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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtcgtgtagtcatgtccaagtttaaacggttcacatgtgagcagatctctatcttgtagaattcgcttaatctgtagcttaaattgtgatttttaacagGACGAAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAGACATATGAAGATGAAAATGTCACTGATGATGAGTCGGATATTGACCTAG

Basic information

species Physcomitrella patens
transcript PP1S9_386V6.1
intron # 2
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|162275962|gb|FC452030.1|FC452030
EST:     GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACG                         GACGAAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAG
genomic: GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACGgtatacgttg ... tttttaacagGACGAAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAG
EST: gi|18358114|gb|BJ190173.1|BJ190173
EST:     GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACG                         GACGAAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAG
genomic: GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACGgtatacgttg ... tttttaacagGACGAAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAG
EST: gi|67702514|gb|BJ962747.1|BJ962747
EST:     GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACG                         GACGAAGCANAGAGCGATGATGACAT
genomic: GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACGgtatacgttg ... tttttaacagGACGAAGCAGAGAGCGATGATGACAT
EST: gi|100399659|gb|BY972829.1|BY972829
EST:     GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACG                         GACGAAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAG
genomic: GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACGgtatacgttg ... tttttaacagGACGAAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAG
EST: gi|100427615|gb|BY977586.1|BY977586
EST:     GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACG                         GACGAAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAG
genomic: GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACGgtatacgttg ... tttttaacagGACGAAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAG
EST: gi|22492231|gb|BU052154.1|BU052154
EST:     GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACG                         GACGAAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAG
genomic: GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACGgtatacgttg ... tttttaacagGACGAAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAG
EST: gi|208347568|gb|DC912827.1|DC912827
EST:     GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACG                         GACGAAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAG
genomic: GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACGgtatacgttg ... tttttaacagGACGAAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAG
EST: gi|100417743|gb|BY975631.1|BY975631
EST:     GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACG                         GACGAAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAG
genomic: GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACGgtatacgttg ... tttttaacagGACGAAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAG
EST: gi|67717655|gb|BJ967914.1|BJ967914
EST:     GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACG                         GACGAAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAG
genomic: GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACGgtatacgttg ... tttttaacagGACGAAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAG
EST: gi|100416732|gb|BY993060.1|BY993060
EST:     GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACG                         GACGAAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAG
genomic: GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACGgtatacgttg ... tttttaacagGACGAAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAG
EST: gi|18348196|gb|BJ180243.1|BJ180243
EST:     GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACG                         GACGAAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAG
genomic: GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACGgtatacgttg ... tttttaacagGACGAAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAG
EST: gi|100446593|gb|CJ970892.1|CJ970892
EST:     GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACG                         GACGAAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAG
genomic: GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACGgtatacgttg ... tttttaacagGACGAAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAG
EST: gi|162164761|gb|FC340483.1|FC340483
EST:     GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACG                         GACGGAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAG
genomic: GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACGgtatacgttg ... tttttaacagGACGAAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAG
EST: gi|208373792|gb|DC936577.1|DC936577
EST:     GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACG                         GACGAAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCCAAG
genomic: GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACGgtatacgttg ... tttttaacagGACGAAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAG
EST: gi|208349326|gb|DC910385.1|DC910385
EST:     GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACG                         GACGAAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAG
genomic: GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACGgtatacgttg ... tttttaacagGACGAAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAG
EST: gi|67704132|gb|BJ964365.1|BJ964365
EST:     GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACG                         GACGAAGCANAGAGCGATGATGACAT
genomic: GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACGgtatacgttg ... tttttaacagGACGAAGCAGAGAGCGATGATGACAT
EST: gi|208344626|gb|DC912572.1|DC912572
EST:     GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACG                         GACGAAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAG
genomic: GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACGgtatacgttg ... tttttaacagGACGAAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAG
EST: gi|67719577|gb|BJ969836.1|BJ969836
EST:     GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACG                         GACGAAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAG
genomic: GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACGgtatacgttg ... tttttaacagGACGAAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAG
EST: gi|67717904|gb|BJ968163.1|BJ968163
EST:     GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACG                         GACGAAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAG
genomic: GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACGgtatacgttg ... tttttaacagGACGAAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAG
EST: gi|67702495|gb|BJ962728.1|BJ962728
EST:     GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACG                         GACGAAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAG
genomic: GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACGgtatacgttg ... tttttaacagGACGAAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAG
EST: gi|100393447|gb|BY953403.1|BY953403
EST:     GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACG                         GACGAAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAG
genomic: GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACGgtatacgttg ... tttttaacagGACGAAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAG
EST: gi|18353366|gb|BJ185421.1|BJ185421
EST:     GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACG                         GACGAAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAG
genomic: GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACGgtatacgttg ... tttttaacagGACGAAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAG
EST: gi|162249194|gb|FC421537.1|FC421537
EST:     GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACG                         GACGGAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAG
genomic: GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACGgtatacgttg ... tttttaacagGACGAAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAG
EST: gi|208358732|gb|DC942926.1|DC942926
EST:     GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACG                         GACGAAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAG
genomic: GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACGgtatacgttg ... tttttaacagGACGAAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAG
EST: gi|100401417|gb|BY990992.1|BY990992
EST:     GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACG                         GACGAAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAG
genomic: GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACGgtatacgttg ... tttttaacagGACGAAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAG
EST: gi|162150303|gb|FC326388.1|FC326388
EST:     GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACG                         GACGGAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAG
genomic: GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACGgtatacgttg ... tttttaacagGACGAAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAG
EST: gi|208368260|gb|DC935643.1|DC935643
EST:     GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACG                         GACGAAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAG
genomic: GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACGgtatacgttg ... tttttaacagGACGAAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAG
EST: gi|18362966|gb|BJ195038.1|BJ195038
EST:     GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACG                         GACGAAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAG
genomic: GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACGgtatacgttg ... tttttaacagGACGAAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAG
EST: gi|18352940|gb|BJ184995.1|BJ184995
EST:     GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACG                         GACGAAGCAGAGAGCGATGATGACAT
genomic: GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACGgtatacgttg ... tttttaacagGACGAAGCAGAGAGCGATGATGACAT
EST: gi|67704727|gb|BJ964960.1|BJ964960
EST:     GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACG                         GACGAAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAG
genomic: GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACGgtatacgttg ... tttttaacagGACGAAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAG
EST: gi|100428929|gb|BY959504.1|BY959504
EST:     GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACG                         GACGAAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAG
genomic: GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACGgtatacgttg ... tttttaacagGACGAAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAG
EST: gi|18359430|gb|BJ191491.1|BJ191491
EST:     GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACG                         GACGAAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAG
genomic: GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACGgtatacgttg ... tttttaacagGACGAAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAG
EST: gi|67719148|gb|BJ969407.1|BJ969407
EST:     GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACG                         GACGAAGCANAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAG
genomic: GCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACGgtatacgttg ... tttttaacagGACGAAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAG

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: 28 (upstream exon), 34 (downstream exon)
Score: 18

GACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGCCGGTGGTTGCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGTCCTGCAACGgtatacgttg ... tttttaacagGACGAAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAGACATATGAAGATGAAAATGTCACTGATGATGAGTCGGATATTGACCTAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctctatcttgtagaattcgcttaatctgtagcttaaattgtgatttttaacagGACGAAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAGACATATGAAGATGAAAATGTCACTGATGATGAGTCGGATATTGACCTAG
                    gcttaat  putative branch site (score: 18)
                                             ttttt  putative PPT
                                  ttaaattgtgattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtcgtgtagtcatgtccaagtttaaacggttcacatgtgagcagatctctatcttgtagaattcgcttaatctgtagcttaaattgtgatttttaacagGACGAAGCAGAGAGCGATGATGACATGGAGGAGAAATCTATGCCACCTAAGACATATGAAGATGAAAATGTCACTGATGATGAGTCGGATATTGACCTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG