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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTCAGTCTTCTTGGGCCTGTGGATGAGATGTTCATTGACGTTTACGACAGGTTTGAACCAGTGAATGACTGGACACTGGATAACTGCTTTATTTCCAAGgtgatgctccatttctctccagaaaaaggatgttgctaatcatccatcgttggcttttttcag

Basic information

species Selaginella moellendorffii
transcript EFJ11673
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ11673 (Selaginella moellendorffii), 5'ss of exon 11
lower sequence: GLYMA07G30050.1 (Glycine max), 5'ss of exon 11
GCTCAGTCTTCTTGGGCCTGTGGATGAGATGTTCATTGACGTTTACGACAGGTTTGAACCAGTGAATGACTGGACACTGGATAACTGCTTTATTTCCAAGgtgatgctccatttc--tctccagaaaaaggatgttgctaatcatccatcgttggcttttttcag-----------------------------------
  |    |||||||| ||||| ||||| || |||  |||| |||||||||||||||||||    |||||      |   |||   || || || || |  || |   |  | |    ||||    |     || ||  |  || |   | |||  ||| ||||                                     
TATTGACCTTCTTGGACCTGTTGATGAAATATTCTATGACATTTACGACAGGTTTGAACCCTGCAATGATCATGAAGCTGATGGTTGTTTCATCTCTACAgtaagtattgagtagaatctctgacatgcatattttatttttcttttgttgttttcttatttcctcctaaccattgtgaagtggcactggcaatcgcaat
















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|169057386|gb|FE466821.1|FE466821
EST:     GGTTTGAACCAGTGAATGACTGGACACTGGATAACTGCTTTATTTCCAAG                         AGCTACGACCCAACCACACACTTTGAGACTACAGTGCAAGATGTTCTTGCC
genomic: GGTTTGAACCAGTGAATGACTGGACACTGGATAACTGCTTTATTTCCAAGgtgatgctcc ... cttttttcagAGCTACGACCCAACCACACACTTTGAGACTACAGTGCAAGATGTTCTTGCC
EST: gi|169038887|gb|FE449604.1|FE449604
EST:     GGTTTGAACCAGTGAATGACTGGACACTGGATAACTGCTTTATTTCCAAG                         AGCTACGACCCAACCACACACTTTGAGACTACAGTGCAAGATGTTCTTGCC
genomic: GGTTTGAACCAGTGAATGACTGGACACTGGATAACTGCTTTATTTCCAAGgtgatgctcc ... cttttttcagAGCTACGACCCAACCACACACTTTGAGACTACAGTGCAAGATGTTCTTGCC
EST: gi|169070710|gb|FE477309.1|FE477309
EST:     GGTTTGAACCAGTGAATGACTGGACACTGGATAACTGCTTTATTTCCAAG                         AGCTACGACCCAACCACACACTTTGAGACTACAGTGCAAGATGTTCTTGCC
genomic: GGTTTGAACCAGTGAATGACTGGACACTGGATAACTGCTTTATTTCCAAGgtgatgctcc ... cttttttcagAGCTACGACCCAACCACACACTTTGAGACTACAGTGCAAGATGTTCTTGCC
EST: gi|169093396|gb|FE492700.1|FE492700
EST:     GGTTTGAACCAGTGAATGACTGGACACTGGATAACTGCTTTATTTCCAAG                         AGCTACGACCCAACCACACACTTTGAGACTACAGTGCAAGATGTTCTTGCC
genomic: GGTTTGAACCAGTGAATGACTGGACACTGGATAACTGCTTTATTTCCAAGgtgatgctcc ... cttttttcagAGCTACGACCCAACCACACACTTTGAGACTACAGTGCAAGATGTTCTTGCC
EST: gi|169092637|gb|FE493657.1|FE493657
EST:     GGTTTGAACCAGTGAATGACTGGACACTGGATAACTGCTTTATTTCCAAG                         AGCTACGACCCAACCACACACTTTGAGACTACAGTGCAAGATGTTCTTGCC
genomic: GGTTTGAACCAGTGAATGACTGGACACTGGATAACTGCTTTATTTCCAAGgtgatgctcc ... cttttttcagAGCTACGACCCAACCACACACTTTGAGACTACAGTGCAAGATGTTCTTGCC
EST: gi|169038296|gb|FE445308.1|FE445308
EST:     GGTTTGAACCAGTGAATGACTGGACACTGGATAACTGCTTTATTTCCAAG                         AGCTACGACCCAACCACACACTTTGAGACTACAGTGCAAGATGTTCTTGCC
genomic: GGTTTGAACCAGTGAATGACTGGACACTGGATAACTGCTTTATTTCCAAGgtgatgctcc ... cttttttcagAGCTACGACCCAACCACACACTTTGAGACTACAGTGCAAGATGTTCTTGCC
EST: gi|169083494|gb|FE491925.1|FE491925
EST:     GGTTTGAACCAGTGAATGACTGGACACTGGATAACTGCTTTATTTCCAAG                         AGCTACGACCCAACCACACACTTTGAGACTACAGTGCAAGATGTTCTTGCC
genomic: GGTTTGAACCAGTGAATGACTGGACACTGGATAACTGCTTTATTTCCAAGgtgatgctcc ... cttttttcagAGCTACGACCCAACCACACACTTTGAGACTACAGTGCAAGATGTTCTTGCC

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 2 RNA-Seq libraries.


Block sizes: 28 (upstream exon), 8 (downstream exon)
Score: 1

GCTCAGTCTTCTTGGGCCTGTGGATGAGATGTTCATTGACGTTTACGACAGGTTTGAACCAGTGAATGACTGGACACTGGATAACTGCTTTATTTCCAAGgtgatgctcc ... cttttttcagAGCTACGACCCAACCACACACTTTGAGACTACAGTGCAAGATGTTCTTGCCATGTACACCCGCATAACCGGAAAG


Block sizes: 35 (upstream exon), 35 (downstream exon)
Score: 108

GCTCAGTCTTCTTGGGCCTGTGGATGAGATGTTCATTGACGTTTACGACAGGTTTGAACCAGTGAATGACTGGACACTGGATAACTGCTTTATTTCCAAGgtgatgctcc ... cttttttcagAGCTACGACCCAACCACACACTTTGAGACTACAGTGCAAGATGTTCTTGCCATGTACACCCGCATAACCGGAAAG




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