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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCTGTAAAATCAAAGCGAGACTACCTCAAACATCGAAGTAGCTTTAACTGGTTATATCTTTCACGTCTTGCGGCTCTCAAGGAATTTGCTTTCATGAAGgtagtggctttcaatctttcagcttttttttttgtttttatgctttgttcag

Basic information

species Selaginella moellendorffii
transcript EFJ10419
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ10419 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: LOC_Os01g66520.1 (Oryza sativa), 5'ss of exon 5
AGCTGTAAAATCAAAGCGAGACTACCTCAAACATCGAAGTAGCTTTAACTGGTTATATCTTTCACGTCTTGCGGCTCTCAAGGAATTTGCTTTCATGAAGgtagtggctttcaat-ctttcagcttttttttttgtttttatgctt-tgttcag-------------------------------------
 ||||| ||||| ||||| |||||  |   ||| || || |||||||| |||||||| || ||||| || ||||| || |||||||||||||| ||||||||  | |||  | || ||||        ||  ||||   ||   |  | ||                                        
GGCTGTGAAATCCAAGCGTGACTATTTGGCACACCGGAGGAGCTTTAATTGGTTATACCTGTCACGACTAGCGGCCCTAAAGGAATTTGCTTTTATGAAGgtttttgctgactatacttttcatcaagttagttgtagctagattcatatttgcttgataatcatttctagtttactttatgaaattccag

upper sequence: EFJ10419 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: GLYMA11G33320.1 (Glycine max), 5'ss of exon 5
AGCTGTAAAATCAAAGCGAGACTACCTCAAACATCGAAGTAGCTTTAACTGGTTATATCTTTCACGTCTTGCGGCTCTCAAGGAATTTGCTTTCATGAAGgtagtggctt-tcaatctttcagcttttttttttgt--ttttatgctttgttcag---------------------------------------------
|||||| ||||| ||||| |||||| | | |||||| ||||| | ||||||| | ||| | || || ||||| || || || ||||||||||||||||||||  ||  ||  |   || |||  |||  | | |||   | ||| |||   |                                                
AGCTGTCAAATCTAAGCGTGACTACTTGAGACATCGCAGTAGTTATAACTGGCTCTATTTGTCTCGCCTTGCTGCGCTTAAAGAATTTGCTTTCATGAAGgttttgttttaccttcctctcatttttagtctatgtaactgtatacttgaattgttatattttgtttgatttgctagtgacatatgctttgcttgagcag

upper sequence: EFJ10419 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: AT3G51270.2 (Arabidopsis thaliana), 5'ss of exon 6
AGCTGTAAAATCAAAGCGAGACTACCTCAAACATCGAAGTAGCTTTAACTGGTTATATCTTTCACGTCTTGCGGCTCTCAAGGAATTTGCTTTCATGAAGgtagtggctttcaatctttcagct-----tttttttttgtttttatgctttgttcag------------------------------------------
 ||||| ||||| ||||| |||||| | |  ||||| ||||| || | |||||| ||||| || || ||||| ||||||||||| |||||||| ||||||||  | || |||   |  | |  |     | || || ||  | |||  | | || |                                           
GGCTGTCAAATCTAAGCGTGACTACTTGAGGCATCGCAGTAGTTTCAGCTGGTTGTATCTCTCCCGACTTGCAGCTCTCAAGGAGTTTGCTTTTATGAAGgttattgccttcttccactaatgtaacactattcttgtgggtgtatcatctttttattttatttttggcctaatgtttgtttggcttctgggtgagcag

upper sequence: EFJ10419 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: PP1S40_20V6.1 (Physcomitrella patens), 5'ss of exon 5
AGCTGTAAAATCAAAGCGAGACTACCTCAAACATCGAAGTAGCTTTAACTGGTTATATCTTTCACGTCTTGCGGCTCTCAAGGAATTTGCTTTCATGAAGgtag------------tggctt-tcaatctttcagcttttttttttgtttttatgctttgttcag-----------------------------------
 ||||| || ||||||||||| ||| | |||||||| | ||||| ||  ||| | ||||| ||  | || |||||||||||||| | |||||||||||||||              ||| || ||| ||  |    |||||||||||||||| |  ||| || |                                    
GGCTGTTAAGTCAAAGCGAGATTACTTGAAACATCGCAATAGCTATAGTTGGCTGTATCTGTCGAGACTGGCGGCTCTCAAGGAGTATGCTTTCATGAAGgtgaggcccactctactggtttgtcattcggttgtattttttttttgtttttgttgtttttttaaaaggtgttttggggttttgttttgtcttgttttgt

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|169060196|gb|FE467558.1|FE467558
EST:     GGTTATATCTTTCACGTCTTGCGGCTCTCAAGGAATTTGCTTTCATGAAG                         GCTCTGCATGAACATGGATTTCCCACTCCAAAAGCAGTTGATTGGAATCGA
genomic: GGTTATATCTTTCACGTCTTGCGGCTCTCAAGGAATTTGCTTTCATGAAGgtagtggctt ... ctttgttcagGCTCTGCATGAACATGGATTTCCCACTCCAAAAGCAGTTGATTGGAATCGA
EST: gi|169054045|gb|FE462280.1|FE462280
EST:     GGTTATATCTTTCACGTCTTGCGGCTCTGAAGGAATTTGCTTTCATGAAG                         GCTCTGCATGAACATGGATTCCCCACTCCAAAAGCAGTTGATTGGAATCGA
genomic: GGTTATATCTTTCACGTCTTGCGGCTCTCAAGGAATTTGCTTTCATGAAGgtagtggctt ... ctttgttcagGCTCTGCATGAACATGGATTTCCCACTCCAAAAGCAGTTGATTGGAATCGA

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCTGTAAAATCAAAGCGAGACTACCTCAAACATCGAAGTAGCTTTAACTGGTTATATCTTTCACGTCTTGCGGCTCTCAAGGAATTTGCTTTCATGAAGgtagtggctttcaatctttcagcttttttttttgtttttatgctttgttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA