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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGCGTTTCAAAATGCGTTCGTGTTCTGGAGCGCTTAACCAGGAGCCAAGATATTCCTCAGGAGTACACATACTACGGTATTCCATCTCCTTGGCTCCAGgtttgtttttcgtcgatgtttttgcggttgactttgggaacaccatatttactctttctgtttagtgatttgagcag

Basic information

species Selaginella moellendorffii
transcript EFJ21842
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ34224 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: GRMZM2G137236_T01 (Zea mays), 5'ss of exon 7
CTGCGTTTCAAAATGCGTTCGTGTTCTGGAGCGCTTAACCAGGAGCCAAGATATTCCTCAGGAGTACACATACTACGGTATTCCATCTCCTTGGCTCCAGgtttgt--ttttcgtcgatgtttttg-cggttgactttgggaacaccatatttactcttt--ctgtttagtgatttgagcag------------------
 ||  || | ||||| ||  |  |  ||||| | ||| | || |  ||||||||||| || |||||||| ||||| || ||||||||||||||||| |||||  ||  ||  | |  ||||  |   |  || |    |      | ||   ||   ||   ||   ||   |||| |  |                   
TTGTCTTCCTAAATGTGTGAGAATATTGGAGAGGTTAGCAAGAAATCAAGATATTCCACAAGAGTACACTTACTATGGAATTCCATCTCCTTGGCTTCAGgtacgtacttccctttcatgtcatcatccattcatccagcttgatctatcagtaaaattaggctagatatgtatttaattactggtcattaggccgttac

upper sequence: EFJ34224 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: GRMZM2G700148_T01 (Zea mays), 5'ss of exon 6
CTGCGTTTCAAAATGCGTTCGTGTTCTGGAGCGCTTAACCAGGAGCCAAGATATTCCTCAGGAGTACACATACTACGGTATTCCATCTCCTTGGCTCCAGgt--ttgtttttcgt--cgatgtttttgcggttgactttggg-aacaccatatttactctttctgtttagtgat--ttgagcag-----------------
 ||  || ||||||| ||  |  |  ||||| | ||| | || |  ||||||||||| || |||||||| || || || ||||||||||||||||| |||||  ||   |||| |  |  | |   | |      |||     |  |  | | |||  | || |  |||||  |  ||  || |                 
TTGTCTTCCAAAATGTGTAAGAATATTGGAGAGATTAGCAAGAAATCAAGATATTCCACAAGAGTACACTTATTATGGAATTCCATCTCCTTGGCTTCAGgtacttccctttcatgccattatccattcaaccagcttcatttattagtaaagttaggcctt-tacttagtagtcattaggctgttaccttctattaagct

upper sequence: EFJ34224 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: GLYMA12G30520.1 (Glycine max), 5'ss of exon 6
CTGCGTTTCAAAATGCGTTCGTGTTCTGGAGCGCTTAACCAGGAGCCAAGATATTCCTCAGGAGTACACATACTACGGTATTCCATCTCCTTGGCTCCAGgtttgttt-ttcgtcgatgtttttgcggttgactttgggaacaccatatttactctttctgtttagtgatttgagcag-------------------------------------------------------------
 ||  || | || ||  |     || | || ||  |  | |||| ||| ||||| || || || ||||| ||||||||||| |||||||| ||||| |||||||||   ||     || ||||||      ||| |   | || | |  ||    |        |     |||| |                                                               
TTGTCTTCCTAAGTGTATCAAAATTTTAGAACGGCTTGCTAGGAACCAGGATATCCCACAAGAATACACTTACTACGGTATCCCATCTCCCTGGCTTCAGgtttgtaaatttaggaatatttttgaatgctactctt--accagcttgcttttattgagaaccaaaaatgttgaactaaattttttcttatccagcaagttaaccttttttagtgtttaacaatttttgcttactgtag

upper sequence: EFJ34224 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: GLYMA17G05410.1 (Glycine max), 5'ss of exon 6
CTGCGTTTCAAAATGCGTTCGTGTTCTGGAGCGCTTAACCAGGAGCCAAGATATTCCTCAGGAGTACACATACTACGGTATTCCATCTCCTTGGCTCCAGgtttgt---------ttttcgtcga---tgtttttgc---ggtt--gactttgggaacaccat---at-ttactctttctgtttagtgat-ttgagcag-----------------------------------------------------------------------------
 ||  || | || ||  |     || | || ||  |  | |||| ||| ||||| || || || ||||| ||||||||||| |||||||| ||||| |||||||||         ||||| || |   | ||| ||    || |  |  ||| |||| |   |   ||  ||||||| | | ||  |  | ||||| |                                                                              
TTGTCTTCCTAAGTGTATCAAAATTTTAGAACGGCTTGCTAGGAACCAGGATATCCCACAAGAATACACTTACTACGGTATCCCATCTCCCTGGCTTCAGgtttgtgaatttttcttttcatcaaatatatttctgtattggcttgggttttaggaagatttttgaatgctactcttacagcttgcttttattgagaaccaaaagtgttgaactaaattttttcttatccagcaagttaaccttttttagtgtttaacaatttttgcttaatgtag

upper sequence: EFJ34224 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: AT5G22770.1 (Arabidopsis thaliana), 5'ss of exon 6
CTGCGTTTCAAAATGCGTTCGTGTTCTGGAGCGCTTAACCAGGAGCCAAGATATTCCTCAGGAGTACACATACTACGGTATTCCATCTCCTTGGCTCCAGgtttgtttttcgtcgatgtttttgc----ggttgactttgggaacaccatatttactctttctgtttagtgatt-tgagcag--------------------------------------------------------------------------------------------------------------------
 ||  |  | ||||| ||     |  | || ||| |  | |||| ||||||| |||||||||||||||||||||| || || |||||||||||||||||||||||  ||   |||   | ||  |    | || |       || |   | |   | | | || || |   ||  || |||                                                                                                                     
TTGTCTACCTAAATGTGTCAAAATATTAGAACGCCTTGCTAGGAACCAAGATGTTCCTCAGGAGTACACATACTATGGCATCCCATCTCCTTGGCTCCAGgtttgacttaactcggcttattcactcttgtttaatagcttaaatattctttaatcgcatccttttcacaaatcctgtgcattttaaacattttatgtgaaattagcttatgaaaatagaggcttggcccagctttggtgtatttttgttactcagttaaagatatcgtggatacttatatatctttggttagtacag

upper sequence: EFJ34224 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: AT5G22780.1 (Arabidopsis thaliana), 5'ss of exon 6
CTGCGTTTCAAAATGCGTTCGTGTTCTGGAGCGCTTAACCAGGAGCCAAGATATTCCTCAGGAGTACACATACTACGGTATTCCATCTCCTTGGCTCCAGgtttgtttttcgtcgat--gtttttgcggttgactttgggaacaccatatttactctttc-----tgtttagtgatttgagcag---------------------------------------------------------------------------------
 ||  |  | ||||| ||     |  | || ||| |  | |||| ||| ||| |||||||||||||||||||||| || || |||||||||||||||||||||||| ||   ||| |   |   | |  |    |||    ||| | | ||  |  | ||     | || |    |||  |                                                                                    
TTGTCTACCTAAATGTGTCAAAATATTAGAACGCCTTGCTAGGAACCAGGATGTTCCTCAGGAGTACACATACTATGGCATCCCATCTCCTTGGCTCCAGgtttgtcttaactcggttaatacgttcaatattttttaatcacatccttttcccaatctcatgcattttaaacattttatgtgaaattagcttatgaaaatagaggcttgccccagctttggtatgttgtggttgttggatacttatatatctttggcagtacag

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|169032760|gb|FE438294.1|FE438294
EST:     ATATTCCTCAGGAGTACACATACTACGGTATTCCATCTCCTTGGCTCCAG                         GTAAAAACAATGCGAGTTTTGCAATATTTCCCGGCGATTGATGATCCGAAC
genomic: ATATTCCTCAGGAGTACACATACTACGGTATTCCATCTCCTTGGCTCCAGgtttgttttt ... atttgagcagGTAAAAACAATGCGAGTTTTGCAATATTTCCCGGCGATTGATGATCCGAAC
EST: gi|169032761|gb|FE438295.1|FE438295
EST:     ATATTCCTCAGGAGTACACATACTACGGTATTCCATCTCCTTGGCTCCAG                         GTAAAAACAATGCGAGTTTTGCAATATTTCCCGGCGATTGATGATCCGAAC
genomic: ATATTCCTCAGGAGTACACATACTACGGTATTCCATCTCCTTGGCTCCAGgtttgttttt ... atttgagcagGTAAAAACAATGCGAGTTTTGCAATATTTCCCGGCGATTGATGATCCGAAC

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: 27 (upstream exon), 35 (downstream exon)
Score: 15

CTGCGTTTCAAAATGCGTTCGTGTTCTGGAGCGCTTAACCAGGAGCCAAGATATTCCTCAGGAGTACACATACTACGGTATTCCATCTCCTTGGCTCCAGgtttgttttt ... atttgagcagGTAAAAACAATGCGAGTTTTGCAATATTTCCCGGCGATTGATGATCCGAACATTAGGCGATCCCTTTTTGAG




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