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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATGTTCGTCGTGGGTGTGAACGAGAGCGAATACAAGGACGATATGGACATCGTTTCCAACGCGAGTTGCACTACCAATTGTCTTGCGCCTCTTGCGAAGgtgtgttgcgagcttccattgtctttccgtcaaagtttctcgactgttcgatgtttctgataatcttctccag

Basic information

species Selaginella moellendorffii
transcript EFJ30760
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ30760 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: GLYMA18G01330.1 (Glycine max), 5'ss of exon 6
AATGTTCGTCGTGGGTGTGAACGAGAGCGAATACAAGGACGATATGGACATCGTTTCCAACGCGAGTTGCACTACCAATTGTCTTGCGCCTCTTGCGAAGgtgtgttgcgagcttccattgtctttccgtcaaagtttctcgactgttcgatgtttctgataatcttctccag------------------------------------
 ||||| || || ||||| |||||||  || ||||||   ||  | ||||| |||||||| || || |||||||||||||||||||| || || || ||||| | ||  ||  ||  |   |  |    |     ||| | |    ||| || | | | ||||  ||                                          
CATGTTTGTTGTTGGTGTTAACGAGAAGGAGTACAAGCCAGAGCTTGACATTGTTTCCAATGCTAGCTGCACTACCAATTGTCTTGCTCCCCTCGCCAAGgtttattttga-tttatacccttgtgatatatttatttattgctgcttccatctgtattataaatttgcatttttcttaatgaaattattaaatcttaattttgtacag

upper sequence: EFJ30760 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: Vv01s0010g02460.t01 (Vitis vinifera), 5'ss of exon 6
AATGTTCGTCGTGGGTGTGAACGAGAGCGAATACAAGGACGATATGGACATCGTTTCCAACGCGAGTTGCACTACCAATTGTCTTGCGCCTCTTGCGAAGgtgtgttgcgagcttccattgtctttccgtcaaagtttctcgac----tgttcgatgtttctga--taatcttctccag--------------
 ||||| ||  ||||||| || ||||  |||||||||  |||||| ||||| |||||||| || || ||||||||||| |||||||| ||||| || ||||| || | |||    ||||||| |||   || ||||||     |    |||| | ||||  |    | |  || || |               
CATGTTTGTTATGGGTGTCAATGAGAAGGAATACAAGCCCGATATCGACATTGTTTCCAATGCTAGCTGCACTACCAACTGTCTTGCTCCTCTGGCTAAGgt-tgcttcga-tacccattgtattttgatctaagttttattgcaacttgtttgttgttcattgccttagattttctatgtgaaattttacag

upper sequence: EFJ30760 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: Vv17s0000g10430.t01 (Vitis vinifera), 5'ss of exon 6
AATGTTCGTCGTGGGTGTGAACGAGAGCGAATACAAGGACGATATGGACATCGTTTCCAACGCGAGTTGCACTACCAATTGTCTTGCGCCTCTTGCGAAGgtg-----tgttgcgagct-tccattgtctttccgtcaaagtttctcga-------ctgttcgatgtttctgataatcttctccag----
 |||||||| || || || |||||||  |||||||||   ||  |  |||| |||||||| || ||||||||||| || || ||||| ||||||||||||||      | ||   |  | || ||  | ||    |||   |  || ||        |||  | || || | |     ||  | |     
TATGTTCGTTGTTGGAGTTAACGAGAAGGAATACAAGCCAGAACTCCACATTGTTTCCAATGCTAGTTGCACTACAAACTGCCTTGCTCCTCTTGCGAAGgttctaccttttatcacttctcgataatgttatgatcaggttaacttgagccaaaattgtgaggtggttttaacttcattgactatgcag

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|169110647|gb|FE514174.1|FE514174
EST:     TCGTTTCCAACGCGAGTTGCACTACCAATTGTCTTGCGCCTCTTGCGAAG                         GTCATCCATGACAAGTTCGGCATCGTGGAGGGCCTCATGACCACTGTGCAC
genomic: TCGTTTCCAACGCGAGTTGCACTACCAATTGTCTTGCGCCTCTTGCGAAGgtgtgttgcg ... tcttctccagGTCATCCATGACAAGTTCGGCATCGTGGAGGGCCTCATGACCACTGTGCAC
EST: gi|169058408|gb|FE466305.1|FE466305
EST:     TCGTTTCCAACGCGAGTTGCACTACCAATTGTCTTGCGCCTCTTGCGAAG                         GTCATCCATGACAAGTTCGGCATCGTGGAGGGCCTCATGACCACTGTGCAC
genomic: TCGTTTCCAACGCGAGTTGCACTACCAATTGTCTTGCGCCTCTTGCGAAGgtgtgttgcg ... tcttctccagGTCATCCATGACAAGTTCGGCATCGTGGAGGGCCTCATGACCACTGTGCAC
EST: gi|169055484|gb|FE465869.1|FE465869
EST:     TCGTTTCCAACGCGAGTTGCACTACCAATTGTCTTGCGCCTCTTGCGAAG                         GTCATCCATGACAAGTTCGGCATCGTGGAGGGCCTCATGACCACTGTGCAC
genomic: TCGTTTCCAACGCGAGTTGCACTACCAATTGTCTTGCGCCTCTTGCGAAGgtgtgttgcg ... tcttctccagGTCATCCATGACAAGTTCGGCATCGTGGAGGGCCTCATGACCACTGTGCAC
EST: gi|169101963|gb|FE504991.1|FE504991
EST:     TCGTTTCCAACGCGAGTTGCACTACCAATTGTCTTGCGCCTCTTGCGAAG                         GTCATCCATGACAAGTTCGGCATCGTGGAGGGCCTCATGACCACTGTGCAC
genomic: TCGTTTCCAACGCGAGTTGCACTACCAATTGTCTTGCGCCTCTTGCGAAGgtgtgttgcg ... tcttctccagGTCATCCATGACAAGTTCGGCATCGTGGAGGGCCTCATGACCACTGTGCAC
EST: gi|169067187|gb|FE474955.1|FE474955
EST:     TCGTTTCCAACGCGAGTTGCACTACCAATTGTCTTGCGCCTCTTGCGAAG                         GTCATCCATGACAAGTTCGGCATCGTGGAGGGCCTCATGACCACTGTGCAC
genomic: TCGTTTCCAACGCGAGTTGCACTACCAATTGTCTTGCGCCTCTTGCGAAGgtgtgttgcg ... tcttctccagGTCATCCATGACAAGTTCGGCATCGTGGAGGGCCTCATGACCACTGTGCAC
EST: gi|169069038|gb|FE477743.1|FE477743
EST:     TCGTTTCCAACGCGAGTTGCACTACCAATTGTCTTGCGCCTCTTGCGAAG                         GTCATCCATGACAAGTTCGGCATCGTGGAGGGCCTCATGACCACTGTGCAC
genomic: TCGTTTCCAACGCGAGTTGCACTACCAATTGTCTTGCGCCTCTTGCGAAGgtgtgttgcg ... tcttctccagGTCATCCATGACAAGTTCGGCATCGTGGAGGGCCTCATGACCACTGTGCAC
EST: gi|169043069|gb|FE453983.1|FE453983
EST:     TCGTTTCCAACGCGAGTTGCACTACCAATTGTCTTGCGCCTCTTGCGAAG                         GTCATCCATGACAAGTTCGGCATCGTGGAGGGCCTCATGACCACTGTGCAC
genomic: TCGTTTCCAACGCGAGTTGCACTACCAATTGTCTTGCGCCTCTTGCGAAGgtgtgttgcg ... tcttctccagGTCATCCATGACAAGTTCGGCATCGTGGAGGGCCTCATGACCACTGTGCAC
EST: gi|169069052|gb|FE477744.1|FE477744
EST:     TCGTTTCCAACGCGAGTTGCACTACCAATTGTCTTGCGCCTCTTGCGAAG                         GTCATCCATGACAAGTTCGGCATCGTGGAGGGCCTCATGACCACTGTGCAC
genomic: TCGTTTCCAACGCGAGTTGCACTACCAATTGTCTTGCGCCTCTTGCGAAGgtgtgttgcg ... tcttctccagGTCATCCATGACAAGTTCGGCATCGTGGAGGGCCTCATGACCACTGTGCAC

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: 32 (upstream exon), 35 (downstream exon)
Score: 17

AATGTTCGTCGTGGGTGTGAACGAGAGCGAATACAAGGACGATATGGACATCGTTTCCAACGCGAGTTGCACTACCAATTGTCTTGCGCCTCTTGCGAAGgtgtgttgcg ... tcttctccagGTCATCCATGACAAGTTCGGCATCGTGGAGGGCCTCATGACCACTGTGCACTCACTAACTG




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