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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTACACTTACATGCGACCCAGACTGCGGTCCTCAAGGTTGATGCCTCACCGCAACTTGCTCGACAGATCCCTGACACACTATTTGGAATATTTTTTGAGgtaagccgtgagacatatacagtaattctgtttttcacaattgcactgtatcactatatcctttcctctggcacttttttgttaggatgctcaagtgcattagcatgcccagaataatccaggtagattatacatgttccaccatgtcctgatgataatgatcttggctaatattgtag

Basic information

species Oryza sativa
transcript LOC_Os11g03730.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g03730.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G006130_T06 (Zea mays), 5'ss of exon 2
GTTACACTTACATGCGACCCAGACTGCGGTCCTCAAGGTTGATGCCTCACCGCAACTTGCTCGACAGATCCCTGACACACTATTTGGAATATTTTTTGAGgtaagccgtgagacatatacagtaattctgtttttcacaatt-gcactgtatcactatatcctttcctctggcacttttttgttaggatgctcaagtgcattagcatgcccagaataatccaggtagattatacatgttccaccatgtcctgatgataatgatcttggctaatattgtag
 ||  |  || | || |||||||| || | |||||||||||||||||| || || ||||| ||  |||||||||| ||||| ||||| |||||||||||||| || |   ||   |||      || ||  ||   |   ||  |    ||| |  | |     |  ||    |  |  |   | |  | ||  ||                                                                                    
TTTGGAAATAGAGGCCACCCAGACAGCAGCCCTCAAGGTTGATGCCTCGCCACAGCTTGCCCGGAAGATCCCTGAAACACTGTTTGGGATATTTTTTGAGgtgaggcagtagtt-tatcggtagatgctagttcctatgttttaccacatataatcagaaagaataatccaa-atatactgcatggcctactgtag------------------------------------------------------------------------------------
















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|88763952|gb|CI773368.1|CI773368
EST:     CGCAACTTGCTCGACAGATCCCTGACACACTATTTGGAATATTTTTTGAG                         GAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAAC
genomic: CGCAACTTGCTCGACAGATCCCTGACACACTATTTGGAATATTTTTTGAGgtaagccgtg ... aatattgtagGAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAAC
EST: gi|29632559|gb|CB637568.1|CB637568
EST:     CGCAACTTGCTCGACAGATCCCTGACACACTATTTGGAATATTTTTTGAG                         GAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAAC
genomic: CGCAACTTGCTCGACAGATCCCTGACACACTATTTGGAATATTTTTTGAGgtaagccgtg ... aatattgtagGAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAAC
EST: gi|88734903|gb|CI758411.1|CI758411
EST:     CGCAACTTGCTCGACAGATCCCTGACACACTATTTGGAATATTTTTTGAG                         GAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAAC
genomic: CGCAACTTGCTCGACAGATCCCTGACACACTATTTGGAATATTTTTTGAGgtaagccgtg ... aatattgtagGAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAAC
EST: gi|88299972|gb|CI580033.1|CI580033
EST:     CGCAACTTGCTCGACAGATCCCTGACACACTATTTGGAATATTTTTTGAG                         GAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAAA
genomic: CGCAACTTGCTCGACAGATCCCTGACACACTATTTGGAATATTTTTTGAGgtaagccgtg ... aatattgtagGAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAAC
EST: gi|88740536|gb|CI764044.1|CI764044
EST:     CGCAACTTGCTCGACAGATCCCTGACACACTATTTGGAATATTTTTTGAG                         GAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAAC
genomic: CGCAACTTGCTCGACAGATCCCTGACACACTATTTGGAATATTTTTTGAGgtaagccgtg ... aatattgtagGAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAAC
EST: gi|29673416|gb|CB669691.1|CB669691
EST:     CGCAACTTGCTCGACAGATCCCTGACACACTATTTGGAATATTTTTTGAG                         GAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAAC
genomic: CGCAACTTGCTCGACAGATCCCTGACACACTATTTGGAATATTTTTTGAGgtaagccgtg ... aatattgtagGAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAAC
EST: gi|29638131|gb|CB643140.1|CB643140
EST:     CGCAACTTGCTCGACAGATCCCTGACACACTATTTGGAATATTTTTTGAG                         GAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAAC
genomic: CGCAACTTGCTCGACAGATCCCTGACACACTATTTGGAATATTTTTTGAGgtaagccgtg ... aatattgtagGAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAAC
EST: gi|88745225|gb|CI768585.1|CI768585
EST:     CGCAACTTGCTCGACAGATCCCTGACACACTATTTGGAATATTTTTTGAG                         GAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAAC
genomic: CGCAACTTGCTCGACAGATCCCTGACACACTATTTGGAATATTTTTTGAGgtaagccgtg ... aatattgtagGAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAAC
EST: gi|88735131|gb|CI758639.1|CI758639
EST:     CGNAACTTGCTCGACAGATCCCTGACACACTATTTGGAATATTTTTTGAG                         GAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAAC
genomic: CGCAACTTGCTCGACAGATCCCTGACACACTATTTGGAATATTTTTTGAGgtaagccgtg ... aatattgtagGAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAAC
EST: gi|29680212|gb|CB676487.1|CB676487
EST:     CGCAACTTGCTCGACAGATCCCTGACACACTATTTGGAATATTTTTTGAG                         GAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAAC
genomic: CGCAACTTGCTCGACAGATCCCTGACACACTATTTGGAATATTTTTTGAGgtaagccgtg ... aatattgtagGAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAAC
EST: gi|29674874|gb|CB671149.1|CB671149
EST:     CGCAACTTGCTCGACAGATCCCTGACACACTATTTGGAATATTTTTTGAG                         GAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAAC
genomic: CGCAACTTGCTCGACAGATCCCTGACACACTATTTGGAATATTTTTTGAGgtaagccgtg ... aatattgtagGAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAAC
EST: gi|29681802|gb|CB678077.1|CB678077
EST:     CGCAACTTGCTCGACAGATCCCTGACACACTATTTGGAATATTTTTTGAG                         GAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAAC
genomic: CGCAACTTGCTCGACAGATCCCTGACACACTATTTGGAATATTTTTTGAGgtaagccgtg ... aatattgtagGAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAAC
EST: gi|29634180|gb|CB639189.1|CB639189
EST:     CGCAACTTGCTCGACAGATCCCTGACACACTATTTGGAATATTTTTTGAG                         GAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAAC
genomic: CGCAACTTGCTCGACAGATCCCTGACACACTATTTGGAATATTTTTTGAGgtaagccgtg ... aatattgtagGAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAAC
EST: gi|88737430|gb|CI760938.1|CI760938
EST:     CGCAACTTGCTCGACAGATCCCTGACACACTATTTGGAATATTTTTTGAG                         GAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAAC
genomic: CGCAACTTGCTCGACAGATCCCTGACACACTATTTGGAATATTTTTTGAGgtaagccgtg ... aatattgtagGAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAAC
EST: gi|29628283|gb|CB633294.1|CB633294
EST:     CGCAACTTGCTCGACAGATCCCTGACACACTATTTGGAATATTTTTTGAG                         GAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAAC
genomic: CGCAACTTGCTCGACAGATCCCTGACACACTATTTGGAATATTTTTTGAGgtaagccgtg ... aatattgtagGAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAAC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 75 (upstream exon), 55 (downstream exon)
Score: 44

GTTACACTTACATGCGACCCAGACTGCGGTCCTCAAGGTTGATGCCTCACCGCAACTTGCTCGACAGATCCCTGACACACTATTTGGAATATTTTTTGAGgtaagccgtg ... aatattgtagGAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAG




<











<


<