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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATACAACTCATCCGGATCGAGATTCGCGTCCCCGAGTATGGCTGGACCACGCAGAAGGTCTTCCATTTGCTGAATTTCCTTGTAAATGGAGgtgagattcttccatcttagaactttggattgatctcttcgtttgctag

Basic information

species Selaginella moellendorffii
transcript EFJ23006
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ23006 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GRMZM2G426306_T01 (Zea mays), 5'ss of exon 3
ATACAACTCATCCGGATCGAGATTCGCGTCCCCGAGTATGGCTGGACCACGCAGAAGGTCTTCCATTTGCTGAATTTCCTTGTAAATGGAGgtgag-----att-------cttccatcttagaactttggattgatctcttcgtttgctag-----------------------------------
 |  || | ||| | ||||||    | || || |||||||| ||||| ||||||||||| |||||||| || || |||||||| ||||| ||||||     |||       ||| |||     | |||  | | | | | ||  |||| | |                                   
GTCAAATTAATCAGAATCGAGTGCAGGGTGCCAGAGTATGGATGGACAACGCAGAAGGTGTTCCATTTTCTAAACTTCCTTGTGAATGGCGgtgagccagcatttgtgccgcttgcattacttagcttctgctaggtgt-ttgatttggtggactgatcaatgtaaatgctctattcctgctcatag

upper sequence: EFJ23006 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GRMZM2G003076_T02 (Zea mays), 5'ss of exon 2
ATACAACTCATCCGGATCGAGATTCGCGTCCCCGAGTATGGCTGGACCACGCAGAAGGTCTTCCATTTGCTGAATTTCCTTGTAAATGGAGgtgag-----attcttccatcttagaac-tttggattgatct-----cttcgtttgctag-----------------------------------
 | ||| | ||| | ||||||  | | || || |||||||| ||||| ||||||||||| |||||||| || || |||||||| || || ||||||     |||  | |  |||  ||   || | ||   ||      ||  |||| | |                                   
GTCCAATTAATCAGAATCGAGTGTAGGGTGCCAGAGTATGGATGGACAACGCAGAAGGTGTTCCATTTTCTAAACTTCCTTGTGAACGGCGgtgagccagcatttgtgccgcttgcaatacttagcttctgctaggtgtttaatttggtggactgatcgatgtgaatgctctattcctgctcgcag

upper sequence: EFJ23006 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GRMZM2G055462_T01 (Zea mays), 5'ss of exon 3
ATACAACTCATCCGGATCGAGATTCGCGTCCCCGAGTATGGCTGGACCACGCAGAAGGTCTTCCATTTGCTGAATTTCCTTGTAAATGGAGgtgag-----att-------cttccatcttagaactttggattgatctcttcgtttgctag-----------------------------------
 | ||| | ||| | ||||||    | || || |||||||| ||||| ||||||||||| |||||||| || || |||||||| || || ||||||     |||       ||| |||     | |||  | | | | | ||  |||| | |                                   
GTCCAATTAATCAGAATCGAGTGCAGGGTGCCAGAGTATGGATGGACAACGCAGAAGGTGTTCCATTTTCTAAACTTCCTTGTGAACGGCGgtgagccagcatttgtgtcgcttgcattacttagcttctgctaggtgt-ttgatttggtggactgatcgatgtgaatgctctatttctgctcgcag

upper sequence: EFJ23006 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GLYMA08G07670.2 (Glycine max), 5'ss of exon 2
ATACAACTCATCCGGATCGAGATTCGCGTCCCCGAGTATGGCTGGACCACGCAGAAGGTCTTCCATTTGCTGAATTTCCTTGTAAATGGAGgtgagattcttccatcttagaactttggattgatctcttcgtttgctag--------------------------------------------
 | |||||  | || ||  | |   | || || |||||||| ||||| ||||||||||| ||||||||| |||||||  |||| |||||| || ||         |       || |  |  | ||| ||   ||  | |                                            
GTGCAACTGGTACGAATTCAAAGGAGGGTACCTGAGTATGGGTGGACAACGCAGAAGGTTTTCCATTTGATGAATTTTGTTGTCAATGGATGTAAgtaagagtagtgaatactctataaacagctctgttaacttatttgttttgaatttatgcttgatgaatccttgttacatttgcagtgag

upper sequence: EFJ23006 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GLYMA08G07670.1 (Glycine max), 5'ss of exon 2
ATACAACTCATCCGGATCGAGATTCGCGTCCCCGAGTATGGCTGGACCACGCAGAAGGTCTTCCATTTGCTGAATTTCCTTGTAAATGGAGgtgagattcttccatcttagaactttggattgatctcttcgtttgctag----------------------------------------
 | |||||  | || ||  | |   | || || |||||||| ||||| ||||||||||| ||||||||| |||||||  |||| |||||| || ||         |       || |  |  | ||| ||   ||  | |                                        
GTGCAACTGGTACGAATTCAAAGGAGGGTACCTGAGTATGGGTGGACAACGCAGAAGGTTTTCCATTTGATGAATTTTGTTGTCAATGGATgtaagtaagagtagtgaatactctataaacagctctgttaacttatttgttttgaatttatgcttgatgaatccttgttacatttgcag

upper sequence: EFJ23006 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GLYMA08G09640.1 (Glycine max), 5'ss of exon 2
ATACAACTCATCCGGATCGAGATTCGCGTCCCCGAGTATGGCTGGACCACGCAGAAGGTCTTCCATTTGCTGAATTTCCTTGTAAATGGAGgtgagattcttccatcttagaactttggattgatctcttcgtttgctag------------------------------------------------------------
 | ||| |  | || ||  |     | || || |||||||| |||||||||||||||||||| || || || |||||| |||| ||||| |||  |  || | |   |      ||   |||  | | ||  | |  | |                                                            
GTTCAATTAGTTCGAATACAATGGAGAGTGCCGGAGTATGGTTGGACCACGCAGAAGGTCTTTCACTTTCTCAATTTCATTGTGAATGGGGgtttgtatcattctaatatttttttctaattatttttttaatctatttgtatttgtttcatgattgacgtttttttggtgcaaagttgatgctcgttctggttttgcag

upper sequence: EFJ23006 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GLYMA05G26630.2 (Glycine max), 5'ss of exon 2
ATACAACTCATCCGGATCGAGATTCGCGTCCCCGAGTATGGCTGGACCACGCAGAAGGTCTTCCATTTGCTGAATTTCCTTGTAAATGGAGgtgagattcttcc--atcttagaactttggattgatctcttcgtttgctag-----------------------------------------------------------------
 | ||| |  | || ||  |  |  | || || || ||||| |||||||||||||||||||| || || || |||||| |||| ||||| |||  |  || | |  |||||     | |   || || | |   |||   |                                                                  
GTTCAATTAGTGCGAATACAATTGAGAGTGCCGGAATATGGTTGGACCACGCAGAAGGTCTTTCACTTTCTCAATTTCATTGTGAATGGGGgtttgtatcattctaatctttcttttctttttttatttgtaattttaaaaaaattgaatctatttgtatttgtttggtgattgacatttttgtggatgctctttctggttttgcag

upper sequence: EFJ23006 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: AT1G14530.1 (Arabidopsis thaliana), 5'ss of exon 2
ATACAACTCATCCGGATCGAGATTCGCGTCCCCGAGTATGGCTGGACCACGCAGAAGGTCTTCCATTTGCTGAATTTCCTTGTAAATGGAGgtgagattctt----ccatcttagaactttggattgatctct---tcgtttgctag-----------------------
|| ||| |  |  | ||  |  |  | || || || ||||||||||| |||||||||||||| ||||| || |||||| | || || ||||||| | || ||     | | ||||   ||    ||| | | |   || |||| |                         
ATTCAATTGGTAAGAATACAATTGAGAGTTCCAGAATATGGCTGGACGACGCAGAAGGTCTTTCATTTTCTCAATTTCATGGTTAACGGAGgtgggtttgtttgtctcttgttagtttttgattttgttttgtgtatcttttgttgattggctcgtcttcttctttgtag

upper sequence: EFJ23006 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: Vv01s0010g01740.t01 (Vitis vinifera), 5'ss of exon 2
ATACAACTCATCCGGATCGAGATTCGCGTCCCCGAGTATGGCTGGACCACGCAGAAGGTCTTCCATTTGCTGAATTTCCTTGTAAATGGAGgtgagattct----------tccat-cttagaactttggattg-atctcttcgtttgctag-----------------------------
 | |||||  | |||||  |  |  | ||||| |||||||| ||||||||||||||||| ||||| || || |||||||| || ||||| |||  |  |||          | ||| ||| |  || ||||||  |    || || |  |                               
GTTCAACTGGTTCGGATACAATTGAGAGTCCCAGAGTATGGTTGGACCACGCAGAAGGTGTTCCACTTTCTCAATTTCCTGGTGAATGGGGgtttgtatctaagttcataattcatactttgtgctatggattataatcttttgtgtatttttattgaatatggtctcatgcgttctgcag

upper sequence: EFJ23006 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: PP1S295_30V6.1 (Physcomitrella patens), 5'ss of exon 2
ATACAACTCATCCGGATCGAGATTCGCGTCCCCGAGTATGGCTGGACCACGCAGAAGGTCTTCCATTTGCTGAATTTCCTTGTAAATGGAGgtgag-attcttcca----tcttagaactttgga--ttgatctct-tcgtttgctag---------------------------------------
 | ||||| || ||||| ||||| || || || ||||||||||||||||| ||||| ||||| ||| || |||||||| |||| |||||| ||||| | ||| |||    |   |  ||||| ||  | | | ||| | ||  |  ||                                       
GTGCAACTAATTCGGATAGAGATGCGAGTTCCGGAGTATGGCTGGACCACTCAGAAAGTCTTTCATCTGTTGAATTTCATTGTTAATGGATgtgagtactctgccaatcgttccaagacttttgacgtcggtttctgttgtcagtcagcgctgattatctggaaatttgtataattttgtgctgcag

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|169049298|gb|FE458222.1|FE458222
EST:     CTGGACCACGCAGAAGGTCTTCCATTTGCTGAATTTCCTTGTAAATGGAG                         TCCGAGCTGTGGTGTTCTTCTTCCGGCGCCAAGTCCAGTTCCTTGAGCCCC
genomic: CTGGACCACGCAGAAGGTCTTCCATTTGCTGAATTTCCTTGTAAATGGAGgtgagattct ... cgtttgctagTCCGAGCTGTGGTGTTCTTCTTCCGGCGCCAAGTCCAGTTCCTTGAGCCCC
EST: gi|169087158|gb|FE493105.1|FE493105
EST:     CTGGACGACGCAGAAGGTCTTCCATTTGCTGAATTTCCTTGTAAATGGAG                         TCCGAGCTGTGGTGTTCTTCTTCCGGCGCCAAGTCCAGTTCCTTGAGCCCC
genomic: CTGGACCACGCAGAAGGTCTTCCATTTGCTGAATTTCCTTGTAAATGGAGgtgagattct ... cgtttgctagTCCGAGCTGTGGTGTTCTTCTTCCGGCGCCAAGTCCAGTTCCTTGAGCCCC

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: 32 (upstream exon), 34 (downstream exon)
Score: 32

ATACAACTCATCCGGATCGAGATTCGCGTCCCCGAGTATGGCTGGACCACGCAGAAGGTCTTCCATTTGCTGAATTTCCTTGTAAATGGAGgtgagattct ... cgtttgctagTCCGAGCTGTGGTGTTCTTCTTCCGGCGCCAAGTCCAGTTCCTTGAGCCCCGG




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