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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTAAGCACCTTGAAGTTTGCTGAACGGGTTTCTGGCGTGGAGTTAGGCGCTGCTCGTAGCAACAAAGAGGGGAGGGATGTGAGAGAACTTATGGAGCAGgttatttctatttttgaatgcattttacttggatgttttagttatcagcgaagcaccaaatgttatgaattggaattttagttattcattttgtttttta...

Basic information

species Glycine max
transcript GLYMA05G37800.1
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G37800.1 (Glycine max), 5'ss of exon 18
lower sequence: LOC_Os05g44560.1 (Oryza sativa), 5'ss of exon 18
TGTAAGCACCTTGAAGTTTGCTGAACGGGTTTCTGGCGTGGAGTTAGGCGCTGCTCGTAGCAACAAAGAGGGGAGGGATGTGAGAGAACTTATGGAGCAGgttatttctatttttgaatgcattttacttggatgttttagttatcagc-gaagcaccaaatgttatgaattggaattttagttattcattttgtttttta----------
| |||||||  | |||||||||||| |||||||||| || |||||||| |||||  | || || |||||||| | |||| | | ||| ||  |||| |||||| || || ||| ||      || |   ||       |  | || | | |||    |     || ||  ||  |   ||  | |   |||| ||| |             
TATAAGCACTCTAAAGTTTGCTGAAAGGGTTTCTGGAGTTGAGTTAGGTGCTGCAAGAAGTAATAAAGAGGGAAAGGATATAAAAGAGCTGCTGGAACAGgttcttgctttttatg------ttctgtctga-----ctcatcattaactgaaatttctttgcttttgttttacataattgctgaactatttagttctaggaagaagggga

upper sequence: GLYMA05G37800.1 (Glycine max), 5'ss of exon 18
lower sequence: GRMZM2G323622_T01 (Zea mays), 5'ss of exon 9
TGTAAGCACCTTGAAGTTTGCTGAACGGGTTTCTGGCGTGGAGTTAGGCGCTGCTCGTAGCAACAAAGAGGGGAGGGATGTGAGAGAACTTATGGAGCAGgttatttctatttttgaatgcattttacttggatgttttagttatcagcgaagcaccaaatgttatgaattggaattt---tagttattcattttgtttttta--
  ||||||| ||||||||||||||| |||||||||| || |||||||| |||||  | || ||||||||||| |  ||| | | ||| ||  | || |||||  || | | | |    |  || |   | |    |||  |||   | ||        ||   || |||    | |||    |    || | ||    ||  |  
AATAAGCACTTTGAAGTTTGCTGAAAGGGTTTCTGGAGTTGAGTTAGGTGCTGCAAGAAGTAACAAAGAGGGTAAAGATATAAAAGAGCTGCTAGAACAGgtctttgcaactgtctcgtatatatatatagataatttctgtttctatcg-----ttcaacactaggaagaaaactttgtacaaacttttacttgagcttccagg

upper sequence: GLYMA05G37800.1 (Glycine max), 5'ss of exon 18
lower sequence: GRMZM2G124883_T01 (Zea mays), 5'ss of exon 9
TGTAAGCACCTTGAAGTTTGCTGAACGGGTTTCTGGCGTGGAGTTAGGCGCTGCTCGTAGCAACAAAGAGGGGAGGGATGTGAGAGAACTTATGGAGCAGgttatttctatttttgaatgcattttacttggatg-ttttagttatcagcg--aagcacca---aatgttatgaattggaattttagttattcattttgtttttta
  ||||||| ||||||||||||||| |||||||||| || |||||||| |||||  | || ||||||||||| |  ||| | | ||| ||  | || |||||| || | | | |   |   ||   | |  |||  ||||||||     |    | ||| |   |    | |  ||   || || | ||   ||||      |   
AATAAGCACTTTGAAGTTTGCTGAAAGGGTTTCTGGAGTTGAGTTAGGTGCTGCAAGAAGTAACAAAGAGGGTAAAGATATAAAAGAGCTGCTAGAACAGgttcttacaactgtctcacatat---attcagataattttagtttctgtcattcaacactaggaagcaatctttatacaaacttaacttgagcattcaacact---

upper sequence: GLYMA05G37800.1 (Glycine max), 5'ss of exon 18
lower sequence: GRMZM5G845682_T02 (Zea mays), 5'ss of exon 5
TGTAAGCACCTTGAAGTTTGCTGAACGGGTTTCTGGCGTGGAGTTAGGCGCTGCTCGTAGCAACAAAGAGGGGAGGGATGTGAGAGAACTTATGGAGCAGgttatttctatttttgaatgcattttacttggatgt-tttagttatcagcgaagcaccaaatgttatgaattggaattttagttattcattttgtttttta
| ||||||| || |||||||||||| |||| ||||| || |||||||| |||||  | |||||||| ||||| | |||| | | ||| ||  |||| |||||| ||    ||||||| |     | ||| |  | | |||  || |||    |       || | |  ||||  | ||||   ||   | | || |     
TATAAGCACTTTAAAGTTTGCTGAAAGGGTGTCTGGAGTAGAGTTAGGTGCTGCAAGAAGCAACAAGGAGGGAAAGGATATAAAAGAGCTACTGGAACAGgttcttgtactttttgactttcactaactggagtttgtttgtttctcattctatttgattatctgagcaattttagtttttaataaatagtatgctgaaa-

upper sequence: GLYMA05G37800.1 (Glycine max), 5'ss of exon 18
lower sequence: GRMZM2G093391_T01 (Zea mays), 5'ss of exon 3
TGTAAGCACCTTGAAGTTTGCTGAACGGGTTTCTGGCGTGGAGTTAGGCGCTGCTCGTAGCAACAAAGAGGGGAGGGATGTGAGAGAACTTATGGAGCAGgttatttctatttttgaatgcattttacttggatgttttagttatcagcgaagcaccaaatgttatgaattgg-aattttagttattcattttgtttttta--------
| |||| || ||||||||||||||| |||||||||| |||||| |||| ||  |       || ||||| || |  ||| | |||||| ||||||| ||||| ||    | | |||  | | |||| |   |||   ||| | ||   |   |||  | ||   ||| |||   ||| ||  || |   | || |    |         
TTTAAGTACTTTGAAGTTTGCTGAAAGGGTTTCTGGAGTGGAGCTAGGTGCCTCAAAGGCGAATAAAGAAGGCAAAGATATTAGAGAATTTATGGAACAGgtgataa--actattgttttccttttgcc--gatcccttattcat--acatggcagtagat---atggattaccaatgtttattttctgtattatccaatgggtgagac

upper sequence: GLYMA05G37800.1 (Glycine max), 5'ss of exon 18
lower sequence: AT1G63640.1 (Arabidopsis thaliana), 5'ss of exon 18
TGTAAGCACCTTGAAGTTTGCTGAACGGGTTTCTGGCGTGGAGTTAGGCGCTGCTCGTAGCAACAAAGAGGGGAGGGATGTGAGAGAACTTATGGAGCAGgttatttctatttttgaatgcattttacttggatgttttagttat--cagcgaagcaccaaatgttatgaattggaattttagttattcattttgtttttta------
 |||||||| ||||| || || ||| |||||||||| ||||||||||| |||||    || |  ||||||||  | ||||| ||| |||| ||||| ||||||  |  | | |||   |   | |  ||   | | |||| || |  |     |     |||    |  ||   |   ||    |||| || ||| ||  ||      
AGTAAGCACTTTGAAATTCGCCGAAAGGGTTTCTGGTGTGGAGTTAGGTGCTGCCAAAAGTAGTAAAGAGGGTCGAGATGTAAGACAACTCATGGAACAGgtttgtattctctttctctctctatctctctcaagatttaattttggctattgaaagttaaagagcacaaa---ggtattcgtatattgatattgcttgatataacag

upper sequence: GLYMA05G37800.1 (Glycine max), 5'ss of exon 18
lower sequence: Vv02s0025g03480.t01 (Vitis vinifera), 5'ss of exon 19
TGTAAGCACCTTGAAGTTTGCTGAACGGGTTTCTGGCGTGGAGTTAGGCGCTGCTCGTAGCAACAAAGAGGGGAGGGATGTGAGAGAACTTATGGAGCAGgttatt---tctatttttgaatgcatttt---acttggatgttttagttatcagcgaagcaccaaatgttatgaattggaattttagttattcattttgtttttta--
| |||| |||||||||||||| ||  | || ||||| || |||||||| |||||  | |||||||||||||| |||||||| |||||||||||||||||||| |||   | |||| |    | |||| |   ||||  |||  |||    |    ||||  |       |     |||  || ||     | | | ||| | || |  
TATAAGTACCTTGAAGTTTGCCGAGAGAGTCTCTGGTGTTGAGTTAGGTGCTGCAAGGAGCAACAAAGAGGGAAGGGATGTTAGAGAACTTATGGAGCAGgtcattacgtttattataattttcattgtttgacttctatgcattaagattttatgaagtgctgttcccttgtgtttgctatcttctgattccctgttgatcttgaag

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTAAGCACCTTGAAGTTTGCTGAACGGGTTTCTGGCGTGGAGTTAGGCGCTGCTCGTAGCAACAAAGAGGGGAGGGATGTGAGAGAACTTATGGAGCAGgttatttctatttttgaatgcattttacttggatgttttagttatcagcgaagcaccaaatgttatgaattggaattttagttattcattttgtttttta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG