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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAGAATATACTGGCAAACTCAGACTGCAAATTGAAAATATGTGATTTCGGACTTGCCCGAGCATCATTCAATGATGCCCCTTCAGCAATATTTTGGACGgtaaggtgcttatatgagattttacattcctctttaagtctttatgttattaattatgttctactttgtgaag

Basic information

species Oryza sativa
transcript LOC_Os06g49430.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g49430.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G135904_T02 (Zea mays), 5'ss of exon 3
CAAGAATATACTGGCAAACTCAGACTGCAAATTGAAAATATGTGATTTCGGACTTGCCCGAGCATCATTCAATGATGCCCCTTCAGCAATATTTTGGACGgtaaggtgcttat-atgagatttta-cattcctctttaagtctttatgttattaat-----tatgttctactttgtgaag
||||||||||||||| ||||| ||||||||| ||||||||||||| || ||||||||||| |||||||||||||||||||||||||| ||||||||||| |||||  ||||   ||   ||   | ||||| | ||  |   ||   ||| |||||     | || | | || | |||||
CAAGAATATACTGGCTAACTCGGACTGCAAACTGAAAATATGTGACTTTGGACTTGCCCGTGCATCATTCAATGATGCCCCTTCAGCTATATTTTGGACAgtaagacgcttgccattttatggaagcattcatgttcca-ctttcccgtttttaatgtgcttctgcttttctgtttgaag

upper sequence: LOC_Os06g49430.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G306028_T02 (Zea mays), 5'ss of exon 3
CAAGAATATACTGGCAAACTCAGACTGCAAATTGAAAATATGTGATTTCGGACTTGCCCGAGCATCATTCAATGATGCCCCTTCAGCAATATTTTGGACGgtaaggtgctt--------atatgagattttacattcctctttaagtctttatgttattaattatgttctactttgtgaag
||||||||||||||| ||||| ||||||||| ||||||||||||| || || |||||||| |||||||| ||||||||||||||||| ||||||||||| |||||   |||        ||   ||  || |  |||| ||||   | ||| |  | |  ||  || | | || | |||||
CAAGAATATACTGGCTAACTCGGACTGCAAACTGAAAATATGTGACTTTGGTCTTGCCCGTGCATCATTTAATGATGCCCCTTCAGCTATATTTTGGACAgtaagacccttgccatcttatggaagcattcatgttccactttgc-tatttttaatgtgcatc-tgcttttctatttgaag
















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|29645354|gb|CB650361.1|CB650361
EST:     GACTTGCCCGAGCATCATTCAATGATGCCCCTTCAGCAATATTTTGGACG                         GATTATGTTGCAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTT
genomic: GACTTGCCCGAGCATCATTCAATGATGCCCCTTCAGCAATATTTTGGACGgtaaggtgct ... ctttgtgaagGATTATGTTGCAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTT
EST: gi|29664602|gb|CB660877.1|CB660877
EST:     GACTTGCCCGAGCATCATTCAATGATGCCCCTTCAGCAATATTTTGGACG                         GATTATGTTGCAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTT
genomic: GACTTGCCCGAGCATCATTCAATGATGCCCCTTCAGCAATATTTTGGACGgtaaggtgct ... ctttgtgaagGATTATGTTGCAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTT
EST: gi|33795692|gb|CF323716.1|CF323716
EST:     GACTTGCCCGAGCATCATTCAATGATGCCCCTTCAGCAATATTTTGGACG                         GATTATGTTGCAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTT
genomic: GACTTGCCCGAGCATCATTCAATGATGCCCCTTCAGCAATATTTTGGACGgtaaggtgct ... ctttgtgaagGATTATGTTGCAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTT
EST: gi|58687543|gb|CK076230.1|CK076230
EST:     GACTTGCCCGAGCATCATTCAATGATGCCCCTTCAGCAATATTTTGGACG                         GATTATGTTGCAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTT
genomic: GACTTGCCCGAGCATCATTCAATGATGCCCCTTCAGCAATATTTTGGACGgtaaggtgct ... ctttgtgaagGATTATGTTGCAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTT
EST: gi|58652759|gb|CK041439.1|CK041439
EST:     GACTTGCCCGAGCATCATTCAATGATGCCCCTTCAGCAATGTTTTGGACG                         GATTATGTTGCAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTT
genomic: GACTTGCCCGAGCATCATTCAATGATGCCCCTTCAGCAATATTTTGGACGgtaaggtgct ... ctttgtgaagGATTATGTTGCAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTT
EST: gi|58663889|gb|CK052575.1|CK052575
EST:     GACTTGCCCGAGCATCATTCAATGATGCCCCTTCAGCAATATTTTGGACG                         GATTATGTTGCAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTT
genomic: GACTTGCCCGAGCATCATTCAATGATGCCCCTTCAGCAATATTTTGGACGgtaaggtgct ... ctttgtgaagGATTATGTTGCAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTT
EST: gi|58693904|gb|CK082591.1|CK082591
EST:     GACTTGCCCGAGCATCATTCAATGATGCCCCTTCAGCAATATTTTGGACG                         GATTATGTTGCAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTT
genomic: GACTTGCCCGAGCATCATTCAATGATGCCCCTTCAGCAATATTTTGGACGgtaaggtgct ... ctttgtgaagGATTATGTTGCAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTT
EST: gi|58663177|gb|CK051863.1|CK051863
EST:     GACTTGCCCGAGCATCATTCAATGATGCCCCTTCAGCAATATTTTGGACG                         GATTATGTTGCAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTT
genomic: GACTTGCCCGAGCATCATTCAATGATGCCCCTTCAGCAATATTTTGGACGgtaaggtgct ... ctttgtgaagGATTATGTTGCAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTT
EST: gi|58668308|gb|CK056994.1|CK056994
EST:     GACTTGCCCGAGCATCATTCAATGATGCCCCTTCAGCAATATTTTGGACG                         GATTATGTTGCAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTT
genomic: GACTTGCCCGAGCATCATTCAATGATGCCCCTTCAGCAATATTTTGGACGgtaaggtgct ... ctttgtgaagGATTATGTTGCAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTT
EST: gi|33675107|gb|CF303346.1|CF303346
EST:     GACTTGCCCGAGCATCATTCAATGATGCCCCTTCAGCAATATTTTGGACG                         GATTATGTTGCAACG
genomic: GACTTGCCCGAGCATCATTCAATGATGCCCCTTCAGCAATATTTTGGACGgtaaggtgct ... ctttgtgaagGATTATGTTGCAACG
EST: gi|66913253|gb|CX100101.1|CX100101
EST:     GACTTGCCCGAGCATCATTCAATGATGCCCGTTCAGCAATATTTTGGACG                         GATTATGTTGCAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTT
genomic: GACTTGCCCGAGCATCATTCAATGATGCCCCTTCAGCAATATTTTGGACGgtaaggtgct ... ctttgtgaagGATTATGTTGCAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTT
EST: gi|58661035|gb|CK049715.1|CK049715
EST:     ACTTGCCCGAGGGGTCATTCAATGATGCCCCTTCAGCAATATTTTGGACG                         GATTATGTTGCAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTT
genomic: ACTTGCCCGA-GCATCATTCAATGATGCCCCTTCAGCAATATTTTGGACGgtaaggtgct ... ctttgtgaagGATTATGTTGCAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTT
EST: gi|29627483|gb|CB632494.1|CB632494
EST:     GACTTGCCCGAGCATCATTCAATGATGCCCCTTCAGCAATATTTTGGACG                         GATTATGTTGCAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTT
genomic: GACTTGCCCGAGCATCATTCAATGATGCCCCTTCAGCAATATTTTGGACGgtaaggtgct ... ctttgtgaagGATTATGTTGCAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTT
EST: gi|33675390|gb|CF303629.1|CF303629
EST:     GACTTGCCCGAGCATCATTCAATGATGCCCCTTCAGCAATATTTTGGACG                         GATTATGTTGCAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCA
genomic: GACTTGCCCGAGCATCATTCAATGATGCCCCTTCAGCAATATTTTGGACGgtaaggtgct ... ctttgtgaagGATTATGTTGCAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCA
EST: gi|58668784|gb|CK057470.1|CK057470
EST:     GACTTGCCCGAGCATCATTCAATGATGCCCCTTCAGCAATATTTAGGACG                         GATTATGTTGCAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTT
genomic: GACTTGCCCGAGCATCATTCAATGATGCCCCTTCAGCAATATTTTGGACGgtaaggtgct ... ctttgtgaagGATTATGTTGCAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTT