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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAATGGGAAAATCGGTCATGTAAATCAAGGCAACAATATGTACCTTTTCCCAGGgtgtgtaaattcttcatgtggttttcaacgcgtttaaaaccgctgttttctattag

Basic information

species Selaginella moellendorffii
transcript EFJ21048
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ21048 (Selaginella moellendorffii), 5'ss of exon 15
lower sequence: GLYMA09G39870.1 (Glycine max), 5'ss of exon 15
AGAATGGGAAAATCGGTCATGTAAATCAAGGCAACAATATGTACCTTTTCCCAGGgtgtgtaaattcttcatgtggttttcaacgcgtttaaaaccgctgttttctattag---------------------------------------
  |||||  || | || ||||||||||||| |||||| |||||||| ||||||||||  | |    |||  || | |||  ||    || |  |    ||      | | |                                       
GAAATGGAGAAGTTGGCCATGTAAATCAAGCCAACAACATGTACCTGTTCCCAGGgtaggcatgc-ctttgtg-gctttataattttttcatgaatcatgccactcagtggaaacattgttgtaatttctattgaaacattccatttcag

upper sequence: EFJ21048 (Selaginella moellendorffii), 5'ss of exon 15
lower sequence: GLYMA03G01680.1 (Glycine max), 5'ss of exon 15
AGAATGGGAAAATCGGTCATGTAAATCAAGGCAACAATATGTACCTTTTCCCAGGgt---gtgtaaattcttcatgtg-gttttcaacgcgtttaaaaccgctgttt--tctattag---------------------------------------
  ||||| ||| | ||||||||||||||||  ||||| |||||||| ||||||||||   || ||  | |||  | ||  | |||  |    ||| | | |     |    ||||||                                       
GTAATGGAAAAGTGGGTCATGTAAATCAAGCAAACAACATGTACCTCTTCCCAGGgtagggtttatctccttggtttgtatattcttctgaattatacctgtcagctgaattattagtgtaacttactaacttctagtttaactttttcattccag

upper sequence: EFJ21048 (Selaginella moellendorffii), 5'ss of exon 15
lower sequence: GLYMA07G08110.1 (Glycine max), 5'ss of exon 15
AGAATGGGAAAATCGGTCATGTAAATCAAGGCAACAATATGTACCTTTTCCCAGGgt---gtgtaaattcttcatgtg-gttttcaacgcgtttaaaaccgctgttt--tctattag---------------------------------------
  ||||| |   | ||||||||||||||||  ||||| |||||||| ||||||||||   || ||  | |||    ||  | |||  |    ||| | | |    ||    ||||||                                       
GTAATGGAATTGTGGGTCATGTAAATCAAGCAAACAACATGTACCTCTTCCCAGGgtagggtttatctccttggcttgtatattcttctgaattatacctgtcaattgaattattagtgtaacttactaacttctagtttaactttttcattccag

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|169073337|gb|FE481101.1|FE481101
EST:     GGGAAAATCGGTCATGTAAATCAAGGCAACAATATGTACCTTTTCCCAGG                         AATTGGACTCGGCACGCTCCTCTGTGGAGCAAGAACAGTTACAGATCGAAT
genomic: GGGAAAATCGGTCATGTAAATCAAGGCAACAATATGTACCTTTTCCCAGGgtgtgtaaat ... tttctattagAATTGGACTCGGCACGCTCCTCTGTGGAGCAAGAACAGTTACAGATCGAAT
EST: gi|169094681|gb|FE492494.1|FE492494
EST:     GGGAAAATCGGTCATGTAAATCAAGGCAACAATATGTACCTTTTCCCAGG                         AATTGGACTCGGCACGCTCCTCTGTGGAGCAAGAACAGTTACAGATCGAAT
genomic: GGGAAAATCGGTCATGTAAATCAAGGCAACAATATGTACCTTTTCCCAGGgtgtgtaaat ... tttctattagAATTGGACTCGGCACGCTCCTCTGTGGAGCAAGAACAGTTACAGATCGAAT
EST: gi|169056283|gb|FE464106.1|FE464106
EST:     GGGAAAATCGGTCATGTAAATCAAGGCAACAATATGTACCTTTTCCCAGG                         AATTGGACTCGGCACGCTCCTCTGTGGAGCAAGAACAGTTACAGATCGAAT
genomic: GGGAAAATCGGTCATGTAAATCAAGGCAACAATATGTACCTTTTCCCAGGgtgtgtaaat ... tttctattagAATTGGACTCGGCACGCTCCTCTGTGGAGCAAGAACAGTTACAGATCGAAT
EST: gi|169088830|gb|FE494394.1|FE494394
EST:     GGGAAAATCGGTCATGTAAATCAAGGCAACAATATGTACCTTTTCCCAGG                         AATTGGACTCGGCACGCTCCTCTGTGGAGCAAGAACAGTTACAGATCGAAT
genomic: GGGAAAATCGGTCATGTAAATCAAGGCAACAATATGTACCTTTTCCCAGGgtgtgtaaat ... tttctattagAATTGGACTCGGCACGCTCCTCTGTGGAGCAAGAACAGTTACAGATCGAAT
EST: gi|169022197|gb|FE431806.1|FE431806
EST:     GGGAAAATCGGTCATGTAAATCAAGGCAACAATATGTACCTTTTCCCAGG                         AATTGGACTCGGCACGCTCCTCTGTGGAGCAAGAACAGTTACAGATCGAAT
genomic: GGGAAAATCGGTCATGTAAATCAAGGCAACAATATGTACCTTTTCCCAGGgtgtgtaaat ... tttctattagAATTGGACTCGGCACGCTCCTCTGTGGAGCAAGAACAGTTACAGATCGAAT
EST: gi|169026051|gb|FE434468.1|FE434468
EST:     GGGAAAATCGGTCATGTAAATCAAGGCAACAATATGTACCTTTTCCCAGG                         AATTGGACTCGGCACGCTCCTCTGTGGAGCAAGAACAGTTACAGATCGAAT
genomic: GGGAAAATCGGTCATGTAAATCAAGGCAACAATATGTACCTTTTCCCAGGgtgtgtaaat ... tttctattagAATTGGACTCGGCACGCTCCTCTGTGGAGCAAGAACAGTTACAGATCGAAT

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: 33

AGAATGGGAAAATCGGTCATGTAAATCAAGGCAACAATATGTACCTTTTCCCAGGgtgtgtaaat ... tttctattagAATTGGACTCGGCACGCTCCTCTGTGGAGCAAGAACAGTTACAGATCGAATGTTAAGCTCCGCCGCAGCAAG




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