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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTCTCCTTCCATTCTGGTCATTCTAACAATGTTTTCCAGGCCAAGATCATGCCTCACTCTGATGATCGAACCATTGTCACCTGTGCTGCCGATGGACAGgtctagttttattaatcattcttagattattgttttttcgtaattgtgtcaattctatattatag

Basic information

species Glycine max
transcript GLYMA20G23960.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G23960.1 (Glycine max), 5'ss of exon 2
lower sequence: AT4G35140.1 (Arabidopsis thaliana), 5'ss of exon 2
ACTCTCCTTCCATTCTGGTCATTCTAACAATGTTTTCCAGGCCAAGATCATGCCTCACTCTGATGATCGAACCATTGTCACCTGTGCTGCCGATGGACAGgtctagttttattaatcattcttaga---ttattgttttttcgtaattgtgtcaattctatattatag---------------------
 || ||||||||||| || ||  |||| || ||||| || || ||| | ||||||  ||||||||||||||| || || ||||||||||| ||||||  |||  | |  | | | |   | | |||   |   |||| |||  |  | ||||||    |   ||| |                      
GCTTTCCTTCCATTCAGGACACGCTAATAACGTTTTTCAAGCAAAGTTTATGCCTTTCTCTGATGATCGAACGATAGTAACCTGTGCTGCTGATGGAATGgtaaaatcctttgagttgctttaagaaactctctgttgttttctgttagtgtcacactttacttagattaaatctccaaacatctttag

upper sequence: GLYMA20G23960.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv03s0038g02940.t01 (Vitis vinifera), 5'ss of exon 4
ACTCTCCTTCCATTCTGGTCATTCTAACAATGTTTTCCAGGCCAAGATCATGCCTCACTCTGATGATCGAACCATTGTCACCTGTGCTGCCGATGGACAGgtctagttttattaatcattcttagattattgtttttt------cgtaat-tgtgtcaattctatattatag------------------------------
||| || ||  | |||||||||  ||||||||||||||| || ||| |||||||| || | |||||||||| |||||| || || || || ||||| |||||  | ||    |  | |    | || |  | || |        | | || ||   ||    ||| | ||                                
ACTTTCATTTGAATCTGGTCATATTAACAATGTTTTCCAAGCAAAGTTCATGCCTTACACAGATGATCGAAGCATTGTTACTTGCGCAGCAGATGGCCAGgt--aattcctgtgtttaaaagtggaatgcttttctggggagagcatgatgtggagcatccttatttcattaggagttggtacctaattcatgactggcatt

upper sequence: GLYMA20G23960.1 (Glycine max), 5'ss of exon 2
lower sequence: EFJ09381 (Selaginella moellendorffii), 5'ss of exon 1
ACTCTCCTTCCATTCTGGTCATTCTAACAATGTTTTCCAGGCCAAGATCATGCCTCACTCTGATGATCGAACCATTGTCACCTGTGCTGCCGATGGACAGgtct-----agttttattaa--tcatt--cttagattattgttttttcgtaattgtgtcaattctatattatag--------
|||||| ||  | ||||| |||   |||||||| |||||||||| ||||||||||  |||  | ||||||| | |||| ||||||||||||||||| || ||       | | |||| ||  || ||   |  ||    | || ||  ||  || | |   |  | | || ||         
ACTCTCTTTTAACTCTGGGCATGACAACAATGTGTTCCAGGCCAGGATCATGCCTTTCTCCAACGATCGAAGCGTTGTGACCTGTGCTGCCGATGGCCAAgtacgtgacattcttatcaagttctttgcttccgagctcttttcttctgttttttttttcttcttctcttttacattcacag

upper sequence: GLYMA20G23960.1 (Glycine max), 5'ss of exon 2
lower sequence: EFJ34971 (Selaginella moellendorffii), 5'ss of exon 2
ACTCTCCTTCCATTCTGGTCATTCTAACAATGTTTTCCAGGCCAAGATCATGCCTCACTCTGATGATCGAACCATTGTCACCTGTGCTGCCGATGGACAGgtct-----agttttattaa--tcatt-cttagattattgttttttcgtaattgtgtcaattctatattatag------
|||||| ||  | ||||| |||   |||||||| |||||||||| ||||||||||  |||  | ||||||| | |||| ||||||||||||||||| || ||       | | || | ||  || || |||  |   |  ||| |||    || | |   |||| | ||| |       
ACTCTCTTTTAACTCTGGCCATGACAACAATGTGTTCCAGGCCAGGATCATGCCTTTCTCCAACGATCGAAGCGTTGTGACCTGTGCTGCCGATGGCCAAgtacgtgacattcttctcaagttctttgcttccaagctcttttcttctgttttttttttcttctcttttacattcacag

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|298172696|gb|HO019736.1|HO019736
EST:     TGCCTCACTCTGATGATCGAACCATTGTCACCTGTGCTGCCGATGGACAG                         GTGAGACATGCTCAACTTCTTGAAAATGGACGAGTCGAAACTAAGTGTCTG
genomic: TGCCTCACTCTGATGATCGAACCATTGTCACCTGTGCTGCCGATGGACAGgtctagtttt ... tatattatagGTGAGACATGCTCAACTTCTTGAAAATGGACGAGTCGAAACTAAGTGTCTG
EST: gi|192306557|gb|FG996233.1|FG996233
EST:     TGCCTCACTCTGATGATCGAACCATTGTCACCTGTGCTGCCGATGGACAG                         GTGAGACATGCTCAACTTCTTGAAAATGGACGAGTCGAAACTAAGTGTCTG
genomic: TGCCTCACTCTGATGATCGAACCATTGTCACCTGTGCTGCCGATGGACAGgtctagtttt ... tatattatagGTGAGACATGCTCAACTTCTTGAAAATGGACGAGTCGAAACTAAGTGTCTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTCTCCTTCCATTCTGGTCATTCTAACAATGTTTTCCAGGCCAAGATCATGCCTCACTCTGATGATCGAACCATTGTCACCTGTGCTGCCGATGGACAGgtctagttttattaatcattcttagattattgttttttcgtaattgtgtcaattctatattatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA