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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAACGTAATGGAGACAGTCAATGACAGAAATGCAGGAGAAAACATGGCCCTCAGTGATGAATTTGTTGGGCTTGAAGAAGCCATTCAAGCAACCCTTCAGgtaacttccgctagttacttccgcctttcaaacaatcccgactattatatgttagcctgcaaatgcctgtacgctgtagatgatgcaacctttacaatgagaagtcctctctaaaattgtgctctgtttgcttatag

Basic information

species Physcomitrella patens
transcript PP1S295_6V6.1
intron # 4
splice site 5'
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|22133444|gb|BQ827740.1|BQ827740
EST:     TCAGTGATGAATTTGTTGGGCTTGAAGAAGCCATTCAAGCAACCCTTCAG                         GAAATCGGCAGTGTTCCACGCGGTCCACCCCCAGCATCTAAGGAGGAGGTC
genomic: TCAGTGATGAATTTGTTGGGCTTGAAGAAGCCATTCAAGCAACCCTTCAGgtaacttccg ... ttgcttatagGAAATCGGCAGTGTTCCACGCGGTCCACCCCCAGCATCTAAGGAGGAGGTC
EST: gi|37836793|gb|BJ594801.1|BJ594801
EST:     TCAGTGATGAATTTGTTGGGCTTGAAGAAGCCATTCAAGCAACCCTTCAG                         GAAATCGGCAGTGTTCCACGCGGTCCACCCCCAGCATCTAAGGAGGAGGTC
genomic: TCAGTGATGAATTTGTTGGGCTTGAAGAAGCCATTCAAGCAACCCTTCAGgtaacttccg ... ttgcttatagGAAATCGGCAGTGTTCCACGCGGTCCACCCCCAGCATCTAAGGAGGAGGTC
EST: gi|162237757|gb|FC413372.1|FC413372
EST:     TCAGTGATGAATTTGTTGGGCTTGAAGAAGCCATTCAAGCAACCCTTCAG                         GAAATCGGCAGTGTTCCACGCGGTCCACCCCCAGCATTTAAGGAGGAGGTC
genomic: TCAGTGATGAATTTGTTGGGCTTGAAGAAGCCATTCAAGCAACCCTTCAGgtaacttccg ... ttgcttatagGAAATCGGCAGTGTTCCACGCGGTCCACCCCCAGCATCTAAGGAGGAGGTC
EST: gi|162152798|gb|FC329804.1|FC329804
EST:     TCAGTGATGAATTTGTTGGGCTTGAAGAAGCCATTCAAGCAACCCTTCAG                         GAAATCGGCAGTGTTCCACGCGGTCCACCCCCAGCATCTAAGGAGGAGGTC
genomic: TCAGTGATGAATTTGTTGGGCTTGAAGAAGCCATTCAAGCAACCCTTCAGgtaacttccg ... ttgcttatagGAAATCGGCAGTGTTCCACGCGGTCCACCCCCAGCATCTAAGGAGGAGGTC
EST: gi|162261739|gb|FC437028.1|FC437028
EST:     TCAGTGAGGAATTTGTTGGGCTTGAAGAAGCCATTCAAGCAACCCTTCAG                         GAAATCGGCAGTGTTCCACGCGGTCCACCCCCAGCATCTAAGGAGGAGGTC
genomic: TCAGTGATGAATTTGTTGGGCTTGAAGAAGCCATTCAAGCAACCCTTCAGgtaacttccg ... ttgcttatagGAAATCGGCAGTGTTCCACGCGGTCCACCCCCAGCATCTAAGGAGGAGGTC
EST: gi|67701362|gb|BJ961595.1|BJ961595
EST:     TCAGTGATGAATTTGTTGGGCTTGAAGAAGCCATTCAAGCAACCCTTCAG                         GAAATCGGCAGTGTTCCACGCGGTCCACCCCCAGCATCTAAGGAGGAGGTC
genomic: TCAGTGATGAATTTGTTGGGCTTGAAGAAGCCATTCAAGCAACCCTTCAGgtaacttccg ... ttgcttatagGAAATCGGCAGTGTTCCACGCGGTCCACCCCCAGCATCTAAGGAGGAGGTC
EST: gi|162270005|gb|FC446705.1|FC446705
EST:     TCAGTGATGAATTTGTTGGGCTTGAAGAAGCCATTCAAGCAACCCTTCAG                         GAAATCGGCAGTGTTCCACGCGGTCCACCCCCAGCATCTAAGGAGGAGGTC
genomic: TCAGTGATGAATTTGTTGGGCTTGAAGAAGCCATTCAAGCAACCCTTCAGgtaacttccg ... ttgcttatagGAAATCGGCAGTGTTCCACGCGGTCCACCCCCAGCATCTAAGGAGGAGGTC
EST: gi|67692610|gb|BJ952843.1|BJ952843
EST:     TCAGTGATGAATTTGTTGGGCTTGAAGAAGCCATTCAAGCAACCCTTCAG                         GAAATCGGCAGTGTTCCACGCGGTCCACCCCCAGCATCTAAGGAGGAGGTC
genomic: TCAGTGATGAATTTGTTGGGCTTGAAGAAGCCATTCAAGCAACCCTTCAGgtaacttccg ... ttgcttatagGAAATCGGCAGTGTTCCACGCGGTCCACCCCCAGCATCTAAGGAGGAGGTC
EST: gi|67693675|gb|BJ953908.1|BJ953908
EST:     TCAGTGATGAATTTGTTGGGCTTGAAGAAGCCATTCAAGCAACCCTTCAG                         GAAATCGGCAGTGTTCCACGCGGTCCACCCCCAGCATCTAAGGAGGAGGTC
genomic: TCAGTGATGAATTTGTTGGGCTTGAAGAAGCCATTCAAGCAACCCTTCAGgtaacttccg ... ttgcttatagGAAATCGGCAGTGTTCCACGCGGTCCACCCCCAGCATCTAAGGAGGAGGTC
EST: gi|18341628|gb|BJ173663.1|BJ173663
EST:     TCAGTGATGAATTTGTTGGGCTTGAAGAAGCCATTCAAGCAACCCTTCAG                         GAAATCGGCAGTGTTCCACGCGGTCCACCCCCAGCATCTAAGGAGGAGGTC
genomic: TCAGTGATGAATTTGTTGGGCTTGAAGAAGCCATTCAAGCAACCCTTCAGgtaacttccg ... ttgcttatagGAAATCGGCAGTGTTCCACGCGGTCCACCCCCAGCATCTAAGGAGGAGGTC
EST: gi|208364186|gb|DC947290.1|DC947290
EST:     TCAGTGATGAATTTGTTGGGCTTGAAGAAGCCATTCAAGCAACCCTTCAG                         GAAATCGGCAGTGTTCCACGCGGTCCACCCCCAGCATCTAAGGAGGAGGTC
genomic: TCAGTGATGAATTTGTTGGGCTTGAAGAAGCCATTCAAGCAACCCTTCAGgtaacttccg ... ttgcttatagGAAATCGGCAGTGTTCCACGCGGTCCACCCCCAGCATCTAAGGAGGAGGTC
EST: gi|162275560|gb|FC451302.1|FC451302
EST:     TCAGTGATGAATTTGTTGGGCTTGAAGAAGCCATTCAAGCAACCCTTCAG                         GAAATCGGCAGTGTTCCACGCGGTCCACCCCCAGCATCTAAGGAGGAGGTC
genomic: TCAGTGATGAATTTGTTGGGCTTGAAGAAGCCATTCAAGCAACCCTTCAGgtaacttccg ... ttgcttatagGAAATCGGCAGTGTTCCACGCGGTCCACCCCCAGCATCTAAGGAGGAGGTC

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), 25 (downstream exon)
Score: 12

AAACGTAATGGAGACAGTCAATGACAGAAATGCAGGAGAAAACATGGCCCTCAGTGATGAATTTGTTGGGCTTGAAGAAGCCATTCAAGCAACCCTTCAGgtaacttccg ... ttgcttatagGAAATCGGCAGTGTTCCACGCGGTCCACCCCCAGCATCTAAGGAGGAGGTCGCAAAGCTTCCAATAGTTGAAGTTACGAAGGAGTTTCTTGAGAGAGTAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAACGTAATGGAGACAGTCAATGACAGAAATGCAGGAGAAAACATGGCCCTCAGTGATGAATTTGTTGGGCTTGAAGAAGCCATTCAAGCAACCCTTCAGgtaacttccgctagttacttccgcctttcaaacaatcccgactattatatgttagcctgcaaatgcctgtacgctgtagatgatgcaacctttacaatgagaagtcctctctaaaattgtgctctgtttgcttatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA