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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttaaaagttttcctctcacggtttttttattgtccaacgcctttttgcagATTGTACTCGCTGTGAAGCTAGGGATGGCAGCAGACGAGGCGATTAAATCCGTGTCCACACTGTCTGATGTAGAAGGCTTGTGCGAGGCGTATGCAACTT

Basic information

species Selaginella moellendorffii
transcript EFJ17214
intron # 7
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|169071789|gb|FE476646.1|FE476646
EST:     GAGTGCCGTTTGGCTGCG                         ATTGTACTCGCTGTGAAGCTAGGGACGGCAGCAGACGAGGCGATTAAATCC
genomic: GAGTGCCGTTTGGCTGCGgtaagttaaa ... ctttttgcagATTGTACTCGCTGTGAAGCTAGGGATGGCAGCAGACGAGGCGATTAAATCC
EST: gi|169050266|gb|FE458346.1|FE458346
EST:     CGCGGNCA-CTAATTACAACAATCGAGTTGTTGAGTGCCGTTTGGCTGCG                         ATTGTACTCGCTGTGAAGCTAGGGATGGCAGC
genomic: CGCGG-CAACTAATTACAACAATCGAGTTGTTGAGTGCCGTTTGGCTGCGgtaagttaaa ... ctttttgcagATTGTACTCGCTGTGAAGCTAGGGATGGCAGC
EST: gi|169019355|gb|FE427665.1|FE427665
EST:     CCGCGGCAACTAATTACAACAATCGAGTTGTTGAGTGCCGTTTGGCTGCG                         ATTGTACTCGCTGTGAAGCTAGGGATGGCAGCAGACGAGGCGATTAAATCC
genomic: CCGCGGCAACTAATTACAACAATCGAGTTGTTGAGTGCCGTTTGGCTGCGgtaagttaaa ... ctttttgcagATTGTACTCGCTGTGAAGCTAGGGATGGCAGCAGACGAGGCGATTAAATCC
EST: gi|169063357|gb|FE472191.1|FE472191
EST:     CGCGGCAACTAATTACAACAATCGAGTTGTTGAGTGCCGTTTGGCTGCG                         ATTGTACTCGCTGTGAAGCTAGGGACGGCAGCAGACGAGGCGATTAAATCC
genomic: CGCGGCAACTAATTACAACAATCGAGTTGTTGAGTGCCGTTTGGCTGCGgtaagttaaa ... ctttttgcagATTGTACTCGCTGTGAAGCTAGGGATGGCAGCAGACGAGGCGATTAAATCC
EST: gi|169071790|gb|FE476647.1|FE476647
EST:     CCGCGGCAACTAATTACAACAATCGAGTTGTTGAGTGCCGTTTGGCTGCG                         ATTGTACTCGCTGTGAAGCTAGGGACGGCAGCAGACGAGGCGATTAAATCC
genomic: CCGCGGCAACTAATTACAACAATCGAGTTGTTGAGTGCCGTTTGGCTGCGgtaagttaaa ... ctttttgcagATTGTACTCGCTGTGAAGCTAGGGATGGCAGCAGACGAGGCGATTAAATCC
EST: gi|169019356|gb|FE427666.1|FE427666
EST:     CCGCGGCAACTA-TTACAACAATCGAGTTGTTGAGTGCCGTTTGGCTGCG                         ATTGTACTCGCTGTGAAGCTAGGGATGGCA
genomic: CCGCGGCAACTAATTACAACAATCGAGTTGTTGAGTGCCGTTTGGCTGCGgtaagttaaa ... ctttttgcagATTGTACTCGCTGTGAAGCTAGGGATGGCA
EST: gi|169063356|gb|FE472190.1|FE472190
EST:     GCAACTAATTACAACAATCGAGTTGTTGAGTGCCGTTTGGCTGCG                         ATTGTACTCGCTGTGAAGCTAGGGACGGCAGCAGACGAGGCGATTAAATCC
genomic: GCAACTAATTACAACAATCGAGTTGTTGAGTGCCGTTTGGCTGCGgtaagttaaa ... ctttttgcagATTGTACTCGCTGTGAAGCTAGGGATGGCAGCAGACGAGGCGATTAAATCC

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), 22 (downstream exon)
Score: 7

TGGTACCTTCGTAGTTGCGAACTCGCTTACAGAATCTAACAAGGCTGTAACCGCGGCAACTAATTACAACAATCGAGTTGTTGAGTGCCGTTTGGCTGCGgtaagttaaa ... ctttttgcagATTGTACTCGCTGTGAAGCTAGGGATGGCAGCAGACGAGGCGATTAAATCCGTGTCCACACTGTCTGATGTAGAAGGCTTGTGCGAGGCGTATGCAACTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaagttaaaagttttcctctcacggtttttttattgtccaacgcctttttgcagATTGTACTCGCTGTGAAGCTAGGGATGGCAGCAGACGAGGCGATTAAATCCGTGTCCACACTGTCTGATGTAGAAGGCTTGTGCGAGGCGTATGCAACTT
                 ctctcac  putative branch site (score: 7)
                                          cgccttttt  putative PPT
                          tttttttattgt  TA-rich tract