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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTGAAGAATATTAGAAGACGAATGACCCCCCAACCCTTGAAAATTAGGGCAGATATTGAAATGAAATGTTTTCAATTTGATGGAGTTCTTCACATTAAGgtatttgattatttgtattccttttgttttttactttggttccttttcttttaagcatctaatttgttatatgaatttttattgcctatagcttatcttccaaagtattctcaggttttataatgatttgattatgcag

Basic information

species Glycine max
transcript GLYMA18G02820.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G02820.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os03g18510.1 (Oryza sativa), 5'ss of exon 2
TGTGAAGAATATTAGAAGACGAATGACCCCCCAACCCTTGAAAATTAGGGCAGATATTGAAATGAAATGTTTTCAATTTGATGGAGTTCTTCACATTAAGgtatttgat-tatttgtat-tccttttgttttttactttggttccttttcttttaagcatctaatttgttatatgaatttttattgcctatagcttatcttccaaagtattctcaggttttataatgatttgattatgcag
 || |||||||| || ||  | ||||| || || ||  | || ||  | || ||| |||| ||||||||||| ||||||||||| || ||||||||||||||  ||| | |   ||| | | |  ||    ||||||     |  || |  |       |||  || ||| |                                                                     
AGTTAAGAATATAAGGAGGAGGATGACACCACAGCCACTTAAGATCCGTGCTGATGTTGAGATGAAATGTTTCCAATTTGATGGGGTGCTTCACATTAAGgttcttgttatccctgtgtcttcccttagggtttactgaaactttttcttatggctaattctggttggttttgcag-----------------------------------------------------------------

upper sequence: GLYMA18G02820.1 (Glycine max), 5'ss of exon 4
lower sequence: AT5G05470.1 (Arabidopsis thaliana), 5'ss of exon 4
TGTGAAGAATATTAGAAGACGAATGACCCCCCAACCCTTGAAAATTAGGGCAGATATTGAAATGAAATGTTTTCAATTTGATGGAGTTCTTCACATTAAGgtatttgattatttgtattccttttgttttttactttggttccttttcttttaagcatctaatttgttatatgaatttttattgcctatagcttatcttccaaagtattctcaggttttataatgatttgattatgcag
| ||||| | ||||| ||  ||||||| || || ||  |||| ||| | || ||||||||| |||| |||||||| |||||||||||||| ||||| |||||   |  ||   | | |    | ||||||||  ||| |||  || ||| ||     |||| ||     ||   || |||      |||     || | |                                       
TTTGAAGGACATTAGGAGGAGAATGACACCACAGCCAATGAAGATTCGTGCTGATATTGAATTGAAGTGTTTTCAGTTTGATGGAGTTCTCCACATCAAGgtcagtcttttcctttttcttatctgttttttttttttgtt--ttctctgtttgttttctacttctagctaaagatgtttggctattattatgaatttacag-------------------------------------

upper sequence: GLYMA18G02820.1 (Glycine max), 5'ss of exon 4
lower sequence: AT2G40290.1 (Arabidopsis thaliana), 5'ss of exon 4
TGTGAAGAATATTAGAAGACGAATGACCCCCCAACCCTTGAAAATTAGGGCAGATATTGAAATGAAATGTTTTCAATTTGATGGAGTTCTTCACATTAAGgtatt--tgattatttgtattccttttgttttttactttggttccttttcttttaagcatctaatttgttatatgaatttttattgcctatagcttatcttccaaagtattctcaggttttataatgatttgattatgcag
||||||||| ||||| ||  ||||||| || |||||  |||||||  |||| ||||| ||| |||| |||||||| |||||||||||| |||||||||||||  |     ||||| |  |  ||||   || | |  |   | | || |  |||   ||| | |||| |   |   ||  || |    |  ||                                                
TGTGAAGAACATTAGGAGGAGAATGACACCACAACCAATGAAAATCCGGGCTGATATCGAATTGAAGTGTTTTCAGTTTGATGGAGTTGTTCACATTAAGgtcgtatctcttattagattatctttaacttgtgaaatgaatacattatgattt---catttgattt-tctcacccatgcttgtaattt-cag------------------------------------------------

upper sequence: GLYMA18G02820.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv06s0004g07100.t01 (Vitis vinifera), 5'ss of exon 4
TGTGAAGAATATTAGAAGACGAATGACCCCCCAACCCTTGAAAATTAGGGCAGATATTGAAATGAAATGTTTTCAATTTGATGGAGTTCTTCACATTAAGgtatttgattatttgtattccttttgttttttactttggttccttttcttttaagcatctaatttgttatatgaatttttattgcctatagcttatcttccaaagtattctcaggttttataatgatttgattatgcag
  | ||||| |||||||| |||||||| || ||||| || |||||  | || || || |||||||||||||| || |||||||| ||||||||||| |||||||| |||| ||       |||  | |    ||  |  || ||||   |||     | |  | ||  | |||       |         | ||   |   |  || |     |                         
GATCAAGAACATTAGAAGGCGAATGACACCACAACCATTAAAAATCCGTGCTGACATAGAAATGAAATGTTTCCAGTTTGATGGTGTTCTTCACATCAAGgtatt-gattgtt-------cttccggt----accattatttctttatctttgtaagttt--tgtggaagatggggcacaaccatgctgtgtttgcatgagactgtgtcaatgg-------------------------

upper sequence: GLYMA18G02820.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv13s0067g01710.t01 (Vitis vinifera), 5'ss of exon 4
TGTGAAGAATATTAGAAGACGAATGACCCCCCAACCCTTGAAAATTAGGGCAGATATTGAAATGAAATGTTTTCAATTTGATGGAGTTCTTCACATTAAGgtatttgattatttgtattccttttgttttttactttggttccttttcttttaagcatctaatttgttatatgaatttttattgcctatagcttatcttccaaagtattctcaggttttataatgatttgattatgcag-------
 || ||||||||||| ||| ||||||| || ||||| ||||||||| |||| |||||||||||||||||||| || |||||||| ||||||||||||||||| ||     ||| || | | |    |||   |||||   |  |||| ||| |     ||||| ||||  || | |     ||  || |||   | | |   ||||| | || | ||| ||| |  ||| ||  | ||        
GGTAAAGAATATTAGGAGAAGAATGACTCCACAACCATTGAAAATTCGGGCTGATATTGAAATGAAATGTTTCCAGTTTGATGGTGTTCTTCACATTAAGgtttt-----attggtgtccttc---tttgccacttt---ttattttatttgattggcctaatctgtttcataattgggattttactttaga--accgttttaagtactgtctgctttaatacttgttttatctttcactattcag

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|27423457|gb|CA934977.1|CA934977
EST:     CAGATATTGAAATGAAATGTTTTCAATTTGATGGAGTTCTTCACATTAAG                         GAGGCAATGCGTAAGGCTGAAGCTGTGGGAAATGATGACTGCCCTGTCAAA
genomic: CAGATATTGAAATGAAATGTTTTCAATTTGATGGAGTTCTTCACATTAAGgtatttgatt ... gattatgcagGAGGCAATGCGTAAGGCTGAAGCTGTGGGAAATGATGACTGCCCTGTCAAA
EST: gi|254345907|gb|GR859554.1|GR859554
EST:     CAGATATTGAAATGAAATGTTTTCAATTTGATGGAGTTCTTCACATTAAG                         -AGGCAATGCGTAAG-CTGA-GCTGTGG-AAATGATGACTGCCCTGTCAAA
genomic: CAGATATTGAAATGAAATGTTTTCAATTTGATGGAGTTCTTCACATTAAGgtatttgatt ... gattatgcagGAGGCAATGCGTAAGGCTGAAGCTGTGGGAAATGATGACTGCCCTGTCAAA
EST: gi|208137526|gb|GD938036.1|GD938036
EST:     TTTTCAATTTGATGGAGTTCTTCACATTAAG                         GAGGCAATGCGTAAGGCTGAAGCTGTGGGAAATGATGACTGCCCTGTCAAA
genomic: TTTTCAATTTGATGGAGTTCTTCACATTAAGgtatttgatt ... gattatgcagGAGGCAATGCGTAAGGCTGAAGCTGTGGGAAATGATGACTGCCCTGTCAAA
EST: gi|193585843|gb|FK541243.1|FK541243
EST:     CAGATATTGAAATGAAATGTTTTCAATTTGATGGAGTTCTTCACATTAAG                         GAGGCAATGCGTAAGGCTGAAGCTGTGGGAAATGATGACTGCCCTGTCAAA
genomic: CAGATATTGAAATGAAATGTTTTCAATTTGATGGAGTTCTTCACATTAAGgtatttgatt ... gattatgcagGAGGCAATGCGTAAGGCTGAAGCTGTGGGAAATGATGACTGCCCTGTCAAA
EST: gi|31462199|gb|CD404227.1|CD404227
EST:     GAGTTCTTCACATTAAG                         GAGGCAATGCGTAAGGCTGAAGCTGTGGGAAATGATGACTGCCCTGTCAAA
genomic: GAGTTCTTCACATTAAGgtatttgatt ... gattatgcagGAGGCAATGCGTAAGGCTGAAGCTGTGGGAAATGATGACTGCCCTGTCAAA
EST: gi|120534519|gb|EH262652.1|EH262652
EST:     CAGATATTGAAATGAAATGTTTTCAATTTGATGGAGTTCTTCACATTAAG                         GAGGCAATGCGTAAGGCTGAAGCTGT
genomic: CAGATATTGAAATGAAATGTTTTCAATTTGATGGAGTTCTTCACATTAAGgtatttgatt ... gattatgcagGAGGCAATGCGTAAGGCTGAAGCTGT
EST: gi|207683877|gb|GD666636.1|GD666636
EST:     CAGATATTGAAATGAAATGTTTTCAATTTGATGGAGTTCTTCACATTAAG                         GAGGCAATGCGTAAGG
genomic: CAGATATTGAAATGAAATGTTTTCAATTTGATGGAGTTCTTCACATTAAGgtatttgatt ... gattatgcagGAGGCAATGCGTAAGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTGAAGAATATTAGAAGACGAATGACCCCCCAACCCTTGAAAATTAGGGCAGATATTGAAATGAAATGTTTTCAATTTGATGGAGTTCTTCACATTAAGgtatttgattatttgtattccttttgttttttactttggttccttttcttttaagcatctaatttgttatatgaatttttattgcctatagcttatcttccaaagtattctcaggttttataatgatttgattatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA