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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGCAAGGCCCAAAGGGCGGTGAACCGAGTCCATATCTTACTGAGCTGCTAAGGTTGGAGGAAGTTGCTAAGCAGCAGGGTTTAGGTCGTTGGAGCAAGgttagcaaatctttttgtttctgccccctccccctttttctttgtactgcaagagatgaatgctttattgtttgcttttttatgcatgttctttttaaactttcag

Basic information

species Oryza sativa
transcript LOC_Os02g32350.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g32350.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G136296_T02 (Zea mays), 5'ss of exon 5
GGAGCAAGGCCCAAAGGGCGGTGAACCGAGTCCATATCTTACTGAGCTGCTAAGGTTGGAGGAAGTTGCTAAGCAGCAGGGTTTAGGTCGTTGGAGCAAGgttagcaaatctttttgtttctgccccctccccctttttctttgtactgcaagagatgaatgctttattgtttgcttttttat-gcatgttctttttaaactttcag
|||||||||| | ||||| || ||||  |  ||  | |||  |||| || | ||||| ||||||||||| ||||| |||||| | |||||||||||||||||| ||||   ||||  | |   ||  ||        |  |||||| || | |||||  ||||||  || ||   |||  | | |  || |  || |  || | |||
GGAGCAAGGCTCCAAGGGTGGCGAACAAAACCCGCACCTTGGTGAGTTGTTGAGGTTAGAGGAAGTTGCCAAGCAACAGGGTGTTGGTCGTTGGAGCAAGgttggcaa--tttttcatcttgaccaact--------tattttgtattgaatgagat--atgctt--ttcttgattttgctgttgtgtgcttcttatctacatccag

upper sequence: LOC_Os02g32350.2 (Oryza sativa), 5'ss of exon 4
lower sequence: AC207890.3_FGT002 (Zea mays), 5'ss of exon 4
GGAGCAAGGCCCAAAGGGCGGTGAACCGAGTCCATATCTTACTGAGCTGCTAAGGTTGGAGGAAGTTGCTAAGCAGCAGGGTTTAGGTCGTTGGAGCAAGgttagcaaatctttttgtttctgccccctccccctttttctttgtactgcaagagatgaatgctttattgtttgcttttttatgcatgttctttttaaactttcag
|||||||||||||||||| || ||||  | | | || ||| | |||||| | ||||||||||||||||| || || |||||| | |||||||||||||||||||||||   ||||  | |||      |  ||  ||   |||| | |||| ||||||     ||||||| ||    | | ||  |||||| || || || |||||
GGAGCAAGGCCCAAAGGGGGGCGAACAAAATTCGTACCTTGCCGAGCTGTTGAGGTTGGAGGAAGTTGCCAAACAACAGGGTGTTGGTCGTTGGAGCAAGgttagcaa--tttttcatctct----tgtgaccaattcattttgcattgcatgagatgtgc-ttttattgattttgctgtcat--atgttccttatatacattcag
















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|29622118|gb|CB627129.1|CB627129
EST:     TAAGGTTGGAGGAAGTTGCTAAGCAGCAGGGTTTAGGTCGTTGGAGCAAG                         GAACCTGGTGCTGCTGAAGAATCAATAAGAGATCTTCCACCATCAGCAATT
genomic: TAAGGTTGGAGGAAGTTGCTAAGCAGCAGGGTTTAGGTCGTTGGAGCAAGgttagcaaat ... aaactttcagGAACCTGGTGCTGCTGAAGAATCAATAAGAGATCTTCCACCATCAGCAATT
EST: gi|29674463|gb|CB670738.1|CB670738
EST:     GGAGGAAGTTGCTAACCATCAGGGTTTAGGTCGTTGGAGCAAG                         GAACCTGGTGCTGCTGAAGAATCAATAAGAGATCTTCCACCATCAGCAATT
genomic: GGAGGAAGTTGCTAAGCAGCAGGGTTTAGGTCGTTGGAGCAAGgttagcaaat ... aaactttcagGAACCTGGTGCTGCTGAAGAATCAATAAGAGATCTTCCACCATCAGCAATT
EST: gi|29687922|gb|CB684197.1|CB684197
EST:     TAAGGTTGGAGGAAGTTGCTAAGCAGCAGGGTTTAGGTCGTTGGAGCAAG                         GAACCTGGTGCTGCTGAAGAATCAATAAGAGATCTTCCACCATCAGCAATT
genomic: TAAGGTTGGAGGAAGTTGCTAAGCAGCAGGGTTTAGGTCGTTGGAGCAAGgttagcaaat ... aaactttcagGAACCTGGTGCTGCTGAAGAATCAATAAGAGATCTTCCACCATCAGCAATT
EST: gi|58670976|gb|CK059662.1|CK059662
EST:     TAAGGTTGGAGGAAGTTGCTAAGCAGCAGGGTTTAGGTCGTTGGAGCAAG                         GAACCTGGTGCTGCTGAAGAATCAATAAGAGATCTTCCACCATCAGCAATT
genomic: TAAGGTTGGAGGAAGTTGCTAAGCAGCAGGGTTTAGGTCGTTGGAGCAAGgttagcaaat ... aaactttcagGAACCTGGTGCTGCTGAAGAATCAATAAGAGATCTTCCACCATCAGCAATT
EST: gi|29622580|gb|CB627591.1|CB627591
EST:     TAAGGTTGGAGGAAGTTGCTAAGCAGCAGGGTTTAGGTCGTTGGAGCAAG                         GAACCTGGTGCTGCTGAAGAATCAATAAGAGATCTTCCACCATCAGCAATT
genomic: TAAGGTTGGAGGAAGTTGCTAAGCAGCAGGGTTTAGGTCGTTGGAGCAAGgttagcaaat ... aaactttcagGAACCTGGTGCTGCTGAAGAATCAATAAGAGATCTTCCACCATCAGCAATT
EST: gi|6012905|gb|AU078722.1|AU078722
EST:     TAANGTTGGAGGAAGTTGCTAAGCAGCAGGGTTTAGGTCGTTGGAGCAAG                         GANC-TGGTGCTGCTGAAGAATCAATAAGAGATCTTCCACCATCAGCAAAT
genomic: TAAGGTTGGAGGAAGTTGCTAAGCAGCAGGGTTTAGGTCGTTGGAGCAAGgttagcaaat ... aaactttcagGAACCTGGTGCTGCTGAAGAATCAATAAGAGATCTTCCACCATCAGCAA-T
EST: gi|29627292|gb|CB632303.1|CB632303
EST:     TAAGGTTGGAGGAAGTTGCTAAGCAGCAGGGTTTAGGTCGTTGGAGCAAG                         GAACCTGGTGCTGCTGAAGAATCAATAAGAGATCTTCCACCATCAGCAATT
genomic: TAAGGTTGGAGGAAGTTGCTAAGCAGCAGGGTTTAGGTCGTTGGAGCAAGgttagcaaat ... aaactttcagGAACCTGGTGCTGCTGAAGAATCAATAAGAGATCTTCCACCATCAGCAATT
EST: gi|117240306|gb|CT842733.1|CT842733
EST:     TAAGGTTGGAGGAAGTTGCTAAGCAGCAGGGTTTAGGTCGTTGGAGCAAG                         GAACCTGGTGCTGCTGAAGAATCAATAAGAGATCTTCCACCATCAGCAATT
genomic: TAAGGTTGGAGGAAGTTGCTAAGCAGCAGGGTTTAGGTCGTTGGAGCAAGgttagcaaat ... aaactttcagGAACCTGGTGCTGCTGAAGAATCAATAAGAGATCTTCCACCATCAGCAATT

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGCAAGGCCCAAAGGGCGGTGAACCGAGTCCATATCTTACTGAGCTGCTAAGGTTGGAGGAAGTTGCTAAGCAGCAGGGTTTAGGTCGTTGGAGCAAGgttagcaaatctttttgtttctgccccctccccctttttctttgtactgcaagagatgaatgctttattgtttgcttttttatgcatgttctttttaaactttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG