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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGACGTGCTTTGCTCCGTCTGCGAGATGGCTGTTGTTTGGGTCCAGAACCAGCTCAGGCAAAACCGTACCAAGCAACAGATTGAGGACTACCTCAATCAGgtatttatgcggaaaccatagctaacaaccttcctgctgcgatggtttcgattacttcgtgtatttgcag

Basic information

species Selaginella moellendorffii
transcript EFJ34434
intron # 9
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|169113000|gb|FE515480.1|FE515480
EST:     AGCTCAGGCAAAACCGTACCAAGCAACAAATTGAGGACTACCTCAATCAG                         CTATGCGAACGGTT
genomic: AGCTCAGGCAAAACCGTACCAAGCAACAGATTGAGGACTACCTCAATCAGgtatttatgc ... gtatttgcagCTATGCGAACGGTT
EST: gi|169031797|gb|FE438482.1|FE438482
EST:     AGCTCAGGCAAAACCGTACCAAGCAACAGATTGAGGACTACCTCAATCAG                         CTATGCGAACGGTTGCCGAGCCCGAATGGCCAGTCCGTTGTTGAGTGCGCG
genomic: AGCTCAGGCAAAACCGTACCAAGCAACAGATTGAGGACTACCTCAATCAGgtatttatgc ... gtatttgcagCTATGCGAACGGTTGCCGAGCCCGAATGGCCAGTCCGTTGTTGAGTGCGCG
EST: gi|169031872|gb|FE438505.1|FE438505
EST:     AGCTCAGGCAAAACCGTACCAAGCAACAGATTGAGGACTACCTCAATCAG                         CTATGCGAACGGTTGCCGAGCCCGAATGGCCAGTCCGTTGTTGAGTGCGCG
genomic: AGCTCAGGCAAAACCGTACCAAGCAACAGATTGAGGACTACCTCAATCAGgtatttatgc ... gtatttgcagCTATGCGAACGGTTGCCGAGCCCGAATGGCCAGTCCGTTGTTGAGTGCGCG
EST: gi|169112151|gb|FE513494.1|FE513494
EST:     AGCTCAGGCAAAACCGTACCAAGCAACAGATTGAGGACTACCTCAATCAG                         CTATGCGAACGGTTGCCGAGCCCGAATGGCCAGTCCGTTGTTGAGTGCGCG
genomic: AGCTCAGGCAAAACCGTACCAAGCAACAGATTGAGGACTACCTCAATCAGgtatttatgc ... gtatttgcagCTATGCGAACGGTTGCCGAGCCCGAATGGCCAGTCCGTTGTTGAGTGCGCG
EST: gi|169060203|gb|FE467565.1|FE467565
EST:     AGCTCAGGCAAAACCGTACCAAGCAACAGATTGAGGACTACCTCAATCAG                         CTATGCGAACGGTTGCCGAGCCCGAATGGCCAGTCCGTTGTTGAGTGCGCG
genomic: AGCTCAGGCAAAACCGTACCAAGCAACAGATTGAGGACTACCTCAATCAGgtatttatgc ... gtatttgcagCTATGCGAACGGTTGCCGAGCCCGAATGGCCAGTCCGTTGTTGAGTGCGCG
EST: gi|169110929|gb|FE509334.1|FE509334
EST:     AGCTCAGGCAAAACCGTACCAAGCAACAGATTGAGGACTACCTCAATCAG                         CTATGCGAACGGTTGCCGAGCCCGAATGGCCAGTCCGTTGTTGAGTGCGCG
genomic: AGCTCAGGCAAAACCGTACCAAGCAACAGATTGAGGACTACCTCAATCAGgtatttatgc ... gtatttgcagCTATGCGAACGGTTGCCGAGCCCGAATGGCCAGTCCGTTGTTGAGTGCGCG
EST: gi|169112990|gb|FE515470.1|FE515470
EST:     AGCTCAGGCAAAACCGTACCAAGCAACAAATTGAGGACTACCTCAATCAG                         CTATGCGAACGGTTGCCGAGCCCGAATGGCCAGTCCGTTGTTGAGTGCGCG
genomic: AGCTCAGGCAAAACCGTACCAAGCAACAGATTGAGGACTACCTCAATCAGgtatttatgc ... gtatttgcagCTATGCGAACGGTTGCCGAGCCCGAATGGCCAGTCCGTTGTTGAGTGCGCG
EST: gi|169058238|gb|FE466005.1|FE466005
EST:     AGCTCAGGCAAAACCGTACCAAGCAACAGATTGAGGACTACCTCAATCAG                         CTATGCGAACGGTTGCCGAGCCCGAATGGCCAGTCCGTTGTTGAGTGCGCG
genomic: AGCTCAGGCAAAACCGTACCAAGCAACAGATTGAGGACTACCTCAATCAGgtatttatgc ... gtatttgcagCTATGCGAACGGTTGCCGAGCCCGAATGGCCAGTCCGTTGTTGAGTGCGCG
EST: gi|169031935|gb|FE440661.1|FE440661
EST:     AGCTCAGGCAAAACCGTACCAAGCAACAGATTGAGGACTACCTCAATCAG                         CTATGCGAACGGTTGCCGAGCCCGAATGGCCAGTCCGTTGTTGAGTGCGCG
genomic: AGCTCAGGCAAAACCGTACCAAGCAACAGATTGAGGACTACCTCAATCAGgtatttatgc ... gtatttgcagCTATGCGAACGGTTGCCGAGCCCGAATGGCCAGTCCGTTGTTGAGTGCGCG
EST: gi|169114468|gb|FE516538.1|FE516538
EST:     AGCTCAGGCAAAACCGTACCAAGCAACAGATTGAGGACTACCTCAATCAG                         CTATGCGAACGGTTGCCGAGCCCGAATGGCCAGTCCGTTGTTGAGTGCGCG
genomic: AGCTCAGGCAAAACCGTACCAAGCAACAGATTGAGGACTACCTCAATCAGgtatttatgc ... gtatttgcagCTATGCGAACGGTTGCCGAGCCCGAATGGCCAGTCCGTTGTTGAGTGCGCG
EST: gi|169065200|gb|FE474024.1|FE474024
EST:     AGCTCAGGCAAAACCGTACCAAGCAACAGATTGAGGACTACCTCAATCAG                         CTATGCGAACGGTTGCCGAGCCCGAATGGCCAGTCCGTTGTTGAGTGCGCG
genomic: AGCTCAGGCAAAACCGTACCAAGCAACAGATTGAGGACTACCTCAATCAGgtatttatgc ... gtatttgcagCTATGCGAACGGTTGCCGAGCCCGAATGGCCAGTCCGTTGTTGAGTGCGCG
EST: gi|169112152|gb|FE513495.1|FE513495
EST:     AGCTCAGGCAAAACCGTACCAAGCAACAGATTGAGGACTACCTCAATCAG                         CTATGCGAACGGTTGCCGAGCCCGAATGGCCAGTCCGTTGTTGAGTGCGCG
genomic: AGCTCAGGCAAAACCGTACCAAGCAACAGATTGAGGACTACCTCAATCAGgtatttatgc ... gtatttgcagCTATGCGAACGGTTGCCGAGCCCGAATGGCCAGTCCGTTGTTGAGTGCGCG
EST: gi|169096046|gb|FE500024.1|FE500024
EST:     AGCTCAGGCAAAACCGTACCAAGCAACAGATTGAGGACTACCTCAATCAG                         CTATGCGAACGGTTGC
genomic: AGCTCAGGCAAAACCGTACCAAGCAACAGATTGAGGACTACCTCAATCAGgtatttatgc ... gtatttgcagCTATGCGAACGGTTGC
EST: gi|169040181|gb|FE448948.1|FE448948
EST:     AGCTCAGGCAAAACCGTACCAAGCAACAGATTGAGGACTACCTCAATCAG                         CTATGCGAACGGTTGCCGAGCCCGAATGGCCAGTCCGTTGTTGAGTGCGCG
genomic: AGCTCAGGCAAAACCGTACCAAGCAACAGATTGAGGACTACCTCAATCAGgtatttatgc ... gtatttgcagCTATGCGAACGGTTGCCGAGCCCGAATGGCCAGTCCGTTGTTGAGTGCGCG
EST: gi|169021618|gb|FE432137.1|FE432137
EST:     AGCTCAGGCAAAACCGTACCAAGCAACAGATTGAGGACTACCTCAATCAG                         CTATGCGAACGGTTGCCGAGCCCGAATGGCCAGTCCGTTGTTGAGTGCGCG
genomic: AGCTCAGGCAAAACCGTACCAAGCAACAGATTGAGGACTACCTCAATCAGgtatttatgc ... gtatttgcagCTATGCGAACGGTTGCCGAGCCCGAATGGCCAGTCCGTTGTTGAGTGCGCG
EST: gi|169096045|gb|FE500023.1|FE500023
EST:     AGCTCAGGCAAAACCGTACCAAGCAACAGATTGAGGACTACCTCAATCAG                         CTATGCGAACGGTTGCCGAGCCCGAATGGCCAGTCCGTTGTTGAGTGCGCG
genomic: AGCTCAGGCAAAACCGTACCAAGCAACAGATTGAGGACTACCTCAATCAGgtatttatgc ... gtatttgcagCTATGCGAACGGTTGCCGAGCCCGAATGGCCAGTCCGTTGTTGAGTGCGCG
EST: gi|169093446|gb|FE495727.1|FE495727
EST:     AGCTCAGGCAAAACCGTACCAAGCAACAGATTGAGGACTACCTCAATCAG                         CTATGCGAACGGTTGCCGAGCCCGAATGGCCAGTCCGTTGTTGAGTGCGCG
genomic: AGCTCAGGCAAAACCGTACCAAGCAACAGATTGAGGACTACCTCAATCAGgtatttatgc ... gtatttgcagCTATGCGAACGGTTGCCGAGCCCGAATGGCCAGTCCGTTGTTGAGTGCGCG
EST: gi|169039672|gb|FE448606.1|FE448606
EST:     AGCTCAGGCAAAACCGTACCAAGCAACAGATTGAGGACTACCTCAATCAG                         CTATGCGAACGGTTGCCGAGCCCGAATGGCCAGTCCGTTGTTGAGTGCGCG
genomic: AGCTCAGGCAAAACCGTACCAAGCAACAGATTGAGGACTACCTCAATCAGgtatttatgc ... gtatttgcagCTATGCGAACGGTTGCCGAGCCCGAATGGCCAGTCCGTTGTTGAGTGCGCG
EST: gi|169044448|gb|FE451072.1|FE451072
EST:     AGCTCAGGCAAAACCGTACCAAGCAACAGATTGAGGACTACCTCAATCAG                         CTATGCGAACGGTTGCCGAGCCCGAATGGCCAGTCCGTTGTTGAGTGCGCG
genomic: AGCTCAGGCAAAACCGTACCAAGCAACAGATTGAGGACTACCTCAATCAGgtatttatgc ... gtatttgcagCTATGCGAACGGTTGCCGAGCCCGAATGGCCAGTCCGTTGTTGAGTGCGCG
EST: gi|169021619|gb|FE432138.1|FE432138
EST:     AGCTCAGGCAAAACCGTACCAAGCAACAGATTGAGGACTACCTCAATCAG                         CTATGCGAACGGTTGCCGAGCCCGAATGGCCAGTCCGTTGTTGAGTGCGCG
genomic: AGCTCAGGCAAAACCGTACCAAGCAACAGATTGAGGACTACCTCAATCAGgtatttatgc ... gtatttgcagCTATGCGAACGGTTGCCGAGCCCGAATGGCCAGTCCGTTGTTGAGTGCGCG
EST: gi|169021385|gb|FE431176.1|FE431176
EST:     AGCTCAGGCAAAACCGTACCAAGCAACAGATTGAGGACTACCTCAATCAG                         CTATGCGAACGGTTGCCGAGCCCGAATGGCCAGTCCGTTGTTGAGTGCGCG
genomic: AGCTCAGGCAAAACCGTACCAAGCAACAGATTGAGGACTACCTCAATCAGgtatttatgc ... gtatttgcagCTATGCGAACGGTTGCCGAGCCCGAATGGCCAGTCCGTTGTTGAGTGCGCG

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: 76

CGACGTGCTTTGCTCCGTCTGCGAGATGGCTGTTGTTTGGGTCCAGAACCAGCTCAGGCAAAACCGTACCAAGCAACAGATTGAGGACTACCTCAATCAGgtatttatgc ... gtatttgcagCTATGCGAACGGTTGCCGAGCCCGAATGGCCAGTCCGTTGTTGAGTGCGCGAAAATCTCCTCCCTCCCGAACGTCTCATTCACCATCGCAAATCAAACGT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGACGTGCTTTGCTCCGTCTGCGAGATGGCTGTTGTTTGGGTCCAGAACCAGCTCAGGCAAAACCGTACCAAGCAACAGATTGAGGACTACCTCAATCAGgtatttatgcggaaaccatagctaacaaccttcctgctgcgatggtttcgattacttcgtgtatttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA