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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGGCGCTACCCTACAGCAAATGATTTTGGATCAGAAATTTTGCCTGCTTCAGCAAAAGAGTACAACGTGCAGgtcggtctttcgtttgtttgttggtgaatgtctgctcaactgcgtagttcacag

Basic information

species Selaginella moellendorffii
transcript EFJ28514
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ28514 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: LOC_Os03g52460.1 (Oryza sativa), 5'ss of exon 9
ATGGCGCTACCCTACAGCAAATGATTTTGGATCAGAAATTTTGCCTGCTTCAGCAAAAGAGTACAACGTGCAGgtcggtctttcgtttg------tttgttggtgaatgtctgctca-actgcgtagttcacag-------------------------------------------------------------------------------------------------------------------------------------------
|||||| |  || ||||||||||| |||||||| |||||  | |||||||||||||||||   ||| ||  ||||  |  |||    |       |   || |  | |||   || | | |||    ||  ||                                                                                                                                            
ATGGCGTTTTCCCACAGCAAATGACTTTGGATCTGAAATCATTCCTGCTTCAGCAAAAGAAATCAATGTAAAGgtaaggatttaacataataagttccatttggtagtgttctctaatattgcactattggcatcagatttacacaaatttattcaataataatactgcatatgtatgatgtattatttattttcttacaatcaacttcagtatcatgtcagaaactagccttgaacatctcaggcacagttgtaacctagaactcattgcag
















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|169103890|gb|FE508374.1|FE508374
EST:     ATTTTGGATCAGAAATTTTGCCTGCTTCAGCAAAAGAGTACAACGTGCAG                         GCTTATTTGTTTTATGATTACTGGGAGGACATCGGGACGATCAAGTCGTTC
genomic: ATTTTGGATCAGAAATTTTGCCTGCTTCAGCAAAAGAGTACAACGTGCAGgtcggtcttt ... tagttcacagGCTTATTTGTTTAATGATTACTGGGAGGACATCGGGACGATCAAGTCGTTC
EST: gi|169114213|gb|FE515748.1|FE515748
EST:     ATTTTGGATCAGAAATTTTGCCTGCTTCAGCAAAAGAGTACAACGTGCAG                         GCTTATTTGTTTAATGATTACTGGGAGGACATCGGGACGATCAAGTCGTTC
genomic: ATTTTGGATCAGAAATTTTGCCTGCTTCAGCAAAAGAGTACAACGTGCAGgtcggtcttt ... tagttcacagGCTTATTTGTTTAATGATTACTGGGAGGACATCGGGACGATCAAGTCGTTC
EST: gi|169097606|gb|FE499244.1|FE499244
EST:     ATTTTGGATCAGAAATTTTGCCTGCTTCAGCAAAAGAGTACAACGTGCAG                         GCTTATTTGTTTAATGATTACTGGGAGGACATCGGGACGATCAAGTCGTTC
genomic: ATTTTGGATCAGAAATTTTGCCTGCTTCAGCAAAAGAGTACAACGTGCAGgtcggtcttt ... tagttcacagGCTTATTTGTTTAATGATTACTGGGAGGACATCGGGACGATCAAGTCGTTC
EST: gi|169067020|gb|FE474437.1|FE474437
EST:     ATTTTGGATCAGAAATTTTGCCTGCTTCAGCAAAAGAGTACAACGTGCAG                         GCTTATTTGTTTAATGATTACTGGGAGGACATCGGGACGATCAAGTCGTTC
genomic: ATTTTGGATCAGAAATTTTGCCTGCTTCAGCAAAAGAGTACAACGTGCAGgtcggtcttt ... tagttcacagGCTTATTTGTTTAATGATTACTGGGAGGACATCGGGACGATCAAGTCGTTC
EST: gi|169103889|gb|FE508373.1|FE508373
EST:     ATTTTGGATCAGAAATTTTGCCTGCTTCAGCAAAAGAGTACAACGTGCAG                         GCTTATTTGTTTAATGATTACTGGGAGGACATCGGGACGATCAAGTCGTTC
genomic: ATTTTGGATCAGAAATTTTGCCTGCTTCAGCAAAAGAGTACAACGTGCAGgtcggtcttt ... tagttcacagGCTTATTTGTTTAATGATTACTGGGAGGACATCGGGACGATCAAGTCGTTC
EST: gi|169044330|gb|FE453268.1|FE453268
EST:     ATTTTGGATCAGAAATTTTGCCTGCTTCAGCAAAAGAGTACAACGTGCAGTCCACAG                   
genomic: ATTTTGGATCAGAAATTTTGCCTGCTTCAGCAAAAGAGTACAACGT---G----CAGgtcggtcttt ... tagt
EST: gi|169106983|gb|FE505954.1|FE505954
EST:     ATTTTGGATCAGAAATTTTGCCTGCTTCAGCAAAAGAGTACAACGTGCAG                         GCTTATTTGTTTAATGATTACTGGGAGGACATCGGGACGATCAAGTCGTTC
genomic: ATTTTGGATCAGAAATTTTGCCTGCTTCAGCAAAAGAGTACAACGTGCAGgtcggtcttt ... tagttcacagGCTTATTTGTTTAATGATTACTGGGAGGACATCGGGACGATCAAGTCGTTC

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: 6

ATGGCGCTACCCTACAGCAAATGATTTTGGATCAGAAATTTTGCCTGCTTCAGCAAAAGAGTACAACGTGCAGgtcggtcttt ... tagttcacagGCTTATTTGTTTAATGATTACTGGGAGGACATCGGGACGATCAAGTCGTTCTATGAAGCAAATCTTGCTCTTACTTGCCAG




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