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

ACTCCGCTGGCAAATGATACAAGCTGTGAATCAAATGTGACTACCCCTCAAAACCCTTTAAGGGATGCAAGTAACCCCTCTGGgtaagtaaatagttctgagtgactcaggtagaattattgttggatggacttgctctttcgatatcatgctatcttaactgccttttatcttgttctag

Basic information

species Oryza sativa
transcript LOC_Os03g01890.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g01890.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G109987_T01 (Zea mays), 5'ss of exon 4
ACTCCGCTGGCAAATGATACAAGCTGTGAATCAAATGTGACTACCCCTCAAAACCCTTTAAGGGATGCAAGTAACCCCTCTGGgtaagtaaatagttctgagtgactcaggtagaattattgttggatggacttgctctttcgatatcatgcta-tcttaactgcctttta--tcttgttctag
||| |  |||| ||||| |||||||||||||||||||| |||||||||| ||||||| ||||||| ||||||||||| ||||||||||| |||  |||||     ||   | || ||| ||||||  |   |||||  |||| | |  || ||| || |||   | ||  |  |||||||  ||
ACTTCATTGGCCAATGACACAAGCTGTGAATCAAATGTCACTACCCCTCCAAACCCTATAAGGGACGCAAGTAACCCTTCTGGgtaagtgaatcattctggccatctggagaaggattcttgttgcgtaaccttgccatttcaagactatcctaatcataataccattccaattcttgtttcag

upper sequence: LOC_Os03g01890.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G042250_T03 (Zea mays), 5'ss of exon 4
ACTCCGCTGGCAAATGATACAAGCTGTGAATCAAATGTGACTACCCCTCAAAACCCTTTAAGGGATGCAAGTAACCCCTCTGGgtaagtaaatagttctgagtgactcaggtagaattattgttggatggacttgctctttcgatatcatgctatcttaactgcctttt---atcttgttctag
||| |  |||| |||||||||||||||||||||||||| ||| |||||| |||| || ||||||||||||||||||| ||||||||||| ||| ||||||     ||   | || ||| ||||||  |   |||||  ||  || |   | |||     | |||| |||   ||||||||  ||
ACTTCATTGGCCAATGATACAAGCTGTGAATCAAATGTCACTGCCCCTCCAAACGCTATAAGGGATGCAAGTAACCCTTCTGGgtaagtgaatcgttctggccatctggagaaggatttttgttgcgtaaccttgccatt--gagactgtcctaatcatagtgccatttcaaatcttgtttcag
















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|29634707|gb|CB639716.1|CB639716
EST:     AATGTGACTACCCCTCAAAACCCTTTAAGGGATGCAAGTAACCCCTCTGG                         GCTCCTTTCAATTGCAGAGGAGACCTTGACAGAGTTCCTCTCAAAGGCTAC
genomic: AATGTGACTACCCCTCAAAACCCTTTAAGGGATGCAAGTAACCCCTCTGGgtaagtaaat ... cttgttctagGCTCCTTTCAATTGCAGAGGAGACCTTGACAGAGTTCCTCTCAAAGGCTAC
EST: gi|29642722|gb|CB647729.1|CB647729
EST:     AATGTGACTACCCCTCAAAACCCTTTAAGGGATGCAAGTAACCCCTCTGG                         GCTCCTTTCAATTGCAGAGGAGACCTTGACAGAGTTCCTCTCAAAGGCTAC
genomic: AATGTGACTACCCCTCAAAACCCTTTAAGGGATGCAAGTAACCCCTCTGGgtaagtaaat ... cttgttctagGCTCCTTTCAATTGCAGAGGAGACCTTGACAGAGTTCCTCTCAAAGGCTAC
EST: gi|58663402|gb|CK052088.1|CK052088
EST:     AATGTGACTACCCCTCAAAACCCTTTAAGGGATGCAAGTAACCCCTCTGG                         GGCTCCTTTCAATTGCAGAGGAGACCTTGACAGAGTTCCTCTCAAAGGCTA
genomic: AATGTGACTACCCCTCAAAACCCTTTAAGGGATGCAAGTAACCCCTCTGGgtaagtaaat ... cttgttctagG-CTCCTTTCAATTGCAGAGGAGACCTTGACAGAGTTCCTCTCAAAGGCTA
EST: gi|88205580|gb|CI205429.1|CI205429
EST:     AATGTGACTACCCCTCAAAACCCTTTAAGGGATGCAAGTAACCCCTCTGG                         GCTCCTTTCAATTGCAGAGGAGACCTTGACAGAGTTCCTCTCAAAGGCTAC
genomic: AATGTGACTACCCCTCAAAACCCTTTAAGGGATGCAAGTAACCCCTCTGGgtaagtaaat ... cttgttctagGCTCCTTTCAATTGCAGAGGAGACCTTGACAGAGTTCCTCTCAAAGGCTAC
EST: gi|29678474|gb|CB674749.1|CB674749
EST:     AATGTGACTACCCCTCAAAACCCTTTAAGGGATGCAAGTAACCCCTCTGG                         GCTCCTTTCAATTGCAGAGGAGACCTTGACAGAGTTCCTCTCAAAGGCTAC
genomic: AATGTGACTACCCCTCAAAACCCTTTAAGGGATGCAAGTAACCCCTCTGGgtaagtaaat ... cttgttctagGCTCCTTTCAATTGCAGAGGAGACCTTGACAGAGTTCCTCTCAAAGGCTAC

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: 54 (upstream exon), 70 (downstream exon)
Score: 19

ACTCCGCTGGCAAATGATACAAGCTGTGAATCAAATGTGACTACCCCTCAAAACCCTTTAAGGGATGCAAGTAACCCCTCTGGgtaagtaaat ... cttgttctagGCTCCTTTCAATTGCAGAGGAGACCTTGACAGAGTTCCTCTCAAAGGCTACTGGTACAGCTATTGATTGGGTCCAGATGCCTGGGATGAAG




<











<


<