RNA editing

Note: The canonic definition of editing implies a post-transcriptional event, but in virology this term is also used for polymerase slippage.

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Some viruses encode genes that express multiple proteins by using overlapping open reading frames (ORFs) through a process known as RNA editing. In these viruses, the RNA polymerase reads the same template base more than once, creating insertions (0, 1, 2, etc, base insertions), leading to different mRNAs, thereby generating different types of proteins.


Editing of genomic template would be disastrous, therefore this happens only during transcription in negative stranded RNA viruses.

co-transcriptional editing, Negative stranded RNA virus

Genus Virus Major insertions Protein % Upstream sequence Position Reference
Respirovirus BPIV3 1 to 6 Gs P / V / D 33-33-33 AGGGAAUUAAAAAAGGG 707-723
Respirovirus hPIV3 1 to 6 Gs P / V / D 33-33-33 AAAGAAUUAAAAAAGGG 707-723
Henipavirus Nipah virus 1 G P / V / W 50-25-25 AGGGAAUUAAAAAAGGG 707-723
Respirovirus Sendai virus 1 G P / V / W 70-25-5 GACUCAACAAAAAAGGG 934-950
Morbilivirus Measles virus 1 G P / V / W 60-35-5 ACACCCAUUAAAAAGGG 676-692
Morbilivirus Phocine distemper virus 1 G P / V / W - GAACCCAUUAAAAAGGG 676-692
Morbilivirus Rinderpest virus 1 G P / V / W - AAACCCAUUAAAAAGGG 676-692
Morbilivirus Canine distemper virus 1 G P / V / W - GGAUCCAUUAAAAAGGG 675-691
Morbilivirus Dolphin morbillivirus 1 G P / V / W - AAAUCCAUUAAAAAGGG 676-692
Rubulavirus Simian virus 5 2 G V / P - CAUCGAUUUUAAGAGGG 474-490
Rubulavirus Mumps virus 2 G V / P - AACAGAAUUUAAGAGGG 447-463
Rubulavirus Parainfluenza virus type 4 2 G V / P - CAGGAUAUUUAAGAGGG 441-457 -
Rubulavirus La piedad, Michoacan virus 2 G V / P - AGCAGUUUUAAAAAGGG 486-502
Rubulavirus Parainfluenza virus type 2 2 G V / P - CCCCAACUUUAAGAGGG 470-486
Ebolavirus Ebolavirus 1 A sGP / GP / ssGP - GACCCUUUGAUUUUUUU 870-886


co-transcriptional editing, Positive stranded RNA virus

Genus Virus Major insertions Protein % Upstream sequence Position Reference
Potyvirus Turnip mosaic virus 1 A P3 / P3N-PIPO 98-2 CUCCAUUUUGGAAAAAA 2954
Potyvirus Plum Pox Virus 1 A P3 / P3N-PIPO 98.4-1.6 ......GUGGAAAAAA 2913
Potyvirus Sweet potato feathery mottle virus 1 A P1 / P1N-PISPO 88.2/11.8 .......AUGGAAAAAA 1389
Potyvirus Sweet potato feathery mottle virus +1 A or -1 A P3 / P3N-PIPO 98.2/1.2 or 0.6 UGAGCUUAUGGAAAAAA 3955


Matching UniProtKB/Swiss-Prot entries

129 entries grouped by strain (browse by keywords)

3 entries

Hendra virus (isolate Horse/Autralia/Hendra/1994) reference strain

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PHOSP_HENDH Phosphoprotein (Protein P)
W_HENDH Protein W
V_HENDH Non-structural protein V

3 entries

Newcastle disease virus (strain Chicken/United States/B1/48) (NDV) reference strain

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V_NDVB1 Protein V
W_NDVB1 Protein W
PHOSP_NDVB1 Phosphoprotein (Protein P)

3 entries

Nipah virus reference strain

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W_NIPAV Protein W
V_NIPAV Non-structural protein V
PHOSP_NIPAV Phosphoprotein (Protein P)

1 entry

Sendai virus (strain Ohita) (SeV) reference strain

PHOSP_SENDO Phosphoprotein (Protein P)

3 entries

Sendai virus (strain Z) (SeV) (Sendai virus (strain HVJ)) reference strain

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PHOSP_SENDZ Phosphoprotein (Protein P)
V_SENDZ Protein V
W_SENDZ Protein W

3 entries

Sudan ebolavirus (strain Human/Uganda/Gulu/2000) (SEBOV) (Sudan Ebola virus) reference strain

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VSGP_EBOSU Pre-small/secreted glycoprotein (pre-sGP) [Cleaved into: Small/secreted glycoprotein (sGP); ...
VGP_EBOSU Envelope glycoprotein (GP1,2) (GP) [Cleaved into: GP1; GP2; Shed GP (GP1,2-delta)]
VSSGP_EBOSU Super small secreted glycoprotein (SsGP)

3 entries

Zaire ebolavirus (strain Mayinga-76) (ZEBOV) (Zaire Ebola virus) reference strain

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VSGP_EBOZM Pre-small/secreted glycoprotein (pre-sGP) [Cleaved into: Small/secreted glycoprotein (sGP); ...
VGP_EBOZM Envelope glycoprotein (GP1,2) (GP) [Cleaved into: Shed GP (GP1,2-delta); GP1; GP2]
VSSGP_EBOZM Super small secreted glycoprotein (SsGP)

2 entries

Hepatitis delta virus genotype I (isolate D380) (HDV) reference strain

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SHDAG_HDVD3 Small delta antigen (S-HDAg) (p24)
LHDAG_HDVD3 Large delta antigen (L-HDAg) (p27)

2 entries

Human parainfluenza 2 virus (strain Toshiba) (HPIV-2) reference strain

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V_PI2HT Non-structural protein V
PHOSP_PI2HT Phosphoprotein (Protein P)

2 entries

Measles virus (strain Ichinose-B95a) (MeV) (Subacute sclerose panencephalitis virus) reference strain

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PHOSP_MEASC Phosphoprotein (Protein P)
V_MEASC Non-structural protein V

2 entries

Mumps virus (strain Miyahara vaccine) (MuV) reference strain

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PHOSP_MUMPM Phosphoprotein (Protein P)
V_MUMPM Non-structural protein V (Non-structural protein NS1)

2 entries

Parainfluenza virus 5 (strain W3) (PIV5) (Simian virus 5) reference strain

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PHOSP_PIV5 Phosphoprotein (Protein P)
V_PIV5 Non-structural protein V

1 entry

Simian virus 41 (SV41) reference strain

V_SV41 Non-structural protein V

2 entries

Tupaia paramyxovirus (TPMV) reference strain

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PHOSP_TPMV Phosphoprotein (Protein P)
V_TPMV Non-structural protein V

3 entries

Reston ebolavirus (strain Philippines-96) (REBOV) (Reston Ebola virus)

Select_allDeselect_all
VGP_EBORE Envelope glycoprotein (GP1,2) (GP) [Cleaved into: GP1; GP2; Shed GP (GP1,2-delta)]
VSSGP_EBORE Super small secreted glycoprotein (SsGP)
VSGP_EBORE Pre-small/secreted glycoprotein (pre-sGP) [Cleaved into: Small/secreted glycoprotein (sGP); ...

3 entries

Reston ebolavirus (strain Reston-89) (REBOV) (Reston Ebola virus)

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VGP_EBORR Envelope glycoprotein (GP1,2) (GP) [Cleaved into: GP1; GP2; Shed GP (GP1,2-delta)]
VSSGP_EBORR Super small secreted glycoprotein (SsGP)
VSGP_EBORR Pre-small/secreted glycoprotein (pre-sGP) [Cleaved into: Small/secreted glycoprotein (sGP); ...

3 entries

Sendai virus (strain Fushimi) (SeV)

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PHOSP_SENDF Phosphoprotein (Protein P)
V_SENDF Protein V
W_SENDF Protein W

3 entries

Sendai virus (strain Hamamatsu) (SeV)

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PHOSP_SENDA Phosphoprotein (Protein P)
W_SENDA Protein W
V_SENDA Protein V

3 entries

Sendai virus (strain Harris) (SeV)

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PHOSP_SENDH Phosphoprotein (Protein P)
V_SENDH Protein V
W_SENDH Protein W

2 entries

Sendai virus (strain Ohita) (SeV)

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V_SENDO Protein V
W_SENDO Protein W

3 entries

Zaire ebolavirus (strain Kikwit-95) (ZEBOV) (Zaire Ebola virus)

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VSSGP_EBOZ5 Super small secreted glycoprotein (SsGP)
VGP_EBOZ5 Envelope glycoprotein (GP1,2) (GP) [Cleaved into: GP1; GP2; Shed GP (GP1,2-delta)]
VSGP_EBOZ5 Pre-small/secreted glycoprotein (pre-sGP) [Cleaved into: Small/secreted glycoprotein (sGP); ...

2 entries

Hepatitis delta virus genotype I (isolate American) (HDV)

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SHDAG_HDVAM Small delta antigen (S-HDAg) (p24)
LHDAG_HDVAM Large delta antigen (L-HDAg) (p27)

2 entries

Hepatitis delta virus genotype I (isolate Italian) (HDV)

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SHDAG_HDVIT Small delta antigen (S-HDAg) (p24)
LHDAG_HDVIT Large delta antigen (L-HDAg) (p27)

2 entries

Hepatitis delta virus genotype I (isolate Japanese M-1) (HDV)

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SHDAG_HDVM1 Small delta antigen (S-HDAg) (p24)
LHDAG_HDVM1 Large delta antigen (L-HDAg) (p27)

2 entries

Hepatitis delta virus genotype I (isolate Japanese M-2) (HDV)

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SHDAG_HDVM2 Small delta antigen (S-HDAg) (p24)
LHDAG_HDVM2 Large delta antigen (L-HDAg) (p27)

2 entries

Hepatitis delta virus genotype I (isolate Japanese S-2) (HDV)

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SHDAG_HDVS2 Small delta antigen (S-HDAg) (p24)
LHDAG_HDVS2 Large delta antigen (L-HDAg) (p27)

2 entries

Hepatitis delta virus genotype I (isolate Lebanon-1) (HDV)

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LHDAG_HDVL1 Large delta antigen (L-HDAg) (p27)
SHDAG_HDVL1 Small delta antigen (S-HDAg) (p24)

2 entries

Hepatitis delta virus genotype I (isolate Nauru) (HDV)

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SHDAG_HDVNA Small delta antigen (S-HDAg) (p24)
LHDAG_HDVNA Large delta antigen (L-HDAg) (p27)

2 entries

Hepatitis delta virus genotype I (isolate US-2) (HDV)

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SHDAG_HDVU2 Small delta antigen (S-HDAg) (p24)
LHDAG_HDVU2 Large delta antigen (L-HDAg) (p27)

2 entries

Hepatitis delta virus genotype I (isolate Woodchuck) (HDV)

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SHDAG_HDVWO Small delta antigen (S-HDAg) (p24)
LHDAG_HDVWO Large delta antigen (L-HDAg) (p27)

2 entries

Hepatitis delta virus genotype II (isolate 7/18/83) (HDV)

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SHDAG_HDV83 Small delta antigen (S-HDAg) (p24)
LHDAG_HDV83 Large delta antigen (L-HDAg) (p27)

2 entries

Hepatitis delta virus genotype II (isolate Japanese S-1) (HDV)

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SHDAG_HDVS1 Small delta antigen (S-HDAg) (p24)
LHDAG_HDVS1 Large delta antigen (L-HDAg) (p27)

2 entries

Hepatitis delta virus genotype II (isolate TW2476) (HDV)

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SHDAG_HDVTW Small delta antigen (S-HDAg) (p24)
LHDAG_HDVTW Large delta antigen (L-HDAg) (p27)

2 entries

Hepatitis delta virus genotype III (isolate Peru-1) (HDV)

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LHDAG_HDVP1 Large delta antigen (L-HDAg) (p27)
SHDAG_HDVP1 Small delta antigen (S-HDAg) (p24)

2 entries

Hepatitis delta virus genotype III (isolate VnzD8349) (HDV)

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SHDAG_HDVV2 Small delta antigen (S-HDAg) (p24)
LHDAG_HDVV2 Large delta antigen (L-HDAg) (p27)

2 entries

Hepatitis delta virus genotype III (isolate VnzD8375) (HDV)

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SHDAG_HDVV3 Small delta antigen (S-HDAg) (p24)
LHDAG_HDVV3 Large delta antigen (L-HDAg) (p27)

2 entries

Hepatitis delta virus genotype III (isolate VnzD8624) (HDV)

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SHDAG_HDVV1 Small delta antigen (S-HDAg) (p24)
LHDAG_HDVV1 Large delta antigen (L-HDAg) (p27)

2 entries

Human parainfluenza 2 virus (HPIV-2)

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PHOSP_PI2H Phosphoprotein (Protein P)
V_PI2H Non-structural protein V

2 entries

Human parainfluenza 4a virus (strain Toshiba) (HPIV-4a)

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PHOSP_PI4HA Phosphoprotein (Protein P)
V_PI4HA Non-structural protein V

2 entries

Human parainfluenza 4b virus (strain 68-333) (HPIV-4b)

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PHOSP_PI4HB Phosphoprotein (Protein P)
V_PI4HB Non-structural protein V

2 entries

Measles virus (strain Edmonston) (MeV) (Subacute sclerose panencephalitis virus)

Select_allDeselect_all
PHOSP_MEASE Phosphoprotein (Protein P)
V_MEASE Non-structural protein V

2 entries

Measles virus (strain Edmonston-AIK-C vaccine) (MeV) (Subacute sclerose panencephalitis virus)

Select_allDeselect_all
V_MEASA Non-structural protein V
PHOSP_MEASA Phosphoprotein (Protein P)

2 entries

Measles virus (strain IP-3-Ca) (MeV) (Subacute sclerose panencephalitis virus)

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PHOSP_MEASI Phosphoprotein (Protein P)
V_MEASI Non-structural protein V

2 entries

Measles virus (strain Yamagata-1) (MeV) (Subacute sclerose panencephalitis virus)

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PHOSP_MEASY Phosphoprotein (Protein P)
V_MEASY Non-structural protein V

2 entries

Mumps virus (strain Enders) (MuV)

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PHOSP_MUMPE Phosphoprotein (Protein P)
V_MUMPE Non-structural protein V (Non-structural protein NS1)

2 entries

Mumps virus (strain SBL) (MuV)

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PHOSP_MUMPS Phosphoprotein (Protein P)
V_MUMPS Non-structural protein V (Non-structural protein NS1)

2 entries

Mumps virus (strain SBL-1) (MuV)

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V_MUMP1 Non-structural protein V (Non-structural protein NS1)
PHOSP_MUMP1 Phosphoprotein (Protein P)

2 entries

Newcastle disease virus (strain Ulster/2C) (NDV)

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PHOSP_NDVU2 Phosphoprotein (Protein P)
V_NDVU2 Non-structural protein V

2 entries

Phocine distemper virus (PDV)

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V_PHODV Non-structural protein V
PHOSP_PHODV Phosphoprotein (Protein P)

2 entries

Reston ebolavirus (strain Siena/Philippine-92) (REBOV) (Reston Ebola virus)

Select_allDeselect_all
VSGP_EBORS Pre-small/secreted glycoprotein (pre-sGP) [Cleaved into: Small/secreted glycoprotein (sGP); ...
VGP_EBORS Envelope glycoprotein (GP1,2) (GP) [Cleaved into: GP1; GP2; Shed GP (GP1,2-delta)]

2 entries

Rinderpest virus (strain Kabete O) (RDV)

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PHOSP_RINDK Phosphoprotein (Protein P)
V_RINDK Non-structural protein V

2 entries

Rinderpest virus (strain RBOK) (RDV)

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PHOSP_RINDR Phosphoprotein (Protein P)
V_RINDR Non-structural protein V

1 entry

Simian virus 41 (SV41)

PHOSP_SV41 Phosphoprotein (Protein P)

2 entries

Sudan ebolavirus (strain Boniface-76) (SEBOV) (Sudan Ebola virus)

Select_allDeselect_all
VSGP_EBOSB Pre-small/secreted glycoprotein (pre-sGP) [Cleaved into: Small/secreted glycoprotein (sGP); ...
VGP_EBOSB Envelope glycoprotein (GP1,2) (GP) [Cleaved into: GP1; GP2; Shed GP (GP1,2-delta)]

2 entries

Sudan ebolavirus (strain Maleo-79) (SEBOV) (Sudan Ebola virus)

Select_allDeselect_all
VSGP_EBOSM Pre-small/secreted glycoprotein (pre-sGP) [Cleaved into: Small/secreted glycoprotein (sGP); ...
VGP_EBOSM Envelope glycoprotein (GP1,2) (GP) [Cleaved into: GP1; GP2; Shed GP (GP1,2-delta)]

2 entries

Tai Forest ebolavirus (strain Cote d'Ivoire-94) (TAFV) (Cote d'Ivoire Ebola virus)

Select_allDeselect_all
VSGP_TAFVC Pre-small/secreted glycoprotein (pre-sGP) [Cleaved into: Small/secreted glycoprotein (sGP); ...
VGP_TAFVC Envelope glycoprotein (GP1,2) (GP) [Cleaved into: GP1; GP2; GP2-delta]

2 entries

Zaire ebolavirus (strain Eckron-76) (ZEBOV) (Zaire Ebola virus)

Select_allDeselect_all
VSGP_EBOEC Pre-small/secreted glycoprotein (pre-sGP) [Cleaved into: Small/secreted glycoprotein (sGP); ...
VGP_EBOEC Envelope glycoprotein (GP1,2) (GP) [Cleaved into: GP1; GP2; Shed GP (GP1,2-delta)]

2 entries

Zaire ebolavirus (strain Gabon-94) (ZEBOV) (Zaire Ebola virus)

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VSGP_EBOG4 Pre-small/secreted glycoprotein (pre-sGP) [Cleaved into: Small/secreted glycoprotein (sGP); ...
VGP_EBOG4 Envelope glycoprotein (GP1,2) (GP) [Cleaved into: GP1; GP2; Shed GP (GP1,2-delta)]

1 entry

Bovine parainfluenza 3 virus (BPIV-3)

PHOSP_PI3B Phosphoprotein (Protein P)

1 entry

Canine distemper virus (strain Onderstepoort) (CDV)

PHOSP_CDVO Phosphoprotein (Protein P)

1 entry

Human parainfluenza 3 virus (strain Wash/47885/57) (HPIV-3) (Human parainfluenza 3 virus (strain NIH 47885))

PHOSP_PI3H4 Phosphoprotein (Protein P)

1 entry

Sendai virus (strain 6/94) (SeV)

PHOSP_SEND6 Phosphoprotein (Protein P)