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'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   		24  
 5'  3'   		25  
 5'  3'   		26  
 5'  3'   		27  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTTTGGTGAAGGAGAGAAGTTTGTGAAAGCTGTATTTTCACTGGCAAGCAAAATTGCTCCAAGTGTTATTTTCGTGGATGAGgtaagtaaattgtaattgatcaatcacaacgcctttctgaattccctgtgatgtttgctttctagtttatcttcttcatcttgtgttgtatag

Basic information

species Oryza sativa
transcript LOC_Os03g22420.1
intron # 23
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g22420.1 (Oryza sativa), 5'ss of exon 23
lower sequence: GRMZM2G042074_T02 (Zea mays), 5'ss of exon 18
TGGTTTGGTGAAGGAGAGAAGTTTGTGAAAGCTGTATTTTCACTGGCAAGCAAAATTGCTCCAAGTGTTATTTTCGTGGATGAGgtaagtaa--attgtaat-tgatcaatca-caacgcctttctgaattccctgtg--atgtttgctttctagtt-tatcttcttcatcttgtgtt---gtatag----------------------------------------
||| ||||||||||||| || || ||||||||||| |||||||||||||| ||||||||||||||||| ||||| ||||| ||||||||| |   | ||  | ||||| || | |||   || | |   |   ||||   | |    |    ||  | ||  || |  |||  || ||   | |||                                         
TGGCTTGGTGAAGGAGAAAAATTCGTGAAAGCTGTTTTTTCACTGGCAAGTAAAATTGCTCCAAGTGTAATTTTTGTGGACGAGgtaagttatagtagtgttgtgatccatgaacaatttctatttatttgatctgtaccaggacaccacaatatctgtagtttgtcaatcccgtattaatgcatacttttctgctcatttatcctgctcttgtttttattttttag

upper sequence: LOC_Os03g22420.1 (Oryza sativa), 5'ss of exon 23
lower sequence: GRMZM2G438355_T01 (Zea mays), 5'ss of exon 2
TGGTTTGGTGAAGGAGAGAAGTTTGTGAAAGCTGTATTTTCACTGGCAAGCAAAATTGCTCCAAGTGTTATTTTCGTGGATGAGgtaagtaa-------attgtaattgat---caatcacaacgcctttctgaattccctgtgatgtttgc---tttctagtttatcttcttcatcttgt-gttgtatag---------------------------------
||| ||||||||||| | ||  ||||||||||||| ||||||||| |||| ||||| ||||||||||| ||||| ||||| ||||||||| |        |||| ||| ||   || |  | ||   ||||  | |   ||  ||      |   ||| |||||| |  ||     | | | | || |||                                  
TGGCTTGGTGAAGGAAAAAA--TTGTGAAAGCTGTGTTTTCACTGACAAGAAAAAT-GCTCCAAGTGTAATTTTTGTGGACGAGgtaagttatagtagtgttgtgattcatgtacattttctacttatttc-aattgtactaggacaccaccatatttgtagtttgttgtcaattccatattgatgcatactttcttgctcatttatcatgccctagtttttag

upper sequence: LOC_Os03g22420.1 (Oryza sativa), 5'ss of exon 23
lower sequence: GLYMA17G13850.1 (Glycine max), 5'ss of exon 21
TGGTTTGGTGAAGGAGAGAAGTTTGTGAAAGCTGTATTTTCACTGGCAAGCAAAATTGCTCCAAGTGTTATTTTCGTGGATGAGgtaagtaaattgtaattgatcaatcacaacgcctttctgaattccctgtgatgtttgctttctagtttatcttcttcatcttgtgttgtatag
||||||||||| || ||||| | |||||||||||| || || ||||| || |||||| | || |||||||| || || |||||||||||    || |||   |      |    |   |  ||| |||  ||  || |    || |||| ||   |||                   
TGGTTTGGTGAGGGTGAGAAATATGTGAAAGCTGTTTTCTCTCTGGCGAGTAAAATTTCACCTAGTGTTATATTTGTTGATGAGgtaagcc--ttttaaccaa--gggtattgtgttgtattga-ttcattg-aatataactttactagctttgtttcag-----------------

upper sequence: LOC_Os03g22420.1 (Oryza sativa), 5'ss of exon 23
lower sequence: GLYMA10G02410.1 (Glycine max), 5'ss of exon 19
TGGTTTGGTGAAGGAGAGAAGTTTGTGAAAGCTGTATTTTCACTGGCAAGCAAAATTGCTCCAAGTGTTATTTTCGTGGATGAGgtaagtaaattgtaattgatcaatcacaacgcctt--tctgaattccctgtgatg-tttgctttctag----tttatcttcttcatcttgtgttgtatag--
||||||||||||||||| || | ||| ||||| || ||||| ||||| |||||||||||||||||||||||||| || ||||||||  ||| |   ||  |  ||  |       | ||  | | |||   ||    |  ||| | || |      |||||  | | ||| |||||||||  ||  
TGGTTTGGTGAAGGAGAAAAATATGTCAAAGCAGTCTTTTCTCTGGCCAGCAAAATTGCTCCAAGTGTTATTTTTGTTGATGAGgttggtataacatatatcttccttttttttactttgttttaaatattctaaatttctttacattttgaccgttttataatgtccat-ttgtgttgt-cagtt

upper sequence: LOC_Os03g22420.1 (Oryza sativa), 5'ss of exon 23
lower sequence: GLYMA10G02400.1 (Glycine max), 5'ss of exon 22
TGGTTTGGTGAAGGAGAGAAGTTTGTGAAAGCTGTATTTTCACTGGCAAGCAAAATTGCTCCAAGTGTTATTTTCGTGGATGAGgtaagtaaattgtaattgatcaatcacaacgcctttctgaattccctgtgatgtttgctttctagtttatcttcttcatcttgtg----ttgtatag-------
|||||||||||||||||||||| ||| |||||||| ||||| || || |||||||||||||||||||||||||| || || |||||   |  ||  |  |   |   | | |       | |||| | |   |    |||  |||  |  |||| ||    |  || |     |  |||         
TGGTTTGGTGAAGGAGAGAAGTATGTCAAAGCTGTCTTTTCTCTAGCCAGCAAAATTGCTCCAAGTGTTATTTTTGTTGACGAGgttgctttatcatg-tcatttgtttata---ttcctttgaagttctcttttcctttattttaaatattatttttaatactttttagaattcatatgagccattt

upper sequence: LOC_Os03g22420.1 (Oryza sativa), 5'ss of exon 23
lower sequence: GLYMA06G17940.1 (Glycine max), 5'ss of exon 23
TGGTTTGGTGAAGGAGAGAAGTTTGTGAAAGCTGTATTTTCACTGGCAAGCAAAATTGCTCCAAGTGTTATTTTCGTGGATGAGgtaagtaaattgtaattgatcaatcacaacgcctttctgaattccctgtgatgtttgctttctagtttatcttcttcatcttgtgttgtatag
||||||||||| || || || |  ||||||||||| ||||| |||||||| ||||||||||| || || || || || || || |||||    |||||  | |    ||  |  |  | | | |||||     | ||     |   |   | |        ||    | ||||||||
TGGTTTGGTGAGGGTGAAAAATACGTGAAAGCTGTTTTTTCCCTGGCAAGTAAAATTGCTCCTAGCGTGATATTTGTTGACGAAgtaagccttttgta--taaatgttctta--gtttgtatcaattcaaca-gctgaaaaataaatcagtgaaaactagtatggcttcttgtatag

upper sequence: LOC_Os03g22420.1 (Oryza sativa), 5'ss of exon 23
lower sequence: GLYMA04G37050.1 (Glycine max), 5'ss of exon 6
TGGTTTGGTGAAGGAGAGAAGTTTGTGAAAGCTGTATTTTCACTGGCAAGCAAAATTGCTCCAAGTGTTATTTTCGTGGATGAGgtaagtaaattgtaattgatcaatcacaacgcctttctgaattccctgtgatgtttgctttctagtttatcttcttcatcttgtgttgtatag
||||||||||| || || |||| ||| |||||||| ||||| ||||| || ||||||||||| || || || || || || || |||||    ||| |    |    |   ||    | ||   | | | | || ||     |   |   |||     |  ||    | ||||||||
TGGTTTGGTGAGGGTGAAAAGTATGTCAAAGCTGTTTTTTCCCTGGCTAGTAAAATTGCTCCTAGCGTGATATTTGTTGACGAAgtaagccttttgca--caaatgtttttaatttgtatc---aattcatctgctgcaaaataaatcagttaaaacttgtatggcttcttgtatag

upper sequence: LOC_Os03g22420.1 (Oryza sativa), 5'ss of exon 23
lower sequence: GLYMA02G17400.1 (Glycine max), 5'ss of exon 19
TGGTTTGGTGAAGGAGAGAAGTTTGTGAAAGCTGTATTTTCACTGGCAAGCAAAATTGCTCCAAGTGTTATTTTCGTGGATGAGgtaagtaaattgta---attgatcaatcacaacgcctttctgaattccctgtgatg-tttgctttctag----tttatcttcttcatcttgtgttgtatag
||||||||||||||||| || | ||| ||||| || ||||| ||||| |||||||||||||||||||||||||| || ||||||||  ||| ||   |   ||    |  |     |    || | |||   ||    |  ||| | || |      |||||  | | ||| |||||||||    
TGGTTTGGTGAAGGAGAAAAATATGTCAAAGCAGTCTTTTCTCTGGCCAGCAAAATTGCTCCAAGTGTTATTTTTGTTGATGAGgttggtatataacatatatcttccttttttttcttggttttaaatattctaaatttctttacattttgaccgttttataatatccat-ttgtgttgtcgga

upper sequence: LOC_Os03g22420.1 (Oryza sativa), 5'ss of exon 23
lower sequence: GLYMA05G03270.1 (Glycine max), 5'ss of exon 19
TGGTTTGGTGAAGGAGAGAAGTTTGTGAAAGCTGTATTTTCACTGGCAAGCAAAATTGCTCCAAGTGTTATTTTCGTGGATGAGgtaagtaaattgtaattgatcaatcacaacgcctt-tctgaattccctgtgatgtttgctttctagtttatcttcttcatcttgtgttgtatag
|||||||| || || ||||| | |||||||||||| || || ||||| || |||||| | || |||||||| || || |||||||||||    || ||| |    ||    |  |  || | |  ||||  || |||||    || |||| ||   |||                   
TGGTTTGGGGAGGGTGAGAAATATGTGAAAGCTGTTTTCTCTCTGGCGAGTAAAATTTCACCTAGTGTTATATTTGTTGATGAGgtaagcc--ttttaact---taagggtattgttttgtattgattcattg-gatgtaactttactagctttgtttcag-----------------

upper sequence: LOC_Os03g22420.1 (Oryza sativa), 5'ss of exon 23
lower sequence: GLYMA02G17410.1 (Glycine max), 5'ss of exon 18
TGGTTTGGTGAAGGAGAGAAGTTTGTGAAAGCTGTATTTTCACTGGCAAGCAAAATTGCTCCAAGTGTTATTTTCGTGGATGAGgtaagtaaattgta--attgatcaatcac------aacgcctttctgaattccctgtga-tgtttgctttctagtttatcttcttcatcttgtgttgtatag
|||||||||||||||||||| | ||| ||||| || ||||| ||||| |||||||||||||||||||||||||| || || |||||   |  ||| |   |||  |  |||        ||    | | |   ||   | | | | |||  |||  |  || |   | |     || |   | |  
TGGTTTGGTGAAGGAGAGAAATATGTCAAAGCAGTCTTTTCTCTGGCCAGCAAAATTGCTCCAAGTGTTATTTTTGTTGACGAGgttgctttattatgtcatttgtttatcttcctttgaatttttcttttcctttattttaaatattttttttaaaactttttacccttcatatgagccattt--

upper sequence: LOC_Os03g22420.1 (Oryza sativa), 5'ss of exon 23
lower sequence: AT4G02480.1 (Arabidopsis thaliana), 5'ss of exon 22
TGGTTTGGTGAAGGAGAGAAGTTTGTGAAAGCTGTATTTTCACTGGCAAGCAAAATTGCTCCAAGTGTTATTTTCGTGGATGAGgtaagtaaattgtaattgatcaatcacaacgcct-ttctgaattccctgtgatgtttgctttctagtttatcttcttcatcttgtg-ttgtatag-------------
||||||||||| ||||||||||  || |||||||| || ||  | || ||||| ||||| |||||||| ||||| || ||||||||| ||   ||| |  |  | ||   |     || ||||      ||| ||| |   |  || |  | ||  ||||  ||||  || ||||  |              
TGGTTTGGTGAGGGAGAGAAGTACGTTAAAGCTGTCTTCTCCTTAGCGAGCAAGATTGCGCCAAGTGTCATTTTTGTTGATGAGgtatgt---ttgaagatattaaaaagcgttctctgttctctcccacctttgaagccagtctttttatgtactttctcgatctgatgattgtggaaaatcattattcag

upper sequence: LOC_Os03g22420.1 (Oryza sativa), 5'ss of exon 23
lower sequence: Vv07s0005g00200.t01 (Vitis vinifera), 5'ss of exon 22
TGGTTTGGTGAAGGAGAGAAGTTTGTGAAAGCTGTATTTTCACTGGCAAGCAAAATTGCTCCAAGTGTTATTTTCGTGGATGAGgtaagtaaattgtaatt----gatcaatcacaacgcctttctgaattccctgtgatgtttgctttctagtttatcttcttcatcttgt--gttgtatag--------------------------------------------------------------------------------------
|||||||| ||||||||||| | ||| |||||||| || || || || || |||||||| || |||||| |||| || || |||||||||  | |  |  |      |||  ||||||   |     |||   |     | |||  ||    ||  ||    ||  |   |     |||  |                                                                                       
TGGTTTGGGGAAGGAGAGAAATATGTCAAAGCTGTGTTCTCTCTAGCTAGTAAAATTGCACCTAGTGTTGTTTTTGTTGACGAGgtaagttgaataaatctttaaattcatccacaacttttgctataatgttcctcactcttt--ttatgggtccatggatttagtgacggtaactgttcaatccttttaattcgccattctgatctttagtttctttcttcttttcctgttaaaaaatttattgttaacttagatttattgtttcag

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|58688470|gb|CK077157.1|CK077157
EST:     TATTTTCACTGGCAAGCAAAATTGCTCCAAGTGTTATTTTCGTGGATGAG                         GTTGATGGCATGTTGGGTAGGCGTGAAAACCC
genomic: TATTTTCACTGGCAAGCAAAATTGCTCCAAGTGTTATTTTCGTGGATGAGgtaagtaaat ... tgttgtatagGTTGATGGCATGTTGGGTAGGCGTGAAAACCC
EST: gi|58662327|gb|CK051007.1|CK051007
EST:     TATTTTCACTGGCAAGCAAAATTGCTCCAAGTGTTATTTTCGTGGATGAG                         GTTGATGGCATGTTGGGTAGGCGTGAAAACCCTGGAGAACATGAAGCAATG
genomic: TATTTTCACTGGCAAGCAAAATTGCTCCAAGTGTTATTTTCGTGGATGAGgtaagtaaat ... tgttgtatagGTTGATGGCATGTTGGGTAGGCGTGAAAACCCTGGAGAACATGAAGCAATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGTTTGGTGAAGGAGAGAAGTTTGTGAAAGCTGTATTTTCACTGGCAAGCAAAATTGCTCCAAGTGTTATTTTCGTGGATGAGgtaagtaaattgtaattgatcaatcacaacgcctttctgaattccctgtgatgtttgctttctagtttatcttcttcatcttgtgttgtatag

- - - - - - - - - - - - - - - - - - - - - - -  AAGCAA