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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTCCTTTATATATGgtaatattcatgtccttatactggttataactaccaataatttgccatatatgttctaagctgttgattcggatgcag

Basic information

species Oryza sativa
transcript LOC_Os12g04990.1
intron # 19
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g04990.3 (Oryza sativa), 5'ss of exon 18
lower sequence: GRMZM2G176546_T01 (Zea mays), 5'ss of exon 10
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTCCTTTATATATGgtaatattcatgtccttatactggttata--actaccaataatttgccatatatgttctaag-ctgttgattcggatgcag
||||||||||||||||||||||||||||||||||||||||| ||||||||||| ||||||||||| || |||||||| ||||| || |  |||||||||||||||||| |||    | |  ||| ||||  || | || | ||  ||||   |||||||||  || ||| ||||| |||||
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATATATGgtaatatttatgattctgtgttggctatatgaccatcagttatg-gccaagcatgttctaaatctcttgtttcggttgcag

upper sequence: LOC_Os12g04990.3 (Oryza sativa), 5'ss of exon 18
lower sequence: GLYMA10G39540.1 (Glycine max), 5'ss of exon 19
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTCCTTTATATATGgtaat------attcatgtccttatactggttataactaccaataatttgccatatatgttctaagctgttgattcggatgcag
||||| || || ||||| || ||||| || ||||| ||||| ||||||||||| ||||| || || || ||||| ||| | ||||||| |||| ||||||||||       | ||||  ||  | | | | | |   |    ||  ||||   ||  |     | |||  |  || |  || ||
AAGAATATCTTTAAGTTGGCACAAGGCGAGTACATTGCTCCTGAGAAGATTGAAAATGTATACGCCAAATGCAAATTTGTGGCGCAGTGCTTTGTATATGgtaaggaaataaatcattcccacaaattcggtgtgtgtg---atcgtttgtactagcttgctgatgcttcttttttgtttgtag

upper sequence: LOC_Os12g04990.3 (Oryza sativa), 5'ss of exon 18
lower sequence: Vv05s0020g03080.t01 (Vitis vinifera), 5'ss of exon 19
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTCCTTTATATATGgtaatattcatgtccttatactggttataactaccaataatttgccatatatgttctaagctgttgattcggatgcag
||||||||||| ||||| || |||||||| ||||||||||| ||||| ||||||||||| |||||||| ||||| ||| |||| |||| |||| |||||||||| |   |||   || |||   |      | |  ||  ||||||   |   | ||    | ||  |  |     ||
AAGAACATTTTTAAGTTGGCACAAGGAGAGTACATAGCTCCAGAGAAAATTGAGAATGTATATGCTAAATGCAAATTTGTTGCCCAGTGCTTTGTATATGgtaagaaaaatgagattttacaaatctctctttc--atcttttgcctgctgactgct----tatttctctgatgatag

upper sequence: LOC_Os12g04990.3 (Oryza sativa), 5'ss of exon 18
lower sequence: Vv14s0128g00720.t01 (Vitis vinifera), 5'ss of exon 19
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTCCTTTATATATGgtaatattcatg---tccttatactggttataactaccaataatttgccatatatgttctaagctgttgattcggatgcag
|||||||| |||||| | || || || ||||| ||||| || ||||| ||||||||||| ||||| |||||||| ||| || | || |  ||||| ||||||||     |||   |     | | | ||    |  ||     |  |   | | || |     ||| | | | |  |  ||
AAGAACATCTTCAAGCTGGCACAGGGTGAATATATAGCACCAGAGAAAATTGAGAATGTATATGCCAAGTGCAAATTTGTTTCCCAATGTTTTATCTATGgtaaggcagatggagtttacttgcagattgggccctccccagctaagttctctttgct---gactgcttaattgattttag

upper sequence: LOC_Os12g04990.3 (Oryza sativa), 5'ss of exon 18
lower sequence: PP1S408_23V6.1 (Physcomitrella patens), 5'ss of exon 21
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTCCTTTATATATGgtaatattcatgtccttatactggttataactaccaataatttgccatatatgttctaagctgttgattcggatgcag--------------------------
||||| || || ||||| ||||||||||| ||||| || || |||||||| |||||||||||   |    |    || ||  | ||||  |  ||| |||||| | ||||| |  ||| |  |     ||||    ||   |||   | ||        ||   || |   ||||                             
AAGAATATCTTTAAGTTGGCTCAAGGAGAGTACATTGCCCCGGAGAAGATCGAGAATGTCTACCTTCGCAGTCGTTTCATAACACAGTGTTACATACATGgta-tgttcat-tttttaaatgga--ggaactcttcatttcttgtggtctaaacaagttgcaactggtgtagatgacttaagatttttttttcatctgaaatga

upper sequence: LOC_Os12g04990.3 (Oryza sativa), 5'ss of exon 18
lower sequence: PP1S33_126V6.1 (Physcomitrella patens), 5'ss of exon 22
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTCCTTTATATATGgtaatattcatgtccttatactggttataactaccaataatttgccatatatgttctaagctgttgattc--ggatgcag---------------------
||||| || |||||||| ||||| ||||| ||||| || ||||||||||||||||| |||||        |   ||| ||||| |||| ||||||  |||||    |||||    |||     |  ||  || |  ||  | |     || || |    | ||      |  || | | |                     
AAGAATATCTTCAAGTTGGCTCAGGGAGAGTACATTGCGCCCGAGAAGATTGAGAACGTCTACCTGCGAAGTCGGTTCATTGCACAGTGCTTTATTCATGgtg-cgttcattcaattaatggaggcatcccttctcattgtctcagtcatctgcttgtggttgaaacaccatggttactggggttgtgggtgctttaagag

upper sequence: LOC_Os12g04990.3 (Oryza sativa), 5'ss of exon 18
lower sequence: PP1S12_178V6.2 (Physcomitrella patens), 5'ss of exon 21
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTCCTTTATATATGgta--------------atattcatgtccttatactggttata-actaccaata-atttgccatatatgttcta-agctgttgattcggatgcag------------------------------------------------------------------------
||||||||||||||||||||||||||||||||||| || || || |||||||||||  | |||  |    |   ||||||| ||||||  ||  ||||||||               |   ||   || || || || ||  |   |||   |   | || |  | | ||     | ||| || | || || | |                                                                        
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATTGCACCGGAAAAGATTGAGAACATTTATCTTCGCAGTCGGTTTATTTCGCAGTGTTTCGTATATGgtgcgttcatttaatcgacggtcgcatctttttaatgattgcacgttactttttcgtgtgacggaaacgtgtagcaactggtgttacgtatactggaaaaactaccaactcattgaaatccaatcattcttaccaatcgtataattggttggtggtgaattgcacag

upper sequence: LOC_Os12g04990.3 (Oryza sativa), 5'ss of exon 18
lower sequence: EFJ33980 (Selaginella moellendorffii), 5'ss of exon 20
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTCCTTTATATATGgtaatattcatgtccttatactggttataactaccaataatttgccatatatgttctaagctgttgattcggatgcag
||||||||||| ||| | || || || ||||||||||| || |||||||||||||||||||||  |||  |||||||  |||| ||||  ||  | || ||| | |   ||    || |  ||  | || | | |  |  |||| || |  | |  |    |||              
AAGAACATTTTTAAGCTTGCACAGGGTGAATACATAGCGCCAGAGAAGATTGAGAATGTCTATCATAAAAGCAAGTTCGTTGCTCAGTGTTTCGTCTACGgtgagaacaat---tttgttttgtgtctagcgagcggt--tttgacacaattctcttcgattgtaacag---------

upper sequence: LOC_Os12g04990.3 (Oryza sativa), 5'ss of exon 18
lower sequence: EFJ37488 (Selaginella moellendorffii), 5'ss of exon 20
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTCCTTTATATATGgt---aatattcatgtcct---tatactggttataactaccaataat-----ttgccatatatgtt--ctaagctgttgattcggatgcag-----------------------------------
||||||||||| ||| | || || || ||||||||||| || |||||||||||||||||||||   ||  |||||||  |||| ||||  ||  | || |||   || | |  |||  |   | ||  |  |  | ||  | | |       | ||   |||   |  | ||| | |         ||                                      
AAGAACATTTTTAAGCTTGCACAGGGTGAATACATAGCGCCAGAGAAGATTGAGAATGTCTATCAAAAAAGCAAGTTCGTTGCTCAGTGTTTCGTCTACGgtgagaacaattttgttttgtgtctagcgagtccacctggcgaaaggatcggtcgctgaatagcatggcaaagttttctccctatgtgtgactcggttttgacacaattctcttcgattgtaacag

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|29630787|gb|CB635796.1|CB635796
EST:     TGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTCCTTTATATATG                         GTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGATG
genomic: TGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTCCTTTATATATGgtaatattca ... tcggatgcagGTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGATG
EST: gi|29625658|gb|CB630669.1|CB630669
EST:     TGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTCCTTTATATATG                         GTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGATG
genomic: TGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTCCTTTATATATGgtaatattca ... tcggatgcagGTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGATG
EST: gi|29622085|gb|CB627096.1|CB627096
EST:     TGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTCCTTTATATATG                         GTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGATG
genomic: TGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTCCTTTATATATGgtaatattca ... tcggatgcagGTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGATG
EST: gi|29626658|gb|CB631669.1|CB631669
EST:     TGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTCCTTTATATATG                         GTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGATG
genomic: TGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTCCTTTATATATGgtaatattca ... tcggatgcagGTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGATG
EST: gi|313081138|gb|HO213724.1|HO213724
EST:     TGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTCCTTTATATATG                         GTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGATG
genomic: TGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTCCTTTATATATGgtaatattca ... tcggatgcagGTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGATG
EST: gi|25806439|gb|CA762400.1|CA762400
EST:     TGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTCCTTTATATATG                         GTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGATG
genomic: TGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTCCTTTATATATGgtaatattca ... tcggatgcagGTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGATG
EST: gi|29665115|gb|CB661390.1|CB661390
EST:     TGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTCCTTTATATATG                         GTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGATG
genomic: TGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTCCTTTATATATGgtaatattca ... tcggatgcagGTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGATG
EST: gi|29674288|gb|CB670563.1|CB670563
EST:     TGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTCCTTTATATATG                         GTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGATG
genomic: TGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTCCTTTATATATGgtaatattca ... tcggatgcagGTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGATG
EST: gi|86851191|gb|CI312592.1|CI312592
EST:     CAAGTTTATTGCGCAGTCCTTTATATATG                         GTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGATG
genomic: CAAGTTTATTGCGCAGTCCTTTATATATGgtaatattca ... tcggatgcagGTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGATG