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'   		18  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagggtagcacgttcttctctactgtttacttttgttgcaaatacttgcatgttgtgtctgtgcagagtactcacatccacatttctatgattatcatgtgcttacttagattgacgtagatatttttgtgacatttatgtttgatgtgcagGAGACTGAAGAAAAAGCACTGGGTGATAGAGTGTGACCCTCTTGTGCATGAGGGGTTTGAAAGCACT

Basic information

species Oryza sativa
transcript LOC_Os06g44230.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g44230.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G475968_T01 (Zea mays), 3'ss of exon 2
gtagggtagcacgttcttctctactgtttacttttgttgcaaatacttgcatgttgtgtctgtgcagagtactcacatc----cacatttctatgattatc---atgtgcttacttagattgacgtaga-tatttttgtgacatttatgtttgatgtgcagGAGACTGAAGAAAAAGCACTGGGTGATAGAGTGTGACCCTCTTGTGCATGAGGGGTTTGAAAGCACT
||||||  |    || |||| |||     | |  | |||||          || |||   ||  | | |    |   |     |||  | ||||| || |       |||||    ||||  | | ||  |  |||||||| |||| | ||| |  |||||||| || ||||| ||||| |||||||||||      || ||||||||||||||||||||||||||||
gtagggctgtgt-tttttctttac-----aatcgtattgcaccgttccatgtgctgttgttgcactgggatgccttgtttcatcaccatcctatgcttgtttaggcatgcttgtgcagatgcatgaagggtccttttgtgatatttctctttaacttgcagGAGGCTAAAGAAGAAGCATTGGGTGATAGA------CCATCTTGTGCATGAGGGGTTTGAAAGCACT

upper sequence: LOC_Os06g44230.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G319000_T01 (Zea mays), 3'ss of exon 1
gtagggtagcacgttcttctctactgtttacttttgttgcaaatacttgcatgttgtgtctgtgcagagtactcacatccacatttctatgattatcatgtgcttacttagattgacgtaga-tatttttgtgacatttatgtttgatgtgcagGAGACTGAAGAAAAAGCACTGGGTGATAGAGTGTGACCCTCTTGTGCATGAGGGGTTTGAAAGCACT
                                            ||| | |||   ||| |         |    |||||   | |   || |||     |||||    ||||  | | ||  |  |||||||  |||| | ||| |  |||||||| || ||||| ||||| |||||||||||      || ||||||||||||||||||||||||||||
------------------------------------------gcactgggatgccttgttt--------catcaccatcc---tatgcttgtttag-gcatgcttgtgcagatgcatgaagggtccttttgtggtatttctctttaacctgcagGAGGCTAAAGAAGAAGCATTGGGTGATAGA------CCATCTTGTGCATGAGGGGTTTGAAAGCACT

upper sequence: LOC_Os06g44230.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G135218_T02 (Zea mays), 3'ss of exon 6
gtagggtagcacgttcttctctactgtttacttttgttg--caaatacttgcatgttgtgtctgtgcagagtactcacatccacatttctatgattatc---atgtgcttacttagattgacgtaga-tatttttgtgacatttatgtttgatgtgcagGAGACTGAAGAAAAAGCACTGGGTGATAGAGTGTGACCCTCTTGTGCATGAGGGGTTTGAAAGCACT---------------------------------
||||||  |    || |||| |||  |    ||    ||  | |  |  ||  |||||   ||| |  |  |  |  |||| ||  | ||||| || |       |||||    ||||  | | ||  |  | |||| | |||| | ||| |  |||||||| || ||||| ||||| ||||||||||||||||||| ||||||||||||||||||||||||||||                                 
gtagggctgtgt-tttttctttacaatcgtattgcactgttccatgagctgt-tgttgca-ctgggatgccttgtttcatc-accatcctatgcttgtttaggcatgcttgtgcagatgcatgaagggtcctcttgtaatatttctctttaacttgcagGAGGCTAAAGAAGAAGCATTGGGTGATAGAGTGTGACCATCTTGTGCATGAGGGGTTTGAAAGCACTGTAAGTTTACTTTGCCCTGCCAACCACATCGGT

upper sequence: LOC_Os06g44230.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G325129_T01 (Zea mays), 3'ss of exon 1
gtagggtagcacgttcttctctactgtttacttttgttg--caaatacttgcatgttgtgtctgtgcagagtact-cacatccacatttctatgattatcatgtgcttacttagattgacgtagatat-ttttgtgacatttatgtttgatgtgcagGAGACTGAAGAAAAAGCACTGGGTGATAGAGTGTGACCCTCTTGTGCATGAGGGGTTTGAAAGCACT
||||||  |    || |||| |||  |    ||    ||  | |  |  ||  |||||     |       |  | ||   |||   |    || ||      |||||    ||||  | | ||  |  |||||||| |||| | ||| |  |||||||| || ||||| ||||| ||||||||||||||||||| ||||||||||||||||||||||||| ||
gtagggctgtgt-tttttctttacaatcgtattgcactgttccatgagctgt-tgttgcactgggatgccttgtttcatcaccatcctatgctggtttaggcatgcttgtgcagatgcatgaagggaccttttgtgatatttctctttaacctgcagGAGGCTAAAGAAGAAGCATTGGGTGATAGAGTGTGACCATCTTGTGCATGAGGGGTTTGAAAGCTCT

upper sequence: LOC_Os06g44230.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G135218_T01 (Zea mays), 3'ss of exon 7
gtagggtagcacgttcttctctactgtttacttttgttg--caaatacttgcatgttgtgtctgtgcagagtactcacatccacatttctatgattatc---atgtgcttacttagattgacgtaga-tatttttgtgacatttatgtttgatgtgcagGAGACTGAAGAAAAAGCACTGGGTGATAGAGTGTGACCCTCTTGTGCATGAGGGGTTTGAAAGCACT
||||||  |    || |||| |||  |    ||    ||  | |  |  ||  |||||   ||| |  |  |  |  |||| ||  | ||||| || |       |||||    ||||  | | ||  |  | |||| | |||| | ||| |  |||||||| || ||||| ||||| ||||||||||||||||||| ||||||||||||||||||||||||||||
gtagggctgtgt-tttttctttacaatcgtattgcactgttccatgagctgt-tgttgca-ctgggatgccttgtttcatc-accatcctatgcttgtttaggcatgcttgtgcagatgcatgaagggtcctcttgtaatatttctctttaacttgcagGAGGCTAAAGAAGAAGCATTGGGTGATAGAGTGTGACCATCTTGTGCATGAGGGGTTTGAAAGCACT

upper sequence: LOC_Os06g44230.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G370326_T01 (Zea mays), 3'ss of exon 2
gtagggtagcacgttcttctctactgtttacttttgttgcaaatacttgcatgttgtgtctgtgcagagtactcacatccacatttctatgattatcatgtgcttacttagattgacgtagatatttttgtgacatttatgtttgatgtgcagGAGACTGAAGAAAAAGCACTGGGTGATAGAGTGTGACCCTCTTGTGCATGAGGGGTTTGAAAGCACT
                                                |||      | |||  |   |   |   ||  |   |  ||| |  ||| | | || |||   ||| |    | |  |||||||| |||| | ||| |  |||||||| || ||||| ||||| |||||||||||      || ||||||||||||||||||||||||||||
---------------------------------------------gccgcaatccccgcctgccctccgctgtt-tattaattctggtatcaaaatc-tctactaact---attaa---gggtccttttgtgatatttctctttaacctgcagGAGGCTAAAGAAGAAGCAGTGGGTGATAGA------CCATCTTGTGCATGAGGGGTTTGAAAGCACT

upper sequence: LOC_Os06g44230.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G115564_T01 (Zea mays), 3'ss of exon 3
gtagggtagcacgttcttct--ctactgtttacttttgttgcaaatacttgcatgttgtgtctgtgcagagtactcacatccacatttctatgattatc-atgtg-cttacttagattgacgtaga-tatttttgtgacatttatgtttgatgtgcagGAGACTGAAGAAAAAGCACTGGGTGATAGAGTGTGACCCTCTTGTGCATGAGGGGTTTGAAAGCACT
||||||  |    || |  |  | |  || |     |||| ||  ||||    |||||   ||| |  |  |  |  ||||  |||  ||||| || |  | ||  |||    ||||  | | ||  | ||||||||| |||| | ||| |  |||||||| || ||||| ||||| ||||||||||||||||||| ||||||||||||||||||||||||||||
gtagggctgtgttttttctttacaatcgtattgcactgttccatgtactgt--tgttgca-ctgggatgccttgtttcatcagcatc-ctatgcttgtttaggtatcttgtgcagatgcatgaagggtctttttgtgatatttctctttaacctgcagGAGGCTAAAGAAGAAGCATTGGGTGATAGAGTGTGACCATCTTGTGCATGAGGGGTTTGAAAGCACT

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: 74 (upstream exon), 33 (downstream exon)
Score: 8

CAGCTTTTGTACAGTCACCAGCTGACCAAACACCAGAGAGTTCTCCAGATATTCGACCAGCATTTAAACACGTACTTCGACAACCTATAGTAGAAAATGGgtagggtagc ... tgatgtgcagGAGACTGAAGAAAAAGCACTGGGTGATAGAGTGTGACCCTCTTGTGCATGAGGGGTTTGAAAGCACT




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgcttacttagattgacgtagatatttttgtgacatttatgtttgatgtgcagGAGACTGAAGAAAAAGCACTGGGTGATAGAGTGTGACCCTCTTGTGCATGAGGGGTTTGAAAGCACT
                    tagatattttt  TA-rich tract