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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtaacaactcgatacgtcttgtcgcccgttactaacatgaggtatttcttttcagTGCCACCTCAGGAAGAAGCATCCAAATGTCTTTGCGGCGCTCTTCTCTTCGACCTTCCGCCCCTGGGACATTGCACGCGGTGACACACTGGCTCCGCGAC

Basic information

species Selaginella moellendorffii
transcript EFJ17159
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|169045759|gb|FE451186.1|FE451186
EST:     GGGTGCCTTTGATTTGCAAGAGCACTCGTTGTCCAGATGTGCTCCAAGCT                         TGCCACCTCAGGAAGAAGCATCCAAATGTCTTTGCGGCGCNNNNNNNNNCG
genomic: GGGTGCCTTTGATTTGCAAGAGCACTCGTTGTCCAGATGTGCTCCAAGCTgtgagtaaca ... ttcttttcagTGCCACCTCAGGAAGAAGCATCCAAATGTCTTTGCGGCGCTCTTCTCTTCG
EST: gi|169070813|gb|FE480649.1|FE480649
EST:     GGGTGCCTTTGATTTGCAAGAGCACTCGTTGTCCAGATGTGCTCCAAGCT                         TGCCACCTCAGGAAGAAGCATCCAAATGTCTTTGCGGCGCTCTTCTCTTCG
genomic: GGGTGCCTTTGATTTGCAAGAGCACTCGTTGTCCAGATGTGCTCCAAGCTgtgagtaaca ... ttcttttcagTGCCACCTCAGGAAGAAGCATCCAAATGTCTTTGCGGCGCTCTTCTCTTCG
EST: gi|169081337|gb|FE488768.1|FE488768
EST:     GGGTGCCTTTGATTTGCAAGAGCACTCGTTGTCCAGATGTGCTCCAAGCT                         TGCCACCTCAGGAAGAAGCATCCAAATGTCTTTGCGGCGCTCTTCTCTTCG
genomic: GGGTGCCTTTGATTTGCAAGAGCACTCGTTGTCCAGATGTGCTCCAAGCTgtgagtaaca ... ttcttttcagTGCCACCTCAGGAAGAAGCATCCAAATGTCTTTGCGGCGCTCTTCTCTTCG
EST: gi|169115457|gb|FE516198.1|FE516198
EST:     GGGTGCCTTTGATTTGCAAGAGCACTCGTTGTCCAGATGTGCTCCAAGCT                         TGCCACCTCAGGAAGAAGCATCCAAATGTCTTTGCGGCGCTCTTCTCTTCG
genomic: GGGTGCCTTTGATTTGCAAGAGCACTCGTTGTCCAGATGTGCTCCAAGCTgtgagtaaca ... ttcttttcagTGCCACCTCAGGAAGAAGCATCCAAATGTCTTTGCGGCGCTCTTCTCTTCG
EST: gi|169081338|gb|FE488769.1|FE488769
EST:     GGGTGCCTTTGATTTGCAAGAGCACTCGTTGTCCAGATGTGCTCCAAGCT                         TGCCACCTCAGGAAGAAGCATCCAAATGTCTTTGCGGCGCTCTTCTCTTCG
genomic: GGGTGCCTTTGATTTGCAAGAGCACTCGTTGTCCAGATGTGCTCCAAGCTgtgagtaaca ... ttcttttcagTGCCACCTCAGGAAGAAGCATCCAAATGTCTTTGCGGCGCTCTTCTCTTCG
EST: gi|169088108|gb|FE493360.1|FE493360
EST:     GGGTGCCTTTGATTTGCAAGAGCACTCGTTGTCCAGATGTGCTCCAAGCT                         TGCCACCTCAGGAAGAAGCATCCAAATGTCTTTGCGGCGCTCTTCTCTTCG
genomic: GGGTGCCTTTGATTTGCAAGAGCACTCGTTGTCCAGATGTGCTCCAAGCTgtgagtaaca ... ttcttttcagTGCCACCTCAGGAAGAAGCATCCAAATGTCTTTGCGGCGCTCTTCTCTTCG

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), 34 (downstream exon)
Score: 64

AGTCCTATCAGCATGCTGCTTCTCTTTCTCGACTGGGACAAGAGCGGGTGCCTTTGATTTGCAAGAGCACTCGTTGTCCAGATGTGCTCCAAGCTgtgagtaaca ... ttcttttcagTGCCACCTCAGGAAGAAGCATCCAAATGTCTTTGCGGCGCTCTTCTCTTCGACCTTCCGCCCCTGGGACATTGCACGCGGTGACACACTGGCTCCGCGAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaacaactcgatacgtcttgtcgcccgttactaacatgaggtatttcttttcagTGCCACCTCAGGAAGAAGCATCCAAATGTCTTTGCGGCGCTCTTCTCTTCGACCTTCCGCCCCTGGGACATTGCACGCGGTGACACACTGGCTCCGCGAC
                             tactaac  putative branch site (score: 64)
                                          tatttcttttc  putative PPT
                                          tatttctttt  TA-rich tract