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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagccacatctttcactcctctatagcaaagatcaccataacattcgcttgtgtgtttccaaaagGTTGAGCTTCATCCAGTGTGGCAGCAGCGAAAGCTTCGAGACTTTTGCAGCAGCATGGGGATCCAAGTCGTGGCATGGTCTCCACTGGGTGGTCTTGGAA

Basic information

species Selaginella moellendorffii
transcript EFJ25928
intron # 3
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|169071013|gb|FE480693.1|FE480693
EST:     AGCTCCAGGACTTGATGGAGCATGCCAAAGTCATCCCAGCAGTTAACCAG                         GTTGAGCTTCATCCAGTGTGGCAGCAGCGAAAGCTTCGAGACTTTTGCAGC
genomic: AGCTCCAGGACTTGATGGAGCATGCCAAAGTCATCCCAGCAGTTAACCAGgtagccacat ... tttccaaaagGTTGAGCTTCATCCAGTGTGGCAGCAGCGAAAGCTTCGAGACTTTTGCAGC
EST: gi|169095805|gb|FE498379.1|FE498379
EST:     AGCTCCAGGACTTGATGGAGCATGCCAAAGTCATCCCAGCAGTTAACCAG                         GTTGAGCTTCATCCAGTGTGGCAGCAGCGAAAGCTTCGAGACTTTTGCAGC
genomic: AGCTCCAGGACTTGATGGAGCATGCCAAAGTCATCCCAGCAGTTAACCAGgtagccacat ... tttccaaaagGTTGAGCTTCATCCAGTGTGGCAGCAGCGAAAGCTTCGAGACTTTTGCAGC
EST: gi|169082071|gb|FE486462.1|FE486462
EST:     AGCTCCAGGACTTGATGGAGCATGCCAAAGTCATCCCAGCAGTTAACCAG                         GTTGAGCTTCATCCAGTGTGGCAGCAGCGAAAGCTTCGAGACTTTTGCAGC
genomic: AGCTCCAGGACTTGATGGAGCATGCCAAAGTCATCCCAGCAGTTAACCAGgtagccacat ... tttccaaaagGTTGAGCTTCATCCAGTGTGGCAGCAGCGAAAGCTTCGAGACTTTTGCAGC
EST: gi|169037551|gb|FE446292.1|FE446292
EST:     AGCTCCAGGACTTGATGGAGCATGCCAAAGTCATCCCAGCAGTTAACCAG                         GTTGAGCTTCATCCAGTGTGGCAGCAGCGAAAGCTTCGAGACTTTTGCAGC
genomic: AGCTCCAGGACTTGATGGAGCATGCCAAAGTCATCCCAGCAGTTAACCAGgtagccacat ... tttccaaaagGTTGAGCTTCATCCAGTGTGGCAGCAGCGAAAGCTTCGAGACTTTTGCAGC
EST: gi|169082070|gb|FE486461.1|FE486461
EST:     AGCTCCAGGACTTGATGGAGCATGCCAAAGTCATCCCAGCAGTTAACCAG                         GTTGAGCTTCATCCAGTGTGGCAGCAGCGAAAGCTTCGAGACTTTTGCAGC
genomic: AGCTCCAGGACTTGATGGAGCATGCCAAAGTCATCCCAGCAGTTAACCAGgtagccacat ... tttccaaaagGTTGAGCTTCATCCAGTGTGGCAGCAGCGAAAGCTTCGAGACTTTTGCAGC
EST: gi|70669580|gb|DN838157.1|DN838157
EST:     AGCTCCAGGACTTGATGGAGCATGCCAAAGTCATCCCAGCAGTTAACCAG                         GTTGAGCTTCATCCAGTGTGGCAGCAGCGAAAGCTTCGAGACTTTTGCAGC
genomic: AGCTCCAGGACTTGATGGAGCATGCCAAAGTCATCCCAGCAGTTAACCAGgtagccacat ... tttccaaaagGTTGAGCTTCATCCAGTGTGGCAGCAGCGAAAGCTTCGAGACTTTTGCAGC
EST: gi|169100748|gb|FE502182.1|FE502182
EST:     AGCTCCAGGACTTGATGGAGCATGCCAAAGTCATCCCAGCAGTTAACCAG                         GTTGAGCTTCATCCAGTGTGGCAGCAGCGAAAGCTTCGAGACTTTTGCAGC
genomic: AGCTCCAGGACTTGATGGAGCATGCCAAAGTCATCCCAGCAGTTAACCAGgtagccacat ... tttccaaaagGTTGAGCTTCATCCAGTGTGGCAGCAGCGAAAGCTTCGAGACTTTTGCAGC
EST: gi|169037552|gb|FE446293.1|FE446293
EST:     AGCTCCAGGACTTGATGGAGCATGCCAAAGTCATCCCAGCAGTTAACCAG                         GTTGAGCTTCATCCAGTGTGGCAGCAGCGAAAGCTTCGAGACTTTTGCAGC
genomic: AGCTCCAGGACTTGATGGAGCATGCCAAAGTCATCCCAGCAGTTAACCAGgtagccacat ... tttccaaaagGTTGAGCTTCATCCAGTGTGGCAGCAGCGAAAGCTTCGAGACTTTTGCAGC

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: 30

GCAGCAGGGTCTTGCTCGAGCGATTGGAGTGAGTAACTTTAGCGTGAAAAAGCTCCAGGACTTGATGGAGCATGCCAAAGTCATCCCAGCAGTTAACCAGgtagccacat ... tttccaaaagGTTGAGCTTCATCCAGTGTGGCAGCAGCGAAAGCTTCGAGACTTTTGCAGCAGCATGGGGATCCAAGTCGTGGCATGGTCTCCACTGGGTGGTCTTGGAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcactcctctatagcaaagatcaccataacattcgcttgtgtgtttccaaaagGTTGAGCTTCATCCAGTGTGGCAGCAGCGAAAGCTTCGAGACTTTTGCAGCAGCATGGGGATCCAAGTCGTGGCATGGTCTCCACTGGGTGGTCTTGGAA
                         ccataac  putative branch site (score: 30)
                                           tgtttcc  putative PPT
                           ataacatt  TA-rich tract