RNA editing

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

image

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, resulting in insertions (0, 1, 2, etc. base insertions) that lead to different mRNAs, producing different types of proteins.


Editing the genomic template would be disastrous because the change is irreversible. Therefore, this only occurs during transcription in negative-stranded RNA viruses; no editing occurs during replication.

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

(all links/actions below point to uniprot.org website)

129 entries grouped by strain (browse by keywords)

3 entries

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

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

3 entries

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

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

3 entries

Nipah virus reference strain

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

2 entries

Sendai virus (strain Hamamatsu) (SeV) reference strain

Select_allDeselect_all
V_SENDA Protein V
PHOSP_SENDA 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

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

3 entries

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

Select_allDeselect_all
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

Select_allDeselect_all
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

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

1 entry

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

PHOSP_MEASA Phosphoprotein (Protein P)

2 entries

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

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

2 entries

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

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

1 entry

Simian virus 41 (SV41) reference strain

V_SV41 Non-structural protein V

2 entries

Tupaia paramyxovirus (TPMV) reference strain

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

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)]
VSGP_EBORE Pre-small/secreted glycoprotein (pre-sGP) [Cleaved into: Small/secreted glycoprotein (sGP); ...
VSSGP_EBORE Super small secreted glycoprotein (SsGP)

3 entries

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

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

3 entries

Sendai virus (strain Fushimi) (SeV)

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

1 entry

Sendai virus (strain Hamamatsu) (SeV)

W_SENDA Protein W

3 entries

Sendai virus (strain Harris) (SeV)

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

2 entries

Sendai virus (strain Ohita) (SeV)

Select_allDeselect_all
V_SENDO Protein V
W_SENDO Protein W

3 entries

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

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

3 entries

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

Select_allDeselect_all
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); ...
VSSGP_EBOZ5 Super small secreted glycoprotein (SsGP)

2 entries

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

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

2 entries

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

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

2 entries

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

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

2 entries

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

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

2 entries

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

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

2 entries

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

Select_allDeselect_all
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)

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

2 entries

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

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

2 entries

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

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

2 entries

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

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

2 entries

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

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

2 entries

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

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

2 entries

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

Select_allDeselect_all
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)

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

2 entries

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

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

2 entries

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

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

2 entries

Human parainfluenza 2 virus (HPIV-2)

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

2 entries

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

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

2 entries

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

Select_allDeselect_all
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

1 entry

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

V_MEASA Non-structural protein V

2 entries

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

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

2 entries

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

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

2 entries

Mumps virus (strain Enders) (MuV)

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

2 entries

Mumps virus (strain SBL) (MuV)

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

2 entries

Mumps virus (strain SBL-1) (MuV)

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

2 entries

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

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

2 entries

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

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

2 entries

Phocine distemper virus (PDV)

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

2 entries

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

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

2 entries

Rinderpest virus (strain Kabete O) (RDV)

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

2 entries

Rinderpest virus (strain RBOK) (RDV)

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

2 entries

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

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

2 entries

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

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

2 entries

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

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

2 entries

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

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

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)