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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACAAGTTCTTGGTGAAGCGGAATGGCAACAGCAGCGCCTCGGTGCAATTCAGCAGCGAGCCCAACAATCTCTACAATCTCAACACCTACAAGTACTCAGgtgagaaagatcgtctccagctcttttagaaatcccgatgaatgccgcgaatcgtctgttgctggattgatcgcattctctcttttcag

Basic information

species Selaginella moellendorffii
transcript EFJ31412
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ31412 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA13G42830.1 (Glycine max), 5'ss of exon 1
AACAAGTTCTTGGTGAAGCGGAATGGCAACAGCAGCGCCTCGGTGCAATTCAGCAGCGAGCCCAACAATCTCTACAATCTCAACACCTACAAGTACTCAGgtgagaaagatcgt--ctccagctcttttagaaatcccgatgaatgccgcgaatcgtctgttgctggattgatcgcattctctcttttcag------------------
|||   || ||||||||   |   || |   |||        ||||| |||||||| |||||||||||||||||||| |||||||| | ||||||||| ||| | ||  |||||  ||  | |    | |||  |       ||||  | || |  ||   || || ||  | | |||| | |  ||   |                  
AACTCCTTTTTGGTGAAAGAGTTCGGAAGGGGCACTCAGAGCGTGCAGTTCAGCAGAGAGCCCAACAATCTCTACAACCTCAACACTTTCAAGTACTCCGgtaataatcatcgtatctttaaccaagtgagacttattctcaaatgt-gtgattaatcgtatg-tgaataaagctcattttatgcttgtggggcgtatggtattgatag

upper sequence: EFJ31412 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA15G02610.1 (Glycine max), 5'ss of exon 1
AACAAGTTCTTGGTGAAGCGGAATGGCAACAGCAGCGCCTCGGTGCAATTCAGCAGCGAGCCCAACAATCTCTACAATCTCAACACCTACAAGTACTCAGgtgag-----------------aaagatcgtctccagctcttttagaaatcccgatgaat----gccgcgaatc-gtctgttgc----tggattgatcgcattctctcttttcag-----------
|||   |||||||||||   |   || |   |||        ||||| |||||||| |||||||||||||||||||| |||||||| | ||||||||| ||| |                   ||  |  | | ||  | | |||  ||||  |   ||     ||   ||||  |  | || |    || ||  | | |||| | | ||| | |           
AACTCTTTCTTGGTGAAAGAGTTCGGAAGGGGCACTCAGAGCGTGCAGTTCAGCAGAGAGCCCAACAATCTCTACAACCTCAACACTTTCAAGTACTCCGgtaattatctctttacccaagcgaaagttattttcaaatgtgttattaatcgtggaaaactgaagcgttgaattaggtttttacattgtgaataaagctcattttatgtttgcggtggtatgatag
















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|169080152|gb|FE490001.1|FE490001
EST:     CAGCAGCGAGCCCAACAATCTCTACAATCTCAACACCTACAAGTACTCAG                         GCTTGGCTAACAAGAAGACCGTCGCTGTGGCCCCGGCTGGAGAGAAAATGG
genomic: CAGCAGCGAGCCCAACAATCTCTACAATCTCAACACCTACAAGTACTCAGgtgagaaaga ... ctcttttcagGCTTGGCTAACAAGAAGACCGTCGCTGTGGCCCCGGCTGGAGAGAAAATGG
EST: gi|169068162|gb|FE476906.1|FE476906
EST:     CAGCAGCGAGCCCAACAATCTCTACAATCTCAACACCTACAAGTACTCAG                         GCTTGGCTAACAAGAAGACCGTCGCTGTGGCCCCGGCTGGAGAGAAAATGG
genomic: CAGCAGCGAGCCCAACAATCTCTACAATCTCAACACCTACAAGTACTCAGgtgagaaaga ... ctcttttcagGCTTGGCTAACAAGAAGACCGTCGCTGTGGCCCCGGCTGGAGAGAAAATGG
EST: gi|169026830|gb|FE434207.1|FE434207
EST:     CAGCAGCGAGCCCAACAATCTCTACAATCTCAACACCTACAAGTACTCAG                         GCTTGGCTAACAAGAAGACCGTCGCTGTGGCCCCGGCTGGAGAGAAAATGG
genomic: CAGCAGCGAGCCCAACAATCTCTACAATCTCAACACCTACAAGTACTCAGgtgagaaaga ... ctcttttcagGCTTGGCTAACAAGAAGACCGTCGCTGTGGCCCCGGCTGGAGAGAAAATGG
EST: gi|169026831|gb|FE434208.1|FE434208
EST:     CAGCAGCGAGCCCAACAATCTCTACAATCTCAACACCTACAAGTACTCAG                         GCTTGGCTAACAAGAAGACCGTCGCTGTGGCCCCGGCTGGAGAGAAAATGG
genomic: CAGCAGCGAGCCCAACAATCTCTACAATCTCAACACCTACAAGTACTCAGgtgagaaaga ... ctcttttcagGCTTGGCTAACAAGAAGACCGTCGCTGTGGCCCCGGCTGGAGAGAAAATGG
EST: gi|169080151|gb|FE490000.1|FE490000
EST:     CAGCAGCGAGCCCAACAATCTCTACAATCTCAACACCTACAAGTACTCAG                         GCTTGGCTAACAAGAAGACCGTCGCTGTGGCCCCGGCTGGAGAGAAAATGG
genomic: CAGCAGCGAGCCCAACAATCTCTACAATCTCAACACCTACAAGTACTCAGgtgagaaaga ... ctcttttcagGCTTGGCTAACAAGAAGACCGTCGCTGTGGCCCCGGCTGGAGAGAAAATGG

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: 66

AACAAGTTCTTGGTGAAGCGGAATGGCAACAGCAGCGCCTCGGTGCAATTCAGCAGCGAGCCCAACAATCTCTACAATCTCAACACCTACAAGTACTCAGgtgagaaaga ... ctcttttcagGCTTGGCTAACAAGAAGACCGTCGCTGTGGCCCCGGCTGGAGAGAAAATGGACATCGTTCTCACCACCACCAAGAAGAAGAAGAGCAACAAGCCCGCATC




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