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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAATGGGATATCCTACAGTCCAGATCAGGTGCTGGTGAGCAATGGAGCTAAGCAATGCATTACGCAAGCCGTACTTGCCGTTTGCTCACCTGGTGATGAGgtttggcctctgtcttgctaatgctagttgctacgctgcgatgtattgaacatctatagtatctaggagaacaaaaacacaaatctcattagttccttta...

Basic information

species Oryza sativa
transcript LOC_Os01g65090.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g65090.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G400604_T01 (Zea mays), 5'ss of exon 4
AAATGGGATATCCTACAGTCCAGATCAGGTGCTGGTGAGCAATGGAGCTAAGCAATGCATTACGCAAGCCGTACTTGCCGTTTGCTCACCTGGTGATGAGgtttggcctctgtcttgcta-atgctagt-tgctacgctgcgatgtattgaacatctat-agtatctaggagaacaaaaacacaaatctcattagttccttta-
 || ||| ||||||||   |||||| |||||||||||||||||||||||||||||||||| || ||||| || ||||| |||||||||||||||||||||||     || | || ||||| |   ||||     |  || | |  |  |||   | ||| || |||||     |    | ||||| |  ||||  |||||    
GAACGGGGTATCCTACCTCCCAGATGAGGTGCTGGTGAGCAATGGAGCTAAGCAATGCATCACACAAGCTGTGCTTGCAGTTTGCTCACCTGGTGATGAGgtgaccactttttcctgctacaccgtagtgcatcaaacttctac-tgctgatgctatattagaatctatat--atgtgagcacaagtaccattt-ttcctaggt

upper sequence: LOC_Os01g65090.2 (Oryza sativa), 5'ss of exon 4
lower sequence: PP1S63_52V6.2 (Physcomitrella patens), 5'ss of exon 5
AAATGGGATATCCTACAGTCCAGATCAGGTGCTGGTGAGCAATGGAGCTAAGCAATGCATTACGCAAGCCGTACTTGCCGTTTGCTCACCTGGTGATGAGgt-ttggcctctgt-------cttgc--taatgctagttgctacgctgcgatgtattgaacat--ctatagtatctaggagaacaaa-----aacacaaatctcattagttccttta-------------------------------------------
||||||| | |||||||  || ||| || | || || || ||||| || |||||| |||||| |||||| ||||| ||||| || || |||||||||||||| ||   |||  |       |||||  |||   | |||   |  || || |  | |     |   |||  | ||||    ||   |      | |      || | |||  | |                                             
AAATGGGTTGTCCTACAAACCTGATGAGATTCTAGTTAGTAATGGCGCCAAGCAAAGCATTATGCAAGCTGTACTCGCCGTATGTTCCCCTGGTGATGAGgtattattctcactgatgatccttgcattaaacttggttagcat-cttcgctaaactagttgtgattattatgtctaatgtaatggactttggatatcttaatcgtcagtagcctcggagaacctcgggcattgaagttgtggctttcgttggactgtag

upper sequence: LOC_Os01g65090.2 (Oryza sativa), 5'ss of exon 4
lower sequence: EFJ32940 (Selaginella moellendorffii), 5'ss of exon 3
AAATGGGATATCCTACAGTCCAGATCAGGTGCTGGTGAGCAATGGAGCTAAGCAATGCATTACGCAAGCCGTACTTGCCGTTTGCTCACCTGGTGATGAGgtttggcctctgtcttgctaatgctagttgctacgctgcgatgtattgaacatctatagtatctaggagaacaaaaacacaaatctcattagttccttta
||||||| |  | ||||   | ||  || | || |||||||||||||| || ||||| || |||||||| || ||| |||||||||| |||||||||||||| ||         ||   |  | |  ||  |  |||  | |  |                                                       
AAATGGGCTCACGTACAAAACGGACGAGATCCTTGTGAGCAATGGAGCGAAACAATGTATCACGCAAGCTGTTCTTTCCGTTTGCTCGCCTGGTGATGAGgtatgttgagaactttagaatggttgttttatgagctttgtttcag------------------------------------------------------

upper sequence: LOC_Os01g65090.2 (Oryza sativa), 5'ss of exon 4
lower sequence: EFJ15807 (Selaginella moellendorffii), 5'ss of exon 3
AAATGGGATATCCTACAGTCCAGATCAGGTGCTGGTGAGCAATGGAGCTAAGCAATGCATTACGCAAGCCGTACTTGCCGTTTGCTCACCTGGTGATGAGgtttggcctctgtcttgctaatgctagttgctacgctgcgatgtattgaacatctatagtatctaggagaacaaaaacacaaatctcattagttccttta
||||||| |  | ||||   | ||  || | || |||||||||||||| || ||||| || |||||||| || ||| |||||||||| |||||||||||||| ||         ||   |  | |  ||  |  |||  | |  |                                                       
AAATGGGCTCACGTACAAAACGGACGAGATCCTTGTGAGCAATGGAGCGAAACAATGTATCACGCAAGCTGTTCTTTCCGTTTGCTCGCCTGGTGATGAGgtatgttgagaactttagaatggttgttttatgagctatgtttcag------------------------------------------------------

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|88396984|gb|CI578133.1|CI578133
EST:     AGCAATGCATTACGCAAGCCGTACTTGCCGTTTGCTCACCTGGTGATGAG                         GTTTTGATACCAGCACCATACTGGGTCAGTTATCCTGAGATGGCTACATTG
genomic: AGCAATGCATTACGCAAGCCGTACTTGCCGTTTGCTCACCTGGTGATGAGgtttggcctc ... tttcttttagGTTTTGATACCAGCACCATACTGGGTCAGTTATCCTGAGATGGCTACATTG
EST: gi|29645872|gb|CB650879.1|CB650879
EST:     AGCAATGCATTACGCAAGCCGTACTTGCCGTTTGCTCACCTGGTGATGAG                         GTTTTGATACCAGCACCATACTGGGTCAGTTATCCTGAGATGGCTACATTG
genomic: AGCAATGCATTACGCAAGCCGTACTTGCCGTTTGCTCACCTGGTGATGAGgtttggcctc ... tttcttttagGTTTTGATACCAGCACCATACTGGGTCAGTTATCCTGAGATGGCTACATTG
EST: gi|109974688|gb|DT807048.1|DT807048
EST:     TGCCGTTTGCTCACCTGGTGATGAG                         GTTTTGATACCAGCACCATACTGGGTCAGTTATCCTGAGATGGCTACATTG
genomic: TGCCGTTTGCTCACCTGGTGATGAGgtttggcctc ... tttcttttagGTTTTGATACCAGCACCATACTGGGTCAGTTATCCTGAGATGGCTACATTG