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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttattctggtcagtattagacatgcatgattattttttatcatcctaacaagctttcatgttgcaagttgctaaacttgttcctgttcattttccccagATGGTTATGGCAGTTTTTGCATACATATATCACCAATCATTCATATCGCCCCAAAACTACTCTGTTGAGCTAATCTTGGAACAG

Basic information

species Oryza sativa
transcript LOC_Os01g55360.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g55360.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM5G825110_T02 (Zea mays), 3'ss of exon 10
tttattctggtcagtatta--gacatgcatgattattttt-tatcatcctaacaagctttcatgttgcaagttgctaaacttgttcctgttcattttccccagATGGTTATGGCAGTTTTTGCATACATATATCACCAATCATTCATATCGCCCCAAAACTACTCTGTTGAGCTAATCTTGGAACAG
  | ||  ||  |  | |   | || ||   |  |      ||  ||  || ||  || | |   |  |  ||   | |  | |     | | |||||||||||||||||||||||| |||||||||||||| ||||| ||||||||  | || || |||| |||||||||| |||||||||| |||
--tgttgggggaaaaaatcctgccaagctgaagaaaccccgtactataataccagtctgt-actctatagcttaacataaatttctgcttgctttttccccagATGGTTATGGCAGTGTTTGCATACATATACCACCAGTCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAG

upper sequence: LOC_Os01g55360.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G452529_T03 (Zea mays), 3'ss of exon 2
tttattctggtcagtatta-gacatgcatgattattttttatcatcctaacaagctttcatgttgcaagttgctaaacttgttcctgttcattttccccagATGGTTATGGCAGTTTTTGCATACATATATCACCAATCATTCATATCGCCCCAAAACTACTCTGTTGAGCTAATCTTGGAACAG
 || ||  ||  |  ||   | || ||   |  |          |  | || ||  |  | | |  |  ||     |  | |     | | |||||||||||||||||||||||| |||||||||||||| ||||||||||||||  | || || |||| |||||||||| |||||||||| |||
-ttgttagggaaaaaatcctgtcaagctgaagaaaccccgtattttattaccagtctgtaggctatagattaacgtaaatttctgcttgccttttccccagATGGTTATGGCAGTGTTTGCATACATATACCACCAATCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAG

upper sequence: LOC_Os01g55360.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA10G32660.1 (Glycine max), 3'ss of exon 9
tttattctggtcagtattagacatgcatgattattttttatcatcctaacaagctttcatgttgcaagttg--ctaaacttgttcctgttcattt--tccccagATGGTTATGGCAGTTTTTGCATACATATATCACCAATCATTCATATCGCCCCAAAACTACTCTGTTGAGCTAATCTTGGAACAG
|||  | || | ||   |||   || | |   |     ||  |   || | |||||| ||||   |||| |  | |||  ||  |   ||   ||  |    ||||||||||||| || ||||||||||||||||| || |||||  |   ||| ||||    ||| |||||  | || ||||| |||
tttcatttgttgag-gctaggactggaagtcaaaaccatactag--tacccagctttgatgt-ataagtcgagcaaaatctgaccaatttgccttggtgtgtagATGGTTATGGCCGTGTTTGCATACATATATCATCAGTCATTTGTTGTGCCGCAAACTCTCTCGGTTGAAATGATTTTGGACCAG

upper sequence: LOC_Os01g55360.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA20G34940.1 (Glycine max), 3'ss of exon 10
tttattctggtcagtattagacatgcatgattattttttatcatcctaacaagct-ttcatgttgcaagttgc-taaacttgttcctgttcattttccc---cagATGGTTATGGCAGTTTTTGCATACATATATCACCAATCATTCATATCGCCCCAAAACTACTCTGTTGAGCTAATCTTGGAACAG
      ||||  | |  ||    |   |     ||   |     |  |  |  || ||  | |    |||||   ||| ||   ||  ||  | ||       ||||||||||||| || |||||||| |||||||| ||||||||  |   ||| ||||    ||| |||||  | || ||||| |||
-----actggcaactcctatttttcactctcctttacattctgcctcagtacactatttgtatctttagttgagcaaaatttgaccaatttgtcttggtgtgtagATGGTTATGGCGGTGTTTGCATATATATATCATCAATCATTTGTTGTGCCGCAAACTCTCTCAGTTGAAATGATTTTGGACCAG

upper sequence: LOC_Os01g55360.1 (Oryza sativa), 3'ss of exon 10
lower sequence: AT1G62430.1 (Arabidopsis thaliana), 3'ss of exon 10
-----------------------------------------------------tttattctggtcagtattagacatgcatgattattttttatcatcctaacaagctttcatgttgcaagttg-ctaaacttgttcctgttcattttccccagATGGTTATGGCAGTTTTTGCATACATATATCACCAATCATTCATATCGCCCCAAAACTACTCTGTTGAGCTAATCTTGGAACAG
                                                      || |  |   ||  ||| |   |||||  |  | || | | |  || |    |||| |   |  |  |   | | || |  |  | |  ||| |  | |||||||||||||||| ||||| ||||||||||  |||||||| ||     |||||| |   || |||||   |||| | || |||
gtaactctaatgaaactagtatctcttcgtaagattatgattaggtctttagagttttcattcacaagattcgcattgcatattcttcttctctaactctcat---ctttaagcatatacataaaccagacctaatgttatctattgttac-agATGGTTATGGCAGTATTTGCCTACATATATCTTCAATCATTTATTGTCTCCCAAAGCGTTTCGGTTGACAAAATCCTAGACCAG

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|29671303|gb|CB667578.1|CB667578
EST:     GAGACAGCATACCTGGGCATGGTGGGATTACTGACCGAATGGATTGTCAG                         ATGGTTATGGCAGTTTTTGCATACATATATCACCAATCATTCATATCGCCC
genomic: GAGACAGCATACCTGGGCATGGTGGGATTACTGACCGAATGGATTGTCAGgtaagtaatc ... ttttccccagATGGTTATGGCAGTTTTTGCATACATATATCACCAATCATTCATATCGCCC
EST: gi|88828918|gb|CI073788.1|CI073788
EST:     GAGACAGCATACCTGGGCATGGTGGGATTACTGACCGAATGGATTGTCAG                         ATGGTTATGGCAGTTTTTGCATACATATATCACCAATCATTCATATCGCCC
genomic: GAGACAGCATACCTGGGCATGGTGGGATTACTGACCGAATGGATTGTCAGgtaagtaatc ... ttttccccagATGGTTATGGCAGTTTTTGCATACATATATCACCAATCATTCATATCGCCC
EST: gi|86437554|gb|CI119276.1|CI119276
EST:     GAGACAGCATACCTGGGCATGGTGGGATTACTGACCGAATGGATTGTCAG                         ATGGTTATGGCAGTTTTTGCATACATATATCACCAATCATTCATATCGCCC
genomic: GAGACAGCATACCTGGGCATGGTGGGATTACTGACCGAATGGATTGTCAGgtaagtaatc ... ttttccccagATGGTTATGGCAGTTTTTGCATACATATATCACCAATCATTCATATCGCCC
EST: gi|89198721|gb|CI003458.1|CI003458
EST:     CTGACCGAATGGATTGTCAG                         ATGGTTATGGCAGTTTTTGCATACATATATCACCAATCATTCATATCGCCC
genomic: CTGACCGAATGGATTGTCAGgtaagtaatc ... ttttccccagATGGTTATGGCAGTTTTTGCATACATATATCACCAATCATTCATATCGCCC
EST: gi|88844663|gb|CI021238.1|CI021238
EST:     CTGGGCATGGTGGGATTACTGACCGAATGGATTGTCAG                         ATGGTTATGGCAGTTTTTGCATACATATATCACCAATCATTCATATCGCCC
genomic: CTGGGCATGGTGGGATTACTGACCGAATGGATTGTCAGgtaagtaatc ... ttttccccagATGGTTATGGCAGTTTTTGCATACATATATCACCAATCATTCATATCGCCC
EST: gi|29679198|gb|CB675473.1|CB675473
EST:     GAGACAGCATACCTGGGCATGGTGGGATTACTGACCGAATGGATTGTCAG                         ATGGTTATGGCAGTTTTTGCATACATATATCACCAATCATTCATATCGCCC
genomic: GAGACAGCATACCTGGGCATGGTGGGATTACTGACCGAATGGATTGTCAGgtaagtaatc ... ttttccccagATGGTTATGGCAGTTTTTGCATACATATATCACCAATCATTCATATCGCCC
EST: gi|86504386|gb|CI147019.1|CI147019
EST:     GAGACAGCATACCTGGGCATGGTGGGATTACTGACCGAATGGATTGTCAG                         ATGGTTATGGCAGTTTTTGCATACATATATCACCAATCATTCATATCGCCC
genomic: GAGACAGCATACCTGGGCATGGTGGGATTACTGACCGAATGGATTGTCAGgtaagtaatc ... ttttccccagATGGTTATGGCAGTTTTTGCATACATATATCACCAATCATTCATATCGCCC
EST: gi|29681975|gb|CB678250.1|CB678250
EST:     GAGACAGCATACCTGGGCATGGTGGGATTACTGACCGAATGGATTGTCAG                         ATGGTTATGGCAGTTTTTGCATACATATATCACCAATCATTCATATCGCCC
genomic: GAGACAGCATACCTGGGCATGGTGGGATTACTGACCGAATGGATTGTCAGgtaagtaatc ... ttttccccagATGGTTATGGCAGTTTTTGCATACATATATCACCAATCATTCATATCGCCC
EST: gi|29671304|gb|CB667579.1|CB667579
EST:     GAGACAGCATACCTGGGCATGGTGGGATTACTGACCGAATGGATTGTCAG                         ATGGTTATGGCAGTTTTTGCATACATATATCACCAATCATTCATATCGCCC
genomic: GAGACAGCATACCTGGGCATGGTGGGATTACTGACCGAATGGATTGTCAGgtaagtaatc ... ttttccccagATGGTTATGGCAGTTTTTGCATACATATATCACCAATCATTCATATCGCCC
EST: gi|313081133|gb|HO213719.1|HO213719
EST:     GAGACAGCATACCTGGGCATGGTGGGATTACTGACCGAATGGATTGTCAG                         ATGGTTATGGCAGTTTTTGCATACATATATCACCAATCATTCATATCGCCC
genomic: GAGACAGCATACCTGGGCATGGTGGGATTACTGACCGAATGGATTGTCAGgtaagtaatc ... ttttccccagATGGTTATGGCAGTTTTTGCATACATATATCACCAATCATTCATATCGCCC
EST: gi|86433541|gb|CI093884.1|CI093884
EST:     TACTGACCGAATGGATTGTCAG                         ATGGTTATGGCAGTTTTTGCATACATATATCACCAATCATTCATATCGCCC
genomic: TACTGACCGAATGGATTGTCAGgtaagtaatc ... ttttccccagATGGTTATGGCAGTTTTTGCATACATATATCACCAATCATTCATATCGCCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctaacaagctttcatgttgcaagttgctaaacttgttcctgttcattttccccagATGGTTATGGCAGTTTTTGCATACATATATCACCAATCATTCATATCGCCCCAAAACTACTCTGTTGAGCTAATCTTGGAACAG
                               cttgttcctgttcatt  CT-rich tract
                                         ttcatttt  TA-rich tract