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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACGAGGCGGAGATATCACCATCGACACTGTATGCCATTGCCTGCGTCATGGAGGGTATACCGTTCATTAACGGGAGTCCTCAGAACACCTTTGTGCCTGgtatgtaattttctgtgtagagtagtatgcggtttattttctcaggttcatggcttatttgtttactgtgtacag

Basic information

species Oryza sativa
transcript LOC_Os03g09250.2
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g09250.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G145638_T02 (Zea mays), 5'ss of exon 1
AACGAGGCGGAGATATCACCATCGACACTGTATGCCATTGCCTGCGTCATGGAGGGTATACCGTTCATTAACGGGAGTCCTCAGAACACCTTTGTGCCTGgtatgt--aattttctgtgt----agagtagtatgcggtttattttct---caggttcatggcttatttgtttactgtgtacag
|||||||||||||| || ||||| ||||| |||||||||||||| ||||  |||||  |  ||||||| || ||||| || |||||||| |||||||||||| |||  | |||  |||||    | |||  ||||  |||   |||||   ||    | |    || |||||   ||| |  ||
AACGAGGCGGAGATCTCGCCATCAACACTATATGCCATTGCCTGTGTCACAGAGGGGGTGTCGTTCATCAATGGGAGCCCCCAGAACACTTTTGTGCCTGgtgtgtttagtttggtgtgtttgcaaagttttatggtgttgcatttctgttcaaagacttattatacttgttgcatgtttgtag

upper sequence: LOC_Os03g09250.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G155242_T01 (Zea mays), 5'ss of exon 5
AACGAGGCGGAGATATCACCATCGACACTGTATGCCATTGCCTGCGTCATGGAGGGTATACCGTTCATTAACGGGAGTCCTCAGAACACCTTTGTGCCTGgtatgtaattttctgtgta---gagtagtatgcggtttattttctcaggttcatggcttatttgtttactgtgtacag----------------------------------
|||||||||||| |||||||||| ||||| |||||||||||||| |||||||||||  | |||||||| || ||||| || |||||||||||||||||||||  ||  |||  |||||     |    |    ||| |    | || | | ||  | ||  | || |  | | |                                      
AACGAGGCGGAGGTATCACCATCAACACTATATGCCATTGCCTGTGTCATGGAGGGGGTGCCGTTCATCAATGGGAGCCCCCAGAACACCTTTGTGCCTGgtgcgtggtttggtgtgtttgcaaaagcttcatggtgttgcatttctgttccaaagtttcatggtgttgtatttctgttccaaggcttattatacctgttgcatgttcgtag

upper sequence: LOC_Os03g09250.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G004528_T03 (Zea mays), 5'ss of exon 5
AACGAGGCGGAGATATCACCATCGACACTGTATGCCATTGCCTGCGTCATGGAGGGTATACCGTTCATTAACGGGAGTCCTCAGAACACCTTTGTGCCTGgtatgt--aattttctgtgt----agagtagtatgcggtttattttctc----aggttcatggcttatttgtttactgtgtacag
|||||||||||||| || ||||| ||||| |||||||||||||| |||| ||||||  | |||||||| || ||||| || |||||||| |||||||||||| |||  | |||  |||||    | |||  ||||  |||   | |||     |    | |    || ||||||  ||| |  ||
AACGAGGCGGAGATCTCGCCATCAACACTATATGCCATTGCCTGTGTCACGGAGGGGGTGCCGTTCATCAATGGGAGCCCCCAGAACACTTTTGTGCCTGgtgtgtttagtttggtgtgttcccaaagttttatggtgttgcatctctgttcaaaaaacttattatacttgtttcatgtttgtag

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|218495019|gb|FG965569.1|FG965569
EST:     GGAGGGTATACCGTTCATTAACGGGAGTCCTCAGAACACCTTTGTGCCTG                         GGCTGATCGATCTTGCTATTAAGAACAACTGCCTGATTGGTGGTGATGATT
genomic: GGAGGGTATACCGTTCATTAACGGGAGTCCTCAGAACACCTTTGTGCCTGgtatgtaatt ... ctgtgtacagGGCTGATCGATCTTGCTATTAAGAACAACTGCCTGATTGGTGGTGATGATT
EST: gi|58598823|gb|CK009351.1|CK009351
EST:     GGAGGGTATACCGTTCATTAACGGGAGTCCTCAGAACACCTTTGTGCCTG                         GGCTGATCGATCTTGCTATTAAGAACAACTGCCTGATTGGTGGTGATGATT
genomic: GGAGGGTATACCGTTCATTAACGGGAGTCCTCAGAACACCTTTGTGCCTGgtatgtaatt ... ctgtgtacagGGCTGATCGATCTTGCTATTAAGAACAACTGCCTGATTGGTGGTGATGATT
EST: gi|29686334|gb|CB682609.1|CB682609
EST:     GGAGGGTATACCGTTCATTAACGGGAGTCCTCAGAACACCTTTGTGCCTG                         GGCTGATCGATCTTGCTATTAAGAACAACTGCCTGATTGGTGGTGATGATT
genomic: GGAGGGTATACCGTTCATTAACGGGAGTCCTCAGAACACCTTTGTGCCTGgtatgtaatt ... ctgtgtacagGGCTGATCGATCTTGCTATTAAGAACAACTGCCTGATTGGTGGTGATGATT
EST: gi|3760166|gb|C97424.1|C97424
EST:     GGAGGGTATACCGTTCATTAACGGGAGTCCTCAGAACACCTTTGTGCCTG                         GGCTGATCGATCTTGCTATTAAGAACAACTGCCTGATTGGTGGTGATGATT
genomic: GGAGGGTATACCGTTCATTAACGGGAGTCCTCAGAACACCTTTGTGCCTGgtatgtaatt ... ctgtgtacagGGCTGATCGATCTTGCTATTAAGAACAACTGCCTGATTGGTGGTGATGATT
EST: gi|11443012|gb|BF430899.1|BF430899
EST:     GGAGGGTATACCGTTCATTAACGGGAGTCCTCAGAACACCTTTGTGCCTG                         GGCTGATCGATCTTGCTATTAAGAACAACTGCCTGATTGGTGGTGATGATT
genomic: GGAGGGTATACCGTTCATTAACGGGAGTCCTCAGAACACCTTTGTGCCTGgtatgtaatt ... ctgtgtacagGGCTGATCGATCTTGCTATTAAGAACAACTGCCTGATTGGTGGTGATGATT
EST: gi|218494828|gb|FG945589.1|FG945589
EST:     GGAGGGTATACCGTTCATTAACGGGAGTCCTCAGAACACCTTTGTGCCTG                         GGCTGATCGATCTTGCTATTAAGAACAACTGCCTGATTGGTGGTGATGATT
genomic: GGAGGGTATACCGTTCATTAACGGGAGTCCTCAGAACACCTTTGTGCCTGgtatgtaatt ... ctgtgtacagGGCTGATCGATCTTGCTATTAAGAACAACTGCCTGATTGGTGGTGATGATT
EST: gi|58675021|gb|CK063708.1|CK063708
EST:     GGAGGGTATACCGTTCATTAACGGGAGTCCTCAGAACACCTTTGTGCCTG                         GGCTGATCGATCTTGCTATTAAGAACAACTGCCTGATTGGTGGTGATGATT
genomic: GGAGGGTATACCGTTCATTAACGGGAGTCCTCAGAACACCTTTGTGCCTGgtatgtaatt ... ctgtgtacagGGCTGATCGATCTTGCTATTAAGAACAACTGCCTGATTGGTGGTGATGATT
EST: gi|2312304|gb|C28459.1|C28459
EST:     GGAGGGTATACCGTTCATTAACGGGAGTCCTCAGAACACCTTTGTGCCTG                         GGCTGATCGATCTTGCTATTAAGAACAACTGCCTGATTGGTGGTGATGATT
genomic: GGAGGGTATACCGTTCATTAACGGGAGTCCTCAGAACACCTTTGTGCCTGgtatgtaatt ... ctgtgtacagGGCTGATCGATCTTGCTATTAAGAACAACTGCCTGATTGGTGGTGATGATT
EST: gi|58598555|gb|CK009083.1|CK009083
EST:     GGAGGGTATACCGTTCATTAACGGGAGTCCTCAGAACACCTTTGTGCCTG                         GGCTGATCGATCTTGCTATTAAGAACAACTGCCTGATTGGTGGTGATGATT
genomic: GGAGGGTATACCGTTCATTAACGGGAGTCCTCAGAACACCTTTGTGCCTGgtatgtaatt ... ctgtgtacagGGCTGATCGATCTTGCTATTAAGAACAACTGCCTGATTGGTGGTGATGATT
EST: gi|218485553|gb|FG949786.1|FG949786
EST:     CCTCAGAACACCTTTGTGCCTG                         GGCTGATCGATCTTGCTATTAAGAACAACTGCCTGATTGGTGGTGATGATT
genomic: CCTCAGAACACCTTTGTGCCTGgtatgtaatt ... ctgtgtacagGGCTGATCGATCTTGCTATTAAGAACAACTGCCTGATTGGTGGTGATGATT
EST: gi|218487632|gb|FG964358.1|FG964358
EST:     GGAGGGTATACCGTTCATTAACGGGAGTCCTCAGAACACCTTTGTGCCTG                         GGCTGATCGATCTTGCTATTAAGAACAACTGCCTGATTGGTGGTGATGATT
genomic: GGAGGGTATACCGTTCATTAACGGGAGTCCTCAGAACACCTTTGTGCCTGgtatgtaatt ... ctgtgtacagGGCTGATCGATCTTGCTATTAAGAACAACTGCCTGATTGGTGGTGATGATT

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: 73 (upstream exon), 75 (downstream exon)
Score: 81

AACGAGGCGGAGATATCACCATCGACACTGTATGCCATTGCCTGCGTCATGGAGGGTATACCGTTCATTAACGGGAGTCCTCAGAACACCTTTGTGCCTGgtatgtaatt ... ctgtgtacagGGCTGATCGATCTTGCTATTAAGAACAACTGCCTGATTGGTGGTGATGATTTCAAGAGTGGACAGACAAAGATGAAGTCTGTCTTGGTTGATTTCCTAGT




<











<


<