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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTTTTGCAAAGAAGGGCATCATTGTCCTGCCCGACATCCTTGCAAACTCAGGCGGTGTCACAGTGAGCTACTTCGAATGGGTACAGgtcagtgaggctctttttgtacgcaagttttggtttgagcatttgctatttctctttcatatag

Basic information

species Selaginella moellendorffii
transcript EFJ06181
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ06181 (Selaginella moellendorffii), 5'ss of exon 8
lower sequence: LOC_Os03g58040.3 (Oryza sativa), 5'ss of exon 9
ATTTTTGCAAAGAAGGGCATCATTGTCCTGCCCGACATCCTTGCAAACTCAGGCGGTGTCACAGTGAGCTACTTCGAATGGGTACAGgtcagtgag---gctctttttgtacgcaagttttggtttgagcatttgctatttctctttcatatag--------------------------------------------
||  |  | ||||| ||| |  |  | || || |||||||| || ||||| || ||||||||||||||||||||||| ||||| ||||| ||| |     |  | |   |  || |  ||  |  | |  || |            | |   |                                             
ATCCTGTCCAAGAAAGGCGTTCTCATTCTTCCAGACATCCTCGCGAACTCCGGTGGTGTCACAGTGAGCTACTTCGAGTGGGTTCAGgtaagttactgcacaatctccctgtgctaaattcagagtaaaaatgtaaagcagtcaggttaagcaagagactgatgcatgaagctgctgctgttcttgtggtttgttcag

upper sequence: EFJ06181 (Selaginella moellendorffii), 5'ss of exon 8
lower sequence: GRMZM2G178415_T05 (Zea mays), 5'ss of exon 9
ATTTTTGCAAAGAAGGGCATCATTGTCCTGCCCGACATCCTTGCAAACTCAGGCGGTGTCACAGTGAGCTACTTCGAATGGGTACAGgtcagtgag--gctctttttgtacgcaagttttggttt------gagcatttgctatttctctttcatatag------------------------------
||  |  ||||||| ||| || |  |||| |||||||| || || ||||| || || |||||||||||||||||||| |||||||| ||||||     ||||||       |  ||   || ||       ||  |  |   | |     || |    |                              
ATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAAgtcagtagctcgctcttgcccactgtgagccgtgcttccttacggactacatagcactgtgaatttaacccgtggacaccacacgtgctttcgtctgttcag
















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|169073033|gb|FE483683.1|FE483683
EST:     TCCTTGCAAACTCAGGCGGTGTCACAGTGAGCTACTTCGAATGGGTACAG                         AACAATCAAGGCTTTATGTGGGACGAAGGTAAAGTCAACATGGAGCTGCAG
genomic: TCCTTGCAAACTCAGGCGGTGTCACAGTGAGCTACTTCGAATGGGTACAGgtcagtgagg ... tttcatatagAACAATCAAGGCTTTATGTGGGACGAAGATAAAGTCAACATGGAGCTGCAG
EST: gi|169029682|gb|FE437353.1|FE437353
EST:     TCCTTGCAAACTCAGGCGGTGTCACAGTGAGCTACTTCGAATGGGTACAG                         AACAATCAAGGCTTTATGTGGGACGAAGGTAAAGTCAACATGGAGCTGCAG
genomic: TCCTTGCAAACTCAGGCGGTGTCACAGTGAGCTACTTCGAATGGGTACAGgtcagtgagg ... tttcatatagAACAATCAAGGCTTTATGTGGGACGAAGATAAAGTCAACATGGAGCTGCAG
EST: gi|169020858|gb|FE431962.1|FE431962
EST:     TCCTTGCAAACTCAGGCGGTGTCACAGTGAGCTACTTCGAATGGGTACAG                         AACAATCAAGGCTTTATGTGGGACGAAGGTAAAGTCAACATGGAGCTGCAG
genomic: TCCTTGCAAACTCAGGCGGTGTCACAGTGAGCTACTTCGAATGGGTACAGgtcagtgagg ... tttcatatagAACAATCAAGGCTTTATGTGGGACGAAGATAAAGTCAACATGGAGCTGCAG
EST: gi|169114202|gb|FE515737.1|FE515737
EST:     TCCTTGCAAACTCAGGCGGTGTCACAGTGAGCTACTTCGAATGGGTACAG                         AACAATCAAGGCTTTATGTGGGACGAAGATAAAGTCAACATGGAGCTGCAG
genomic: TCCTTGCAAACTCAGGCGGTGTCACAGTGAGCTACTTCGAATGGGTACAGgtcagtgagg ... tttcatatagAACAATCAAGGCTTTATGTGGGACGAAGATAAAGTCAACATGGAGCTGCAG
EST: gi|169034524|gb|FE444571.1|FE444571
EST:     TCCTTGCAAACTCAGGCGGTGTCACAGTGAGCTACTTCGAATGGGTACAG                         AACAATCAAGGCTTTATGTGGGACGAAGGTAAAGTCAACATGGAGCTGCAG
genomic: TCCTTGCAAACTCAGGCGGTGTCACAGTGAGCTACTTCGAATGGGTACAGgtcagtgagg ... tttcatatagAACAATCAAGGCTTTATGTGGGACGAAGATAAAGTCAACATGGAGCTGCAG
EST: gi|169114203|gb|FE515738.1|FE515738
EST:     TCCTTGCAAACTCAGGCGGTGTCACAGTGAGCTACTTCGAATGGGTACAG                         AACAATCAAGGCTTTATGTGGGACGAAGATAAAGTCAACATGGAGCTGCAG
genomic: TCCTTGCAAACTCAGGCGGTGTCACAGTGAGCTACTTCGAATGGGTACAGgtcagtgagg ... tttcatatagAACAATCAAGGCTTTATGTGGGACGAAGATAAAGTCAACATGGAGCTGCAG
EST: gi|169046220|gb|FE456379.1|FE456379
EST:     TCCTTGCAAACTCAGGCGGTGTCACAGTGAGCTACTTCGAATGGGTACAG                         AACAATCAAGGCTTTATGTGGGACGAAGGTAAAGTCAACATGGAGCTGCAG
genomic: TCCTTGCAAACTCAGGCGGTGTCACAGTGAGCTACTTCGAATGGGTACAGgtcagtgagg ... tttcatatagAACAATCAAGGCTTTATGTGGGACGAAGATAAAGTCAACATGGAGCTGCAG
EST: gi|169022697|gb|FE429724.1|FE429724
EST:     TCCTTGCAAACTCAGGCGGTGTCACAGTGAGCTACTTCGAATGGGTACAG                         AACAATCAAGGCTTTATGTGGGACGAAGATAAAGTCAACATGGAGCTGCAG
genomic: TCCTTGCAAACTCAGGCGGTGTCACAGTGAGCTACTTCGAATGGGTACAGgtcagtgagg ... tttcatatagAACAATCAAGGCTTTATGTGGGACGAAGATAAAGTCAACATGGAGCTGCAG
EST: gi|169030555|gb|FE437888.1|FE437888
EST:     TCCTTGCAAACTCAGGCGGTGTCACAGTGAGCTACTTCGAATGGGTACAG                         AACAATCAAGGCTTTATGTGGGACGAAGATAAAGTCAACATGGAGCTGCAG
genomic: TCCTTGCAAACTCAGGCGGTGTCACAGTGAGCTACTTCGAATGGGTACAGgtcagtgagg ... tttcatatagAACAATCAAGGCTTTATGTGGGACGAAGATAAAGTCAACATGGAGCTGCAG
EST: gi|169054883|gb|FE463487.1|FE463487
EST:     TCCTTGCAAACTCAGGCGGTGTCACAGTGAGCTACTTCGAATGGGTACAG                         AACAATCAAGGCTTTATGTGGGACGAAGGTAAAGTCAACATGGAGCTGCAG
genomic: TCCTTGCAAACTCAGGCGGTGTCACAGTGAGCTACTTCGAATGGGTACAGgtcagtgagg ... tttcatatagAACAATCAAGGCTTTATGTGGGACGAAGATAAAGTCAACATGGAGCTGCAG

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: 34

ATTTTTGCAAAGAAGGGCATCATTGTCCTGCCCGACATCCTTGCAAACTCAGGCGGTGTCACAGTGAGCTACTTCGAATGGGTACAGgtcagtgagg ... tttcatatagAACAATCAAGGCTTTATGTGGGACGAAGATAAAGTCAACATGGAGCTGCAGAGATACATCACCAGTGCATATAAGAGCGTGAAAGAATCATGCAAGACTC




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