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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTCATGGATCTAATGTCCAAGGCCTTGAAACTACTGCCACTTTTGATCCTGCGACCGACGAGTTTGTGATGAACAGCCCAAACCTGACTTCTACAAAGgtaaacaaatctttgcaacgagcattttctaataaagctgttttcag

Basic information

species Selaginella moellendorffii
transcript EFJ35164
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ35164 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: GLYMA05G04940.1 (Glycine max), 5'ss of exon 4
TGGTCATGGATCTAATGTCCAAGGCCTTGAAACTACTGCCACTTTTGATCCTGCGACCGACGAGTTTGTGATGAACAGCCCAAACCTGACTTCTACAAAGgtaa--------acaaatctttgcaacgagcattt--------tctaataaagctgttttcag-------------------------------------
||| |||||||||||||| ||||| |||||||| ||||| || ||||||||    || ||||||||||| ||  | ||||| |   ||||||| |  || || |        | | ||   |     |||| |||        | ||| |    ||||||||                                      
TGGCCATGGATCTAATGTTCAAGGGCTTGAAACAACTGCAACCTTTGATCCCAGAACAGACGAGTTTGTAATTCATAGCCCCACATTGACTTCAAGCAAAgtgagtacaatgagagatggcttatgggagcctttactggtcctttaagatgtgtgttttcatgtatgagattctagaagatgaaattgtgttcattcat

upper sequence: EFJ35164 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: AT2G35690.1 (Arabidopsis thaliana), 5'ss of exon 3
TGGTCATGGATCTAATGTCCAAGGCCTTGAAACTACTGCCACTTTTGATCCTGCGACCGACGAGTTTGTGATGAACAGCCCAAACCTGACTTCTACAAAGgtaa-----acaaatctttgcaacgagc-attttctaataaagctgttttcag---------------------------------
||||||||| |||||||| ||||||||||| || || || |||||||||||   ||| ||  ||||| | ||  |||| ||||  | ||| ||  | || ||||     | || | |   ||   | | |||||    |     |||||  |                                  
TGGTCATGGCTCTAATGTTCAAGGCCTTGAGACAACCGCTACTTTTGATCCAAAGACAGATCAGTTTATCATTCACAGTCCAACTCAGACATCATCCAAAgtaaggggaagaagtatagacagttatctattttgatctctgagtgtttaaattgtgtcttgattttgttttgtttgaaacattag
















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|169062876|gb|FE472886.1|FE472886
EST:     CTGCGACCGACGAGTTTGTGATGAACAGCCCAAACCTGACTTCTACAAAG                         TGGTGGCCTGGTGGTCTAGGCAAAGCCTCTACACACGCTCTAGTGTATGCT
genomic: CTGCGACCGACGAGTTTGTGATGAACAGCCCAAACCTGACTTCTACAAAGgtaaacaaat ... ctgttttcagTGGTGGCCTGGTGGTCTAGGCAAAGCCTCTACACACGCTCTAGTGTATGCT
EST: gi|169063685|gb|FE471791.1|FE471791
EST:     CTGCGACCGACGAGTTTGTGATGAACAGCCCAAACCTGACTTCTACAAAG                         TGGTGGCCTGGTGGTCTAGGCAAAGCCTCTACACACGCTCTAGTGTATGCT
genomic: CTGCGACCGACGAGTTTGTGATGAACAGCCCAAACCTGACTTCTACAAAGgtaaacaaat ... ctgttttcagTGGTGGCCTGGTGGTCTAGGCAAAGCCTCTACACACGCTCTAGTGTATGCT
EST: gi|169023125|gb|FE429177.1|FE429177
EST:     CTGCGACCGACGAGTTTGTGATGAACAGCCCAAACCTGACTTCTACAAAG                         TGGTGGCCTGGTGGTCTAGGCAAAGCCTCTACACACGCTCTAGTGTATGCT
genomic: CTGCGACCGACGAGTTTGTGATGAACAGCCCAAACCTGACTTCTACAAAGgtaaacaaat ... ctgttttcagTGGTGGCCTGGTGGTCTAGGCAAAGCCTCTACACACGCTCTAGTGTATGCT
EST: gi|169024575|gb|FE435683.1|FE435683
EST:     CTGCGACCGACGAGTTTGTGATGAACAGCCCAAACCTGACTTCTACAAAG                         TGGTGGCCTGGTGGTCTAGGCAAAGCCTCTACACACGCTCTAGTGTATGCT
genomic: CTGCGACCGACGAGTTTGTGATGAACAGCCCAAACCTGACTTCTACAAAGgtaaacaaat ... ctgttttcagTGGTGGCCTGGTGGTCTAGGCAAAGCCTCTACACACGCTCTAGTGTATGCT
EST: gi|169099715|gb|FE503112.1|FE503112
EST:     CTGCGACCGACGAGTTTGTGATGAACAGCCCAAACCTGACTTCTACAAAG                         TGGTGGCCTGGTGGTCTAGGCAAAGCCTCTACACACGCTCTAGTGTATGCT
genomic: CTGCGACCGACGAGTTTGTGATGAACAGCCCAAACCTGACTTCTACAAAGgtaaacaaat ... ctgttttcagTGGTGGCCTGGTGGTCTAGGCAAAGCCTCTACACACGCTCTAGTGTATGCT
EST: gi|169025869|gb|FE433168.1|FE433168
EST:     CTGCGACCGACGAGTTTGTGATGAACAGCCCAAACCTGACTTCTACAAAG                         TGGTGGCCTGGTGGTCTAGGCAAAGCCTCTACACACGCTCTAGTGTATGCT
genomic: CTGCGACCGACGAGTTTGTGATGAACAGCCCAAACCTGACTTCTACAAAGgtaaacaaat ... ctgttttcagTGGTGGCCTGGTGGTCTAGGCAAAGCCTCTACACACGCTCTAGTGTATGCT
EST: gi|169037439|gb|FE443333.1|FE443333
EST:     CTGCGACCGACGAGTTTGTGATGAACAGCCCAAACCTGACTTCTACAAAG                         TGGTGGCCTGGTGGTCTAGGCAAAGCCTCTACACACGCTCTAGTGTATGCT
genomic: CTGCGACCGACGAGTTTGTGATGAACAGCCCAAACCTGACTTCTACAAAGgtaaacaaat ... ctgttttcagTGGTGGCCTGGTGGTCTAGGCAAAGCCTCTACACACGCTCTAGTGTATGCT

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: 29

TGGTCATGGATCTAATGTCCAAGGCCTTGAAACTACTGCCACTTTTGATCCTGCGACCGACGAGTTTGTGATGAACAGCCCAAACCTGACTTCTACAAAGgtaaacaaat ... ctgttttcagTGGTGGCCTGGTGGTCTAGGCAAAGCCTCTACACACGCTCTAGTGTATGCTCGACTGATCACCGACAATCACGACTACGGGATCCACG




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