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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTTGTAAGACAAGCTGCGTCAAAAACAAATGACTTGGCTGGTGATGGAACCACCACGTCCGTGGTTTTGGCACAAGGACTTATAAACGAGGGTGTCAAGgtttgttttttctcaagttcatggaagtttcatgaggcaatctggagggtaatttgcag

Basic information

species Selaginella moellendorffii
transcript EFJ36935
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ36935 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GRMZM2G015989_T01 (Zea mays), 5'ss of exon 4
GCTTGTAAGACAAGCTGCGTCAAAAACAAATGACTTGGCTGGTGATGGAACCACCACGTCCGTGGTTTTGGCACAAGGACTTATAAACGAGGGTGTCAAGgttt--gttttttctcaagttcatg----gaagtttcatga--ggcaatctggagggtaatttgcag-----------------------------
  | ||  | ||||||||  | |||||||||||||||||||||||||| || ||||| || || ||  | || |||||  | || |  |||||||| |||||    | |  |    ||  |||||    |  || ||   |  | || | |   ||  |  |  ||                              
ATTGGTCCGCCAAGCTGCTGCTAAAACAAATGACTTGGCTGGTGATGGGACAACCACTTCGGTTGTCCTTGCTCAAGGGATGATTACTGAGGGTGTAAAGgtacacgctagtatataacctcatgtattggggtatctatatcgtcactgttccggccatgtctcaatatctagaggattttgctactttctccag

upper sequence: EFJ36935 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GLYMA08G18760.2 (Glycine max), 5'ss of exon 3
GCTTGTAAGACAAGCTGCGTCAAAAACAAATGACTTGGCTGGTGATGGAACCACCACGTCCGTGGTTTTGGCACAAGGACTTATAAACGAGGGTGTCAAGgtttg-ttttttctcaagttcatggaagtttcatgaggcaatctggagggtaatttgcag-----------------------------------------------
| | || |||||||| ||  | || ||||| ||||||||||||||||||||||| || || || ||| | || || || ||||||   || |||||||||||  | || ||| |    ||  ||||| |||  ||    || ||      || || |                                                  
GTTGGTGAGACAAGCGGCTGCCAAGACAAACGACTTGGCTGGTGATGGAACCACGACCTCGGTTGTTCTTGCTCAGGGTCTTATAGCGGAAGGTGTCAAGgtaggattatttgttgtcttattggaaatttagtgtcataa-ctaataactacttggttttgttttttgtaatgcaactaggcctcattttatgttaattttcgcag

upper sequence: EFJ36935 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GLYMA15G40110.1 (Glycine max), 5'ss of exon 3
GCTTGTAAGACAAGCTGCGTCAAAAACAAATGACTTGGCTGGTGATGGAACCACCACGTCCGTGGTTTTGGCACAAGGACTTATAAACGAGGGTGTCAAGgtttg-ttttttctcaagttcatggaagtttcatgaggcaatctggagggtaatttgcag------------------------------------------
| | || |||||||| ||  | || ||||| ||||||||||||||||||||||| || || || ||| | || || || |||||   ||| || || |||||    || ||| |   |||   |||| | |  ||   ||  ||      || |  |                                             
GTTGGTGAGACAAGCAGCTGCCAAGACAAACGACTTGGCTGGTGATGGAACCACGACTTCGGTTGTTCTAGCTCAGGGTCTTATTGCCGAAGGCGTTAAGgtaaaattatttgttgtgttttcggaaatgtagtgtt-catactaataactactcggttttggattttgtaattaggcctcattttatgttaatttttgcag

upper sequence: EFJ36935 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: Vv09s0002g03930.t01 (Vitis vinifera), 5'ss of exon 3
GCTTGTAAGACAAGCTGCGTCAAAAACAAATGACTTGGCTGGTGATGGAACCACCACGTCCGTGGTTTTGGCACAAGGACTTATAAACGAGGGTGTCAAGgtttgtt----ttttctcaagttcatggaagtttcatgaggcaatctggagggtaatttgcag---------------------------------------
| | || ||||||||||| |||||||| ||||| |||||||||||||| || || || || || ||| |||| |||||  | || |  || ||||| |||||||||     |||| |||  | | |     |||    |  |||  | | | | |   |   |                                       
GTTGGTGAGACAAGCTGCTTCAAAAACCAATGATTTGGCTGGTGATGGGACAACTACTTCTGTTGTTCTGGCTCAAGGCTTGATTACTGAAGGTGTTAAGgtttgtaaaggttttgtcacttgcttttc--tttaggaacacaaattagcgtgaatgcttgggccgatgcttgtaatacttacatggcactgattcgttcag

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|169038912|gb|FE449629.1|FE449629
EST:     CCACCACGTCCGTGGTTTTGGCACAAGGACTTATAAACGAGGGTGTCAAG                         CTAGTCGCAGCGGGAGCTAATCCTATACAAATTGCTCGAGGTATTGACAAG
genomic: CCACCACGTCCGTGGTTTTGGCACAAGGACTTATAAACGAGGGTGTCAAGgtttgttttt ... taatttgcagCTAGTCGCAGCGGGAGCTAATCCTATACAAATTGCTCGAGGTATTGACAAG
EST: gi|169098668|gb|FE500232.1|FE500232
EST:     CCACCACGTCCGTGGTTTTGGCACAAGGACTTATAAACGAGGGTGTCAAG                         CTAGTCGCAGCGGGAGCTAATCCTATACAAATTGCTCGAGGTATTGACAAG
genomic: CCACCACGTCCGTGGTTTTGGCACAAGGACTTATAAACGAGGGTGTCAAGgtttgttttt ... taatttgcagCTAGTCGCAGCGGGAGCTAATCCTATACAAATTGCTCGAGGTATTGACAAG
EST: gi|169028067|gb|FE435425.1|FE435425
EST:     CCACCACGTCCGTGGTTTTGGCACAAGGACTTATAAACGAGGGTGTCAAG                         CTAGTCGCAGCGGGAGCTAATCCTATACAAATTGCTCGAGGTATTGACAAG
genomic: CCACCACGTCCGTGGTTTTGGCACAAGGACTTATAAACGAGGGTGTCAAGgtttgttttt ... taatttgcagCTAGTCGCAGCGGGAGCTAATCCTATACAAATTGCTCGAGGTATTGACAAG
EST: gi|169111607|gb|FE513964.1|FE513964
EST:     CCACCACGTCCGTGGTTTTGGCACAAGGACTTATAAACGAGGGTGTCAAG                         CTAGTCGCAGCGGGAGCTAATCCTATACAAATTGCTCGAGGTATTGACAAG
genomic: CCACCACGTCCGTGGTTTTGGCACAAGGACTTATAAACGAGGGTGTCAAGgtttgttttt ... taatttgcagCTAGTCGCAGCGGGAGCTAATCCTATACAAATTGCTCGAGGTATTGACAAG
EST: gi|169024241|gb|FE435219.1|FE435219
EST:     CCACCACGTCCGTGGTTTTGGCACAAGGACTTATAAACGAGGGTGTCAAG                         CTAGTCGCAGCGGGAGCTAATCCTATACAAATTGCTCGAGGTATTGACAAG
genomic: CCACCACGTCCGTGGTTTTGGCACAAGGACTTATAAACGAGGGTGTCAAGgtttgttttt ... taatttgcagCTAGTCGCAGCGGGAGCTAATCCTATACAAATTGCTCGAGGTATTGACAAG
EST: gi|169021474|gb|FE428561.1|FE428561
EST:     CCACCACGTCCGTGGTTTTGGCACAAGGACTTATAAACGAGGGTGTCAAG                         CTAGTCGCAGCGGGAGCTAATCCTATACAAATTGCTCGAGGTATTGACAAG
genomic: CCACCACGTCCGTGGTTTTGGCACAAGGACTTATAAACGAGGGTGTCAAGgtttgttttt ... taatttgcagCTAGTCGCAGCGGGAGCTAATCCTATACAAATTGCTCGAGGTATTGACAAG
EST: gi|169077168|gb|FE486094.1|FE486094
EST:     CCACCACGTCCGTGGTTTTGGCACAAGGACTTATAAACGAGGGTGTCAAG                         CTAGTCGCAGCGGGAGCTAATCCTATACAAATTGCTCGAGGTATTGACAAG
genomic: CCACCACGTCCGTGGTTTTGGCACAAGGACTTATAAACGAGGGTGTCAAGgtttgttttt ... taatttgcagCTAGTCGCAGCGGGAGCTAATCCTATACAAATTGCTCGAGGTATTGACAAG
EST: gi|169024291|gb|FE432552.1|FE432552
EST:     CCACCACGTCCGTGGTTTTGGCACAAGGACTTATAAACGAGGGTGTCAAG                         CTAGTCGCAGCGGGAGCTAATCCTATACAAATTGCTCGAGGTATTGACAAG
genomic: CCACCACGTCCGTGGTTTTGGCACAAGGACTTATAAACGAGGGTGTCAAGgtttgttttt ... taatttgcagCTAGTCGCAGCGGGAGCTAATCCTATACAAATTGCTCGAGGTATTGACAAG

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: 29 (upstream exon), 35 (downstream exon)
Score: 19

GCTTGTAAGACAAGCTGCGTCAAAAACAAATGACTTGGCTGGTGATGGAACCACCACGTCCGTGGTTTTGGCACAAGGACTTATAAACGAGGGTGTCAAGgtttgttttt ... taatttgcagCTAGTCGCAGCGGGAGCTAATCCTATACAAATTGCTCGAGGTATTGACAAGGTCATCGCAGGCCTTGTCAAGGAACTCAAGACTTTGTCGAAAGAG




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