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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattacttagacaactagcatgtgtaaactgattgcattgaataagcatacaattgctttgttcaaaatagtcttcagaatagaaaaaaaaaacttatgttcaactataaggcatctatcatgcttaaacagttaactgagacatctatcattcacttcaaatttacatgccttattatatagTTTTCAGAAAACTTCACAATTATGTTGTTCCACTATGATGGTCGGACTAATGACTGGGATGAATTTGAGTGGTCAAAAAGGGCCATTCATGTGAGTGTCA

Basic information

species Oryza sativa
transcript LOC_Os01g68260.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g68260.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM5G801369_T01 (Zea mays), 3'ss of exon 6
gtaattacttagacaactagcatgtgtaaactgattgcattgaataagcatacaattgctttgttcaaaatagtcttcagaatagaaaaaaaaaacttatgttcaactataaggcatctatcatgcttaaacagttaactgagacatctatcatt-cacttcaaatttacatgccttat-tatatagTTTTCAGAAAACTTCACAATTATGTTGTTCCACTATGATGGTCGGACTAATGACTGGGATGAATTTGAGTGGTCAAAAAGGGCCATTCATGTGAGTGTCA
                                                                                                             |||| ||||    |||||||||   |     ||   || |||  |     |||| ||| ||||   |  | | || |||||||||| ||||||||||||||||||||||| |||||||||||||| | ||| |||||||||||||||||||||||||||||| | |||||||||||||
------------------------------------------------------------------------------------------------------------gtaagacatcctaaatgcttaaaatatgcgaggaatgatatattgtagtttttcagattcacatatgtcttctctacagTTTTCAGATAACTTCACAATTATGTTGTTCCATTATGATGGTCGGACAACTGAGTGGGATGAATTTGAGTGGTCAAAAAGGGCCGTCCATGTGAGTGTCA

upper sequence: LOC_Os01g68260.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA12G29800.1 (Glycine max), 3'ss of exon 6
gtaattacttagacaactagcatgtgtaaactgattgcattgaataagcatacaattgctttgttcaaaatagtcttcagaatagaaaaaaaaaacttatgttcaactataaggcatctatcatgcttaaacagttaactgagacatctatcattcacttcaaatttacatgcc------ttattatatagTTTTCAGAAAACTTCACAATTATGTTGTTCCACTATGATGGTCGGACTAATGACTGGGATGAATTTGAGTGGTCAAAAAGGGCCATTCATGTGAGTGTCA
                                                                                                ||  | |  ||||     ||| ||| |   || |   ||  |   |  ||| | | |||  ||||||| || |   |       || || | |||||||| ||  | ||  ||||| || | || || |||||||||||||||| ||| |||||| |||||||||||||||  |  || || ||||| ||||  |
--------------------------------------------------------------------------------------------gttattgagattgactacctt-catatataagaatttatttgtatatctac-catttcttattttcttcaaaattgctgactatcaaattgttctgtagTTTTCTGATGATTTTGCAATTTTGCTCTTTCATTATGATGGTCGGACTAGTGAATGGGATCAATTTGAGTGGTCAAGGAATGCAATCCATGTTAGTGCAA

upper sequence: LOC_Os01g68260.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA13G39990.1 (Glycine max), 3'ss of exon 6
gtaattacttagacaactagcatgtgtaaactgattgcattgaataagcatacaattgctttgttcaaaatagtcttcagaatagaaaaaaaaaacttatgttcaactataaggcatctatcatgcttaaacagttaactgagacatctatcattcacttcaaatttacatgccttattatatagTTTTCAGAAAACTTCACAATTATGTTGTTCCACTATGATGGTCGGACTAATGACTGGGATGAATTTGAGTGGTCAAAAAGGGCCATTCATGTGAGTGTCA
                                                                                  |     | |   ||| |  ||||  |||| |  || |||  ||  ||   |   |  | | |  |   |||   | | |  | |  ||    || || | |||||||| ||  | ||  ||||| || | || || |||||||||||||||| ||| |||||| |||||||||||||||  || || || ||||| || |  |
---------------------------------------------------------------------------------gttattgatattgact-accttcatatatatga-atttatt-tgtatatcta-ccatttcatattttcttcaag-attgctgactatcaaa--ttgttctgtagTTTTCTGATGATTTTGCAATTTTGCTCTTTCATTATGATGGTCGGACTAGTGAATGGGATCAATTTGAGTGGTCAAGGAGTGCAATCCATGTCAGCGCAA

upper sequence: LOC_Os01g68260.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv06s0004g02700.t01 (Vitis vinifera), 3'ss of exon 6
gtaattacttagacaactagcatgtgtaaactgattgcattgaataagcatacaattgctttgttcaaaatagtcttcagaatagaaaaaaaaaacttatgttcaactataaggcat-ctatcatgcttaaacagttaactgagacatctat---cattca-cttcaaatttacatgccttattatatagTTTTCAGAAAACTTCACAATTATGTTGTTCCACTATGATGGTCGGACTAATGACTGGGATGAATTTGAGTGGTCAAAAAGGGCCATTCATGTGAGTGTCA
                                                                                                   |  || || || || | | | || ||  | |   | |||  |      | | |    ||| |  |||| ||    |||  || |     ||||||| ||  | |||  |||| || | || |||||||||||||| || | ||| |||||| ||||||||||||||||||  || |||||||| ||||  |
--------------------------------------------------------------------------------------------------gtcatccac-atgagccgttccataattttcatttatttattttgattgtttctggatattgagtttcagatgcttatgttttgtggc--agTTTTCTGAGGATTTCCAAATTTTGCTTTTTCACTATGATGGTCGAACAAGTGAATGGGATCAATTTGAGTGGTCAAAAACTGCAATTCATGTTAGTGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acagttaactgagacatctatcattcacttcaaatttacatgccttattatatagTTTTCAGAAAACTTCACAATTATGTTGTTCCACTATGATGGTCGGACTAATGACTGGGATGAATTTGAGTGGTCAAAAAGGGCCATTCATGTGAGTGTCA
  agttaac  putative branch site (score: 3)
                                          ccttatt  putative PPT
                                            ttattatata  TA-rich tract