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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGCATTTCACTAGAACCTGGCGGTCAGTTTGAACTTAGTGGTGCTCCTCTTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAGgtaatgtgcagtgcatccctgtattaacttcttgctttatttgattttcacttatgatttgcgcattgccatgccatatatatcttcagtccgaaagtttttttgccagcagttgatccaatccgaaacgtctgttcttgtag

Basic information

species Oryza sativa
transcript LOC_Os05g03820.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g03820.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G111579_T01 (Zea mays), 5'ss of exon 3
AAGCATTTCACTAGAACCTGGCGGTCAGTTTGAACTTAGTGGTGCTCCTCTTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAGgtaatgt-----gcagtgcatccctgtattaacttcttgcttta--tttgattttcacttatg-atttgcgcattgccatgccatatatatcttcagtccgaaagtttttttgccagcagttgatccaatccgaaacgtctgttcttgtag
|||||| |||||||||||||| || || |||||||||||||| |||||||| ||||||||||||||||||||||||||||||||||| |||||||| |||||||  |      || ||||| |||     | | |||| |   |  | |||| ||   || ||  | |   ||||    || || | |||  | |||| |                                                   
AAGCATCTCACTAGAACCTGGAGGCCAATTTGAACTTAGTGGCGCTCCTCTCGAAACATTACATCAAACTTGTGCTGAGGTCAATTCGCATCTTTATCAGgtaacttctcttacattgcattccttgtacagcatcttacagaaactatgatcttagtttgtgtgtgttaccattcttttgtcagagataa-tacagtacc--------------------------------------------------

upper sequence: LOC_Os05g03820.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G020096_T01 (Zea mays), 5'ss of exon 3
AAGCATTTCACTAGAACCTGGCGGTCAGTTTGAACTTAGTGGTGCTCCTCTTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAGgtaatgtgcagtgcatccctgtattaacttcttgctttatttgattttcacttatgatttgcgcattgccatgccatatatatcttcagtccgaaagtttttttgccagcagttgatccaatccgaaacgtctgttcttgtag
|||||| |||||||||||||| || || |||||||||||||| |||||||| ||||| |||||||||||||||||||||||||| |||||||| || |||||||           | |   |  | || | ||  |||   ||    ||    |  | ||  |   |   |   | | | | | || | |    |   | |    |   |                                 
AAGCATCTCACTAGAACCTGGAGGCCAATTTGAACTTAGTGGCGCTCCTCTCGAAACGTTACATCAAACTTGTGCTGAGGTCAACTCACATCTATATCAGgtaac----------ttctctttctgacgttttcttttccctgtgcatcttgcagaaattatga--tcttagctcgtgtgtgtttttacttgacattatataagactgacca-------------------------------

upper sequence: LOC_Os05g03820.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA11G02570.1 (Glycine max), 5'ss of exon 2
AAGCATTTCACTAGAACCTGGCGGTCAGTTTGAACTTAGTGGTGCTCCTCTTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAGgtaatgtgcagtgca-tccctgtattaacttcttgctttatttgattttcacttatgatttgcgcattgccatgccatatatatcttcagtccgaaagtttttttgccagcagttgatccaatccgaaacgtctgttcttgtag
||| || ||| |||||||||| ||||| ||||| |||||||||   ||| |  ||||||| ||||||||||||| |||| | ||||||||||| || ||||| | || | ||||| ||  ||   ||||      | | |  | | ||| | | || |||| |    |    | |  |  | |  |  ||   | ||  | ||                                         
AAGTATATCATTAGAACCTGGTGGTCAATTTGAGCTTAGTGGTATGCCTTTGAAAACATTGCATCAAACTTGTGATGAGATTAATTCACATCTCTATCAGgtca-gt-ctgtgcaatctttggcataacaagaatcctaagat-agtttaattcataattt-catcctattttactgttaaaagttgaagcatgcaatgtgtta----------------------------------------

upper sequence: LOC_Os05g03820.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA01G42900.1 (Glycine max), 5'ss of exon 3
AAGCATTTCACTAGAACCTGGCGGTCAGTTTGAACTTAGTGGTGCTCCTCTTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAGgtaatgtgcagtgca-tccctgtattaacttcttgctttatttgattttcacttatgatttgcgcattgccatgccatatatatcttcagtccgaaagtttttttgccagcagttgatccaatccgaaacgtctgttcttgtag
|||||| ||| |||||||||| ||||| ||||| |||||||||   ||| |  ||||||| ||||||||||||| |||| | ||||||||||| || ||||| | || | ||||| ||  ||    |||      | | |  | | ||| | | || |||| |   ||    | |  |  | |  |  |    | ||     |                                         
AAGCATATCATTAGAACCTGGTGGTCAATTTGAGCTTAGTGGTATGCCTTTGAAAACATTGCATCAAACTTGTGATGAGATTAATTCACATCTCTATCAGgtca-gt-ctgtgcaatctttggcacaacaagaatcctgagat-actttaattcataattt-cattttattttactgttgaaagttgaaacatgcaatgcaatg----------------------------------------

upper sequence: LOC_Os05g03820.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA08G01750.1 (Glycine max), 5'ss of exon 4
AAGCATTTCACTAGAACCTGGCGGTCAGTTTGAACTTAGTGGTGCTCCTCTTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAGgtaatgtgcagtgcatccctgtattaacttcttgctttatttgattttcacttatgatttgcgcattgccatgccatatatatcttcagtccgaaagtttttttgccagcagttgatccaatccgaaacgtctgttcttgtag
 ||||| ||| | || ||||| |||||||||||||||||||| |||||||||||||| || ||||| ||||||||||| || ||||  || ||||| |||||| |      | |     |  ||||||||     ||| ||||   ||      ||||||| | |||   |||| ||  |||| |||  | || |    | | |  || || |||                            
GAGCATATCATTGGAGCCTGGTGGTCAGTTTGAACTTAGTGGAGCTCCTCTTGAAACCTTGCATCAGACTTGTGCTGAAGTTAATTTGCACCTTTATCAGgtact---tgtttcgctgatacattaactt-----tttttttgccattaga--gtgatttg-gaatttttatgcaat-catattttc--tacggataaatatgtatcatca-ttg----------------------------

upper sequence: LOC_Os05g03820.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA05G37850.3 (Glycine max), 5'ss of exon 4
AAGCATTTCACTAGAACCTGGCGGTCAGTTTGAACTTAGTGGTGCTCCTCTTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAGgtaatgtgcagtgcatccctgtattaacttcttgctttatttgattttcacttatgatttgcgcattgccatgccatatatatcttcagtccgaaagtttttttgccagcagttgatccaatccgaaacgtctgttcttgtag
 ||||| ||| | || ||||| |||||||||||||||||||| |||||||||||||| || ||||| ||||||||||| || ||||| || ||||| |||||| |      | |     || || |||   ||  | | |||     |      |||||||    ||   | || ||  |||| |||        | | | | |                                       
GAGCATATCATTGGAGCCTGGTGGTCAGTTTGAACTTAGTGGAGCTCCTCTTGAAACCTTGCATCAGACTTGTGCTGAAGTTAATTCCCACCTTTATCAGgtact---tgtttcgctgatgcataaaccattttttcttttttgccattgga-gtgatttgaaattttttacgcgat-catattttctacagatgaatatgtata--------------------------------------

upper sequence: LOC_Os05g03820.2 (Oryza sativa), 5'ss of exon 4
lower sequence: AT4G23100.3 (Arabidopsis thaliana), 5'ss of exon 4
AAGCATTTCACTAGAACCTGGCGGTCAGTTTGAACTTAGTGGTGCTCCTCTTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAGgtaatgtgcagtgcatccctgtattaacttcttgctttatttgattttcacttatgatttgcgcattgccatgccatatatatcttcagtccgaaagtttttttgccagcagttgatccaatccgaaacgtctgttcttgtag
|||||||||||| |||||||| |||||||| || ||||||||||| |||||||| || || ||||||||||||||||| ||||||||||||||||| |||||||| |  |    |    |     |   |||  |  ||     |    | | |  |  |    |  |  ||| || |                                                                 
AAGCATTTCACTTGAACCTGGGGGTCAGTTCGAGCTTAGTGGTGCACCTCTTGAGACTTTGCATCAAACTTGTGCTGAAGTCAATTCACATCTTTATCAGgtaatttcaaagataattattgccaatgctctcaccctaaaacgtgacaaataaccaactatctacgg--atgtcacag----------------------------------------------------------------

upper sequence: LOC_Os05g03820.2 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv02s0025g03530.t01 (Vitis vinifera), 5'ss of exon 4
AAGCATTTCACTAGAACCTGGCGGTCAGTTTGAACTTAGTGGTGCTCCTCTTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAGgtaatgtgcagtgcatccctgtattaacttcttgctttatttgattttcacttatgatttgcgcattgccatgccatatatatcttcagtccgaaagtttttttgccagcagttgatccaatccgaaacgtctgttcttgtag
|||||| ||||| ||||| || ||||||||||| ||||| ||||| ||||||||||| || |||||||| ||||||||||| |||||||| ||||| |||||| | ||   | | || |  | || |  |  | ||||  |   |    ||  | ||| | | |||    ||   ||| ||| || || |   | |  |                                            
AAGCATCTCACTGGAACCCGGTGGTCAGTTTGAGCTTAGCGGTGCCCCTCTTGAAACTTTGCATCAAACCTGTGCTGAGGTTAATTCACACCTTTATCAGgtact-tgtcattcttctccttcttcatcttcttctttgatcactggataccaaagatatcctcatattgat--tata-ataactccaataaaataactaaaag---------------------------------------

upper sequence: LOC_Os05g03820.2 (Oryza sativa), 5'ss of exon 4
lower sequence: PP1S479_14V6.1 (Physcomitrella patens), 5'ss of exon 3
AAGCATTTCACTAGAACCTGGCGGTCAGTTTGAACTTAGTGGTGCTCCTCTTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAGgtaatgtgcagtgcatccctgtattaacttcttgctttatttgattttcacttatgatttgcgcattgccatgccatatatatcttcagtccgaaagtttttttgccagcagttgatccaatccgaaacgtctgttcttgtag
|||  | ||  | ||||| ||||| ||||||||| | ||||| || ||||| || ||| | |||||||| || || ||||||||||||||||| || ||||||  | |   ||    |||   || |  |     | |||     ||| | | || ||       | | ||     | | ||  || | |      | |                                            
AAGTGTATCTTTGGAACCCGGCGGCCAGTTTGAATTGAGTGGAGCGCCTCTGGAGACACTTCATCAAACATGCGCCGAGGTCAATTCACATCTGTATCAGgtatggcgggttgtccaccttctttcatgtgaatatatataaagattttaatcat-atcgtaatctggtcacat--tttgtaattttatttttggggctggac----------------------------------------

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|7219950|gb|AU063307.2|AU063307
EST:     TTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAG                         GTCAAAGCAGTTGGAGAGGAAATGGGGATTGGATTTCTCGGAATTGGTTTT
genomic: TTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAGgtaatgtgca ... gttcttgtagGTCAAAGCAGTTGGAGAGGAAATGGGGATTGGATTTCTCGGAATTGGTTTT
EST: gi|33796283|gb|CF324008.1|CF324008
EST:     TTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAG                         GTCAAAGCAGTTGGAGAGGAAATGGGGATTGGATTTCTCGGAATTGGTTTT
genomic: TTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAGgtaatgtgca ... gttcttgtagGTCAAAGCAGTTGGAGAGGAAATGGGGATTGGATTTCTCGGAATTGGTTTT
EST: gi|88347509|gb|CI637449.1|CI637449
EST:     TTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAG                         GTCAAAGCAGTTGG
genomic: TTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAGgtaatgtgca ... gttcttgtagGTCAAAGCAGTTGG
EST: gi|88573359|gb|CI664930.1|CI664930
EST:     TTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAG                         GTCAAAGCAGTTGGAGAGGAAATGGGGATTG
genomic: TTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAGgtaatgtgca ... gttcttgtagGTCAAAGCAGTTGGAGAGGAAATGGGGATTG
EST: gi|58658531|gb|CK047211.1|CK047211
EST:     TTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAG                         GTCAAAGCAGTTGGAGAGGAAATGGGGATTGGATTTCTCGGAATTGGTTTT
genomic: TTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAGgtaatgtgca ... gttcttgtagGTCAAAGCAGTTGGAGAGGAAATGGGGATTGGATTTCTCGGAATTGGTTTT
EST: gi|29679436|gb|CB675711.1|CB675711
EST:     TTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAG                         GTCAAAGCAGTTGGAGAGGAAATGGGGATTGGATTTCTCGGAATTGGTTTT
genomic: TTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAGgtaatgtgca ... gttcttgtagGTCAAAGCAGTTGGAGAGGAAATGGGGATTGGATTTCTCGGAATTGGTTTT
EST: gi|88336064|gb|CI647258.1|CI647258
EST:     TTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAG                         GTCAAAGCAGTTGGAGAGGAA
genomic: TTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAGgtaatgtgca ... gttcttgtagGTCAAAGCAGTTGGAGAGGAA
EST: gi|29677970|gb|CB674245.1|CB674245
EST:     TTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAG                         GTCAAAGCAGTTGGAGAGGAAATGGGGATTGGATTTCTCGGAATTGGTTTT
genomic: TTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAGgtaatgtgca ... gttcttgtagGTCAAAGCAGTTGGAGAGGAAATGGGGATTGGATTTCTCGGAATTGGTTTT