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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcgttttcccatatgtctctagggacatcagtaactattgtattttttccacagGTTCCCATGACGCGCATCAGGAAAAGAATTGCCACTCGTCTAAAAGATGCTCAAAACACCTTGGCGTTGCTCACGACTTTCAACGAAGTTGACAT

Basic information

species Selaginella moellendorffii
transcript EFJ38519
intron # 4
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|169070985|gb|FE478923.1|FE478923
EST:     CG-GGCCTTCAACAGAACCACAACTACCT-CTAAAG-AAGGGAGCGACGA                         GTTCCCATGACGCGCATCAGGAAAAGAATTGCCACTCGTCTAAAAGATGCT
genomic: CGCTGCCTTCAACAGAACCACAACTACCTCCCAAAGAAAGGGAGCGACGAgtaagcgttt ... ttttccacagGTTCCCATGACGCGCATCAGGAAAAGAATTGCCACTCGTCTAAAAGATGCT
EST: gi|169070986|gb|FE478924.1|FE478924
EST:     CGCGGCCTTCAACAGAACCACAACTACCTCCTAAAGAAAGGGAGCGACGA                         GTTCCCATGACGCGCATCAGGAAAAGAATTGCCACTCGTCTAAAAGATGCT
genomic: CGCTGCCTTCAACAGAACCACAACTACCTCCCAAAGAAAGGGAGCGACGAgtaagcgttt ... ttttccacagGTTCCCATGACGCGCATCAGGAAAAGAATTGCCACTCGTCTAAAAGATGCT

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: 34 (upstream exon), 33 (downstream exon)
Score: 4

TCCACCTCCTCCGCAACCGCCGCCGCCGCCGCCGCCACCGTCCTCACCGCCGCTGCCTTCAACAGAACCACAACTACCTCCCAAAGAAAGGGAGCGACGAgtaagcgttt ... ttttccacagGTTCCCATGACGCGCATCAGGAAAAGAATTGCCACTCGTCTAAAAGATGCTCAAAACACCTTGGCGTTGCTCACGACTTTCAACGAAGTTGACAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcgttttcccatatgtctctagggacatcagtaactattgtattttttccacagGTTCCCATGACGCGCATCAGGAAAAGAATTGCCACTCGTCTAAAAGATGCTCAAAACACCTTGGCGTTGCTCACGACTTTCAACGAAGTTGACAT
                             cagtaac  putative branch site (score: 4)
                                         tattttttcc  putative PPT
                                taactattgtattttt  TA-rich tract