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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatctgtaaagttaagatgtatacattgatgctgctagtggatgagtagtgaatggatggttatcgtggttgctaatgctttccattacacatttttcagGTACTTACCTGAGGAAATGAGGAACCCAACCACCTTTAAAT

Basic information

species Physcomitrella patens
transcript PP1S110_13V6.1
intron # 8
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|37835216|gb|BJ593228.1|BJ593228
EST:     TTCAAAAGATGGTTTATCC                         GTACTTACCTGAGGAAATGAGGAACCCAACCACCTTTAAAT
genomic: TTCAAAAGATGGTTTATCCgtatggctat ... catttttcagGTACTTACCTGAGGAAATGAGGAACCCAACCACCTTTAAAT
EST: gi|37850772|gb|BJ608780.1|BJ608780
EST:     CAGTTGGAGAAGATGATGGAGGACCCAACAGTTCAAAAGATGGTTTATCC                         GTACTTACCTGAGGAAATGAGGAACCCAACCACCNTTTAAAT
genomic: CAGTTGGAGAAGATGATGGAGGACCCAACAGTTCAAAAGATGGTTTATCCgtatggctat ... catttttcagGTACTTACCTGAGGAAATGAGGAACCCAACCACC-TTTAAAT
EST: gi|162179084|gb|FC356485.1|FC356485
EST:     CAGTTGGAGAAGATGATGGAGGACCCAACAGTTCAAAAGATGGTTTATCC                         GTACTTACCTGAGGAAATGAGGAACCCAACCACCTTTAAAT
genomic: CAGTTGGAGAAGATGATGGAGGACCCAACAGTTCAAAAGATGGTTTATCCgtatggctat ... catttttcagGTACTTACCTGAGGAAATGAGGAACCCAACCACCTTTAAAT
EST: gi|162179083|gb|FC356484.1|FC356484
EST:     CAGTTGGAGAAGATGATGGAGGACCCAACAGTTCAAAAGATGGTTTATCC                         GTACTTACCTGAGGAAATGAGGAACCCAACCACCTTTAAAT
genomic: CAGTTGGAGAAGATGATGGAGGACCCAACAGTTCAAAAGATGGTTTATCCgtatggctat ... catttttcagGTACTTACCTGAGGAAATGAGGAACCCAACCACCTTTAAAT
EST: gi|37824986|gb|BJ583052.1|BJ583052
EST:     CAGTTGGAGAAGATGATGGAGGACCCAACAGTTCAAAAGATGGTTTATCC                         GTACTTACCTGAGGAAATGAGGAACCCAACCNCCNTTTAAAT
genomic: CAGTTGGAGAAGATGATGGAGGACCCAACAGTTCAAAAGATGGTTTATCCgtatggctat ... catttttcagGTACTTACCTGAGGAAATGAGGAACCCAACCACC-TTTAAAT
EST: gi|208395403|gb|DC924471.1|DC924471
EST:     CAG-TGGAGAAGATGATGGAGGACCCAACAGTTCAAAAGATGGTTTATCC                         GTACTTACCTGAGGAAATGAGGAACCCAACCACCTTTAAAT
genomic: CAGTTGGAGAAGATGATGGAGGACCCAACAGTTCAAAAGATGGTTTATCCgtatggctat ... catttttcagGTACTTACCTGAGGAAATGAGGAACCCAACCACCTTTAAAT
EST: gi|162176402|gb|FC353587.1|FC353587
EST:     CAGTTGGAGAAGATGATGGAGGACCCAACAGTTCAAAAGATGGTTTATCC                         GTACTTACNTGAGGAAATGAGGAACCCAACCACCTTTAAAT
genomic: CAGTTGGAGAAGATGATGGAGGACCCAACAGTTCAAAAGATGGTTTATCCgtatggctat ... catttttcagGTACTTACCTGAGGAAATGAGGAACCCAACCACCTTTAAAT
EST: gi|162166027|gb|FC340423.1|FC340423
EST:     CAGTTGGAGAAGATGATGGAGGACCCAACAGTTCAAAAGATGTTTTATCC                         GTACTTACCTGAGGAAATGAGGAACCCAACCACCTTTAAAT
genomic: CAGTTGGAGAAGATGATGGAGGACCCAACAGTTCAAAAGATGGTTTATCCgtatggctat ... catttttcagGTACTTACCTGAGGAAATGAGGAACCCAACCACCTTTAAAT
EST: gi|37836231|gb|BJ594239.1|BJ594239
EST:     CAGTTGGAGAAGATGATGGAGGACCCANCAGTTCAAAAGATGGTTTATCC                         GTACTTACCTGAGGAAATGAGGAACCCAACCACCNTTTAAAT
genomic: CAGTTGGAGAAGATGATGGAGGACCCAACAGTTCAAAAGATGGTTTATCCgtatggctat ... catttttcagGTACTTACCTGAGGAAATGAGGAACCCAACCACC-TTTAAAT
EST: gi|208349470|gb|DC921944.1|DC921944
EST:     CAGTTCAAAAGATGGTTTATCC                         GTACTTACCTGAGGAAATGANGAACCCANCCACCTTTAAAT
genomic: CAGTTCAAAAGATGGTTTATCCgtatggctat ... catttttcagGTACTTACCTGAGGAAATGAGGAACCCAACCACCTTTAAAT
EST: gi|162169704|gb|FC345241.1|FC345241
EST:     CAGTTGGAGAAGATGATGGAGGACCCAACAGTTCAAAAGATGGTTTATCC                         GTACTTACCTGAGGAAATGAGGAACCCAACCACCTTTAAAT
genomic: CAGTTGGAGAAGATGATGGAGGACCCAACAGTTCAAAAGATGGTTTATCCgtatggctat ... catttttcagGTACTTACCTGAGGAAATGAGGAACCCAACCACCTTTAAAT
EST: gi|162183778|gb|FC360695.1|FC360695
EST:     CAGTTGGAGAAGATGATGGAGGACCCAACAGTTCAAAAGATGGTTTATCC                         GTACTTACCTGAGGAAATGAGGAACCCAACCACCTTTAAAT
genomic: CAGTTGGAGAAGATGATGGAGGACCCAACAGTTCAAAAGATGGTTTATCCgtatggctat ... catttttcagGTACTTACCTGAGGAAATGAGGAACCCAACCACCTTTAAAT
EST: gi|162244160|gb|FC419811.1|FC419811
EST:     CAGTTGGAGAAGATGATGGAGGACCCAACAGTTCAAAAGATGGTTTATCC                         GTACTTACCTGAGGAAATGAGGAACCCAACCACCTTTAAAT
genomic: CAGTTGGAGAAGATGATGGAGGACCCAACAGTTCAAAAGATGGTTTATCCgtatggctat ... catttttcagGTACTTACCTGAGGAAATGAGGAACCCAACCACCTTTAAAT
EST: gi|208396401|gb|DC920067.1|DC920067
EST:     CAGTTGGAGAAGATGATGGAGGACCCAACAGTTCAAAAGATGGTTTATCC                         GTACTTACCTGAGGAAATGAGGAACCCAACCACCTTTAAAT
genomic: CAGTTGGAGAAGATGATGGAGGACCCAACAGTTCAAAAGATGGTTTATCCgtatggctat ... catttttcagGTACTTACCTGAGGAAATGAGGAACCCAACCACCTTTAAAT

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: 22

CATGGGATTCTGCGGGAAAAGCAAAGCAGACTGTTTTTAGTGTGGAGCAGTTGGAGAAGATGATGGAGGACCCAACAGTTCAAAAGATGGTTTATCCgtatggctat ... catttttcagGTACTTACCTGAGGAAATGAGGAACCCAACCACCTTTAAAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtagtgaatggatggttatcgtggttgctaatgctttccattacacatttttcagGTACTTACCTGAGGAAATGAGGAACCCAACCACCTTTAAAT
                         tgctaat  putative branch site (score: 22)
                                             catttttc  putative PPT
                                            acattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatctgtaaagttaagatgtatacattgatgctgctagtggatgagtagtgaatggatggttatcgtggttgctaatgctttccattacacatttttcagGTACTTACCTGAGGAAATGAGGAACCCAACCACCTTTAAAT

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