Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCGAGAGAGAAATGGACGACTACACGAGGGAAATGATGGACCTGAAGACACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTTGCCAGGATCCGTgtgcgtacataccttagggtttcctcaccgtagatccattcaattctttcaacttagggttattcttccatattttttttttttgtctcag

Basic information

species Glycine max
transcript GLYMA20G38790.3
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G38790.2 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os12g01170.1 (Oryza sativa), 5'ss of exon 1
GTTCGAGAGAGAAATGGACGACTACACGAGGGAAATGATGGACCTGAAGACACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTTGCCAGGATCCGTgtgcgtacataccttagggtttcctcaccgtagatccattcaattctttcaacttagggttattcttccatattttttttttttgtct--cag-------
|   ||  | |  |||||||||||| || |||| |||||||| || ||||| || ||||| ||||| ||||||||||| |||||||| |||| |||| | || |  |    || |     ||| || |      | |   |  ||||    |  |       | ||| |  || |   | |   | |   | |       
GGCGGAAGGGGGGATGGACGACTACGCGCGGGAGATGATGGAGCTCAAGACGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATCAGGgtacaaatcccccatccctcttcttctcttctcttgctcacctttctgcggatctgactcactacttgcggatctcaatctccggcccgccggaattgct

upper sequence: GLYMA20G38790.2 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G099980_T03 (Zea mays), 5'ss of exon 1
GTTCGAGAGAGAAATGGACGACTACACGAGGGAAATGATGGACCTGAAGACACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTTGCCAGGATCCGTgtgcgtacataccttagggtttcctcaccgtag--atccattcaattctttcaacttagggttattcttccatattttttttttttgtctcag-------
 ||  ||   |  |||||||||||| |  |||| |||||||| || ||||| || ||||| ||||| ||||||||||| |||||||| |||| |||  | || ||||| | |       |||| ||      |  |||| |||| |  |              |  | ||     | |   ||||  || |         
ATTTCAGGCCGGGATGGACGACTACGCCCGGGAGATGATGGAGCTCAAGACGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGGgttcgtacttccaacttattttcttcgtttccgccatcccttcattgatccggtgcctcacccacgcctcacggatctagcttttcatcccctccagttt

upper sequence: GLYMA20G38790.2 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G151268_T02 (Zea mays), 5'ss of exon 1
GTTCGAGAGAGAAATGGACGACTACACGAGGGAAATGATGGACCTGAAGACACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTTGCCAGGATCCGTgtgcgtacataccttagggtttcctcaccgt-agatccattcaattctttcaacttagggttattcttccatattttttttttttgtctcag--------
 ||   ||  |  |||||||||||| |  |||| |||||||| |||||||| || ||||| ||||| ||||||||||| ||||| || |||| |||  | || ||||| ||||      || | |||     | |||| |||| |  |              |  |  |   || |   ||||    | |          
ATTTCGGACGGGGATGGACGACTACGCCCGGGAGATGATGGAGCTGAAGACGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGGgttcgtacttaccacttctttccttcatttccacatcccttcattgatccggtgcctcacccacaccccaggatctagcttttcccgccctcccgtttgg

upper sequence: GLYMA20G38790.2 (Glycine max), 5'ss of exon 1
lower sequence: Vv13s0067g03320.t01 (Vitis vinifera), 5'ss of exon 1
GTTCGAGAGAGAAATGGACGACTACACGAGGGAAATGATGGACCTGAAGACACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTTGCCAGGATCCGTgtgcgtacatacc---ttagggtttcctcaccgtagatccattcaattctttcaacttagggttattcttccatattttttttttttgtctcag------
    |    ||| ||||||||||||||  | || ||||||||||| ||||| || |||||||| || || ||||||||||||||||| |||| |||||| ||   | | |  |   ||    | |  |  |   |  | | | |   | || | ||  ||   |   | |     ||    ||||   |   ||      
AGCTGTTGCAGAGATGGACGACTACACTCGAGAGATGATGGACCTCAAGACCCTTGTCACTCGAACCCTAGAGAAGAAAGGCGTCCTCGCCAAGATCCGGgtattttcctttcctttttacctctttttccttcattttcttccgccttttcccacccagatctcggcgttttgtttcaaattttcaatacgagaaacga

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|298186320|gb|HO036953.1|HO036953
EST:     CACTGGTCACTCGCACTCCCGAGAAGAAAGGCGTCCTTGCCAGGATCCGT                         GCCGAACTCAGAGCGAGTGTGTTCGAGGCCATCGAAGAGGAAGATCATGTG
genomic: CACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTTGCCAGGATCCGTgtgcgtacat ... tttgtctcagGCCGAACTCAGAGCGAGTGTGTTCGAGGCCATCGAAGAGGAAGATCATGTG
EST: gi|298168800|gb|HO009730.1|HO009730
EST:     CACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTTGCCAGGATCCGT                         GCCGAACTCAGAGCGAGTGTGTTCGAGGCCATCGAAGAGGAAGATCATGTG
genomic: CACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTTGCCAGGATCCGTgtgcgtacat ... tttgtctcagGCCGAACTCAGAGCGAGTGTGTTCGAGGCCATCGAAGAGGAAGATCATGTG
EST: gi|151405233|gb|EV275047.1|EV275047
EST:     CACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTTGCCAGGATCCGT                         GCCGAACTCAGGGTGAGTGTGTTCGAGGCCATCGAAGAGGAAGATCATGTG
genomic: CACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTTGCCAGGATCCGTgtgcgtacat ... tttgtctcagGCCGAACTCAGAGCGAGTGTGTTCGAGGCCATCGAAGAGGAAGATCATGTG
EST: gi|298191648|gb|HO039127.1|HO039127
EST:     CACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTTGCCAGGATCCGT                         GCCGAACTCAGAGCGAGTGTGTTCGAGGCCATCGAAGAGGAAGATCATGTG
genomic: CACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTTGCCAGGATCCGTgtgcgtacat ... tttgtctcagGCCGAACTCAGAGCGAGTGTGTTCGAGGCCATCGAAGAGGAAGATCATGTG
EST: gi|13563206|gb|BG551426.1|BG551426
EST:     CACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTTGCCAGGATCCGT                         GCCGAACTCAGAGCGAGTGTGTTCGAGGCCATCGAAGAGGAAGATCATGTG
genomic: CACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTTGCCAGGATCCGTgtgcgtacat ... tttgtctcagGCCGAACTCAGAGCGAGTGTGTTCGAGGCCATCGAAGAGGAAGATCATGTG
EST: gi|298198893|gb|HO042256.1|HO042256
EST:     CACCGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTTGCCAGGATCCGT                         GCCGAACTCAGAGCGAGTGTGTTCGAGGCCATCGAAGAGGAAGATCATGTG
genomic: CACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTTGCCAGGATCCGTgtgcgtacat ... tttgtctcagGCCGAACTCAGAGCGAGTGTGTTCGAGGCCATCGAAGAGGAAGATCATGTG
EST: gi|151408547|gb|EV278355.1|EV278355
EST:     CACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTTGCCAGGATCCGT                         GCCGAACTCAGAGCGAGTGTGTTCGAGGCCATCGAAGAGGAAGATCATGTG
genomic: CACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTTGCCAGGATCCGTgtgcgtacat ... tttgtctcagGCCGAACTCAGAGCGAGTGTGTTCGAGGCCATCGAAGAGGAAGATCATGTG
EST: gi|254329094|gb|GR833466.1|GR833466
EST:     CACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTTGCCAGGATCCGT                         GCCGAACTCAGAGCGAGTGTGTTCGAGGCCATCGAAGAGGAAGATCATGTG
genomic: CACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTTGCCAGGATCCGTgtgcgtacat ... tttgtctcagGCCGAACTCAGAGCGAGTGTGTTCGAGGCCATCGAAGAGGAAGATCATGTG
EST: gi|192325538|gb|FK018434.1|FK018434
EST:     CACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTTGCCAGGATCCGT                         GTCGAACTCAGAGCGAGTGTGTTCGAGGCCATCGAAGAGGAAGATCATGTG
genomic: CACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTTGCCAGGATCCGTgtgcgtacat ... tttgtctcagGCCGAACTCAGAGCGAGTGTGTTCGAGGCCATCGAAGAGGAAGATCATGTG
EST: gi|22522110|gb|BU080921.1|BU080921
EST:     CACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTTGCCAGGATCCGT                         GCCGAACTCAGAGCGAGTGTGTTCGAGGCCATCGAAGAGGAAGATCATGTG
genomic: CACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTTGCCAGGATCCGTgtgcgtacat ... tttgtctcagGCCGAACTCAGAGCGAGTGTGTTCGAGGCCATCGAAGAGGAAGATCATGTG
EST: gi|298199357|gb|HO042720.1|HO042720
EST:     CACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTTGCCAGGATCCGT                         GCCGAACTCAGAGCGAGTGTGTTCGAGGCCATCGAAGAGGAAGATCATGTG
genomic: CACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTTGCCAGGATCCGTgtgcgtacat ... tttgtctcagGCCGAACTCAGAGCGAGTGTGTTCGAGGCCATCGAAGAGGAAGATCATGTG
EST: gi|298184578|gb|HO029791.1|HO029791
EST:     CACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTTGCCAGGATCCGT                         GCCGAACTCAGAGCGAGTGTGTTCGAGGCCATCGAAGAGGAAGATCATGTG
genomic: CACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTTGCCAGGATCCGTgtgcgtacat ... tttgtctcagGCCGAACTCAGAGCGAGTGTGTTCGAGGCCATCGAAGAGGAAGATCATGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCGAGAGAGAAATGGACGACTACACGAGGGAAATGATGGACCTGAAGACACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTTGCCAGGATCCGTgtgcgtacataccttagggtttcctcaccgtagatccattcaattctttcaacttagggttattcttccatattttttttttttgtctcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA