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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCGACGTTTTTCCGGTTTGGGAAGCATGGGGTTACGCACTACTTCGGATAGAACATTATGCGCAAGCCAGGCTAAAGTTCAAgcaagtatctttttgtttgaccatcttatcactctaacctggcaacttacag

Basic information

species Selaginella moellendorffii
transcript EFJ21919
intron # 25
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ21919 (Selaginella moellendorffii), 5'ss of exon 25
lower sequence: PP1S109_57V6.1 (Physcomitrella patens), 5'ss of exon 28
ATCGACGTTTTTCCGGTTTGGGAAGCATGGGGTTACGCACTACTTCGGATAGAACATTATGCGCAAGCCAGGCTAAAGTTCAAgcaagtatctttttgtttgaccatcttatcactctaacctggcaacttacag-----------------------------------------------------------------------------------------------------------------------------------------------------
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ATTAATCCGTGCCTAGTTTGGGAAGCATGGGGTTACGCGCTCCTTCGTATTGAGCACTACGCTCAAGCAAGGGTAAAGTTCAAgtgagtaaagctcc--tgcactgtagtattatttgaatgaagtgtattctagagttacattctgtccaacttcagaatattttgcaacataccttcaagagttcccgcttcttaggtttatctgcgttgtttgttgggatcagatgcttgtgcagccgttgaatattgatatctgatcacatacttctttatggctttcag
















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|169115117|gb|FE516690.1|FE516690
EST:     TACGCACTACTTCGGATAGAACATTATGCGCAAGCCAGGCTAAAGTTCAA                         GAAAGCATTTCAATTATACAAGGAAGATTCATCCAAGATTGTTCAGAGAAT
genomic: TACGCACTACTTCGGATAGAACATTATGCGCAAGCCAGGCTAAAGTTCAAgcaagtatct ... caacttacagGAAAGCATTTCAATTATACAAGGAAGATTCATCCAAGATTGTTCAGAGAAT
EST: gi|169046678|gb|FE455420.1|FE455420
EST:     TACGCACTACTTCGGATAGAACATTATGCGCAAGCCAGGCTAAAGTTCAA                         GAAAGCATTTCAATTATACAAGGAAGATTCATCCAAGATTGTTCAGAGAAT
genomic: TACGCACTACTTCGGATAGAACATTATGCGCAAGCCAGGCTAAAGTTCAAgcaagtatct ... caacttacagGAAAGCATTTCAATTATACAAGGAAGATTCATCCAAGATTGTTCAGAGAAT
EST: gi|169055737|gb|FE466668.1|FE466668
EST:     TACGCACTACTTCGGATAGAACATTATGCGCAAGCCAGGCTAAAGTTCAA                         GAAAGCATTTCAATTATACAAGGAAGATTCATCCAAGATCGTTCAGAGAAT
genomic: TACGCACTACTTCGGATAGAACATTATGCGCAAGCCAGGCTAAAGTTCAAgcaagtatct ... caacttacagGAAAGCATTTCAATTATACAAGGAAGATTCATCCAAGATTGTTCAGAGAAT
EST: gi|169076901|gb|FE485294.1|FE485294
EST:     TACGCACTACTTCGGATAGAACATTATGCGCAAGCCAGGCTAAAGTTCAA                         GAAAGCATTTCAATTATACAAGGAAGATTCATCCAAGATTGTTCAGAGAAT
genomic: TACGCACTACTTCGGATAGAACATTATGCGCAAGCCAGGCTAAAGTTCAAgcaagtatct ... caacttacagGAAAGCATTTCAATTATACAAGGAAGATTCATCCAAGATTGTTCAGAGAAT

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: 10

ATCGACGTTTTTCCGGTTTGGGAAGCATGGGGTTACGCACTACTTCGGATAGAACATTATGCGCAAGCCAGGCTAAAGTTCAAgcaagtatct ... caacttacagGAAAGCATTTCAATTATACAAGGAAGATTCATCCAAGATTGTTCAGAGAATAGTTGACAATGTGGAGGCATGCCCTGCTGCTGATGTCCATGCTGCACGT




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