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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCCGCTCGCGTCCCCAAGAAGGTGCTCCAGTTTGCCGGGATCGAGGATGTTTTCACCTCGTCGCGCGGATCGACCAAGACACTCGGCAACTTCGTCAAGgtgaggattggtctgatcgttctttcattctcgacgagtttttcttggtctttcgcag

Basic information

species Selaginella moellendorffii
transcript EFJ24057
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ24057 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA11G02190.1 (Glycine max), 5'ss of exon 1
TGCCGCTCGCGTCCCCAAGAAGGTGCTCCAGTTTGCCGGGATCGAGGATGTTTTCACCTCGTCGCGCGGATCGACCAAGACACTCGGCAACTTCGTCAAGgtgaggat-tggtctgatcgttctttcattctcgacgagtt---tttcttggtctttcgcag--------------------------------------
 || ||| | || |||||||||||||| ||||| || ||||| || |||||||||||||| ||  | ||||| |||||||| |||||||||||||| |||||  |  | |  | | | |  | | | | | |  |    ||   || |        | | |                                       
GGCGGCTAGGGTTCCCAAGAAGGTGCTGCAGTTCGCGGGGATTGATGATGTTTTCACCTCCTCCAGAGGATCCACCAAGACCCTCGGCAACTTCGTTAAGgtttgtgtatttttttaccaatttgttacttttcatattttagattgccgacgacattgtaaaaatttagggcaaattagggtcgtgcttcaaatgtgac

upper sequence: EFJ24057 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA02G09370.1 (Glycine max), 5'ss of exon 1
TGCCGCTCGCGTCCCCAAGAAGGTGCTCCAGTTTGCCGGGATCGAGGATGTTTTCACCTCGTCGCGCGGATCGACCAAGACACTCGGCAACTTCGTCAAGgtgaggattgg----tctgatcgttctttcattctcgacgagtt----tttcttggt--ctttcgcag--------------------------------
 || ||| | || |||||||||||||| |||||||| || || || |||||||||||||| ||  | ||||| |||||||| || ||||||||||| |||||  |  || |    ||| |    | |     | | |||   ||    | || ||     |||    |                                
GGCGGCTAGGGTTCCCAAGAAGGTGCTGCAGTTTGCTGGTATTGATGATGTTTTCACCTCCTCCAGGGGATCCACCAAGACCCTTGGCAACTTCGTTAAGgtttgtttttggtattcttacaagtttgctgcttttgacattttcaactatcatgaaaatttttatggacgaattaaggttgtaattccaatgtcacaat

upper sequence: EFJ24057 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: PP1S10_190V6.1 (Physcomitrella patens), 5'ss of exon 1
TGCCGCTCGCGTCCCCAAGAAGGTGCTCCAGTTTGCCGGGATCGAGGATGTTTTCACCTCGTCGCGCGGATCGACCAAGACACTCGGCAACTTCGTCAAGgtgag---gattggtctgatcgttctttcattct--cgacgagtttttcttggtctt-tcgcag------------------------------------
 ||||| ||||| |||||||||||  | ||||||||||| || |||||||| |||||||| || ||||| || |||||||| ||||| |||||||| ||||||||   | ||  |  |        ||| |  |   || ||  |   | |  | |  | | |                                     
CGCCGCCCGCGTGCCCAAGAAGGTTTTGCAGTTTGCCGGTATTGAGGATGTGTTCACCTCTTCCCGCGGCTCCACCAAGACCCTCGGTAACTTCGTGAAGgtgagctggtttcattcggaatactcttcgtcttagtgatgaagtaggcctaatttgattgtaatgctgtcgatagtatgttgagcattgacttgtgatg

upper sequence: EFJ24057 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: PP1S400_15V6.1 (Physcomitrella patens), 5'ss of exon 1
TGCCGCTCGCGTCCCCAAGAAGGTGCTCCAGTTTGCCGGGATCGAGGATGTTTTCACCTCGTCGCGCGGATCGACCAAGACACTCGGCAACTTCGTCAAGgtgagga---ttggtctgatcgt----tctttcattctcgacgagtttttcttggtctttcgcag-----------------------------------
 || || ||||| |||||||||||  | ||||| ||||| || ||||||||||||||||| || |||||||| |||||||| ||||| || ||||| |||||||| |   ||| |  |  |||    |  ||   | |  | |   | |  |   || |    ||                                   
CGCTGCACGCGTGCCCAAGAAGGTTTTGCAGTTCGCCGGTATTGAGGATGTTTTCACCTCTTCCCGCGGATCCACCAAGACCCTCGGTAATTTCGTGAAGgtgagcaaatttgcttagggcgtgtgatgcttgtgtgttaatgtactgtattaaatcctgattagggtttctcgattcggaactgaaattgtcctagtct

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|169037289|gb|FE443287.1|FE443287
EST:     TTTTCACCTCGTCGCGCGGATCGACCAAGACTCTGGGAAACTTCGTCAAG                         GCTACGTACGACTGTCTGTTGAAGACGTATGGGTTCCTCACCCCGGATCTG
genomic: TTTTCACCTCGTCGCGCGGATCGACCAAGACACTCGGCAACTTCGTCAAGgtgaggattg ... tctttcgcagGCTACGTACGACTGTCTGTTGAAGACGTATGGGTTCCTCACCCCGGATCTG
EST: gi|169101141|gb|FE503485.1|FE503485
EST:     TTTTCACCTCGTCGCGCGGATCGACCAAGACACTCGGCAACTTCGTCAAG                         GCTACGTACGACTGTCTGTTGAAGACGTATGGGTTCCTCACCCCGGATCTG
genomic: TTTTCACCTCGTCGCGCGGATCGACCAAGACACTCGGCAACTTCGTCAAGgtgaggattg ... tctttcgcagGCTACGTACGACTGTCTGTTGAAGACGTATGGGTTCCTCACCCCGGATCTG
EST: gi|169049580|gb|FE457724.1|FE457724
EST:     TTTTCACCTCGTCGCGCGGATCGACCAAGACACTCGGCAACTTCGTCAAG                         GCTACGTACGACTGTCTGTTGAAGACGTATG
genomic: TTTTCACCTCGTCGCGCGGATCGACCAAGACACTCGGCAACTTCGTCAAGgtgaggattg ... tctttcgcagGCTACGTACGACTGTCTGTTGAAGACGTATG
EST: gi|169110290|gb|FE510619.1|FE510619
EST:     TTTTCACCTCGTCGCGGGGATCGACCAAGACACTCGGCAATTTCGTCAAG                         GCTACGTACGACTGTTTGTTGAAGACGTATGGGTTCCTCCCCCCGGATCTG
genomic: TTTTCACCTCGTCGCGCGGATCGACCAAGACACTCGGCAACTTCGTCAAGgtgaggattg ... tctttcgcagGCTACGTACGACTGTCTGTTGAAGACGTATGGGTTCCTCACCCCGGATCTG
EST: gi|169044278|gb|FE453008.1|FE453008
EST:     TTTTCACCTCGTCGCGCGGATCGACCAAGACACTCGGCAACTTCGTCAAG                         GCTACGTACGACTGTCTGTTGAAGACGTATGGGTTCCTCACCCCGGATCTG
genomic: TTTTCACCTCGTCGCGCGGATCGACCAAGACACTCGGCAACTTCGTCAAGgtgaggattg ... tctttcgcagGCTACGTACGACTGTCTGTTGAAGACGTATGGGTTCCTCACCCCGGATCTG
EST: gi|169037290|gb|FE443288.1|FE443288
EST:     TTTTCACCTCGTCGCGCGGATCGACCAAGACTCTGGGAAACTTCGTCAAG                         GCTACGTACGACTGTCTGTTGAAGACGTATGGGTTCCTCACCCCGGATCTG
genomic: TTTTCACCTCGTCGCGCGGATCGACCAAGACACTCGGCAACTTCGTCAAGgtgaggattg ... tctttcgcagGCTACGTACGACTGTCTGTTGAAGACGTATGGGTTCCTCACCCCGGATCTG
EST: gi|169035202|gb|FE442580.1|FE442580
EST:     TTTTCACCTCGTCGCGCGGATCGACCAAGACACTCGGCAACTTCGTCAAG                         GCTACGTACGACTGTCTGTTGAAGACGTATGGGTTCCTCACCCCGGATCTG
genomic: TTTTCACCTCGTCGCGCGGATCGACCAAGACACTCGGCAACTTCGTCAAGgtgaggattg ... tctttcgcagGCTACGTACGACTGTCTGTTGAAGACGTATGGGTTCCTCACCCCGGATCTG
EST: gi|169100295|gb|FE501092.1|FE501092
EST:     TTTTCACCTCGTCGCGCGGATCGACCAAGACTCTGGGAAACTTCGTCAAG                         GCTACGTACGACTGTCTGTTGAAGACGTATGGGTTCCTCACCCCGGATCTG
genomic: TTTTCACCTCGTCGCGCGGATCGACCAAGACACTCGGCAACTTCGTCAAGgtgaggattg ... tctttcgcagGCTACGTACGACTGTCTGTTGAAGACGTATGGGTTCCTCACCCCGGATCTG
EST: gi|169057178|gb|FE464689.1|FE464689
EST:     TTTTCACCTCGTCGCGCGGATCGACCAAGACACTCGGCAACTTCGTCAAG                         GCTACGTACGACTGTCTGTTGAAGACGTATGGGTTCCTCACCCCGGATCTG
genomic: TTTTCACCTCGTCGCGCGGATCGACCAAGACACTCGGCAACTTCGTCAAGgtgaggattg ... tctttcgcagGCTACGTACGACTGTCTGTTGAAGACGTATGGGTTCCTCACCCCGGATCTG

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: 17

TGCCGCTCGCGTCCCCAAGAAGGTGCTCCAGTTTGCCGGGATCGAGGATGTTTTCACCTCGTCGCGCGGATCGACCAAGACACTCGGCAACTTCGTCAAGgtgaggattg ... tctttcgcagGCTACGTACGACTGTCTGTTGAAGACGTATGGGTTCCTCACCCCGGATCTGTGGAAGGAGACCCGGTTTACCAAGTCGCCGTTCCAGGAGTTCACGGACT




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