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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGGAGAGCTTGCCCGTGATGGTGAGCGGTGTCTGGTCTGACGATCCCAACTTGCAAGTCGAGGCGACGACCCAGTTCCGGAAGCTACTGTCAATTGgtagcttttgatgaaaatctattttttcttggtactgacatgggtgtttgtgaag

Basic information

species Selaginella moellendorffii
transcript EFJ31557
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ31557 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GLYMA20G38320.1 (Glycine max), 5'ss of exon 2
CTGGAGAGCTTGCCCGTGATGGTGAGCGGTGTCTGGTCTGACGATCCCAACTTGCAAGTCGAGGCGACGACCCAGTTCCGGAAGCTACTGTCAATTGgtagcttttgatgaaaatct--attttttcttggtactgacatgggtgtttgtgaag--------------------------------
 ||||   | | ||    ||||| |  ||||| ||| |||| |||   ||| ||||  ||||||||||||| |||||||||||||| || || ||||||   ||  |||     |||   | |||  || ||  |    ||  | ||  ||  |                                
TTGGAACACCTACCATCTATGGTTACTGGTGTTTGGACTGATGATAATAACCTGCAGCTCGAGGCGACGACGCAGTTCCGGAAGCTGCTTTCGATTGgt---ttgggatcggtctctctgtgtttaatttgttgtttagtgaattttaatggtgctttggttaatttggttttttgtgtgtatcag
















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|169031969|gb|FE440669.1|FE440669
EST:     CAACTTGCAAGTCGAGGCGACGACCCAGTTCCGGAAGCTACTGTCAATTG                         AGCGAAGGCCTCCGATCGAAGAGGTCATCAAGGCAGGCGTGGTTCCTCGAT
genomic: CAACTTGCAAGTCGAGGCGACGACCCAGTTCCGGAAGCTACTGTCAATTGgtagcttttg ... gtttgtgaagAGCGAAGGCCTCCGATCGAAGAGGTCATCAAGGCAGGCGTGGTTCCTCGAT
EST: gi|169076897|gb|FE485290.1|FE485290
EST:     CAACTTGCAAGTCGAGGCGACGACCCAGTTCCGGAAGCTACTGTCAATTG                         AGCGAAGGCCTCCGATCGAAGAGGTCATCAAGGCAGGCGTGGTTCCTCGAT
genomic: CAACTTGCAAGTCGAGGCGACGACCCAGTTCCGGAAGCTACTGTCAATTGgtagcttttg ... gtttgtgaagAGCGAAGGCCTCCGATCGAAGAGGTCATCAAGGCAGGCGTGGTTCCTCGAT
EST: gi|169035711|gb|FE443180.1|FE443180
EST:     CGACGACCCAGTTCCGGAAGCTACTGTCAATTG                         AGCGAAGCCCTCCGATCGAAGAGGTCATCAAGGCAGGCGTGGTTCCTCGAT
genomic: CGACGACCCAGTTCCGGAAGCTACTGTCAATTGgtagcttttg ... gtttgtgaagAGCGAAGGCCTCCGATCGAAGAGGTCATCAAGGCAGGCGTGGTTCCTCGAT
EST: gi|169045304|gb|FE453617.1|FE453617
EST:     CAACTTGCAAGTCGAGGCGACGACCCAGTTCCGGAAGCTACTGTCAATTG                         AGCGAAGCCCTCCGATCGAAGAGGTCATCAAGGCAGGCGTGGTTCCTCGAT
genomic: CAACTTGCAAGTCGAGGCGACGACCCAGTTCCGGAAGCTACTGTCAATTGgtagcttttg ... gtttgtgaagAGCGAAGGCCTCCGATCGAAGAGGTCATCAAGGCAGGCGTGGTTCCTCGAT
EST: gi|169029571|gb|FE438932.1|FE438932
EST:     CAACTTGCAAGTCGAGGCGACGACCCAGTTCCGGAAGCTACTGTCAATTG                         AGCGAAGCCCTCCGATCGAAGAGGTCATCAAGGCAGGCGTGGTTCCTCGAT
genomic: CAACTTGCAAGTCGAGGCGACGACCCAGTTCCGGAAGCTACTGTCAATTGgtagcttttg ... gtttgtgaagAGCGAAGGCCTCCGATCGAAGAGGTCATCAAGGCAGGCGTGGTTCCTCGAT
EST: gi|169076232|gb|FE485262.1|FE485262
EST:     CAACTTGCAAGTCGAGGCGACGACCCAGTTCCGGAAGCTACTGTCAATTG                         AGCGAAGGCCTCCGATCGAAGAGGTCATCAAGGCAGGCGTGGTTCCTCGAT
genomic: CAACTTGCAAGTCGAGGCGACGACCCAGTTCCGGAAGCTACTGTCAATTGgtagcttttg ... gtttgtgaagAGCGAAGGCCTCCGATCGAAGAGGTCATCAAGGCAGGCGTGGTTCCTCGAT
EST: gi|169102471|gb|FE508021.1|FE508021
EST:     CAACTTGCAAGTCGAGGCGACGACCCAGTTCCGGAAGCTACTGTCAATTG                         AGCGAAGCCCTCCGATCGAAGAGGTCATCAAGGCAGGCGTGGTTCCTCGAT
genomic: CAACTTGCAAGTCGAGGCGACGACCCAGTTCCGGAAGCTACTGTCAATTGgtagcttttg ... gtttgtgaagAGCGAAGGCCTCCGATCGAAGAGGTCATCAAGGCAGGCGTGGTTCCTCGAT
EST: gi|169049984|gb|FE458076.1|FE458076
EST:     CAACTTGCAAGTCGAGGCGACGACCCAGTTCCGGAAGCTACTGTCAATTG                         AGCGAAGCCCTCCGATCGAAGAGGTCATCAAGGCAGGCGTGGTTCCTCGAT
genomic: CAACTTGCAAGTCGAGGCGACGACCCAGTTCCGGAAGCTACTGTCAATTGgtagcttttg ... gtttgtgaagAGCGAAGGCCTCCGATCGAAGAGGTCATCAAGGCAGGCGTGGTTCCTCGAT
EST: gi|169028583|gb|FE440440.1|FE440440
EST:     CAACTTGCAAGTCGAGGCGACGACCCAGTTCCGGAAGCTACTGTCAATTG                         AGCGAAGCCCTCCGATCGAAGAGGTCATCAAGGCAGGCGTGGTTCCTCGAT
genomic: CAACTTGCAAGTCGAGGCGACGACCCAGTTCCGGAAGCTACTGTCAATTGgtagcttttg ... gtttgtgaagAGCGAAGGCCTCCGATCGAAGAGGTCATCAAGGCAGGCGTGGTTCCTCGAT
EST: gi|169024266|gb|FE433060.1|FE433060
EST:     CAACTTGCAAGTCGAGGCGACGACCCAGTTCCGGAAGCTACTGTCAATTG                         AGCGAAGGCCTCCGATCGAAGAGGTCATCAAGGCAGGCGTGGTTCCTCGAT
genomic: CAACTTGCAAGTCGAGGCGACGACCCAGTTCCGGAAGCTACTGTCAATTGgtagcttttg ... gtttgtgaagAGCGAAGGCCTCCGATCGAAGAGGTCATCAAGGCAGGCGTGGTTCCTCGAT
EST: gi|169020135|gb|FE428522.1|FE428522
EST:     CAACTTGCAAGTCGAGGCGACGACCCAGTTCCGGAAGCTACTGTCAATTG                         AGCGAAGCCCTCCGATCGAAGAGGTCATCAAGGCAGGCGTGGTTCCTCGAT
genomic: CAACTTGCAAGTCGAGGCGACGACCCAGTTCCGGAAGCTACTGTCAATTGgtagcttttg ... gtttgtgaagAGCGAAGGCCTCCGATCGAAGAGGTCATCAAGGCAGGCGTGGTTCCTCGAT

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: 40

CTGGAGAGCTTGCCCGTGATGGTGAGCGGTGTCTGGTCTGACGATCCCAACTTGCAAGTCGAGGCGACGACCCAGTTCCGGAAGCTACTGTCAATTGgtagcttttg ... gtttgtgaagAGCGAAGGCCTCCGATCGAAGAGGTCATCAAGGCAGGCGTGGTTCCTCGATTTGTAGAGTTTTTGAAGCGCCACGATTTCCACCAGCTTCAG




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