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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGATTGCGATGAGCACAAGAGTGTGTGCAGCAAGTATGGAGTTTCTGGGTACCCAACAATTCAATGGTTCCCCAAAGGATCCCTGGAGCCCAAAAAgtgaggctgcataacttttgttcaaatacttttgaacatctacaccagacaaaattttcatgatttatatcactacaaccatgtag

Basic information

species Oryza sativa
transcript LOC_Os01g23740.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g23740.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G128171_T04 (Zea mays), 5'ss of exon 3
GTTGATTGCGATGAGCACAAGAGTGTGTGCAGCAAGTATGGAGTTTCTGGGTACCCAACAATTCAATGGTTCCCCAAAGGATCCCTGGAGCCCAAAAAgtgaggctgcataacttttgttcaaatacttttgaacatctacaccagacaaaattt-----tcatgatttatatcactacaaccatgtag
|||||||| ||||||||||||||| |||||||||||||||||||||| ||||| |||||||| ||||||||||| ||||||||| |||||||||||||||||||  ||        |||| ||||  ||    |   ||        |||  | |     |  |||   | ||  ||    | |  |||
GTTGATTGTGATGAGCACAAGAGTTTGTGCAGCAAGTATGGAGTTTCCGGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAAgtgagggagcgcg-----tgtttaaatttttccatat-cctttgtttaccaagttctgtgaattctgacagaaattcctttggcaaattag

upper sequence: LOC_Os01g23740.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA02G01750.1 (Glycine max), 5'ss of exon 3
GTTGATTGCGATGAGCACAAGAGTGTGTGCAGCAAGTATGGAGTTTCTGGGTACCCAACAATTCAATGGTTCCCCAAAGGATCCCTGGAGCCCAAAAAgtgaggc--tgcataacttttgttcaaatacttttgaacatctacaccagacaaaattttcatgattta--tatcactacaaccatgtag------------------------------------------
||||| || ||||||||||||||| |||||||||| |||||||| |||||||||||||||||||| ||||| || |||||||| || || ||||||||||||||   |   |  || |||    |  || ||   |||  |  |  |    || |  |  | |||||  | ||| | ||    | |                                            
GTTGACTGTGATGAGCACAAGAGTTTGTGCAGCAAATATGGAGTCTCTGGGTACCCAACAATTCAGTGGTTTCCAAAAGGATCTCTTGAACCCAAAAAgtgaggagatttttgtctattggaatataacattgacacaattttat-atcttaattcatagttatttacctgtcatttcacatttatcattccttttgcattcaatacttgattttggaaaattcccatag

upper sequence: LOC_Os01g23740.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA06G24520.1 (Glycine max), 5'ss of exon 4
GTTGATTGCGATGAGCACAAGAGTGTGTGCAGCAAGTATGGAGTTTCTGGGTACCCAACAATTCAATGGTTCCCCAAAGGATCCCTGGAGCCCAAAAAgtgaggc--tgcataacttttgttcaaatacttttgaacatctacaccagacaaaattttcatgatttatatcactacaaccatgtag--------------------------------------------
||||| || ||||||||||||||| |||||||||| |||||||| |||||||||||||||||||| ||||| || |||||||| || || ||||||||||||||   |   |  || |||    |  || ||   |||  |  |  |    || |  |  | |||||  |  |      ||| ||                                             
GTTGACTGTGATGAGCACAAGAGTTTGTGCAGCAAATATGGAGTCTCTGGGTACCCAACAATTCAGTGGTTTCCAAAAGGATCTCTTGAACCCAAAAAgtgaggagatttttgtctattggaatataacattgacacaattttat-atcttaattcatagttatttacctgtcatttctcatttatcattccttttgcattcaatacttgattttggaaaattcccatag

upper sequence: LOC_Os01g23740.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA10G01820.1 (Glycine max), 5'ss of exon 4
GTTGATTGCGATGAGCACAAGAGTGTGTGCAGCAAGTATGGAGTTTCTGGGTACCCAACAATTCAATGGTTCCCCAAAGGATCCCTGGAGCCCAAAAAgtgaggctgcataacttttgttcaaatacttt-tgaaca----tctacaccaga---caaaatt-ttcatgatttatatcactacaaccatgtag-------------------------------------
||||| || |||||||| |||||| ||||||||||||||||||| |||||||||||||||||||| ||||| || |||||||| || ||  |||||||||||||    ||    | | ||  ||||     || | |    | || | |  |   || | || || |    | || ||||  | | |||                                         
GTTGACTGTGATGAGCATAAGAGTTTGTGCAGCAAGTATGGAGTCTCTGGGTACCCAACAATTCAGTGGTTTCCAAAAGGATCTCTTGAAGCCAAAAAgtgagg--agatcttctctattggaatataacatggagacgattttatatctcaattcatagttatttacctgtcatttcacatctatcattccttttgcattcaatatttgattttggaaaattcccatag

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|58598802|gb|CK009330.1|CK009330
EST:     GGGTACCCAACAATTCAATGGTTCCCCAAAGGATCCCTGGAGCCCAAAAA                         GTATGAAGGACAACGCAGTGCAGAGGCCCTTGCTGAATTTGTTAACACTGA
genomic: GGGTACCCAACAATTCAATGGTTCCCCAAAGGATCCCTGGAGCCCAAAAAgtgaggctgc ... aaccatgtagGTATGAAGGACAACGCAGTGCAGAGGCCCTTGCTGAATTTGTTAACACTGA