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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATACGATAAGTTTTGTCCGTTCTACAAGTCCGTTTGGATGATGCGAAACATCGTCCATTTCTGCGACCTGTCCACTCAGgtatgcactgccatacctctttcacgtccttgaaattttactttctcttgcag

Basic information

species Selaginella moellendorffii
transcript EFJ30330
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ30330 (Selaginella moellendorffii), 5'ss of exon 18
lower sequence: LOC_Os06g45120.1 (Oryza sativa), 5'ss of exon 17
ATACGATAAGTTTTGTCCGTTCTACAAGTCCGTTTGGATGATGCGAAACATCGTCCATTTCTGCGACCTGTCCACTCAGgta-------tgcactgccatacctctttcacgtccttgaaattttactttctcttgcag-----------------------------------------
||| || ||||| ||||| ||||||||||| |||||||||||||| |||||  | ||||||       |  | | |||||||        |   |   |   ||| ||  ||||||||||  || | || |||  |||                                          
ATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACATTATTCATTTCAATACATTAGCAAATCAGgtaaatctaacgtgtttttaccactccttt-cgtccttgaaccttaaattactcaagcaactttgatttgaaatttgaagtatgaacctgtgaagaatgtt

upper sequence: EFJ30330 (Selaginella moellendorffii), 5'ss of exon 18
lower sequence: GRMZM2G421857_T02 (Zea mays), 5'ss of exon 17
ATACGATAAGTTTTGTCCGTTCTACAAGTCCGTTTGGATGATGCGAAACATCGTCCATTTCTGCGACCTGTCCACTCAGgtatgcactgccatacctctttcacgtccttgaaattttactttctcttgcag------------------------------------------------
||| |||||||| || || |||||||| ||||||||||||||||| |||||  | || |||  |    || | | ||||||| |  ||   || ||     | |    ||| ||    |     | |  ||                                                 
ATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAACATTATTCACTTCAACACATTGGCAAATCAGgtaaggtctttaatgcccacccccctgttttgtaacca-atcaattatcacaatttattgttgctccacctgctatcattgtattgttttgtcaagatttg

upper sequence: EFJ30330 (Selaginella moellendorffii), 5'ss of exon 18
lower sequence: GRMZM2G128877_T02 (Zea mays), 5'ss of exon 17
ATACGATAAGTTTTGTCCGTTCTACAAGTCCGTTTGGATGATGCGAAACATCGTCCATTTCTGCGACCTGTCCACTCAGgtatgcact--gcca-tacctctttcacgtccttgaaattttactttctcttgcag--------------------------------------------
||| |||||||| || || |||||||| ||||||||||||||||| || ||  | || |||  |    || | | ||||||| || ||   | |  |   |||        ||  | |     ||| || |||||                                            
ATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAGgtaagctctcaactagcagtacttctgtaatttttgagtaaatgtttttcctgcagattgttttgcaatgatcaaggaaacttattaaacttctgattgt

upper sequence: EFJ30330 (Selaginella moellendorffii), 5'ss of exon 18
lower sequence: GRMZM2G128877_T04 (Zea mays), 5'ss of exon 1
---------------------ATACGATAAGTTTTGTCCGTTCTACAAGTCCGTTTGGATGATGCGAAACATCGTCCATTTCTGCGACCTGTCCACTCAGgtatgcact--gcca-tacctctttcacgtccttgaaattttactttctcttgcag--------------------------------------------
                     ||| |||||||| || || |||||||| ||||||||||||||||| || ||  | || |||  |    || | | ||||||| || ||   | |  |   |||        ||  | |     ||| || |||||                                            
ACAAGTGTTGTTTAATATTAGATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAGgtaagctctcaactagcagtacttctgtaatttttgagtaaatgtttttcctgcagattgttttgcaatgatcaaggaaacttattaaacttctgattgt

upper sequence: EFJ30330 (Selaginella moellendorffii), 5'ss of exon 18
lower sequence: GLYMA07G00430.1 (Glycine max), 5'ss of exon 18
ATACGATAAGTTTTGTCCGTTCTACAAGTCCGTTTGGATGATGCGAAACATCGTCCATTTCTGCGACCTGTCCACTCAGgtatg-cactgccatacctctttcacgtccttgaaattttactttctcttgcag-----------------------------------------------
||| ||||| ||||| || ||||||||||| |||||||||||||| |||||  ||||||||| | |  || | | |||||||||  | ||  |    ||   || ||  |||   ||||| ||   || | |                                                
ATATGATAAATTTTGCCCCTTCTACAAGTCTGTTTGGATGATGCGCAACATTATCCATTTCTACAATTTGGCAAATCAGgtatggtagtgtaaggaatcaggca-gtttttggtgttttatttatactagaaaaaagaagaaaagtccatgtaatcattggcatctaggttcaagttact

upper sequence: EFJ30330 (Selaginella moellendorffii), 5'ss of exon 18
lower sequence: GLYMA08G23990.1 (Glycine max), 5'ss of exon 18
ATACGATAAGTTTTGTCCGTTCTACAAGTCCGTTTGGATGATGCGAAACATCGTCCATTTCTGCGACCTGTCCACTCAGgtatg-cactgccatacctctttcacgtccttgaaattttactttctcttgcag-----------------------------------------------
||| || || || || || ||||||||||| |||||||||||||| |||||  ||||||||| | |  || | | |||||||||    ||  |    ||   || ||  |||   ||||| ||    | | |                                                
ATATGACAAATTCTGCCCCTTCTACAAGTCTGTTTGGATGATGCGCAACATTATCCATTTCTACAATTTGGCAAATCAGgtatggtggtgtaaggaatcaggca-gtttttggtgttttatttatattagaaaaaagaagaaaagtccatgtaatcattggcatctaggttcaagttact

upper sequence: EFJ30330 (Selaginella moellendorffii), 5'ss of exon 18
lower sequence: AT1G78900.2 (Arabidopsis thaliana), 5'ss of exon 18
ATACGATAAGTTTTGTCCGTTCTACAAGTCCGTTTGGATGATGCGAAACATCGTCCATTTCTGCGACCTGTCCACTCAGgtatgcactgc------catacctctttcacgtccttgaaatt--------ttactttctcttgcag-----------------------------
||| || || || ||||| |||||||||||||| ||||||||||| |||||  ||||||||| | ||||  |||  ||||||   |           |||| |  |   |    | |  |||        ||  ||| ||| |                                
ATATGACAAATTCTGTCCTTTCTACAAGTCCGTGTGGATGATGCGTAACATTATCCATTTCTACAACCTAGCCAACCAGgtaaataagatgagatttatacatactatgctaagtggggattaaggtcaattggtttgtctaggtaaaaacccattaattgttttggatacacag

upper sequence: EFJ30330 (Selaginella moellendorffii), 5'ss of exon 18
lower sequence: Vv09s0054g00890.t01 (Vitis vinifera), 5'ss of exon 18
ATACGATAAGTTTTGTCCGTTCTACAAGTCCGTTTGGATGATGCGAAACATCGTCCATTTCTGCGACCTGTCCACTCAGgta---tgcactgccatacctctttca----cgtccttgaaattttactttctcttgcag----------------------------------------
||| |||||||| || || ||||||||||| |||||||||||||| || ||  |||||||||   |  || ||| |||||||   ||  |  |  |  |||||||     |  |       |||| |||| |||    |                                        
ATATGATAAGTTCTGCCCCTTCTACAAGTCGGTTTGGATGATGCGCAATATTATCCATTTCTATAATTTGGCCAATCAGgtacgatgttcctctctctctctttccaccccccctcccccgttttcctttttctctttgacctattgttgtcatgtttgccaagatcattgtgtctgta

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|169116507|gb|FE517532.1|FE517532
EST:     CCGTTTGGATGATGCGAAACATCGTTCATTTCTGCGACCTGTCCACTCAG                         GCTGTTGAGAAAGCTGCCGGATCCAAGGGTCAGAAAATAACTTTCAACATC
genomic: CCGTTTGGATGATGCGAAACATCGTCCATTTCTGCGACCTGTCCACTCAGgtatgcactg ... tctcttgcagGCTGTTGAGAAAGCTGCCGGATCCAAGGGTCAGAAAATAACTTTCAACATC
EST: gi|169094896|gb|FE491630.1|FE491630
EST:     CCGTTTGGATGATGCGAAACATCGTTCATTTCTGCGACCTGTCCACTCAG                         GCTGTTGAGAAAGCTGCCGGATCCAAGGGTCAGAAAATAACTTTCAACATC
genomic: CCGTTTGGATGATGCGAAACATCGTCCATTTCTGCGACCTGTCCACTCAGgtatgcactg ... tctcttgcagGCTGTTGAGAAAGCTGCCGGATCCAAGGGTCAGAAAATAACTTTCAACATC
EST: gi|169105223|gb|FE504895.1|FE504895
EST:     CCGTTTGGATGATGCGAAACATCGTTCATTTCTGCGACCTGTCCACTCAG                         GCTGTTGAGAAAGCTGCCGGATCCAAGGGTCAGAAAATAACTTTCAACATC
genomic: CCGTTTGGATGATGCGAAACATCGTCCATTTCTGCGACCTGTCCACTCAGgtatgcactg ... tctcttgcagGCTGTTGAGAAAGCTGCCGGATCCAAGGGTCAGAAAATAACTTTCAACATC
EST: gi|169075917|gb|FE482836.1|FE482836
EST:     CCGTTTGGATGATGCGAAACATCGTTCATTTCTGCGACCTGTCCACTCAG                         GCTGTTGAGAAAGCTGCCGGATCCAAGGGTCAGAAAATAACTTTCAACATC
genomic: CCGTTTGGATGATGCGAAACATCGTCCATTTCTGCGACCTGTCCACTCAGgtatgcactg ... tctcttgcagGCTGTTGAGAAAGCTGCCGGATCCAAGGGTCAGAAAATAACTTTCAACATC
EST: gi|169058960|gb|FE467728.1|FE467728
EST:     CCGTTTGGATGATGCGAAACATCGTTCATTTCTGCGACCTGTCCACTCAG                         GCTGTTGAGAAAGCTGCCGGATCCAAGGGTCAGAAAATAACTTTCAACATC
genomic: CCGTTTGGATGATGCGAAACATCGTCCATTTCTGCGACCTGTCCACTCAGgtatgcactg ... tctcttgcagGCTGTTGAGAAAGCTGCCGGATCCAAGGGTCAGAAAATAACTTTCAACATC
EST: gi|169116508|gb|FE517533.1|FE517533
EST:     CCGTTTGGATGATGCGAAACATCGTTCATTTCTGCGACCTGTCCACTCAG                         GCTGTTGAGAAAGCTGCCGGATCCAAGGGTCAGAAAATAACTTTCAACATC
genomic: CCGTTTGGATGATGCGAAACATCGTCCATTTCTGCGACCTGTCCACTCAGgtatgcactg ... tctcttgcagGCTGTTGAGAAAGCTGCCGGATCCAAGGGTCAGAAAATAACTTTCAACATC
EST: gi|169055454|gb|FE465852.1|FE465852
EST:     CCGTTTGGATGATGCGAAACATCGTCCATTTCTGCGACCTGTCCACTCAG                         GCTGTTGAGAAAGCTGCCGGATCCAAGGGTCAGAAAATAACTTTCAACATC
genomic: CCGTTTGGATGATGCGAAACATCGTCCATTTCTGCGACCTGTCCACTCAGgtatgcactg ... tctcttgcagGCTGTTGAGAAAGCTGCCGGATCCAAGGGTCAGAAAATAACTTTCAACATC
EST: gi|169074665|gb|FE480895.1|FE480895
EST:     CCGTTTGGATGATGCGAAACATCGTTCATTTCTGCGACCTGTCCACTCAG                         GCTGTTGAGAAAGCTGCCGGATCCAAGGGTCAGAAAATAACTTTCAACATC
genomic: CCGTTTGGATGATGCGAAACATCGTCCATTTCTGCGACCTGTCCACTCAGgtatgcactg ... tctcttgcagGCTGTTGAGAAAGCTGCCGGATCCAAGGGTCAGAAAATAACTTTCAACATC
EST: gi|169026429|gb|FE434742.1|FE434742
EST:     CCGTTTGGATGATGCGAAACATCGTCCATTTCTGCGACCTGTCCACTCAG                         GCTGTTGAGAAAGCTGCCGGATCCAAGGGTCAGAAAATAACTTTCAACATC
genomic: CCGTTTGGATGATGCGAAACATCGTCCATTTCTGCGACCTGTCCACTCAGgtatgcactg ... tctcttgcagGCTGTTGAGAAAGCTGCCGGATCCAAGGGTCAGAAAATAACTTTCAACATC
EST: gi|169096020|gb|FE500011.1|FE500011
EST:     CCGTTTGGATGATGCGAAACATCGTTCATTTCTGCGACCTGTCCACTCAG                         GCTGTTGAGAAAGCTGCCGGATCCAAGGGTCAGAAAATAACTTTCAACATC
genomic: CCGTTTGGATGATGCGAAACATCGTCCATTTCTGCGACCTGTCCACTCAGgtatgcactg ... tctcttgcagGCTGTTGAGAAAGCTGCCGGATCCAAGGGTCAGAAAATAACTTTCAACATC
EST: gi|169026425|gb|FE435778.1|FE435778
EST:     CCGTTTGGATGATGCGAAACATCGTCCATTTCTGCGACCTGTCCACTCAG                         GCTGTTGAGAAAGCTGCCGGATCCAAGGGTCAGAAAATAACTTTCAACATC
genomic: CCGTTTGGATGATGCGAAACATCGTCCATTTCTGCGACCTGTCCACTCAGgtatgcactg ... tctcttgcagGCTGTTGAGAAAGCTGCCGGATCCAAGGGTCAGAAAATAACTTTCAACATC
EST: gi|169083647|gb|FE495380.1|FE495380
EST:     CCGTTTGGATGATGCGAAACATCGTTCATTTCTGCGACCTGTCCACTCAG                         GCTGTTGAGAAAGCTGCCGGATCCAAGGGTCAGAAAATAACTTTCAACATC
genomic: CCGTTTGGATGATGCGAAACATCGTCCATTTCTGCGACCTGTCCACTCAGgtatgcactg ... tctcttgcagGCTGTTGAGAAAGCTGCCGGATCCAAGGGTCAGAAAATAACTTTCAACATC
EST: gi|169038845|gb|FE446988.1|FE446988
EST:     CCGTTTGGATGATGCGAAACATCGTCCATTTTTGCGACCTGTCCACTCAG                         GCTGTTGAGAAAGCTGCCGGATCCAAGGGTCAGAAAATAACTTTCAACATC
genomic: CCGTTTGGATGATGCGAAACATCGTCCATTTCTGCGACCTGTCCACTCAGgtatgcactg ... tctcttgcagGCTGTTGAGAAAGCTGCCGGATCCAAGGGTCAGAAAATAACTTTCAACATC
EST: gi|169067637|gb|FE475314.1|FE475314
EST:     CCGTTTGGATGATGCGAAACATCGTCCATTTCTGCGACCTGTCCACTCAG                         GCTGTTGAGAAAGCTGCCGGATCCAAGGGTCAGAAAATAACTTTCAACATC
genomic: CCGTTTGGATGATGCGAAACATCGTCCATTTCTGCGACCTGTCCACTCAGgtatgcactg ... tctcttgcagGCTGTTGAGAAAGCTGCCGGATCCAAGGGTCAGAAAATAACTTTCAACATC
EST: gi|169047686|gb|FE454854.1|FE454854
EST:     CCGTTTGGATGATGCGAAACATCGTTCATTTCTGCGACCTGTCCACTCAG                         GCTGTTGAGAAAGCTGCCGTATTCAAGGGTCAGAAAATAACTTTCAACATC
genomic: CCGTTTGGATGATGCGAAACATCGTCCATTTCTGCGACCTGTCCACTCAGgtatgcactg ... tctcttgcagGCTGTTGAGAAAGCTGCCGGATCCAAGGGTCAGAAAATAACTTTCAACATC
EST: gi|169077658|gb|FE484920.1|FE484920
EST:     CCGTTTGGATGATGCGAAACATCGTTCATTTCTGCGACCTGTCCACTCAG                         GCTGTTGAGAAAGCTGCCGGATCCAAGGGTCAGAAAATAACTTTCAACATC
genomic: CCGTTTGGATGATGCGAAACATCGTCCATTTCTGCGACCTGTCCACTCAGgtatgcactg ... tctcttgcagGCTGTTGAGAAAGCTGCCGGATCCAAGGGTCAGAAAATAACTTTCAACATC
EST: gi|169045568|gb|FE452529.1|FE452529
EST:     CCGTTTGGATGATGCGAAACATCGTCCATTTCTGCGACCTGTCCACTCAG                         GCTGTTGAGAAAGCTGCCGGATCCAAGGGTCAGAAAATAACTTTCAACATC
genomic: CCGTTTGGATGATGCGAAACATCGTCCATTTCTGCGACCTGTCCACTCAGgtatgcactg ... tctcttgcagGCTGTTGAGAAAGCTGCCGGATCCAAGGGTCAGAAAATAACTTTCAACATC

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: 23 (upstream exon), 27 (downstream exon)
Score: 14

ATACGATAAGTTTTGTCCGTTCTACAAGTCCGTTTGGATGATGCGAAACATCGTCCATTTCTGCGACCTGTCCACTCAGgtatgcactg ... tctcttgcagGCTGTTGAGAAAGCTGCCGGATCCAAGGGTCAGAAAATAACTTTCAACATCATCAGGCAGCGCCTCGGAGACATCATATACCGTTTAGT




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