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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTGCTGCTCTAGCTTTGGATGATTCAGTTCTAGACGCTGATCAACTGGAAAATCTCATAAAATTTTGCCCAACAAAAGAGGAGATGGAACTTCTAAAGgttgttttaaaattaaagcttatatttccttgcactccttctgtaatctttaatttttctcttctctgaatatcttgcaaaagtaaagtatttgcactttttcctatcag

Basic information

species Oryza sativa
transcript LOC_Os04g17130.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g17130.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G398731_T01 (Zea mays), 5'ss of exon 3
AGTGCTGCTCTAGCTTTGGATGATTCAGTTCTAGACGCTGATCAACTGGAAAATCTCATAAAATTTTGCCCAACAAAAGAGGAGATGGAACTTCTAAAGgttgttttaaaattaaagcttatatttccttgcactccttctgtaatctttaatttttctcttctctgaatatcttgcaaaagtaaagtatttgcactttttcctatcag
|||||||||||||||||||| ||||||||| | || ||||| ||  | |||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||  ||||||    ||  |||||      |             | ||   || | ||||||||||   |   |||| |||| | |   || ||||||| |||||
AGTGCTGCTCTAGCTTTGGACGATTCAGTTTTGGATGCTGACCAGATTGAAAATCTAATAAAATTTTGCCCAACAAAAGAGGAGATGGAACTTCTAAAGgttgtttttgaattaatatctaattttccacatgtt-------------tgaaccatttttttctctgaatccata--aaaaataaattttgcacattttttcc-atcag

upper sequence: LOC_Os04g17130.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA17G11100.1 (Glycine max), 5'ss of exon 10
AGTGCTGCTCTAGCTTTGGATGATTCAGTTCTAGACGCTGATCAACTGGAAAATCTCATAAAATTTTGCCCAACAAAAGAGGAGATGGAACTTCTAAAGgttgt-tttaaaattaaagcttatatttccttgcactccttctgtaatctttaatttttctcttctctga-atatcttgcaaaagtaaagtatttgcactttttcctatcag------------------------------------------
  ||| |  |||||||||||||| |||||  | || | ||||||| ||||||||||||| || ||||| || || |||||||||||||| ||| | |||||    ||||| |         ||| ||| || || || |  | |||   ||||  |||||  | | ||  || |  || || | |||| ||| | |  ||  |   ||  |                                          
GCTGCAGTACTAGCTTTGGATGAGTCAGTATTGGATGTTGATCAAGTGGAAAATCTCATTAAGTTTTGTCCTACCAAAGAGGAGATGGATCTTTTGAAGgtgaagtttaacaaatttatccataattc-ttaca-tcttgttttaacaattaaggtttctagtttgtggtatcttctgtaacactaaaatatatccttttactgtgatttgtttaatttctaattttgtttcctcttgtttatggttgtttag

upper sequence: LOC_Os04g17130.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA06G21190.1 (Glycine max), 5'ss of exon 10
AGTGCTGCTCTAGCTTTGGATGATTCAGTTCTAGACGCTGATCAACTGGAAAATCTCATAAAATTTTGCCCAACAAAAGAGGAGATGGAACTTCTAAAGgttgttttaaaattaaagcttatatt-tccttgcactccttctgtaatctttaatttttctcttctctgaatatcttgcaaaagtaaagtatttgcactttttcctatcag-----------------------------------------------
  ||| |  || ||| |||||||||||||  |||| | ||||||  ||||||||||||| |||||||| || || |||||||| || || ||| |||||||     | ||   ||    || ||  | |||||| || | || | |   ||||   ||||| | ||| |  || ||||       | | ||||  || ||||  | | |                                                
GCTGCAGTACTGGCTATGGATGATTCAGTGTTAGATGTTGATCAGGTGGAAAATCTCATTAAATTTTGTCCTACCAAAGAGGAAATAGAGCTTTTAAAGgtgaagcttaa-caaatttatacatgattcttgca-tcttgctttgacaattaagggttctcatttct-agcat-ttgctgttactatgaatttctaccttttattgtaattttcttgcttttctaattttgattaatcttggttatggtttatatag

upper sequence: LOC_Os04g17130.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA05G00820.1 (Glycine max), 5'ss of exon 8
AGTGCTGCTCTAGCTTTGGATGATTCAGTTCTAGACGCTGATCAACTGGAAAATCTCATAAAATTTTGCCCAACAAAAGAGGAGATGGAACTTCTAAAGgttgt-tttaaaattaaagcttatatttccttgcactccttctgtaatctttaatttttctcttctctga-atatcttgcaaaagtaaagtatttgcactttttcctatcag------------------------------------------
  ||| |  |||||||||||||| || ||  | || | ||||||| ||||||||||||| || ||||| || || |||||||||||||| ||| | |||||    ||||| |         ||| ||| || || || |  | |||   ||||  |||||  | | ||  || |  ||  | | |||| ||| | |  ||  ||  ||  |                                          
GCTGCAGTACTAGCTTTGGATGAGTCGGTATTGGATGTTGATCAAGTGGAAAATCTCATTAAGTTTTGTCCTACCAAAGAGGAGATGGATCTTTTGAAGgtgaagtttaacaaatttatccatacttc-ttaca-tcttgttttaacaattaaggtttctagtttgtggcatcttctgttagactaaaatatatccttttactctgatttgtttaatctctaattttgattcctcttgtttatgattgtttag

upper sequence: LOC_Os04g17130.1 (Oryza sativa), 5'ss of exon 9
lower sequence: AT5G07650.1 (Arabidopsis thaliana), 5'ss of exon 4
AGTGCTGCTCTAGCTTTGGATGATTCAGTTCTAGACGCTGATCAACTGGAAAATCTCATAAAATTTTGCCCAACAAAAGAGGAGATGGAACTTCTAAAGgttgt----tttaa--aattaaagcttatatttcct-tgcactccttctgtaatcttt---aatttttc-----tcttctctgaatatcttgcaaaagta-aagtatttgcactttttcctatcag---------------
| ||| |  || ||  ||||||| || ||  |||| | ||||||| | || || || ||||| |||||||||||||| ||||||||||| ||||| |||||| |    ||| |  | ||  |   | || || || |  | |  || ||| || |||   | || ||      || ||  |    |  ||  |     |   ||  |||  |||| || |    |               
ACTGCAGTCCTGGCAATGGATGAGTCTGTAGTAGATGTTGATCAAATAGAGAAACTTATAAAGTTTTGCCCAACAAATGAGGAGATGGAGCTTCTTAAGgttttgacttttgagtagttgcattatttactttctatttatttattttgtgatatttgtcagttcttggttaatcatcattattcactttttattgacacgggttcttgttctttgtcgtgattgactgatttgttgtag

upper sequence: LOC_Os04g17130.1 (Oryza sativa), 5'ss of exon 9
lower sequence: AT5G07650.1 (Arabidopsis thaliana), 5'ss of exon 18
AGTGCTGCTCTAGCTTTGGATGATTCAGTTCTAGACGCTGATCAACTGGAAAATCTCATAAAATTTTGCCCAACAAAAGAGGAGATGGAACTTCTAAAGgttgttttaaaattaaagcttatatttccttgcactccttctgtaatctttaatttttctcttctctgaatatcttgcaaaagtaaagtatttgcactttttcctatcag
  ||| |  ||||   ||||||| |  || ||||| | ||||||| | || ||||| ||||  |||||||||||||| ||||||||||| ||||| ||||||   |      |     ||   |  | ||     | |  |    |  ||| ||          || | | |    |  || | |    ||||   |            
GCTGCAGTACTAGGAATGGATGAGTATGTACTAGATGTTGATCAAATAGAGAATCTTATAAGGTTTTGCCCAACAAAGGAGGAGATGGAGCTTCTTAAGgttacctcttgcctt---tttgagtagcattatctacttcttaaggttgttacttgacacgagtccttattcttggtcgtaattgactggtttgttgtag----------

upper sequence: LOC_Os04g17130.1 (Oryza sativa), 5'ss of exon 9
lower sequence: AT5G07740.1 (Arabidopsis thaliana), 5'ss of exon 7
AGTGCTGCTCTAGCTTTGGATGATTCAGTTCTAGACGCTGATCAACTGGAAAATCTCATAAAATTTTGCCCAACAAAAGAGGAGATGGAACTTCTAAAGgtt--gttttaaaattaaagc----ttatatttccttgcactccttctgta-atcttt-----aatttttctcttctctg--aatatcttgcaaaagtaa--agtatttgcactttttcctatcag---------------------
  ||| | ||| ||  ||||||| || || ||||| | ||||||| | || ||||| ||||| ||||||||||| || ||||||||||| || || ||||||  || || |  ||  ||     |||| | |   ||   |   | || | ||| ||     ||| | ||  || |  |  |  ||  | ||   || |     ||  |  ||| ||| |    |                     
GCTGCAGTTCTGGCAATGGATGAGTCTGTACTAGATGTTGATCAAATAGAGAATCTTATAAAGTTTTGCCCAACCAAGGAGGAGATGGAGCTACTTAAGgttacgtcttgacttttgagtagcattatctatttctgtctttactttggagatcatttgtgaaatatgtcaattattggttatcattattcacttgttattgacatgagtccttgttcttggtcgtaattgtctggtttgttctag

upper sequence: LOC_Os04g17130.1 (Oryza sativa), 5'ss of exon 9
lower sequence: AT5G07760.1 (Arabidopsis thaliana), 5'ss of exon 16
AGTGCTGCTCTAGCTTTGGATGATTCAGTTCTAGACGCTGATCAACTGGAAAATCTCATAAAATTTTGCCCAACAAAAGAGGAGATGGAACTTCTAAAGgttg--ttttaaaattaaagc----ttatatttccttgcactc-cttctgt-aatctttaatttttctc-ttctctgaatatcttgcaaaagtaaagtatttgcactttttcctatcag----------
  ||| | |||||   ||||||| || || ||||| | ||||||| | || ||||| ||||  |||||||||||||| ||||||||| | ||||| ||||||   | || |  ||  ||      ||| |     ||   |  ||| ||| |||  ||  || |  |  ||| ||   ||  |  ||  ||| |    | |      |     ||  |          
GCTGCAGTTCTAGGAATGGATGAGTCTGTACTAGATGTTGATCAAATAGAGAATCTTATAAGGTTTTGCCCAACAAAGGAGGAGATGAAGCTTCTTAAGgttacctcttgacttttgagtagcactatctacttctgtctttacttttgtcaattcttggttatcattattcacttgttagttgacacgagtcattattcttggtcgtaattgattggtttgttgtag

upper sequence: LOC_Os04g17130.1 (Oryza sativa), 5'ss of exon 9
lower sequence: AT5G07770.2 (Arabidopsis thaliana), 5'ss of exon 7
AGTGCTGCTCTAGCTTTGGATGATTCAGTTCTAGACGCTGATCAACTGGAAAATCTCATAAAATTTTGCCCAACAAAAGAGGAGATGGAACTTCTAAAGgt----tgttttaaaattaaagc--ttatatttccttgcactccttctgtaatctttaatttttctcttctctgaatatcttgcaaaagtaaagtatttgcactttttcctatcag
  ||| |   | ||  ||||||| || || ||||| | ||||||| | || ||||| ||| || ||||||||||||| ||||||||||| ||||| |||||      | || |  ||  ||     |||| | ||||   || || | |||    | ||  ||  ||     || | |||||        || |   |||  ||| |  ||    
GCTGCAGTCATGGCAATGGATGAGTCTGTACTAGATGTTGATCAAATAGAGAATCTTATACAACTTTGCCCAACAAAGGAGGAGATGGAGCTTCTTAAGgtgttacctcttgacttttgagtagcaatatctacttgtg-tctttatttaag---tgatcatttactgacacgagt-tcttgttcgg---aattgactgc--tttgttgtag---

upper sequence: LOC_Os04g17130.1 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv17s0000g06640.t01 (Vitis vinifera), 5'ss of exon 9
AGTGCTGCTCTAGCTTTGGATGATTCAGTTCTAGACGCTGATCAACTGGAAAATCTCATAAAATTTTGCCCAACAAAAGAGGAGATGGAACTTCTAAAGgttgttttaaaattaaagcttatatttccttgcactccttctgtaatctttaat------ttttctcttctctgaatatcttgcaaaagtaaagta-tttgcactttttcctatcag------------------------------------------
  ||| | ||||||  ||||||| ||| || |||| | ||||||| |||||||||||||||| || ||||| || |||||||||||||||||||| |||||      | ||   |||     |||| |||  |    |  |    | || |||        |||||| || |||  || ||     |||| | |  | | |   |||| || ||                                            
GCTGCAGTTCTAGCAATGGATGAGTCAATTTTAGATGTTGATCAAGTGGAAAATCTCATAAAGTTCTGCCCTACTAAAGAGGAGATGGAACTTCTTAAGgtgcagcaataacacaagtcataattttcttctatgtttcattagctattcaatggaagacgttctctgctgtgaggatgtttgttgagtatattggtctacctgtttttctttcttagtttttccccttagactaatgatttctgtttgtttatttag

upper sequence: LOC_Os04g17130.1 (Oryza sativa), 5'ss of exon 9
lower sequence: PP1S246_71V6.1 (Physcomitrella patens), 5'ss of exon 8
AGTGCTGCTCTAGCTTTGGATGATTCAGTTCTAGACGCTGATCAACTGGAAAATCTCATAAAATTTTGCCCAACAAAAGAGGAGATGGAACTTCTAAAGgttgttttaaaattaaagcttatatttccttgcactccttctgtaatctttaatttttctcttctctgaatatcttg-caaaagtaaagtatt-----tgcactttttcctatcag---------------------------------------------------------------
||||  | |||  |||||||    || ||  | ||  | |||||| ||||||||||||| || || |||||||| || |||||||||||  | || |  ||   ||||  ||||   |||  | |     ||  |  |  | || | |  || || |   ||  |||||  | |   |  | || || | ||     ||   ||| ||  ||                                                                  
AGTGGAGTTCTTTCTTTGGACCCATCTGTATTGGATACAGATCAAGTGGAAAATCTCATTAAGTTCTGCCCAACGAAGGAGGAGATGGATATGCTGAGAgtaagtttatcatta---cttcaagtgaaaggctattgtgat-tagtgtagaagttctggattaactgaaagtgtcaacggacgtgaatttttattcatgtggtttctcaaattgccttacattcaccatgagcattgtaattggtaaatttattactttattgccgggatgtttttag

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTGCTGCTCTAGCTTTGGATGATTCAGTTCTAGACGCTGATCAACTGGAAAATCTCATAAAATTTTGCCCAACAAAAGAGGAGATGGAACTTCTAAAGgttgttttaaaattaaagcttatatttccttgcactccttctgtaatctttaatttttctcttctctgaatatcttgcaaaagtaaagtatttgcactttttcctatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA