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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtctcgtttgtctcgtttctatcgtaagacacgcgctaaacgaggctgtgtgttttgtagGCTCTTTTCGTGCGGAACTAGCAAGGAGGGTGACTCATTCCTTGTCGAGTGGAATGAAAGTGAAGGGGCTATCAAACGCACGTACATTGGATTCCGTAAG

Basic information

species Selaginella moellendorffii
transcript EFJ35798
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ35798 (Selaginella moellendorffii), 3'ss of exon 14
lower sequence: GLYMA03G39290.1 (Glycine max), 3'ss of exon 15
------------------------------------------------gtttgtctcgtttgtctcgtttctatcgtaa-------gacacgcgctaaacgaggctgtgtgttttgtagGCTCTTTTCGTGCGGAACTAGCAAGGAGGGTGACTCATTCCTTGTCGAGTGGAATGAAAGTGAAGGGGCTATCAAACGCACGTACATTGGATTCCGTAAG
                                                | |  |    ||||    || |  |    ||        ||| |   |           |   || | ||| || ||||| ||||||||||| || || || || ||||| ||||| || ||||||||||||||||| || || ||  | || |||| ||| ||| | |||
gtaagaaggatttgggtgcggataagtatttaagtttcatgttcaatggataattgaatttgagatgtattaaataaaaccgtattaacatgtcttcctatttatcattatttctatagACTGTTTTCTTGCGGAACTAGTAAAGATGGAGAGTCATTTCTTGTTGAATGGAATGAAAGTGAAGGAGCCATTAAGAGAACATACAATGGGTTCAGAAAG
















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|169025921|gb|FE432882.1|FE432882
EST:     TTGGATGCGCCTGGAAGTTGGTGCACAACAATGGCCTACAATGGCACAAG                         GCTCTTTTCGTGCGGAACTAGCAAGGAGGGTGACTCATTCCTTGTCGAGTG
genomic: TTGGATGCGCCTGGAAGTTGGTGCACAACAATGGCCTACAATGGCACAAGgtttgtctcg ... tgttttgtagGCTCTTTTCGTGCGGAACTAGCAAGGAGGGTGACTCATTCCTTGTCGAGTG
EST: gi|169027203|gb|FE436114.1|FE436114
EST:     TGGATGCGCCTGGAAGTTGGTGCACAACAATGGCCTANCA-TGGCACAAG                         GCTCTTTTCGTGCGGGACTAGCAAGGAGGGTGACTCATTCCTTGTCGAGTG
genomic: TGGATGCGCCTGGAAGTTGGTGCACAACAATGGCCTA-CAATGGCACAAGgtttgtctcg ... tgttttgtagGCTCTTTTCGTGCGGAACTAGCAAGGAGGGTGACTCATTCCTTGTCGAGTG

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: 31

ACGGCAAAATCAAGGCGTGGCTGTACGATTGCTTTGGTTCACGGGGTGACTTGGATGCGCCTGGAAGTTGGTGCACAACAATGGCCTACAATGGCACAAGgtttgtctcg ... tgttttgtagGCTCTTTTCGTGCGGAACTAGCAAGGAGGGTGACTCATTCCTTGTCGAGTGGAATGAAAGTGAAGGGGCTATCAAACGCACGTACATTGGATTCCGTAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttgtctcgtttctatcgtaagacacgcgctaaacgaggctgtgtgttttgtagGCTCTTTTCGTGCGGAACTAGCAAGGAGGGTGACTCATTCCTTGTCGAGTGGAATGAAAGTGAAGGGGCTATCAAACGCACGTACATTGGATTCCGTAAG
                            cgctaaa  putative branch site (score: 31)
          tttctat  TA-rich tract