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'   		28  
 5'  3'   		29  
 5'  3'   		30  
 5'  3'   		31  
 5'  3'   		32  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCGACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGCAGAAGgtttgttctctgtgttcttgctggacaactgtcttgcttggtttctggagataatttttttgagatttcatttaaaggaacaggacccgatcgaaatgaa...

Basic information

species Oryza sativa
transcript LOC_Os04g51610.3
intron # 28
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 28
lower sequence: GRMZM2G140328_T03 (Zea mays), 5'ss of exon 28
TACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCGACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGCAGAAGgtttgttctctgtgttcttgctggacaactgtcttgcttggtttctggagataatttttttgagatttcatttaaaggaacaggacccgatcgaa-atgaa--
| ||||||||||||||||| ||||||||| ||||||| |||||| |||||||||||||||||||  ||||||||||| ||||||| ||||| || |||||||      ||    |   |  || |  | ||| |    || | | ||    ||| || |   | | | | |||    || ||  |  | || | | ||  |  
TGCTGTGGGTTAACCTAATTATGGATACTTTGGGTGCCCTTGCATTGGCGACAGAACCACCTACAAACCATCTTATGGAGAGACCCCCAGTAGGGAGAAGgtagtgaatcaccatctatcttgtagcattgtttaaactg-tgtatgttcgtaaattgtac-acactac-tttctctgatcacaattccattggacattgaca

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 28
lower sequence: GRMZM2G391042_T01 (Zea mays), 5'ss of exon 28
TACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCGACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGCAGAAGgtttgttctctgtgttcttgctggacaactgtcttgcttggtttct---ggagataatttttttgagatttcatttaaaggaacaggacccgatcgaaatgaa-
|  |||||||||||||||| ||||| ||| ||||||| |||||| |||||||||||||||||||  ||||||||||| ||||||| ||||| || |||||||||||||| ||||  | ||||  | |  || ||  | | || |||    |||| |      | | ||     | |           |    || || |||   
TGTTGTGGGTTAACCTAATTATGGACACTTTGGGTGCCCTTGCATTGGCGACAGAACCACCTACAAACCATCTTATGGAGAGACCCCCAGTAGGGAGAAGgtttgttct-tgtgcacgtgct--atatttg-ctcacctagtatcttatagagagaccccagtagggagaaggtatctgattggcaaatattatggacatggca

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 28
lower sequence: GLYMA15G00340.1 (Glycine max), 5'ss of exon 29
TACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCGACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGCAGAAGgtttgttctctgtgttcttgctggacaactgtcttgcttggtttctggagataatttttttgagatttcatttaaaggaacaggacccgatcgaaatgaa
|  ||||||| ||| | |||||||| || || || |||||||||||||| || ||||| || || ||| | |||||||| ||| ||||||||||| |||||||||||     | || || |     ||  |      | || ||    | ||  | | |||| | |||||                              
TTTTGTGGGTCAACGTTATCATGGACACACTTGGGGCTCTTGCACTGGCTACGGAACCGCCAACAGACAACCTTATGCACAGATCACCAGTTGGCCGAAGgtttgtttggctttttatttcaaattaaaagcagacttgggcttactaacatcttatgtttg-gctttcag-----------------------------

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 28
lower sequence: GLYMA07G00630.2 (Glycine max), 5'ss of exon 27
TACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCGACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGCAGAAGgtttg---ttctctgtgttcttgctggacaact--gtcttgcttggtttctggagataatttttttgagatttcatttaaaggaacaggacccgatcgaaatgaa
|  ||||||| ||||| ||||||||||| || || || ||||||||||| || ||||| || || ||||  || ||||| ||| ||||||||||| |||||||||   |  |  |  ||||  ||   ||  |   | ||  | |    ||  | |  ||  |  | ||    ||   ||| || || |  |   |  |  ||  
TTTTGTGGGTCAACCTTATCATGGATACACTTGGGGCGCTTGCACTGGCTACTGAACCGCCAACAGACCGCCTAATGCACAGATCACCAGTTGGCCGAAGgtttggattgattggctttctctctaagcagtttaatatttatggtacccttaatactatactgatcag----cacaaaaacgagcatgcacatgtacacttgg-

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 28
lower sequence: GLYMA08G23760.1 (Glycine max), 5'ss of exon 30
TACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCGACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGCAGAAGgtttg---ttctctgtgttcttgctggacaact--gtcttgcttggtttctggagat----aatttttttgagatttcatttaaaggaacaggacccgatcgaaatgaa
|  ||||||||||||| ||||||||||| || || || ||||||||||| || |||||||| || ||||  || ||||| ||| ||||||||||| |||||||||   |  |  |  ||||  ||   ||  |   | ||  | |  | || || |     || | |  |||  |  ||  |||| | ||| || |   |         
TTTTGTGGGTTAACCTTATCATGGATACACTTGGGGCGCTTGCACTGGCTACTGAACCACCAACAGACCGCCTAATGCACAGATCACCAGTTGGCCGAAGgtttggattgattggctttctcacttagcagtttaatatttatagtatccttgaaagttaaaactatactgatctagcacataaatgcacatgaacatgt---------

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 28
lower sequence: GLYMA13G44990.1 (Glycine max), 5'ss of exon 29
TACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCGACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGCAGAAGgtttgttctc-tgtgttcttgctggacaactgtct-tgcttgg----tttctggagataattttt-ttgagatttc----att-taaaggaacaggacccgatcgaaatgaa-----------------------------------------------------------
|  ||||||| ||||| |||||||| || || || |||||||||||||| || ||||| || || ||| | |||||||| ||| ||||||||||| ||||||||| | |  | || | |   ||||   ||  || | ||  |    ||| |    ||  ||||| |||  |||||    ||| || |  |||| |      || ||||  |                                                           
TTTTGTGGGTCAACCTTATCATGGACACACTTGGGGCTCTTGCACTGGCTACGGAACCGCCAACAGACAACCTTATGCACAGATCACCAGTTGGCCGAAGgtttggtttggtttggtttgattggatctcttactatactatgagaatttatacgcattttttttattgcaatttctaaaattatacaaaaacaaggtt-attcaaaatccaaatactcacttgaagacagacttgggcttactacgatatatcttatgtttggctttcag

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 28
lower sequence: AT3G21180.1 (Arabidopsis thaliana), 5'ss of exon 27
TACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCGACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGCAGAAGgtttgttctctgtgttcttgctggacaactgtcttgcttggtttctggagataatttttttgagatttcatttaaaggaacaggacccgatcgaaatgaa--------
| || ||||| ||||| |||||||||||||| || || |||||||| || ||||| ||||| || || ||||||||||| ||| | || ||||| ||||||| |   |    ||  | || ||     ||       || ||        ||| || | ||| | ||||| |   | |    |     | | |               
TGCTTTGGGTCAACCTTATCATGGATACTCTTGGAGCACTTGCACTAGCTACAGAGCCACCAACCGATCATCTTATGCATAGAACCCCTGTTGGAAGAAGgtataaacatgttgcacatgatgttttcctcatacttttagtgaaacagaatagttatattgtggtttcagtcgtatggttcgtgatggtttgtttcttgatttgcag

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 28
lower sequence: Vv09s0018g02130.t01 (Vitis vinifera), 5'ss of exon 29
TACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCGACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGCAGAAGgtttgttctc-------tgtgttcttgctggacaactgtcttgcttggtttctggagataatttttttga-gatttcatttaaaggaacaggacccgatcgaaatgaa
| || ||||||||||| |||||||||||||| || || |||||| |||| || |||||||| ||||| ||||||||| | ||| | ||||||||  ||||||| |  ||        | |  |  |  ||      |  || |  |  |||    |  |   |||| ||| |  ||  |||         ||  | |||         
TTCTATGGGTTAACCTTATCATGGATACTCTTGGAGCACTTGCATTGGCTACTGAACCACCAACTGATCATCTTATGGAAAGATCTCCAGTTGGTCGAAGgttagaacttgaagtagtatacttctcgtgattttgttcctcgtctaattttataatttggattttatgatgggttgttttcgtatggttgggactgatg--------

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 28
lower sequence: Vv11s0052g00320.t01 (Vitis vinifera), 5'ss of exon 30
TACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCGACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGCAGAAGgtt-tgttctctgtgttcttgctggac-----aactgtcttgcttggtttctggagataatttttttgagatttcatttaaaggaacaggacccgatcgaaatgaa
| || |||||||| || |||||||||||||| || || |||||| |||| || |||||||| || || || || ||||| || || ||||||||  ||||||  | || | | |  | |||   ||      || |    |   |    |  |  || ||||   |      |     |  |||          | |  |      
TCCTCTGGGTTAATCTTATCATGGATACTCTTGGAGCACTTGCATTGGCCACTGAACCACCAACAGATCACCTGATGCACAGGCCTCCAGTTGGTCGAAGgtaattttttttttaatgttgggagatccaataaatactgtttataaactaagtggaaaattgggtcagatctgtccctggaggtttgaattgtgcttca------

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|88351169|gb|CI623391.1|CI623391
EST:     ACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGGAGAAG                         GGAACCCTTGATAACAAATGTCATGTGGAGAAACTTAATCATAATGG
genomic: ACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGCAGAAGgtttgttctc ... ttgttttcagGGAACCCTTGATAACAAATGTCATGTGGAGAAACTTAATCATAATGG
EST: gi|58594188|gb|CF992496.1|CF992496
EST:     CAGAACCACCTACTGACCATCTTATGCCAGAGACCACCAGTTGGCAGAAG                         GGAACCCTTGATAACAAATGTCATGTGGAGAAACTTAATCATAATG
genomic: CAGAACCACCTACTGACCATCTTATGC-AGAGACCACCAGTTGGCAGAAGgtttgttctc ... ttgttttcagGGAACCCTTGATAACAAATGTCATGTGGAGAAACTTAATCATAATG
EST: gi|218500877|gb|FG965670.1|FG965670
EST:     ACAGAACCACCTACTGACCATCTTATGCAGAGACCAACAGTTGGCAGAAG                         GGAACCCTTGAATAACAAATGTCATGTGGAGAAACTTAATCATAATG
genomic: ACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGCAGAAGgtttgttctc ... ttgttttcagGGAACCCTTGA-TAACAAATGTCATGTGGAGAAACTTAATCATAATG