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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCGCTCTACAATGTCTTGGTACAAGTCCAGCCCGAGGCAGTCTTGTGGGGGATTGGGACGGCCCTTGGAGAGCTTCCGCCTTACTTTGTTTCTAGAGCAGgtatcctcatttcatttgcttttaagtttcgtgtcactgacttagaaggtccgcag

Basic information

species Selaginella moellendorffii
transcript EFJ15115
intron # 4
splice site 5'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ15115 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: AT4G14950.1 (Arabidopsis thaliana), 5'ss of exon 4
CCGCTCTACAATGTCTTGGTACAAGTCCAGCCCGAGGCAGTCTTGTGGGGGATTGGGACGGCCCTTGGAGAGCTTCCGCCTTACTTTGTTTCTAGAGCAGgt----------atcctcatttcatttgcttttaagtttcgtgtcactgacttagaaggtccgcag--------------------------------------------
|| ||   ||   | |||  ||||||||||   |||||| |||| ||||| ||||||||||| ||||| |||||||| || || ||  | || || ||||||          || |||  |  || |   | |  | || ||||    | |   | | || |  ||                                            
CCTCTTACCAGCATATTGCCACAAGTCCAGTTGGAGGCAATCTTATGGGGTATTGGGACGGCTCTTGGGGAGCTTCCTCCATATTTCATCTCAAGGGCAGgtttgtatactgattctctctatatatttctctttgatttgtgtagtcgtccatgcatgtgcataggtctcggttgtttattgtgttgtttgctttttctatttttccag
















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|169106011|gb|FE504371.1|FE504371
EST:     GATTGGGACGGCCCTTGGAGAGCTTCCGCCTTACTTTGTTTCTAGAGCAG                         CTCGGTTGTCTGGCGAGCGTCT
genomic: GATTGGGACGGCCCTTGGAGAGCTTCCGCCTTACTTTGTTTCTAGAGCAGgtatcctcat ... aggtccgcagCTCGGTTGTCTGGCGAGCGTCT
EST: gi|169051285|gb|FE457622.1|FE457622
EST:     GATTGGGACGGCGCTTGGAGAGCTTCCGCCTTACTTTGTTTCTAGAGCAG                         CTCGGTTGTCTGGCGAGCGTCTAAAGGCTCTTGACGACATTGAGAATGAGT
genomic: GATTGGGACGGCCCTTGGAGAGCTTCCGCCTTACTTTGTTTCTAGAGCAGgtatcctcat ... aggtccgcagCTCGGTTGTCTGGCGAGCGTCTAAAGGCTCTTGACGACATCGAGAACGAGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCGCTCTACAATGTCTTGGTACAAGTCCAGCCCGAGGCAGTCTTGTGGGGGATTGGGACGGCCCTTGGAGAGCTTCCGCCTTACTTTGTTTCTAGAGCAGgtatcctcatttcatttgcttttaagtttcgtgtcactgacttagaaggtccgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG