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

ACTGCCTTGCAATTCTAGCAAATATGGCCCCTCATGTGCATAGGCTGAGTGCATATGCATCTCAAAGGCTGGTTAGCCTCTTTGACATGCTCTCTCGCAAgtatgctcgctcaatctttctcccagtttatttaccttgaatcttttgttacataagtgacacctaaagttaccttatcttctgcttttatgcaacattcttcag

Basic information

species Oryza sativa
transcript LOC_Os01g56630.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g56630.2 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G078576_T04 (Zea mays), 5'ss of exon 11
ACTGCCTTGCAATTCTAGCAAATATGGCCCCTCATGTGCATAGGCTGAGTGCATATGCATCTCAAAGGCTGGTTAGCCTCTTTGACATGCTCTCTCGCAAgtatgctcgc--tcaatctttctcccagtttatttaccttgaatcttttgttacat-aagtgacacctaaagttaccttatcttctgcttttatgcaacattcttcag
|||| ||||||||| ||||||||||||| || |||||||||||||||||||| |||||||| |||||||| ||||| |||||||||||||| ||||||||||||||| ||  | | |||||  ||   ||||||||| ||   |   |  | || | ||||   ||||||||| | |||      || || |||| | ||| |   ||
ACTGTCTTGCAATTTTAGCAAATATGGCTCCGCATGTGCATAGGCTGAGTGCTTATGCATCACAAAGGCTAGTTAGTCTCTTTGACATGCTTTCTCGCAAgtatgctagcctttactcttttccctgatttatttactttatgttagtgctaacttcaagttgaacctaaagtaatcttgct---tgtttgtatgtaccatgcaatag

upper sequence: LOC_Os01g56630.2 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G079389_T01 (Zea mays), 5'ss of exon 11
ACTGCCTTGCAATTCTAGCAAATATGGCCCCTCATGTGCATAGGCTGAGTGCATATGCATCTCAAAGGCTGGTTAGCCTCTTTGACATGCTCTCTCGCAAgtatgctcgc--tcaatctttctcccagtttatttaccttgaatcttttgttacat-aagtgacacctaaagttaccttatcttctgcttttatgcaacattcttcag--
|||| ||||| ||| ||||||| ||||| ||||||||||||||||||||||| |||||||| |||||||| ||||| ||||| |||||||| ||||||||||||||| ||  | | |||||| |    ||||||||| ||   |   |  | || | ||||   ||||||||| | |||      || || |||| | ||| |   |   
ACTGTCTTGCTATTTTAGCAAACATGGCTCCTCATGTGCATAGGCTGAGTGCTTATGCATCACAAAGGCTAGTTAGTCTCTTCGACATGCTTTCTCGCAAgtatgctagcctttactctttccctagatttatttactttacgttagtcctaacttcaagttgaacctaaagtaatcttgct---tgtttctatgtaccatgcaatatag

upper sequence: LOC_Os01g56630.2 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA10G38920.2 (Glycine max), 5'ss of exon 11
ACTGCCTTGCAATTCTAGCAAATATGGCCCCTCATGTGCATAGGCTGAGTGCATATGCATCTCAAAGGCTGGTTAGCCTCTTTGACATGCTCTCTCGCAAgtatg---ctcgctcaatctttctcccagtttatttaccttgaatcttt---tgttacataagtgacacctaaagttaccttatcttctgcttt-tatgcaacattcttcag
  ||||| ||||   | |||||  |||| |||||||| ||| |  ||||||||||||||||||| ||  | || ||||| ||||| ||||| || ||||||||||   |||  |   |  |  ||  | | | | ||       |||||   | ||| |  | ||  | |    ||||         |  |  | |||       |  | ||
CATGCCTGGCAACCTTGGCAAACGTGGCACCTCATGTTCATCGTTTGAGTGCATATGCATCTCAGAGATTAGTCAGCCTTTTTGATATGCTTTCACGCAAgtatgtcactcttttgtttgtcttcataatgt-tctattccatttctttatgtcttagaacattgtaatcaccggttaaaaatctggccaccatatatttgcttcttattag

upper sequence: LOC_Os01g56630.2 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA20G28880.1 (Glycine max), 5'ss of exon 10
ACTGCCTTGCAATTCTAGCAAATATGGCCCCTCATGTGCATAGGCTGAGTGCATATGCATCTCAAAGGCTGGTTAGCCTCTTTGACATGCTCTCTCGCAAgtatgct-cgctcaatctttctcccagtttatttaccttgaatcttttgttacataagtgacacctaaagttaccttatcttctg-----cttttatgcaacattcttcag
  ||||| ||||   | ||||| ||||| |||||||| ||| |  ||||||||||||||||||| ||  | || ||||| ||||| ||||| || ||||||||||   | ||     || |   ||   | ||    |  | |  ||| |  | ||    |     |    |   | |   ||||     | | |||       |  | ||
CATGCCTGGCAACCTTGGCAAACATGGCACCTCATGTTCATCGTTTGAGTGCATATGCATCTCAGAGATTAGTCAGCCTTTTTGATATGCTTTCACGCAAgtatgtcactcttttgtttgccttcataatgttctattccatttctttatgtcttagaacattgtaatcactggttaaaaatctggccaccatatatttgcttcttattag

upper sequence: LOC_Os01g56630.2 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA10G00550.1 (Glycine max), 5'ss of exon 11
ACTGCCTTGCAATTCTAGCAAATATGGCCCCTCATGTGCATAGGCTGAGTGCATATGCATCTCAAAGGCTGGTTAGCCTCTTTGACATGCTCTCTCGCAAgtatgctcgctcaatctttctcccagtttatttac---cttgaatcttttgttac--ataagtgacacctaaagttaccttatcttctgcttttatgcaacattcttcag---------------------------------
  || || ||||   | ||||| ||||| |||||||| ||  |  ||||||||||||||||||| || || || ||||||||||||||||| || || ||||||| |    || |||||||     || ||  |    ||  | || ||  | ||  | ||   | | ||| |  |  | ||| | |  |||  |   |    | |   |                                 
CATGTCTGGCAACATTGGCAAACATGGCACCTCATGTCCACCGTTTGAGTGCATATGCATCTCAGAGACTAGTCAGCCTCTTTGACATGCTATCACGAAAgtatgttg--ccagtctttctgggctttcataaaaaaactatattcattattcaccaaaaaaaaaaaactatacatttcatatttacatcttgaaatgagtgatttcttgtataatgttgattctaatgttgattatggttag

upper sequence: LOC_Os01g56630.2 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA15G24080.1 (Glycine max), 5'ss of exon 13
ACTGCCTTGCAATTCTAGCAAATATGGCCCCTCATGTGCATAGGCTGAGTGCATATGCATCTCAAAGGCTGGTTAGCCTCTTTGACATGCTCTCTCGCAAgtatgctcgctcaatctttctcccagtttatt-taccttgaatcttttgttacataagtgacacctaaagttaccttatcttctgcttttatgcaacattcttcag
  || || ||||   | |||||  |||| || ||||| ||  |  ||||||||||||||||||| || || || |||||||||| |||||| || || ||||||| |    || ||| |||     || ||  ||   || ||   || ||    ||   |   |     | |  ||   |||| || ||    |  |||      
CATGTCTGGCAACATTGGCAAACCTGGCACCACATGTCCACCGTTTGAGTGCATATGCATCTCAGAGACTAGTCAGCCTCTTTGGCATGCTATCACGGAAgtatgttg--ccagtctatctgggctttcataataaactgtattcattattcaccaaaaaatttcatgtataatgttga-ttctactgttgattatgattag----

upper sequence: LOC_Os01g56630.2 (Oryza sativa), 5'ss of exon 11
lower sequence: Vv05s0020g04100.t01 (Vitis vinifera), 5'ss of exon 11
ACTGCCTTGCAATTCTAGCAAATATGGCCCCTCATGTGCATAGGCTGAGTGCATATGCATCTCAAAGGCTGGTTAGCCTCTTTGACATGCTCTCTCGCAAgtatgctcgctcaatctttctcccagtttatttaccttgaatcttttgttacataagtgacacctaaagttaccttatcttctgcttttatgcaacattc--ttcag
|||| || |||| | | || || ||||| |||||||  ||  |  | ||||| |||||||| || |||||||||||||| ||||| |||||||| |||||||||| |      || | | |   | |||  | |  |||| |   |  || |||        | ||   |    | || ||    |||  || || |||   | |||
ACTGTCTCGCAACTTTGGCGAACATGGCTCCTCATGCCCACCGTTTAAGTGCCTATGCATCACAGAGGCTGGTTAGCCTTTTTGATATGCTCTCACGCAAgtatgtttatgttatatat-tgataatttggtaattttga-taaatgctttcattttcagggcttatgatcttttaatttttccttttattgtaatattggatccag

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|58684083|gb|CK072770.1|CK072770
EST:     GCATATGCATCTCAAAGGCTGGTTAGCCTCTTTGACATGCTCTCTCGCAA                         GTATACCAAATTAGCCGAGTTAAAAAATGACAAAGCTATCAAAGTTATATC
genomic: GCATATGCATCTCAAAGGCTGGTTAGCCTCTTTGACATGCTCTCTCGCAAgtatgctcgc ... cattcttcagGTATACCAAATTAGCCGAGTTAAAAAATGACAAAGCTATCAAAGTTATATC
EST: gi|58678344|gb|CK067031.1|CK067031
EST:     GCATATGCATCTCAAAGGCTGGTTAGCCTCTTTGACATGCTCTCTCGCAA                         GTATACCAAATTAGCCGAGTTAAAAAATGACAAAGCTATCAAAGTTATATC
genomic: GCATATGCATCTCAAAGGCTGGTTAGCCTCTTTGACATGCTCTCTCGCAAgtatgctcgc ... cattcttcagGTATACCAAATTAGCCGAGTTAAAAAATGACAAAGCTATCAAAGTTATATC
EST: gi|29639051|gb|CB644060.1|CB644060
EST:     GCATATGCATCTCAAAGGCTGGTTAGCCTCTTTGACATGCTCTCTCGCAA                         GTATACCAAATTAGCCGAGTTAAAAAATGACAAAGCTATCAAAGTTATATC
genomic: GCATATGCATCTCAAAGGCTGGTTAGCCTCTTTGACATGCTCTCTCGCAAgtatgctcgc ... cattcttcagGTATACCAAATTAGCCGAGTTAAAAAATGACAAAGCTATCAAAGTTATATC