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'   
8  
 5'  3'   
9  
 5'  3'   
10  
 5'  3'   
11  
 5'  3'   
12  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACACCAGAGAAGATTGAAGCTGCTGGTAAGAAGAAAGAAGAAGGAAATGCATTATTTAAAGCTGGTAAATATGCAAGAGCTTCTAAAAGATATGAGAAGgtaataaaaaataaattgaatatttattcattctcttccatttcaatgcattcctgaggcatttttgttaccaaaatcttatcatag

Basic information

species Glycine max
transcript GLYMA16G10730.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G10730.1 (Glycine max), 5'ss of exon 9
lower sequence: GRMZM2G349810_T01 (Zea mays), 5'ss of exon 3
CACACCAGAGAAGATTGAAGCTGCTGGTAAGAAGAAAGAAGAAGGAAATGCATTATTTAAAGCTGGTAAATATGCAAGAGCTTCTAAAAGATATGAGAAGgtaataaaaaataaattgaatatttattcattct---------cttccatttcaatgcattcctgaggcatttttgtt-accaaaatcttatcatag---------------
|| |||||||||||| | |||||||||| ||||| | ||| | |||||||| || ||| | |||||||| |||||||| || |||||||||||||| | | | || || | | ||| |||| | | | | | | | | | || | | | | | ||
CAATGAAGAGAAGATTGAGGTTGCTGGTAAGGAGAAACAGGAATGGAATGCATTGTTCAAATTGGACAAATATGCTAGAGCTTCCAAGCGATATGAGAAGgtacttcatctttctttctgtagtaacccatagcacgaaaaagtcaaaatttgagtcctgtgcagggttgtcctacttcggcttacttctgttttaatcccatgctgccaag

upper sequence: GLYMA16G10730.1 (Glycine max), 5'ss of exon 9
lower sequence: AT5G48570.1 (Arabidopsis thaliana), 5'ss of exon 9
CACACCAGAGAAGATTGAAGCTGCTGGTAAGAAGAAAGAAGAAGGAAATGCATTATTTAAAGCTGGTAAATATGCAAGAGCTTCTAAAAGATATGAGAAGgtaataaaaaataaattgaatatttattcattctcttccatttcaatgcattcctgaggcatttttgttaccaaaatcttatcatag
||||| || | ||| |||||||| || ||||||||||||||||| |||| || || |||||||| ||||| ||||||||||| || ||||| |||| ||| | | | | ||||| | | | | || || |||| | ||| | | || ||
CACACAGGAAAGGATAGAAGCTGCAGGCAAGAAGAAAGAAGAAGGCAATGTGTTGTTCAAAGCTGGAAAATACGCAAGAGCTTCAAAGAGATACGAGAGGgtt-tgggatttggtcctagtatttgctaaagaaact---------tatgtttttgtttagattttaacatcaagttttgattgcag

upper sequence: GLYMA16G10730.1 (Glycine max), 5'ss of exon 9
lower sequence: AT3G25230.1 (Arabidopsis thaliana), 5'ss of exon 9
CACACCAGAGAAGATTGAAGCTGCTGGTAAGAAGAAAGAAGAAGGAAATGCATTATTTAAAGCTGGTAAATATGCAAGAGCTTCTAAAAGATATGAGAAGgtaataaaaaataaattgaatatttattcattctcttccatttcaatgcattcctgaggcatttttgttaccaaaatcttatcatag
||| |||||||||||||||||| |||||||||| |||||||||||| | ||||||| || |||||| | ||||| || ||||||||||||||| || | | || | |||| || || | | | || ||| || | || | | || ||
CACTGAGGAGAAGATTGAAGCTGCTAGTAAGAAGAAGGAAGAAGGAAATTCCAAGTTTAAAGGAGGCAAATATTCCCTGGCTTCCAAGAGATATGAGAAGgta-tatgatacgaactacttattgctttatgagttataagtcgaaca----------acatcttacatggttaagtttcttctcag

upper sequence: GLYMA16G10730.1 (Glycine max), 5'ss of exon 9
lower sequence: Vv00s0958g00020.t01 (Vitis vinifera), 5'ss of exon 5
CACACCAGAGAAGATTGAAGCTGCTGGTAAGAAGAAAGAAGAAGGAAATGCATTATTTAAAGCTGGTAAATATGCAAGAGCTTCTAAAAGATATGAGAAGgtaataaaaaataaattgaatatttattc-attctcttccatttcaatgcattcctgaggcatttttgttaccaaaatcttatcatag-----
||| |||||||||||| |||||||| |||||||| |||||||| |||| |||| || |||||||||||||||||||| || || |||||||||||||||| | | || || ||| || ||| | | | ||||||| | | | | | | | | | |
CACTGAAGAGAAGATTGAGGCTGCTGGCAAGAAGAAGGAAGAAGGCAATGTGCTATTCAAGGCTGGTAAATATGCAAGAGCCTCAAAGAGATATGAGAAGgtaaaatcatatgtggaatatgcttagtctattgattagcggtctctgccattcctctgtcctcaatttatctttcttttggttgcaatgcag

upper sequence: GLYMA16G10730.1 (Glycine max), 5'ss of exon 9
lower sequence: Vv00s0769g00010.t01 (Vitis vinifera), 5'ss of exon 9
CACACCAGAGAAGATTGAAGCTGCTGGTAAGAAGAAAGAAGAAGGAAATGCATTATTTAAAGCTGGTAAATATGCAAGAGCTTCTAAAAGATATGAGAAGgtaataaaaaataaattgaatatttattc-attctcttccatttcaatgcattcctgaggcatttttgttaccaaaatcttatcatag-----
||| |||||||||||| |||||||| |||||||| |||||||| |||| |||| || |||||||||||||||||||| || || |||||||||||||||| | | || || ||| || ||| | | | ||||||| | | | | | | | | | |
CACTGAAGAGAAGATTGAGGCTGCTGGCAAGAAGAAGGAAGAAGGCAATGTGCTATTCAAGGCTGGTAAATATGCAAGAGCCTCAAAGAGATATGAGAAGgtaaaatcatatgtgggatatgcttaatctattgattagcggtctctgccattcctctgtcctcaatttatctttcttttggttgcaatgcag

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|209706891|gb|BW661501.1|BW661501
EST:     AAGATATGAGAAG                         GCTGTAAAGTTCATAGAGTACGATACTGCCTTTAGTGAAGAGGAGAAGAAG
genomic: AAGATATGAGAAGgtaataaaaa ... cttatcatagGCTGTAAAGTTCATAGAGTACGATACTGCCTTTAGTGAAGAGGAGAAGAAG
EST: gi|7284769|gb|AW597319.1|AW597319
EST:     CATTATTTAAAGCTGGTAAATATGCAAGAGCTTCTAAAAGATATGAGAAG                         GCTGTAAAGTTCATAGAGTACGATACTGCCTTTAGTGAAGAGGAGAAGAAG
genomic: CATTATTTAAAGCTGGTAAATATGCAAGAGCTTCTAAAAGATATGAGAAGgtaataaaaa ... cttatcatagGCTGTAAAGTTCATAGAGTACGATACTGCCTTTAGTGAAGAGGAGAAGAAG
EST: gi|58020765|gb|CX707507.1|CX707507
EST:     CATTATTTAAAGCTGGTAAATATGCAAGAGCTTCTAAAAGATATGAGAAG                         GCTGTAAAGTTCATAGAGTACGATACTGCCTTTAGTGAAGAGGAGAAGAAG
genomic: CATTATTTAAAGCTGGTAAATATGCAAGAGCTTCTAAAAGATATGAGAAGgtaataaaaa ... cttatcatagGCTGTAAAGTTCATAGAGTACGATACTGCCTTTAGTGAAGAGGAGAAGAAG
EST: gi|10255841|gb|BE823607.1|BE823607
EST:     CATTATTTAAAGCTGGTAAATATGCAAGAGCNNCTAAAAGATATGAGAAG                         GCTGTAAAGTTCATAGAGTACGATACTGCCTTTAGTGAAGAGGAGAAGAAG
genomic: CATTATTTAAAGCTGGTAAATATGCAAGAGCTTCTAAAAGATATGAGAAGgtaataaaaa ... cttatcatagGCTGTAAAGTTCATAGAGTACGATACTGCCTTTAGTGAAGAGGAGAAGAAG
EST: gi|7146792|gb|AW508714.1|AW508714
EST:     CATTATTTAAAGCTGGTAAATATGCAAGAGCTTCTAAAAGATATGAGAAG                         GCTGTAAAGTTCATAGAGTACGATA
genomic: CATTATTTAAAGCTGGTAAATATGCAAGAGCTTCTAAAAGATATGAGAAGgtaataaaaa ... cttatcatagGCTGTAAAGTTCATAGAGTACGATA
EST: gi|14011452|gb|BG726374.1|BG726374
EST:     CATTATTTAAAGCTGGTAAATATGCAAGAGCTTCTAAAAGATATGAGAAG                         GCTGTAAAGTTCATAGAGTACGATACTGCCTTTAGTGAAGAGGAGAAGAAG
genomic: CATTATTTAAAGCTGGTAAATATGCAAGAGCTTCTAAAAGATATGAGAAGgtaataaaaa ... cttatcatagGCTGTAAAGTTCATAGAGTACGATACTGCCTTTAGTGAAGAGGAGAAGAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACACCAGAGAAGATTGAAGCTGCTGGTAAGAAGAAAGAAGAAGGAAATGCATTATTTAAAGCTGGTAAATATGCAAGAGCTTCTAAAAGATATGAGAAGgtaataaaaaataaattgaatatttattcattctcttccatttcaatgcattcctgaggcatttttgttaccaaaatcttatcatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT