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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgatggtcgaacttcaaattattacctgaagtgtggcacccaggcatttctatcctgatgaattttggttccggctaaaatttggttgtgcgcttgcagCCATCAACGAATTGGTGGCATGCTTCGGGGAGCTCCTGATTGATTTTGTGCCCACGGTTGGCGGTCTATCGCTTGCTGATGCTCCAGCATTTAAGAAAGC

Basic information

species Physcomitrella patens
transcript PP1S127_105V6.1
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|100359641|gb|BY947079.1|BY947079
EST:     GATCCGGAAAGGTGCCACCTCGCCAAGGTCGAATCGCATTGTTGCCCAAG                         CCATCAACGAATTGGTGGCATGCTTCGGGGAGCTCCTGATTGATTTTGTGC
genomic: GATCCGGAAAGGTGCCACCTCGCCAAGGTCGAATCGCATTGTTGCCCAAGgtttgagttc ... gcgcttgcagCCATCAACGAATTGGTGGCATGCTTCGGGGAGCTCCTGATTGATTTTGTGC
EST: gi|100442745|gb|BY981570.1|BY981570
EST:     GATCCGGAGAGGTGCCACCTCGCCAAGGTCGAATCGCATTGTTGCCCAAG                         CCATCAACGAATTGGTGGCATGCTTCGGGGGAGCTCCTGATTGATTTTGTG
genomic: GATCCGGAAAGGTGCCACCTCGCCAAGGTCGAATCGCATTGTTGCCCAAGgtttgagttc ... gcgcttgcagCCATCAACGAATTGGTGGCATGCTTCGGGG-AGCTCCTGATTGATTTTGTG
EST: gi|100364307|gb|BY984547.1|BY984547
EST:     GATCCGGAAAGGTGCCACCTCGCCAAGGTCGAATCGCATTGTTGCCCAAG                         CCATCAACGAATTGGTGGCATGCTTCGGGGAGCTCCTGATTGATTTTGTGC
genomic: GATCCGGAAAGGTGCCACCTCGCCAAGGTCGAATCGCATTGTTGCCCAAGgtttgagttc ... gcgcttgcagCCATCAACGAATTGGTGGCATGCTTCGGGGAGCTCCTGATTGATTTTGTGC
EST: gi|67508040|gb|BJ940913.1|BJ940913
EST:     GATCCGGAAAGGTGCCACCTCGCCAAGGTCGAATCGCATTGTTGCCCAAG                         CCATCAACGAATTGGTGGCATGCTTCGGGGAGCTCCTGATTGATTTTGTGC
genomic: GATCCGGAAAGGTGCCACCTCGCCAAGGTCGAATCGCATTGTTGCCCAAGgtttgagttc ... gcgcttgcagCCATCAACGAATTGGTGGCATGCTTCGGGGAGCTCCTGATTGATTTTGTGC
EST: gi|100368415|gb|BY966999.1|BY966999
EST:     GATCCGGAAAGGTGCCACCTCGCCAAGGTCGAATCGCATTGTTGCCCAAG                         CCATCAACGAATTGGTGGCATGCTTCGGGGAGCTCCTGATTGATTTTGTGC
genomic: GATCCGGAAAGGTGCCACCTCGCCAAGGTCGAATCGCATTGTTGCCCAAGgtttgagttc ... gcgcttgcagCCATCAACGAATTGGTGGCATGCTTCGGGGAGCTCCTGATTGATTTTGTGC
EST: gi|100404763|gb|BY991271.1|BY991271
EST:     GATCCGGAAAGGTGCCACCTCGCCAAGGTCGAATCGCATTGTTGCCCAAG                         CCATCAACGAATTGGTGGCATGCTTCGGGGAGCTCCTGATTGATTTTGTGC
genomic: GATCCGGAAAGGTGCCACCTCGCCAAGGTCGAATCGCATTGTTGCCCAAGgtttgagttc ... gcgcttgcagCCATCAACGAATTGGTGGCATGCTTCGGGGAGCTCCTGATTGATTTTGTGC
EST: gi|100381192|gb|BY950021.1|BY950021
EST:     GATCCGGAAAGGTGCCACCTCGCCAAGGTCGAATCGCATTGTTGCCCAAG                         CCATCAACGAATTGGTGGCATGCTTCGGGGAGCTCCTGATTGATTTTGTGC
genomic: GATCCGGAAAGGTGCCACCTCGCCAAGGTCGAATCGCATTGTTGCCCAAGgtttgagttc ... gcgcttgcagCCATCAACGAATTGGTGGCATGCTTCGGGGAGCTCCTGATTGATTTTGTGC
EST: gi|18327213|gb|BJ159215.1|BJ159215
EST:     GATCCGGAAAGGTGCCACCTCGCCAAGGTCGAATCGCATTGTTGCCCAAG                         CCATCAACGAATTGGTGGCATGCTTCGGGGAGCTCCTGATTGATTTTGTGC
genomic: GATCCGGAAAGGTGCCACCTCGCCAAGGTCGAATCGCATTGTTGCCCAAGgtttgagttc ... gcgcttgcagCCATCAACGAATTGGTGGCATGCTTCGGGGAGCTCCTGATTGATTTTGTGC
EST: gi|162163345|gb|FC339671.1|FC339671
EST:     GATCCGGAAAGGTGCCACCTCGCCAAGGTCGAATCGCATTGTTGCCCAAG                         CCATCAACGAATTGGTGGCATGCTTCGGGGAGCTCCTGATTGATTTTGTGC
genomic: GATCCGGAAAGGTGCCACCTCGCCAAGGTCGAATCGCATTGTTGCCCAAGgtttgagttc ... gcgcttgcagCCATCAACGAATTGGTGGCATGCTTCGGGGAGCTCCTGATTGATTTTGTGC
EST: gi|18327207|gb|BJ159209.1|BJ159209
EST:     GATCCGGAAAGGTGCCACCTCGCCAAGGTCGAATCGCATTGTTGCCCAAG                         CCATCAACGAATTGGTGGCATGCTTCGGGGAGCTCCTGATTGATTTTGTGC
genomic: GATCCGGAAAGGTGCCACCTCGCCAAGGTCGAATCGCATTGTTGCCCAAGgtttgagttc ... gcgcttgcagCCATCAACGAATTGGTGGCATGCTTCGGGGAGCTCCTGATTGATTTTGTGC
EST: gi|208353818|gb|DC906506.1|DC906506
EST:     GATCCGGAAAGGTGCCACCTCGCCAAGGTCGAATCGCATTGTTGCCCAAG                         CCATCAACGAATTGGTGGCATGCTTCGGGGAGCTCCTGATTGATTTTGTGC
genomic: GATCCGGAAAGGTGCCACCTCGCCAAGGTCGAATCGCATTGTTGCCCAAGgtttgagttc ... gcgcttgcagCCATCAACGAATTGGTGGCATGCTTCGGGGAGCTCCTGATTGATTTTGTGC
EST: gi|208360000|gb|DC934917.1|DC934917
EST:     GATCCGGAAAGGTGCCACCTCGCCAAGGTCGAATCGCATTGTTGCCCAAG                         CCATCAACGAATTGGTGGCATGCTTCGGGGAGCTCCTGATTGATTTTGTGC
genomic: GATCCGGAAAGGTGCCACCTCGCCAAGGTCGAATCGCATTGTTGCCCAAGgtttgagttc ... gcgcttgcagCCATCAACGAATTGGTGGCATGCTTCGGGGAGCTCCTGATTGATTTTGTGC
EST: gi|18371173|gb|BJ202775.1|BJ202775
EST:     GATCCGGAAAGGTGCCACCTCGCCAAGGTCGAATCGCATTGTTGCCCAAG                         CCATCAACGAATTGGTGGCATGCTTCGGGGAGCTCCTGATTGATTTTGTGC
genomic: GATCCGGAAAGGTGCCACCTCGCCAAGGTCGAATCGCATTGTTGCCCAAGgtttgagttc ... gcgcttgcagCCATCAACGAATTGGTGGCATGCTTCGGGGAGCTCCTGATTGATTTTGTGC
EST: gi|67716305|gb|BJ966565.1|BJ966565
EST:     GATCCGGAAAGGTGCCACCTCGCCAAGGTCGAATCGCATTGTTGCCCAAG                         CCATCAACGAATTGGTGGCATGCTTCGGGGAGCTCCTGATTGATTTTGTGC
genomic: GATCCGGAAAGGTGCCACCTCGCCAAGGTCGAATCGCATTGTTGCCCAAGgtttgagttc ... gcgcttgcagCCATCAACGAATTGGTGGCATGCTTCGGGGAGCTCCTGATTGATTTTGTGC
EST: gi|18350922|gb|BJ182973.1|BJ182973
EST:     GATCCGGAAAGGTGCCACCTCGCCAAGGTCGAATCGCATTGTTGCCCAAG                         CCATCAACGAATTGGTGGCATGCTTCGGGGAGCTCCTGATTGATTTTGTGC
genomic: GATCCGGAAAGGTGCCACCTCGCCAAGGTCGAATCGCATTGTTGCCCAAGgtttgagttc ... gcgcttgcagCCATCAACGAATTGGTGGCATGCTTCGGGGAGCTCCTGATTGATTTTGTGC
EST: gi|18325903|gb|BJ157901.1|BJ157901
EST:     GATCCGGAAAGGTGCCACCTCGCCAAGGTCGAATCGCATTGTTGCCCAAG                         CCATCAACGAATTGGTGGCATGCTTCGGGGAGCTCCTGATTGATTTTGTGC
genomic: GATCCGGAAAGGTGCCACCTCGCCAAGGTCGAATCGCATTGTTGCCCAAGgtttgagttc ... gcgcttgcagCCATCAACGAATTGGTGGCATGCTTCGGGGAGCTCCTGATTGATTTTGTGC
EST: gi|100416897|gb|BY993143.1|BY993143
EST:     GATCCGGAAAGGTGCCACCTCGCCAAGGTCGAATCGCATTGTTGCCCAAG                         CCATCAACGAATTGGTGGCATGCTTCGGGGAGCTCCTGATTGATTTTGTGC
genomic: GATCCGGAAAGGTGCCACCTCGCCAAGGTCGAATCGCATTGTTGCCCAAGgtttgagttc ... gcgcttgcagCCATCAACGAATTGGTGGCATGCTTCGGGGAGCTCCTGATTGATTTTGTGC

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: 23 (upstream exon), 29 (downstream exon)
Score: 5

CTCGAATCATCTTTTCGCCCCTCTTTTCCCGCTGGTTCTTCTTCCCTAACGATCCGGAAAGGTGCCACCTCGCCAAGGTCGAATCGCATTGTTGCCCAAGgtttgagttc ... gcgcttgcagCCATCAACGAATTGGTGGCATGCTTCGGGGAGCTCCTGATTGATTTTGTGCCCACGGTTGGCGGTCTATCGCTTGCTGATGCTCCAGCATTTAAGAAAGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttctatcctgatgaattttggttccggctaaaatttggttgtgcgcttgcagCCATCAACGAATTGGTGGCATGCTTCGGGGAGCTCCTGATTGATTTTGTGCCCACGGTTGGCGGTCTATCGCTTGCTGATGCTCCAGCATTTAAGAAAGC
                            ggctaaa  putative branch site (score: 5)
                               taaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgatggtcgaacttcaaattattacctgaagtgtggcacccaggcatttctatcctgatgaattttggttccggctaaaatttggttgtgcgcttgcagCCATCAACGAATTGGTGGCATGCTTCGGGGAGCTCCTGATTGATTTTGTGCCCACGGTTGGCGGTCTATCGCTTGCTGATGCTCCAGCATTTAAGAAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA