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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtatctcctttcataggaacgatgtggttttgtttgatctcctcatttaatttcagGCTTGGGCTCGGCTATGTAAATGTTTGGGTCAAGAATTTTTACCGTATATGAATGTTGTTATGCCACCCCTTCTGCGCTCTGCGCAACTTAAACCAGACG

Basic information

species Selaginella moellendorffii
transcript EFJ38876
intron # 6
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|169101638|gb|FE503067.1|FE503067
EST:     GGATGACGATCCAACCATTAGCTACATGCTGCAG                         GCTTGGGCCCGGCTATGTAAATGTTTGGGTCAAGAATTTTTACCGTATATG
genomic: GGATGACGATCCAACCATTAGCTACATGTTGCAGgtttgtatct ... ttaatttcagGCTTGGGCTCGGCTATGTAAATGTTTGGGTCAAGAATTTTTACCGTATATG
EST: gi|169093463|gb|FE496550.1|FE496550
EST:     AGGGTGCGCACTTGGAGGATGACGATCCAACCATTAGCTACATGCTGCAG                         GCTTGGGCCCGGCTATGTAAATGTTTGGGTCAAGAATTTTTACCGTATATG
genomic: AGGGTGCGCACTTGGAGGATGACGATCCAACCATTAGCTACATGTTGCAGgtttgtatct ... ttaatttcagGCTTGGGCTCGGCTATGTAAATGTTTGGGTCAAGAATTTTTACCGTATATG

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: 33 (upstream exon), 20 (downstream exon)
Score: 3

GTGATGGAAGTTCTGATGACCCTCCAGGGTGCGCACTTGGAGGATGACGATCCAACCATTAGCTACATGTTGCAGgtttgtatct ... ttaatttcagGCTTGGGCTCGGCTATGTAAATGTTTGGGTCAAGAATTTTTACCGTATATGAATGTTGTTATGCCACCCCTTCTGCGCTCTGCGCAACTTAAACCAGACG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatctcctttcataggaacgatgtggttttgtttgatctcctcatttaatttcagGCTTGGGCTCGGCTATGTAAATGTTTGGGTCAAGAATTTTTACCGTATATGAATGTTGTTATGCCACCCCTTCTGCGCTCTGCGCAACTTAAACCAGACG
                                           atttaat  putative branch site (score: 3)
                                    tctcctcattt  CT-rich tract
                                         tcatttaattt  TA-rich tract