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

gtaagaccataagagtctcactatttctgctttggtaaaagtattcaatccaacccgtatgtccaatgtaatagtcaccttttgctacattgctcttcagGAAATGAAAATGCTTACTATGAGAGATCACCGATCAACTTTGTTGACAAATTTACATGTCCAGTTATTTTGTTTCAAGGCTTGGATGATAAG

Basic information

species Oryza sativa
transcript LOC_Os06g11180.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g11180.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G120302_T02 (Zea mays), 3'ss of exon 15
gtaagaccataagagtctcactatttctgctttggtaaaagtattcaatccaacccgtatgtccaatgtaa---tagtcaccttttgc-tacattgctcttcagGAAATGAAAATGCTTACTATGAGAGATCACCGATCAACTTTGTTGACAAATTTACATGTCCAGTTATTTTGTTTCAAGGCTTGGATGATAAG
||||||     |  || | |  |||  || |||  | ||  | || || |||     ||  ||  || ||    || | |    |  |  ||||    ||| |||||||||||  |||||||| ||||||||||| |||||||||||  || | ||||| |||||||| |||||||||||||| ||||| ||||||
gtaaga----gacggtattatcatt--tgtttt--tgaagatgtt-aacccactttctagctctgatttacatctatttattcatgacgcacatgttcctttagGAAATGAAAGAGCTTACTACGAGAGATCACCAATCAACTTTGTCAACCAGTTTACTTGTCCAGTCATTTTGTTTCAAGGGTTGGAGGATAAG

upper sequence: LOC_Os06g11180.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GLYMA08G42730.1 (Glycine max), 3'ss of exon 15
gtaagaccataagagtctcactatttctgctttggtaaaagtattcaatccaacccgtatgtccaatgtaatagtca-ccttttgctacattgctcttcagGAAATGAAAATGCTTACTATGAGAGATCACCGATCAACTTTGTTGACAAATTTACATGTCCAGTTATTTTGTTTCAAGGCTTGGATGATAAG
||||| | || |     | || |||        ||||    |  |   |        | ||| | || | ||  |||  || || ||  |||| | | |||||  ||| || |  | |||||| |||||||| |||||   ||||||||||||| | |||||  ||||||| |||||||| |||||||| |||
gtaagtcaatga-----tgaccatt-----caaggtacctattatttctttggtttatttgttcgatttgatgttcagtctattccttaattgat-tgcagGAGGTGAGAAGGGGTGCTATGAAAGATCACCAATCAATCATGTTGACAAATTTTCTTGTCCCATTATTTTATTTCAAGGATTGGATGACAAG

upper sequence: LOC_Os06g11180.1 (Oryza sativa), 3'ss of exon 15
lower sequence: Vv18s0001g11150.t01 (Vitis vinifera), 3'ss of exon 15
----gtaagaccataagag--tctcact----atttctgctttggtaaaagtattcaatccaacccgtatgtcca-atgtaatagtcaccttttgctacattgctcttcagGAAATGAAAATGCTTACTATGAGAGATCACCGATCAACTTTGTTGACAAATTTACATGTCCAGTTATTTTGTTTCAAGGCTTGGATGATAAG
     |||      | ||   | | |      ||| |   ||  || | ||| |  ||| | |      | |||| ||  | || |||     |  |  | || | |||||||| ||||| |||||||| |||||| ||||||||||| |||||||| |||||| | || ||  ||||||| || ||||| ||||| || |||
gtaaataacctttcaggaaatttttatgttgaattacatattctgtgatagtctaaaattcgattatactttccatattgagtattcatgcaattgtcaactggt-ttcagGAAGTGAAAGTGCTTACTTTGAGAGGTCACCGATCAATTTTGTTGATAAATTTTCTTGCCCCATTATTTTATTCCAAGGATTGGAAGACAAG

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|86412718|gb|CI067123.1|CI067123
EST:     GAGAGCAGAGACACACAAATTCGAGTCTCACTATACTGACAATCTTGTAG                         GAAATGAAAATGCTTACTATGAGAGATCACCGATCAACTTTGTTGACAAAT
genomic: GAGAGCAGAGACACACAAATTCGAGTCTCACTATACTGACAATCTTGTAGgtaagaccat ... tgctcttcagGAAATGAAAATGCTTACTATGAGAGATCACCGATCAACTTTGTTGACAAAT
EST: gi|88903654|gb|CI089192.1|CI089192
EST:     GAGAGCAGAGACACACAAATTCGAGTCTCACTATACTGACAATCTTGTAG                         GAAATGAAAATGCTTACTATGAGAGATCACCGATCAACTTTGTTGACAAAT
genomic: GAGAGCAGAGACACACAAATTCGAGTCTCACTATACTGACAATCTTGTAGgtaagaccat ... tgctcttcagGAAATGAAAATGCTTACTATGAGAGATCACCGATCAACTTTGTTGACAAAT
EST: gi|86479713|gb|CI122346.1|CI122346
EST:     GAGAGCAGAGACACACAAATTCGAGTCTCACTATACTGACAATCTTGTAG                         GAAATGAAAATGCTTACTATGAGAGATCACCGATCAACTTTGTTGACAAAT
genomic: GAGAGCAGAGACACACAAATTCGAGTCTCACTATACTGACAATCTTGTAGgtaagaccat ... tgctcttcagGAAATGAAAATGCTTACTATGAGAGATCACCGATCAACTTTGTTGACAAAT
EST: gi|29630392|gb|CB635401.1|CB635401
EST:     GAGAGCAGAGACACACAAATTCGAGTCTCACTATACTGACAATCTTGTAG                         GAAATGAAAATGCTTACTATGAGAGATCACCGATCAACTTTGTTGACAAAT
genomic: GAGAGCAGAGACACACAAATTCGAGTCTCACTATACTGACAATCTTGTAGgtaagaccat ... tgctcttcagGAAATGAAAATGCTTACTATGAGAGATCACCGATCAACTTTGTTGACAAAT
EST: gi|29630391|gb|CB635400.1|CB635400
EST:     GAGAGCAGAGACACACAAATTCGAGTCTCACTATACTGACAATCTTGTAG                         GAAATGAAAATGCTTACTATGAGAGATCACCGATCAACTTTGTTGACAAAT
genomic: GAGAGCAGAGACACACAAATTCGAGTCTCACTATACTGACAATCTTGTAGgtaagaccat ... tgctcttcagGAAATGAAAATGCTTACTATGAGAGATCACCGATCAACTTTGTTGACAAAT
EST: gi|86479598|gb|CI122231.1|CI122231
EST:     AGAGCAGAGACACACAAATTCGAGTCTTCACTATACTGACAATCTTGTAG                         GAAATGAAAATGCTTACTATGAGAGATCACCGATCAACTTTGTTGACAAAT
genomic: AGAGCAGAGACACACAAATTCGAGTC-TCACTATACTGACAATCTTGTAGgtaagaccat ... tgctcttcagGAAATGAAAATGCTTACTATGAGAGATCACCGATCAACTTTGTTGACAAAT

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: 53 (upstream exon), 41 (downstream exon)
Score: 5

ATTGGTGACTTATCTTTGTTGAGAGCAGAGACACACAAATTCGAGTCTCACTATACTGACAATCTTGTAGgtaagaccat ... tgctcttcagGAAATGAAAATGCTTACTATGAGAGATCACCGATCAACTTTGTTGACAAATTTACATGTCCAGTTATTTTGTTTCAAGGCTTGGATGATAAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatccaacccgtatgtccaatgtaatagtcaccttttgctacattgctcttcagGAAATGAAAATGCTTACTATGAGAGATCACCGATCAACTTTGTTGACAAATTTACATGTCCAGTTATTTTGTTTCAAGGCTTGGATGATAAG
                                            ttgctcttc  CT-rich tract
                   aatgtaata  TA-rich tract