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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGACGCGAACGGCATCTTGTCAGTAAGTGCGACTGACAAAGGAACCGGCAAGAAGCAAGACATTACGATCACTGGCGCCAGTACTCTTCCACAAGACGAGgtaaaaacacaagtttttctcttgccagatcttggtttctaacgcgaatacgaatacacgcag

Basic information

species Selaginella moellendorffii
transcript EFJ23703
intron # 7
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|169100202|gb|FE502416.1|FE502416
EST:     AGAAGCAAGACATTACGATCACTGGCGCCAGTACTCTTCCACAAGACGAG                         GTGGAGAGAATGGTGAACGAGGCCGAGAAGTTCAGCAAGGAGGACAAGGAG
genomic: AGAAGCAAGACATTACGATCACTGGCGCCAGTACTCTTCCACAAGACGAGgtaaaaacac ... atacacgcagGTGGAGAGAATGGTGAACGAGGCCGAGAAGTTCAGCAAGGAGGACAAGGAG
EST: gi|169081404|gb|FE487665.1|FE487665
EST:     AGAAGCAAGACATTACGATCACTGGCGCCAGTACTCTTCCACAAGACGAG                         GTGGAGAGAATGGTGAACGAGGCCGAGAAGTTCAGCAAGGAGGACAAGGAG
genomic: AGAAGCAAGACATTACGATCACTGGCGCCAGTACTCTTCCACAAGACGAGgtaaaaacac ... atacacgcagGTGGAGAGAATGGTGAACGAGGCCGAGAAGTTCAGCAAGGAGGACAAGGAG
EST: gi|169114872|gb|FE515821.1|FE515821
EST:     AGAAGCAAGACATTACGATCACTGGCGCCAGTACTCTTCCACAAGACGAG                         GTGGAGAGAATGGTGAACGAGGCCGAGAAGTTCAGCAAGGAGGACAAGGAG
genomic: AGAAGCAAGACATTACGATCACTGGCGCCAGTACTCTTCCACAAGACGAGgtaaaaacac ... atacacgcagGTGGAGAGAATGGTGAACGAGGCCGAGAAGTTCAGCAAGGAGGACAAGGAG
EST: gi|169081403|gb|FE487664.1|FE487664
EST:     AGAAGCAAGACATTACGATCACTGGCGCCAGTACTCTTCCACAAGACGAG                         GTGGAGAGAATGGTGAACGAGGCCGAGAAGTTCAGCAAGGAGGACAAGGAG
genomic: AGAAGCAAGACATTACGATCACTGGCGCCAGTACTCTTCCACAAGACGAGgtaaaaacac ... atacacgcagGTGGAGAGAATGGTGAACGAGGCCGAGAAGTTCAGCAAGGAGGACAAGGAG
EST: gi|169111799|gb|FE511179.1|FE511179
EST:     AGAAGCAAGACATTACGATCACTGGCGCCAGTACTCTTCCACAAGACGAG                         GTGGAGAGAATGGTGAACGAGGCCGAGAAGTTCAGCAAGGAGGACAAGGAG
genomic: AGAAGCAAGACATTACGATCACTGGCGCCAGTACTCTTCCACAAGACGAGgtaaaaacac ... atacacgcagGTGGAGAGAATGGTGAACGAGGCCGAGAAGTTCAGCAAGGAGGACAAGGAG
EST: gi|169111798|gb|FE511178.1|FE511178
EST:     AGAAGCAAGACATTACGATCACTGGCGCCAGTACTCTTCCACAAGACGAG                         GTGGAGAGAATGGTGAACGAGGCCGAGAAGTTCAGCAAGGAGGACAAGGAG
genomic: AGAAGCAAGACATTACGATCACTGGCGCCAGTACTCTTCCACAAGACGAGgtaaaaacac ... atacacgcagGTGGAGAGAATGGTGAACGAGGCCGAGAAGTTCAGCAAGGAGGACAAGGAG
EST: gi|169079167|gb|FE488652.1|FE488652
EST:     AGAAGCAAGACATTACGATCACTGGCGCCAGTACTCTTCCACAAGACGAG                         GTGGAGAGAATGGTGAACGAGGCCGAGAAGTTCAGCAAGGAGGACAAGGAG
genomic: AGAAGCAAGACATTACGATCACTGGCGCCAGTACTCTTCCACAAGACGAGgtaaaaacac ... atacacgcagGTGGAGAGAATGGTGAACGAGGCCGAGAAGTTCAGCAAGGAGGACAAGGAG
EST: gi|169021789|gb|FE429916.1|FE429916
EST:     AGAAGCAAGACATTACGATCACTGGCGCCAGTACTCTTCCACAAGACGAG                         GTGGAGAGAATGGTGAACGAGGCCGAGAAGTTCAGCAAGGAGGACAAGGAG
genomic: AGAAGCAAGACATTACGATCACTGGCGCCAGTACTCTTCCACAAGACGAGgtaaaaacac ... atacacgcagGTGGAGAGAATGGTGAACGAGGCCGAGAAGTTCAGCAAGGAGGACAAGGAG
EST: gi|169081876|gb|FE486423.1|FE486423
EST:     AGAAGCAAGACATTACGATCACTGGCGCCAGTACTCTTCCACAAGACGAG                         GTGGAGAGAATGGTGAACGAGGCCGAGAAGTTCAGCAAGGAGGACAAGGAG
genomic: AGAAGCAAGACATTACGATCACTGGCGCCAGTACTCTTCCACAAGACGAGgtaaaaacac ... atacacgcagGTGGAGAGAATGGTGAACGAGGCCGAGAAGTTCAGCAAGGAGGACAAGGAG
EST: gi|169082125|gb|FE490585.1|FE490585
EST:     AGAAGCAAGACATTACGATCACTGGCGCCAGTACTCTTCCACAAGACGAG                         GTGGAGAGAATGGTGAACGAGGCCGAGAAGTTCAGCAAGGAGGACAAGGAG
genomic: AGAAGCAAGACATTACGATCACTGGCGCCAGTACTCTTCCACAAGACGAGgtaaaaacac ... atacacgcagGTGGAGAGAATGGTGAACGAGGCCGAGAAGTTCAGCAAGGAGGACAAGGAG
EST: gi|169028457|gb|FE440418.1|FE440418
EST:     AGAAGCAAGACATTACGATCACTGGCGCCAGTACTCTTCCACAAGACGAG                         GTGGAGAGAATGGTGAACGAGGCCGAGAAGTTCAGCAAGGAGGACAAGGAG
genomic: AGAAGCAAGACATTACGATCACTGGCGCCAGTACTCTTCCACAAGACGAGgtaaaaacac ... atacacgcagGTGGAGAGAATGGTGAACGAGGCCGAGAAGTTCAGCAAGGAGGACAAGGAG
EST: gi|169082945|gb|FE491145.1|FE491145
EST:     AGAAGCAAGACATTACGATCACTGGCGCCAGTACTCTTCCACAAGACGAG                         GTGGAGAGAATGGTGAACGAGGCCGAGAAGTTCAGCAAGGAGGACAAGGAG
genomic: AGAAGCAAGACATTACGATCACTGGCGCCAGTACTCTTCCACAAGACGAGgtaaaaacac ... atacacgcagGTGGAGAGAATGGTGAACGAGGCCGAGAAGTTCAGCAAGGAGGACAAGGAG
EST: gi|169029192|gb|FE439398.1|FE439398
EST:     AGAAGCAAGACATTACGATCACTGGCGCCAGTACTCTTCCACAAGACGAG                         GTGGAGAGAATGGTGAACGAGGCCGAGAAGTTCAGCAAGGAGGACAAGGAG
genomic: AGAAGCAAGACATTACGATCACTGGCGCCAGTACTCTTCCACAAGACGAGgtaaaaacac ... atacacgcagGTGGAGAGAATGGTGAACGAGGCCGAGAAGTTCAGCAAGGAGGACAAGGAG
EST: gi|169021041|gb|FE430650.1|FE430650
EST:     AGAAGCAAGACATTACGATCACTGGCGCCAGTACTCTTCCACAAGACGAG                         GTGGAGAGAATGGTGAACGAGGCCGAGAAGTTCAGCAAGGAGGACAAGGAG
genomic: AGAAGCAAGACATTACGATCACTGGCGCCAGTACTCTTCCACAAGACGAGgtaaaaacac ... atacacgcagGTGGAGAGAATGGTGAACGAGGCCGAGAAGTTCAGCAAGGAGGACAAGGAG
EST: gi|169028458|gb|FE440419.1|FE440419
EST:     AGAAGCAAGACATTACGATCACTGGCGCCAGTACTCTTCCACAAGACGAG                         GTGGAGAGAATGGTGAACGAGGCCGAGAAGTTCAGCAAGGAGGACAAGGAG
genomic: AGAAGCAAGACATTACGATCACTGGCGCCAGTACTCTTCCACAAGACGAGgtaaaaacac ... atacacgcagGTGGAGAGAATGGTGAACGAGGCCGAGAAGTTCAGCAAGGAGGACAAGGAG
EST: gi|169092853|gb|FE494978.1|FE494978
EST:     AGAAGCAAGACATTACGATCACTGGCGCCAGTACTCTTCCACAAGACGAG                         GTGGAGAGAATGGTGAACGAGGCCGAGAAGTTCAGCAAGGAGGACAAGGAG
genomic: AGAAGCAAGACATTACGATCACTGGCGCCAGTACTCTTCCACAAGACGAGgtaaaaacac ... atacacgcagGTGGAGAGAATGGTGAACGAGGCCGAGAAGTTCAGCAAGGAGGACAAGGAG
EST: gi|169104026|gb|FE505039.1|FE505039
EST:     AGAAGCAAGACATTACGATCACTGGCGCCAGTACTCTTCCACAAGACGAG                         GTGGAGAGAATGGTGAACGAGGCCGAGAAGTTCAGCAAGGAGGACAAGGAG
genomic: AGAAGCAAGACATTACGATCACTGGCGCCAGTACTCTTCCACAAGACGAGgtaaaaacac ... atacacgcagGTGGAGAGAATGGTGAACGAGGCCGAGAAGTTCAGCAAGGAGGACAAGGAG
EST: gi|169092852|gb|FE494977.1|FE494977
EST:     AGAAGCAAGACATTACGATCACTGGCGCCAGTACTCTTCCACAAGACGAG                         GTGGAGAGAATGGTGAACGAGGCCGAGAAGTTCAGCAAGGAGGACAAGGAG
genomic: AGAAGCAAGACATTACGATCACTGGCGCCAGTACTCTTCCACAAGACGAGgtaaaaacac ... atacacgcagGTGGAGAGAATGGTGAACGAGGCCGAGAAGTTCAGCAAGGAGGACAAGGAG
EST: gi|169028426|gb|FE439087.1|FE439087
EST:     AGAAGCAAGACATTACGATCACTGGCGCCAGTACTCTTCCACAAGACGAG                         GTGGAGAGAATGGTGAACGAGGCCGAGAAGTTCAGCAAGGAGGACAAGGAG
genomic: AGAAGCAAGACATTACGATCACTGGCGCCAGTACTCTTCCACAAGACGAGgtaaaaacac ... atacacgcagGTGGAGAGAATGGTGAACGAGGCCGAGAAGTTCAGCAAGGAGGACAAGGAG
EST: gi|169038244|gb|FE445282.1|FE445282
EST:     AGAAGCAAGACATTACGATCACTGGCGCCAGTACTCTTCCACAAGACGAG                         GTGGAGAGAATGGTGAACGAGGCCGAGAAGTTCAGCAAGGAGGACAAGGAG
genomic: AGAAGCAAGACATTACGATCACTGGCGCCAGTACTCTTCCACAAGACGAGgtaaaaacac ... atacacgcagGTGGAGAGAATGGTGAACGAGGCCGAGAAGTTCAGCAAGGAGGACAAGGAG
EST: gi|169038258|gb|FE445283.1|FE445283
EST:     AGAAGCAAGACATTACGATCACTGGCGCCAGTACTCTTCCACAAGACGAG                         GTGGAGAGAATGGTGAACGAGGCCGAGAAGTTCAGCAAGGAGGACAAGGAG
genomic: AGAAGCAAGACATTACGATCACTGGCGCCAGTACTCTTCCACAAGACGAGgtaaaaacac ... atacacgcagGTGGAGAGAATGGTGAACGAGGCCGAGAAGTTCAGCAAGGAGGACAAGGAG
EST: gi|169100203|gb|FE502417.1|FE502417
EST:     GAAAGCA-GACATTACGATCACTGGCGCCAGTACTCTTCCACAAGACGAA                         GTGGAGAGAATGGTGAACG
genomic: GAA-GCAAGACATTACGATCACTGGCGCCAGTACTCTTCCACAAGACGAGgtaaaaacac ... atacacgcagGTGGAGAGAATGGTGAACG
EST: gi|169051044|gb|FE458214.1|FE458214
EST:     AGAAGCAAGACATTACGATCACTGGCGCCAGTACTCTTCCACAAGACGAG                         GTGGAGAGAATGGTGAACGAGGCCGAGAAGTTCAGCAAGGAGGACAAGGAG
genomic: AGAAGCAAGACATTACGATCACTGGCGCCAGTACTCTTCCACAAGACGAGgtaaaaacac ... atacacgcagGTGGAGAGAATGGTGAACGAGGCCGAGAAGTTCAGCAAGGAGGACAAGGAG

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: 35 (upstream exon), 35 (downstream exon)
Score: 73

CGACGCGAACGGCATCTTGTCAGTAAGTGCGACTGACAAAGGAACCGGCAAGAAGCAAGACATTACGATCACTGGCGCCAGTACTCTTCCACAAGACGAGgtaaaaacac ... atacacgcagGTGGAGAGAATGGTGAACGAGGCCGAGAAGTTCAGCAAGGAGGACAAGGAGAAGAGAGAGGCAGTGGACGTGAAGAACCAGGCCGACTCGCTGGTGTATC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGACGCGAACGGCATCTTGTCAGTAAGTGCGACTGACAAAGGAACCGGCAAGAAGCAAGACATTACGATCACTGGCGCCAGTACTCTTCCACAAGACGAGgtaaaaacacaagtttttctcttgccagatcttggtttctaacgcgaatacgaatacacgcag

- - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA