Leaky scanning

Leaky scanning is a phenomenon in which a weak initiation codon triplet on mRNA is sometimes skipped by ribosome in translation initiation. The 40S ribosomal subunit continues scanning to further initiation codon. The weak initiation codon can be an ACG, or an ATG in a weak Kozak consensus context.
This way a mRNA can encode for several different proteins if the AUG are not in frame, or for proteins with different N-terminus if the AUG are in the same frame.
Upstream ORFs (uORF) are small coding regions preceding an ORF, The latter must be translated by leaky scanning or termination-reinitiation. Many eukaryotic genes encode for uORF to downregulate the translation/mRNA ratio of a gene. These genes are described in the uORF database
The leaky scanning is favored in case of cellular stress in which EIF2alpha is phosphorylated , like in case of dsRNA/PKR activation. Many eukaryotic stress response genes are under the transcription control of a uORF. Viruses may use this regulatory system for their own purpose.


Family Host Genus Virus Products RefSeq Ref.
Bunyaviridae Orthobunyavirus Bunyamwera virus NS/NSs NC_001927
Hantavirus Andes virus NS/NSs NC_003466
Phlebovirus Rift valley fever virus NSm-Gn, NSm, NSm' NC_014396
Caliciviridae Norovirus Murine norovirus ORF4/CP NC_008311
Hepadnaviridae Orthohepadnavirus Hepatitis B virus HBeAg/C/P NC_003977
M/S? NC_003977
Hepeviridae Hepevirus Hepatitis E virus ORF3/CP NC_001434
Herpesviridae Simplexvirus Human herpesvirus 1 uORF/UL30 NC_001806
Cytomegalovirus Human cytomegalovirus uORF2/gp74 NC_006273
Rhadinovirus Kaposi’s sarcoma-associated herpesvirus uORF1+ORF35/
uORF28+ORF36
NC_009333
Orthomyxoviridae Influenza virus A A/Puerto Rico/8/34 PB1/PN1-F2/N40 NC_002021
Influenza virus B B/Lee/1940 NB/NA NC_002209
Papillomaviridae Alphapapillomavirus HPV16 E6/E7 NC_001526
Polyomaviridae Polyomavirus SV40 Agno/VP2/VP3? NC_001669
Paramyxoviridae Aquaparamyxovirus Sendai virus P/C EU156171
Respirovirus Sendai virus C'/P/C/Y1/Y2 NC_001552
Morbilivirus Measles virus P/C NC_001498
Henipavirus Hendra virus P/C NC_001906
Reoviridae Rotavirus Rotavirus A VP7.1/VP7.2, NC_011503
NSP5/NSP6 NC_011505
Orbivirus Bluetongue virus Vp6a, NS4 NC_006008
NS3a NC_006015
Orthoreovirus Mammalian orthoreovirus Sigma1/sigma1s NC_004277
MuNS/MuNSC NC_004281
Coronaviridae Betacoronavirus Bovine coronavirus N/I NC_003045
Arteriviridae Arterivirus Equine arteritis virus E/GP2 NC_002532
ORF5a/GP5 NC_002532
Alphatetraviridae Omegatetravirus Helicoverpa armigera stunt virus P17/CP NC_004060
Baculoviridae Alphabaculovirus Autographa californica multiple nucleopolyhedrovirus uORF/gp64 NC_004323
Alphaflexviridae Potexvirus Potato virus X TGB2/TGB3 NC_011620
Caulimoviridae Tungrovirus Rice tungro bacilliform virus ORF1/ORF2/ORF3 NC_001914
Luteoviridae Luteovirus Barley yellow dwarf virus P3a/CP/MP NC_004750
Polerovirus Potato leafroll virus P0/P1 NC_001747
P3a/CP/MP NC_001747
Enamovirus Pea enation mosaic virus P0/P1 NC_003629
Tombusviridae Aureusvirus Pothos latent virus MP/P14 NC_000939
Machlomovirus Maize chlorotic mottle virus ORF1/ORF2 NC_003627
Unassigned Sobemovirus Southern bean mosaic virus MP/X/ORF2A NC_004060
Tymoviridae Tymovirus Turnip yellow mosaic virus MVP/ORF1 NC_004063
Virgaviridae Hordeivirus Barley stripe mosaic virus TGB2/TGB3 NC_003481
Pecluvirus Peanut clump virus CP/P39 NC_003668
TGB2/TGB3