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

gtgagataacacctgttttcatatttacctgtgtgcacatgcacgccttgttctcattgttgcacaaactaatgctgattcctctaatccaattgctagACATGTCCTCCACAAGTATATAAATGAGGATGTTTCATTAGGAAGTTGGTTTATTGGATTAGATGTCGAGCATATCGACGACCGGAGACTTTGTTGTGGT

Basic information

species Oryza sativa
transcript LOC_Os02g06840.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g06840.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G132866_T01 (Zea mays), 3'ss of exon 9
gtgagataacacctgttttcatatttacctgtgtgcacatgcacgccttgttctc-attgttgcacaaactaatgctgattcctctaatccaattgc--tagACATGTCCTCCACAAGTATATAAATGAGGATGTTTCATTAGGAAGTTGGTTTATTGGATTAGATGTCGAGCATATCGACGACCGGAGACTTTGTTGTGGT
|||||  | ||   |  |      | |  | | |  | ||  ||   | ||| |  |   || ||   ||| | ||||   |   |||||  |  |    || ||| |||| |||||||| ||||| || || ||||| ||||||  |||||| || ||  ||||||| ||||||||||| |||||||| ||||| ||||| 
gtgagtcagcaatagcatgggc-ctgaattttctcgagatttacagttcgttttggagccttacattgactta-gctg---ctaataatctgaccgtaacagGCATATCCTTCACAAGTACATAAACGAAGACGTTTCGTTAGGATCTTGGTTCATCGGGCTAGATGTTGAGCATATCGATGACCGGAGGCTTTGCTGTGGC

upper sequence: LOC_Os02g06840.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA06G46230.2 (Glycine max), 3'ss of exon 9
----gtgag-ataacacctgttttcatatttacctgtgtgcacatgcacgccttgttctcattgttgcacaaactaatgctgattcctctaatccaattgctagACATGTCCTCCACAAGTATATAAATGAGGATGTTTCATTAGGAAGTTGGTTTATTGGATTAGATGTCGAGCATATCGACGACCGGAGACTTTGTTGTGGT
    ||| |  |||  |   |||  |  || |      |  |    |       ||||| ||  |||  |   || |  |||  |       |     |   ||  |||| || |||||||||   || |||||||| ||| |||||   |||||||||||| | ||||| |||||||| || || || |||||||||||||| 
gagtgtgtgtgtaattcacctttgtaagttaaatcaaatcaatgaac-taaaaggttcttat-attgtgc--tctcaccctgtgtgtatatgtttttctttcagGAATGTTCTTCACAAGTATGCCAACGAGGATGTGTCACTAGGATCCTGGTTTATTGGACTTGATGTGGAGCATATAGATGATCGAAGACTTTGTTGTGGC

upper sequence: LOC_Os02g06840.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA12G10520.1 (Glycine max), 3'ss of exon 9
-----gtgag-ataacacctgttttcatatttacctgtgtgcacatgcacgccttgttctcattgttgcacaaactaatgctgattcctctaatccaattgctagACATGTCCTCCACAAGTATATAAATGAGGATGTTTCATTAGGAAGTTGGTTTATTGGATTAGATGTCGAGCATATCGACGACCGGAGACTTTGTTGTGGT
     |||||   ||  |   |||  | ||| |      |  |    |       ||||| ||  |||  |   || |  ||| |   | ||       |   ||  |||| || |||||||||   || |||||||| ||| |||||   |||||||||||| | ||||| |||||||| || || || |||||||||||||| 
ctggagtgagtggaattcacctttataaattaaatcaaatcaatgaac-taaaaggttcttat-attgtgc--tctcaccctg-tgtgtatatgttttctttcagGAATGTTCTTCACAAGTATGCCAACGAGGATGTGTCACTAGGATCCTGGTTTATTGGACTTGATGTGGAGCATATAGATGATCGAAGACTTTGTTGTGGC

upper sequence: LOC_Os02g06840.2 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv19s0090g00560.t01 (Vitis vinifera), 3'ss of exon 9
gtgagataacacctgttttcatatttacctgtgtgcacatg-cacgccttgttctcattgttgcacaaactaatgctgattcctctaatccaattgctagACATGTCCTCCACAAGTATATAAATGAGGATGTTTCATTAGGAAGTTGGTTTATTGGATTAGATGTCGAGCATATCGACGACCGGAGACTTTGTTGTGGT
|| || |  ||  ||   |  |    |   |||   |  |  || |||    | |      ||| |  |||  || ||  ||   ||||    |  |||| ||||| || |||||||||   ||||||||||||||||| |||  |||||||||||| || || |  |||||||| || |||||| |||| ||||| |||
gtaagtttccaaatgccgtttttagaaaaagtgactaattatcatgccaaaatttt----ctgccctgact--tggtg-ctctcataatg-gttatctagGCATGTGCTTCACAAGTATGCTAATGAGGATGTTTCATTGGGATCTTGGTTTATTGGTTTGGACGCAGAGCATATTGATGACCGGCGACTGTGTTGCGGT

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|29682551|gb|CB678826.1|CB678826
EST:     CAATTGTATGCTATTTCAAAAGATCTAGCACCCTACATATCTATAAACAG                         ACATGTCCTCCACAAGTATATAAATGAGGATGTTTCATTAGGAAGTTGGTT
genomic: CAATTGTATGCTATTTCAAAAGATCTAGCAACCTACATATCTATAAACAGgtgagataac ... caattgctagACATGTCCTCCACAAGTATATAAATGAGGATGTTTCATTAGGAAGTTGGTT
EST: gi|86868611|gb|CI332988.1|CI332988
EST:     CAATTGTATGCTATTTCAAAAGATCTAGCAACCTACATATCTATAAACAG                         ACATGTCCTCCACAAGTATATAAATGAGGATGTTTCATTAGGAAGTTGGTT
genomic: CAATTGTATGCTATTTCAAAAGATCTAGCAACCTACATATCTATAAACAGgtgagataac ... caattgctagACATGTCCTCCACAAGTATATAAATGAGGATGTTTCATTAGGAAGTTGGTT
EST: gi|88274436|gb|CI394842.1|CI394842
EST:     CAATTGTATGCTATTTCAAAAGATCTAGCAACCTACATATCTATAAACAG                         ACATGTCCTCCACAAGTATATAAATGAGGATGTTTCATTAGGAAGTTGGTT
genomic: CAATTGTATGCTATTTCAAAAGATCTAGCAACCTACATATCTATAAACAGgtgagataac ... caattgctagACATGTCCTCCACAAGTATATAAATGAGGATGTTTCATTAGGAAGTTGGTT
EST: gi|29657303|gb|CB653578.1|CB653578
EST:     CAATTGTATGCTATTTCAAAAGATCTAGCAACCTACATATCTATAAACAG                         ACATGTCCTCCACAAGTATATAAATGAGGATGTTTCATTAGGAAGTTGGTT
genomic: CAATTGTATGCTATTTCAAAAGATCTAGCAACCTACATATCTATAAACAGgtgagataac ... caattgctagACATGTCCTCCACAAGTATATAAATGAGGATGTTTCATTAGGAAGTTGGTT
EST: gi|87006638|gb|CI295021.1|CI295021
EST:     CAATTGTATGCTATTTCAAAAGATCTAGCAACCTACATATCTATAAACAG                         ACATGTCCTCCACAAGTATATAAATGAGGATGTTTCATTAGGAAGTTGGTT
genomic: CAATTGTATGCTATTTCAAAAGATCTAGCAACCTACATATCTATAAACAGgtgagataac ... caattgctagACATGTCCTCCACAAGTATATAAATGAGGATGTTTCATTAGGAAGTTGGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccttgttctcattgttgcacaaactaatgctgattcctctaatccaattgctagACATGTCCTCCACAAGTATATAAATGAGGATGTTTCATTAGGAAGTTGGTTTATTGGATTAGATGTCGAGCATATCGACGACCGGAGACTTTGTTGTGGT
                     aaactaat  TA-rich tract