacgatgttttcatgttgacacctttcctcactatttgtacacgtgggttccccagGAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG