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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaggaagagatgaagggatttcatgtaaactaagttaggtccatcacatagcttacaggtgtactaatcaaattcttcgttacctacgctggaatctcagATTGTGCCAGGATATGACTGTGCTGGAGTGGTGGTGAAATTGGGCGATCAAGCCTCCAAGTTCGAAGTGGACGACGAGGTGTATGGCATGACTTCTGAAA

Basic information

species Physcomitrella patens
transcript PP1S47_72V6.1
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|18362096|gb|BJ194163.1|BJ194163
EST:     ACAACAAGCGCCGAACTGGCTACCTTGGGGATAAGGATTCTCCACTTCCG                         ATTGTGCCAGGATATGACTGTGCTGGAGTGGTGGTGAAATTGGGCGATCAA
genomic: ACAACAAGCGCCGAACTGGCTACCTTGGGGATAAGGATTCTCCACTTCCGgtattacgcg ... ggaatctcagATTGTGCCAGGATATGACTGTGCTGGAGTGGTGGTGAAATTGGGCGATCAA
EST: gi|18355778|gb|BJ187837.1|BJ187837
EST:     ACAACAAGCGCCGAACTGGCTACCTTGGGGATAAGGATTCTCCACTTCCG                         ATTGTGCCAGGATATGACTGTGCTGGAGTGGTGGTGAAATTGGGCGATCAA
genomic: ACAACAAGCGCCGAACTGGCTACCTTGGGGATAAGGATTCTCCACTTCCGgtattacgcg ... ggaatctcagATTGTGCCAGGATATGACTGTGCTGGAGTGGTGGTGAAATTGGGCGATCAA
EST: gi|100417052|gb|BY993220.1|BY993220
EST:     ACAACAAGCGCCGAACTGGCTACCTTGGGGATAAGGATTCTCCACTTCCG                         ATTGTGCCAGGATATGACTGTGCTGGAGTGGTGGTGAAATTGGGCGATCAA
genomic: ACAACAAGCGCCGAACTGGCTACCTTGGGGATAAGGATTCTCCACTTCCGgtattacgcg ... ggaatctcagATTGTGCCAGGATATGACTGTGCTGGAGTGGTGGTGAAATTGGGCGATCAA
EST: gi|100364422|gb|BY984605.1|BY984605
EST:     ACAACAAGCGCCGAACTGGCTACCTTGGGGATAAGGATTCTCCACTTCCG                         ATTGTGCCAGGATATGACTGTGCTGGAGTGGTGGTGAAATTGGGCGATCAA
genomic: ACAACAAGCGCCGAACTGGCTACCTTGGGGATAAGGATTCTCCACTTCCGgtattacgcg ... ggaatctcagATTGTGCCAGGATATGACTGTGCTGGAGTGGTGGTGAAATTGGGCGATCAA
EST: gi|18358548|gb|BJ190607.1|BJ190607
EST:     ACAACAAGCGCCGAACTGGCTACCTTGGGGATAAGGATTCTCCACTTCCG                         ATTGTGCCAGGATATGACTGTGCTGGAGTGGTGGTGAAATTGGGCGATCAA
genomic: ACAACAAGCGCCGAACTGGCTACCTTGGGGATAAGGATTCTCCACTTCCGgtattacgcg ... ggaatctcagATTGTGCCAGGATATGACTGTGCTGGAGTGGTGGTGAAATTGGGCGATCAA
EST: gi|18327978|gb|BJ159982.1|BJ159982
EST:     ACAACAAGCGCCGAACTGGCTACCTTGGGGATAAGGATTCTCCACTTCCG                         ATTGTGCCAGGATATGACTGTGCTGGAGTGGTGGTGAAATTGGGCGATCAA
genomic: ACAACAAGCGCCGAACTGGCTACCTTGGGGATAAGGATTCTCCACTTCCGgtattacgcg ... ggaatctcagATTGTGCCAGGATATGACTGTGCTGGAGTGGTGGTGAAATTGGGCGATCAA
EST: gi|18342862|gb|BJ174898.1|BJ174898
EST:     ACAACAAGCGCCGAACTGGCTACCTTGGGGATAAGGATTCTCCACTTCCG                         ATTGTGCCAGGATATGACTGTGCTGGAGTGGTGGTGAAATTGGGCGATCAA
genomic: ACAACAAGCGCCGAACTGGCTACCTTGGGGATAAGGATTCTCCACTTCCGgtattacgcg ... ggaatctcagATTGTGCCAGGATATGACTGTGCTGGAGTGGTGGTGAAATTGGGCGATCAA
EST: gi|67573682|gb|BJ946506.1|BJ946506
EST:     ACAACAAGCGCCGAACTGGCTACCTTGGGGATAAGGATTCTCCACTTCCG                         ATTGTGCCAGGATATGACTGTGCTGGAGTGGTGGTGAAATTGGGCGATCAA
genomic: ACAACAAGCGCCGAACTGGCTACCTTGGGGATAAGGATTCTCCACTTCCGgtattacgcg ... ggaatctcagATTGTGCCAGGATATGACTGTGCTGGAGTGGTGGTGAAATTGGGCGATCAA
EST: gi|100364095|gb|BY966712.1|BY966712
EST:     ACAACAAGCGCCGAACTGGCTACCTTGGGGATAAGGATTCTCCACTTCCG                         ATTGTGCCAGGATATGACTGTGCTGGAGTGGTGGTGAAATTGGGCGATCAA
genomic: ACAACAAGCGCCGAACTGGCTACCTTGGGGATAAGGATTCTCCACTTCCGgtattacgcg ... ggaatctcagATTGTGCCAGGATATGACTGTGCTGGAGTGGTGGTGAAATTGGGCGATCAA
EST: gi|18361870|gb|BJ193937.1|BJ193937
EST:     ACAACAAGCGCCGAACTGGCTACCTTGGGGATAAGGATTCTCCACTTCCG                         ATTGTGCCAGGATATGACTGTGCTGGAGTGGTGGTGAAATTGGGCGATCAA
genomic: ACAACAAGCGCCGAACTGGCTACCTTGGGGATAAGGATTCTCCACTTCCGgtattacgcg ... ggaatctcagATTGTGCCAGGATATGACTGTGCTGGAGTGGTGGTGAAATTGGGCGATCAA
EST: gi|100373826|gb|BY967820.1|BY967820
EST:     ACAACAAGCGCCGAACTGGCTACCTTGGGGATAAGGATTCTCCACTTCCG                         ATTGTGCCAGGATATGACTGTGCTGGAGTGGTGGTGAAATTGGGCGATCAA
genomic: ACAACAAGCGCCGAACTGGCTACCTTGGGGATAAGGATTCTCCACTTCCGgtattacgcg ... ggaatctcagATTGTGCCAGGATATGACTGTGCTGGAGTGGTGGTGAAATTGGGCGATCAA
EST: gi|18353649|gb|BJ185704.1|BJ185704
EST:     ACAACAAGCGCCGAACTGGCTACCTTGGGGATAAGGATTCTCCACTTCCG                         ATTGTGCCAGGATATGACTGTGCTGGAGTGGTGGTGAAATTGGGCGATCA
genomic: ACAACAAGCGCCGAACTGGCTACCTTGGGGATAAGGATTCTCCACTTCCGgtattacgcg ... ggaatctcagATTGTGCCAGGATATGACTGTGCTGGAGTGGTGGTGAAATTGGGCGATCA
EST: gi|162196625|gb|FC374915.1|FC374915
EST:     ACAACAAGCGCCGAACTGGCTACCTTGGGGATAAGGATTCTCCACTTCCG                         ATTGTGCCAGGATATGACTGTGCTGGAGTGGTGGTGAAATTGGGCGATCAA
genomic: ACAACAAGCGCCGAACTGGCTACCTTGGGGATAAGGATTCTCCACTTCCGgtattacgcg ... ggaatctcagATTGTGCCAGGATATGACTGTGCTGGAGTGGTGGTGAAATTGGGCGATCAA
EST: gi|67507802|gb|BJ940679.1|BJ940679
EST:     ACAACAAGCGCCGAACTGGCTACCTTGGGGATAAGGATTCTCCACTTCCG                         ATTGTGCCAGGATATGACTGTGCTGGAGTGGTGGTGAAATTGGGCGATCAA
genomic: ACAACAAGCGCCGAACTGGCTACCTTGGGGATAAGGATTCTCCACTTCCGgtattacgcg ... ggaatctcagATTGTGCCAGGATATGACTGTGCTGGAGTGGTGGTGAAATTGGGCGATCAA
EST: gi|100404502|gb|BY973610.1|BY973610
EST:     ACAACAAGCGCCGAACTGGCTACCTTGGGGATAAGGATTCTCCACTTCCG                         ATTGTGCCAGGATATGACTGTGCTGGAGTGGGGGTGAAATTGGGCGATCAA
genomic: ACAACAAGCGCCGAACTGGCTACCTTGGGGATAAGGATTCTCCACTTCCGgtattacgcg ... ggaatctcagATTGTGCCAGGATATGACTGTGCTGGAGTGGTGGTGAAATTGGGCGATCAA
EST: gi|100385061|gb|BY987524.1|BY987524
EST:     ACAACAAGCGCCGAACTGGCTACCTTGGGGATAAGGATTCTCCACTTCCG                         ATTGTGCCAGGATATGACTGTGCTGGAGTGGTGGTGAAATTGGGCGATCAA
genomic: ACAACAAGCGCCGAACTGGCTACCTTGGGGATAAGGATTCTCCACTTCCGgtattacgcg ... ggaatctcagATTGTGCCAGGATATGACTGTGCTGGAGTGGTGGTGAAATTGGGCGATCAA
EST: gi|18366065|gb|BJ198143.1|BJ198143
EST:     ACAACAAGCGCCGAACTGGCTACCTTGGGGATAAGGATTCTCCACTTCCG                         ATTGTGCCAGGATATGACTGTGCTGGAGTGGTGGTGAAATTGGGCGATCAA
genomic: ACAACAAGCGCCGAACTGGCTACCTTGGGGATAAGGATTCTCCACTTCCGgtattacgcg ... ggaatctcagATTGTGCCAGGATATGACTGTGCTGGAGTGGTGGTGAAATTGGGCGATCAA
EST: gi|100439739|gb|BY962083.1|BY962083
EST:     ACAACAAGCGCCGAACTGGCTACCTTGGGGATAAGGATTCTCCACTTCCG                         ATTGTGCCAGGATATGACTGTGCTGGAGTGGTGGTGAAATTGGGCGATCAA
genomic: ACAACAAGCGCCGAACTGGCTACCTTGGGGATAAGGATTCTCCACTTCCGgtattacgcg ... ggaatctcagATTGTGCCAGGATATGACTGTGCTGGAGTGGTGGTGAAATTGGGCGATCAA
EST: gi|18349768|gb|BJ181818.1|BJ181818
EST:     ACAACAAGCGCCGAACTGGCTACCTTGGGGATAAGGATTCTCCACTTCCG                         ATTGTGCCANGATATGACTGTGCTGGAGTGGTGGTGAAATTGGGCGATCAA
genomic: ACAACAAGCGCCGAACTGGCTACCTTGGGGATAAGGATTCTCCACTTCCGgtattacgcg ... ggaatctcagATTGTGCCAGGATATGACTGTGCTGGAGTGGTGGTGAAATTGGGCGATCAA
EST: gi|18360612|gb|BJ192675.1|BJ192675
EST:     ACAACAAGCGCCGAACTGGCTACCTTGGGGATAAGGATTCTCCACTTCCG                         ATTGTGCCAGGATATGACTGTGCTGGAGTGGTGGTGAAATTGGGCGATCAA
genomic: ACAACAAGCGCCGAACTGGCTACCTTGGGGATAAGGATTCTCCACTTCCGgtattacgcg ... ggaatctcagATTGTGCCAGGATATGACTGTGCTGGAGTGGTGGTGAAATTGGGCGATCAA
EST: gi|18374854|gb|BJ206432.1|BJ206432
EST:     ACAACAAGCGCCGAACTGGCTACCTTGGGGATAAGGATTCTCCACTTCCG                         ATTGTGCCAGGATATGACTGTGCTGGAGTGGTGGTGAAATTGGGCGATCAA
genomic: ACAACAAGCGCCGAACTGGCTACCTTGGGGATAAGGATTCTCCACTTCCGgtattacgcg ... ggaatctcagATTGTGCCAGGATATGACTGTGCTGGAGTGGTGGTGAAATTGGGCGATCAA
EST: gi|18359391|gb|BJ191452.1|BJ191452
EST:     ACAACAAGCGCCGAACTGGCTACCTTGGGGATAAGGATTCTCCACTTCCG                         ATTGTGCCAGGATATGACTGTGCTGGAGTGGTGGTGAAATTGGGCGATCAA
genomic: ACAACAAGCGCCGAACTGGCTACCTTGGGGATAAGGATTCTCCACTTCCGgtattacgcg ... ggaatctcagATTGTGCCAGGATATGACTGTGCTGGAGTGGTGGTGAAATTGGGCGATCAA

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: 30 (upstream exon), 34 (downstream exon)
Score: 13

GCCAAATCAGGTCCTTATCAAGGTGAAGGCTGCGGCCATCAACCCTGTCGACAACAAGCGCCGAACTGGCTACCTTGGGGATAAGGATTCTCCACTTCCGgtattacgcg ... ggaatctcagATTGTGCCAGGATATGACTGTGCTGGAGTGGTGGTGAAATTGGGCGATCAAGCCTCCAAGTTCGAAGTGGACGACGAGGTGTATGGCATGACTTCTGAAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatagcttacaggtgtactaatcaaattcttcgttacctacgctggaatctcagATTGTGCCAGGATATGACTGTGCTGGAGTGGTGGTGAAATTGGGCGATCAAGCCTCCAAGTTCGAAGTGGACGACGAGGTGTATGGCATGACTTCTGAAA
                tactaat  putative branch site (score: 13)
                   taatcaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaggaagagatgaagggatttcatgtaaactaagttaggtccatcacatagcttacaggtgtactaatcaaattcttcgttacctacgctggaatctcagATTGTGCCAGGATATGACTGTGCTGGAGTGGTGGTGAAATTGGGCGATCAAGCCTCCAAGTTCGAAGTGGACGACGAGGTGTATGGCATGACTTCTGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA