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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGTGGTGGACAGCGTGAAAAAAGACTTTGGCAGCATTGATATTCTCGTTCATTCTCTTGCGAATGGTCCAGAAgtaagagattcagattcctctaatcctgatcgtcgatttcttttgttcatcgtggttccttgtttcgatctcag

Basic information

species Selaginella moellendorffii
transcript EFJ10940
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ10940 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: LOC_Os08g23810.2 (Oryza sativa), 5'ss of exon 7
GAAGTGGTGGACAGCGTGAAAAAAGACTTTGGCAGCATTGATATTCTCGTTCATTCTCTTGCGAATGGTCCAGAAgta-agagattcagattcctctaatcctgatcgtcgatttcttttgtt-----catcgtggttccttgtttcgatctcag---------------------------
||||| |  ||    || || || ||||||||||||||||| ||| | || |||||||| || ||||||||||| ||| || |  || |   ||| || ||||    |   | | ||  || |      || ||   | | |||| || | |||                            
GAAGTTGCTGAGTCAGTCAAGAATGACTTTGGCAGCATTGACATTTTGGTGCATTCTCTAGCTAATGGTCCAGAGgtatagtgcctctg---cctatattcctctgtgcttactgctagtgatgaaattattgtccatacgtgttacgctttcaactaatgatcacctacctctgtttgaag

upper sequence: EFJ10940 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: AT2G05990.1 (Arabidopsis thaliana), 5'ss of exon 6
GAAGTGGTGGACAGCGTGAAAAAAGACTTTGGCAGCATTGATATTCTCGTTCATTCTCTTGCGAATGGTCCAGAAgtaagagattcagatt--cctctaatcctgatcgtcgatttcttttgttcatcg--tggttccttgtttcgatctcag----------
||||  |  ||  | ||||||||||| ||||| |||||||| ||||| || ||||| ||||| ||||| ||||| |||    | ||  ||       |  |     |    |  || | ||||  |     |  |||||  |   | || ||           
GAAGCTGCTGAATGTGTGAAAAAAGATTTTGGAAGCATTGACATTCTTGTCCATTCCCTTGCAAATGGCCCAGAGgtagagaactcgtatcgattattggttacagtaagtgcattgtgttgtatacaaactatttcctaatggtgttcacatgtgggtttag
















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|169109266|gb|FE514068.1|FE514068
EST:     ACTTTGGCAGCATTGATATTCTCGTTCATTCTCTTGCGAATGGTCCGGAA                         GTGTCGAAGCCTCTTCTAGAGACTTCGAGGAAAGGATACCTCGCGGCTAGC
genomic: ACTTTGGCAGCATTGATATTCTCGTTCATTCTCTTGCGAATGGTCCAGAAgtaagagatt ... tcgatctcagGTGTCGAAGCCTCTTCTAGAGACTTCGAGGAAAGGATACCTCGCGGCTAGC
EST: gi|169029497|gb|FE438897.1|FE438897
EST:     ACTTTGGCAGCATTGATATTCTCGTTCATTCTCTTGCGAATGGTCCAGAA                         GTGTCGAAGCCTCTTCTAGAGACTTCGAGGAAAGGATACCTCGCGGCTAGC
genomic: ACTTTGGCAGCATTGATATTCTCGTTCATTCTCTTGCGAATGGTCCAGAAgtaagagatt ... tcgatctcagGTGTCGAAGCCTCTTCTAGAGACTTCGAGGAAAGGATACCTCGCGGCTAGC
EST: gi|169041054|gb|FE450354.1|FE450354
EST:     ACTTTGGCAGCATTGATATTCTCGTTCATTCTCTTGCGAATGGTCCAGAA                         GTGTCGAAGCCTCTTCTAGAGACTTCGAGGAAAGGATACCTCGCGGCTAGC
genomic: ACTTTGGCAGCATTGATATTCTCGTTCATTCTCTTGCGAATGGTCCAGAAgtaagagatt ... tcgatctcagGTGTCGAAGCCTCTTCTAGAGACTTCGAGGAAAGGATACCTCGCGGCTAGC
EST: gi|169024460|gb|FE434385.1|FE434385
EST:     ACTTTGGCAGCATTGATATTCTCGTTCATTCTCTTGCGAATGGTCCAGAA                         GTGTCGAAGCCTCTTCTAGAGACTTCGAGGAAAGGATACCTCGCGGCTAGC
genomic: ACTTTGGCAGCATTGATATTCTCGTTCATTCTCTTGCGAATGGTCCAGAAgtaagagatt ... tcgatctcagGTGTCGAAGCCTCTTCTAGAGACTTCGAGGAAAGGATACCTCGCGGCTAGC
EST: gi|169106433|gb|FE507445.1|FE507445
EST:     CTTTGGCAGCA-TGATATTTCTCGTTCATTCTCTTGCGAATGGTCCGGAA                         GTGTCGAAGCCTCTTCTAGAGACTTCGAGGAAAGGATACCTCGCGGCTAGC
genomic: CTTTGGCAGCATTGATA-TTCTCGTTCATTCTCTTGCGAATGGTCCAGAAgtaagagatt ... tcgatctcagGTGTCGAAGCCTCTTCTAGAGACTTCGAGGAAAGGATACCTCGCGGCTAGC
EST: gi|169041055|gb|FE450355.1|FE450355
EST:     ACTTTGGCAGCATTGATATTCTCGTTCATTCTCTTGCGAATGGTCCAGAA                         GTGTCGAAGCCTCTTCTAGAGACTTCGAGGAAAGGATACCTCGCGGCTAGC
genomic: ACTTTGGCAGCATTGATATTCTCGTTCATTCTCTTGCGAATGGTCCAGAAgtaagagatt ... tcgatctcagGTGTCGAAGCCTCTTCTAGAGACTTCGAGGAAAGGATACCTCGCGGCTAGC
EST: gi|169069401|gb|FE480524.1|FE480524
EST:     ACTTTGGCAGCATTGATATTCTCGTTCATTCTCTTGCGAATGGTCCAGAA                         GTGTCGAAGCCTCTTCTAGAGACTTCGAGGAAAGGATACCTCGCGGCTAGC
genomic: ACTTTGGCAGCATTGATATTCTCGTTCATTCTCTTGCGAATGGTCCAGAAgtaagagatt ... tcgatctcagGTGTCGAAGCCTCTTCTAGAGACTTCGAGGAAAGGATACCTCGCGGCTAGC
EST: gi|169083532|gb|FE495876.1|FE495876
EST:     ACTTTGGCAGCATTGATATTCTCGTTCATTCTCTTGCGAATGGTCCGGAA                         GTGTCGAAGCCTCTTCTAGAGACTTCGAGGAAAGGATACCTCGCGGCTAGC
genomic: ACTTTGGCAGCATTGATATTCTCGTTCATTCTCTTGCGAATGGTCCAGAAgtaagagatt ... tcgatctcagGTGTCGAAGCCTCTTCTAGAGACTTCGAGGAAAGGATACCTCGCGGCTAGC
EST: gi|169069400|gb|FE480523.1|FE480523
EST:     CTTTGGCAGCATTGATATTCTCGTTCATTCTC-TGNCGAATGGTCCAGAA                         GTGTCGAAGCCTCTTCTAGAGACTTCGAGGAAAGGATACCTCGCGGCTAGC
genomic: CTTTGGCAGCATTGATATTCTCGTTCATTCTCTTG-CGAATGGTCCAGAAgtaagagatt ... tcgatctcagGTGTCGAAGCCTCTTCTAGAGACTTCGAGGAAAGGATACCTCGCGGCTAGC
EST: gi|169039555|gb|FE449945.1|FE449945
EST:     ACTTTGGCAGCATTGATATTCTCGTTCATTCTCTTGCGAATGGTCCGGAA                         GTGTCGAAGCCTCTTCTAGAGACTTCGAGGAAAGGGATAC-TCGCGGCTAG
genomic: ACTTTGGCAGCATTGATATTCTCGTTCATTCTCTTGCGAATGGTCCAGAAgtaagagatt ... tcgatctcagGTGTCGAAGCCTCTTCTAGAGACTTCGAGGAAAGG-ATACCTCGCGGCTAG
EST: gi|169106434|gb|FE507446.1|FE507446
EST:     ACTTTGGCAGCATTGATATTCTCGTTCATTCTCTTGCGAATGGTCCGGAA                         GTGTCGAAGCCTCTTCTAGAGACTTCGAGGAAAGGATAC-TCGCGGCTAGC
genomic: ACTTTGGCAGCATTGATATTCTCGTTCATTCTCTTGCGAATGGTCCAGAAgtaagagatt ... tcgatctcagGTGTCGAAGCCTCTTCTAGAGACTTCGAGGAAAGGATACCTCGCGGCTAGC

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: 34 (upstream exon), 34 (downstream exon)
Score: 8

GAAGTGGTGGACAGCGTGAAAAAAGACTTTGGCAGCATTGATATTCTCGTTCATTCTCTTGCGAATGGTCCAGAAgtaagagatt ... tcgatctcagGTGTCGAAGCCTCTTCTAGAGACTTCGAGGAAAGGATACCTCGCGGCTAGCTCCGCATCAGCGTATTCACATGTCTCTCTCCTCAGACATTTTGCTCCAA




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