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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcatgaatcaatttgtttcacaaaatcgtttcatctttcgccttgtgcagGATATCAAGAAAAGTTTTATTTCAACCCCGGAGACACAGGCTTCAAG

Basic information

species Selaginella moellendorffii
transcript EFJ07601
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ07601 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GRMZM2G073950_T01 (Zea mays), 3'ss of exon 4
---------gtatgcatgaatcaatttgtttcaca--aaatcgtttcatcttt----cgccttgtg-----cagGATATCAAGAAAAGTTTTATTTCAACCCCGGAGACACAGGCTTCAAG
          || || |       | ||    |||     |  | |||||| |    |  ||| ||     ||||||||||||| |||||||||||||||||||| ||||| ||||| |||
gtaaggtcaataggcttttcctgttctgccatacattgggttatctcatctataaagccgcttctgtttgtcagGATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG
















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|169066302|gb|FE472978.1|FE472978
EST:     TGGAACGGACCTTGGGCTCTACCGAAAATCTCACATTCCCGACGGCCCAG                         GATATCAAGAAAAGTTTTATTTCAACCCCGGAGACACAGGCTTCAAG
genomic: TGGAACGGACCTTGGGCTCTACCGAAAATCTCACATTCCCGACGGCCCAGgtatgcatga ... ccttgtgcagGATATCAAGAAAAGTTTTATTTCAACCCCGGAGACACAGGCTTCAAG
EST: gi|169066303|gb|FE472979.1|FE472979
EST:     TGGAACGGACCTTGGGCTCTACCGAAAATCTCACATTCCCGACGGCCCAG                         GATATCAAGAAAAGTTTTATTTCAACCCCGGAGACACAGGCTTCAAG
genomic: TGGAACGGACCTTGGGCTCTACCGAAAATCTCACATTCCCGACGGCCCAGgtatgcatga ... ccttgtgcagGATATCAAGAAAAGTTTTATTTCAACCCCGGAGACACAGGCTTCAAG
EST: gi|169067004|gb|FE475981.1|FE475981
EST:     TGGAACGGACCTTGGGCTCTACCGAAAATCTCACATTCCCGACGGCCCAG                         GATATCAAGAAAAGTTTTATTTCAACCCCGGAGACACAGGCTTCAAG
genomic: TGGAACGGACCTTGGGCTCTACCGAAAATCTCACATTCCCGACGGCCCAGgtatgcatga ... ccttgtgcagGATATCAAGAAAAGTTTTATTTCAACCCCGGAGACACAGGCTTCAAG
EST: gi|169044683|gb|FE452477.1|FE452477
EST:     TGGAACGGACCTTGGGCTCTACCGAAAATCTCACATTCCCGACGGCCCAG                         GATATCAAGAAAAGTTTTATTTCAACCCCGGAGACACAGGCTTCAAG
genomic: TGGAACGGACCTTGGGCTCTACCGAAAATCTCACATTCCCGACGGCCCAGgtatgcatga ... ccttgtgcagGATATCAAGAAAAGTTTTATTTCAACCCCGGAGACACAGGCTTCAAG
EST: gi|169058558|gb|FE464284.1|FE464284
EST:     TGGAACGGACCTTGGGCTCTACCGAAAATCTCACATTCCCGACGGCCCAG                         GATATCAAGAAAAGTTTTATTTCAACCCCGGAGACACAGGCTTCAAG
genomic: TGGAACGGACCTTGGGCTCTACCGAAAATCTCACATTCCCGACGGCCCAGgtatgcatga ... ccttgtgcagGATATCAAGAAAAGTTTTATTTCAACCCCGGAGACACAGGCTTCAAG
EST: gi|169094622|gb|FE494548.1|FE494548
EST:     TGGAACGGACCTTGGGCTCTACCGAAAATCTCACATTCCCGACGGCCCAG                         GATATCAAGAAAAGTTTTATTTCAACCCCGGAGACACAGGCTTCAAG
genomic: TGGAACGGACCTTGGGCTCTACCGAAAATCTCACATTCCCGACGGCCCAGgtatgcatga ... ccttgtgcagGATATCAAGAAAAGTTTTATTTCAACCCCGGAGACACAGGCTTCAAG
EST: gi|169094623|gb|FE494549.1|FE494549
EST:     TGGAACGGACCTTGGGCTCTACCGAAAATCTCACATTCCCGACGGCCCAG                         GATATCAAGAAAAGTTTTATTTCAACCCCGGAGACACAGGCTTCAAG
genomic: TGGAACGGACCTTGGGCTCTACCGAAAATCTCACATTCCCGACGGCCCAGgtatgcatga ... ccttgtgcagGATATCAAGAAAAGTTTTATTTCAACCCCGGAGACACAGGCTTCAAG
EST: gi|169067005|gb|FE475982.1|FE475982
EST:     TGGAACGGACCTTGGGCTCTACCGAAAATCTCACATTCCCGACGGCCCAG                         GATATCAAGAAAAGTTTTATTTCAACCCCGGAGACACAGGCTTCAAG
genomic: TGGAACGGACCTTGGGCTCTACCGAAAATCTCACATTCCCGACGGCCCAGgtatgcatga ... ccttgtgcagGATATCAAGAAAAGTTTTATTTCAACCCCGGAGACACAGGCTTCAAG
EST: gi|169044684|gb|FE452478.1|FE452478
EST:     TGGAACGGACCTTGGGCTCTACCGAAAATCTCACATTCCCGACGGCCCAG                         GATATCAAGAAAAGTTTTATTTCAACCCCGGAGACACAGGCTTCAAG
genomic: TGGAACGGACCTTGGGCTCTACCGAAAATCTCACATTCCCGACGGCCCAGgtatgcatga ... ccttgtgcagGATATCAAGAAAAGTTTTATTTCAACCCCGGAGACACAGGCTTCAAG
EST: gi|169058559|gb|FE464285.1|FE464285
EST:     TGGAACGGACCTTGGGCTCTACCGAAAATCTCACATTCCCGACGGCCCAG                         GATATCAAGAAAAGTTTTATTTCAACCCCGGAGACACAGGCTTCAAG
genomic: TGGAACGGACCTTGGGCTCTACCGAAAATCTCACATTCCCGACGGCCCAGgtatgcatga ... ccttgtgcagGATATCAAGAAAAGTTTTATTTCAACCCCGGAGACACAGGCTTCAAG

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: 25 (upstream exon), 31 (downstream exon)
Score: 5

GAGGAGGCAAACAATGCACACTATAACTCTATTGTTATCATAGATGCCGATGGAACGGACCTTGGGCTCTACCGAAAATCTCACATTCCCGACGGCCCAGgtatgcatga ... ccttgtgcagGATATCAAGAAAAGTTTTATTTCAACCCCGGAGACACAGGCTTCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatgcatgaatcaatttgtttcacaaaatcgtttcatctttcgccttgtgcagGATATCAAGAAAAGTTTTATTTCAACCCCGGAGACACAGGCTTCAAG
                                 tttcatctttcgcctt  CT-rich tract
          aatcaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcatgaatcaatttgtttcacaaaatcgtttcatctttcgccttgtgcagGATATCAAGAAAAGTTTTATTTCAACCCCGGAGACACAGGCTTCAAG

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