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Vaccina Orthologs

Overview

This table provides our list of all transcribed genes coded for by Vaccinia virus strain Western Reserve (VACV-WR; NC_006998) along with their corresponding orthologs in Vaccinia virus strain Copenhagen (VACV-COP; M35027). This list is based on our assessment of ORFs that have the potential to be transcribed, and has been determined based on a number of parameters including conservation across Orthopoxvirus species - especially Cowpox (CPXV-GRI; X94355) - and on the presence of characteristic promoter sites in the region upstream of the putative translation initiation codon.

All genes annotated in the original GenBank records for VACV-WR & VACV-COP are listed, except the VACV-COP genes annotated as "X_ORF_X". These "X_ORF_X" genes are predicted not to be expressed.

We welcome your feedback on this table. If you can verify or refute any of the predictions, we want to know. Additionally, if you can add to the list of literature references, we will gladly update the chart.

To download a copy of this table in Excel format, please click here.

Key

VACWR###
pseudogene
no ortholog
  • "VACWR###": Vaccinia WR genes listed in the original GenBank record, but predicted not to be expressed
  • "pseudogene": Fragmented genes that have lost their promoter sequences and are therefore predicted not to be expressed.
  • "no ortholog": There is no remnant of this gene in the nucleotide sequence of the indicated strain.

Additionally, if neither the VACV-WR nor the VACV-COP orthologs is transcribed, then the Predicted and Description columns have been shaded gray as well.

Temporal Expression
  • Predicted: Temporal expression based on our prediction of early and late transcriptional promoters. No prediction is made for intermediate transcriptional promoters.
  • Known: Expression based on published experimental results.
  • References: Citations supporting the data listed in "Known".
ITR Paralogs
 Diploid copy of genes that are duplicated at opposite ends of the genome within the Inverted Terminal Repeats (ITR). The locations of the ITRs are as follows:
SpeciesITR Length3' ITR5' ITR
VACV-WR101851..10186184517..194711
M3502711966102..12068179671..191637

Ortholog Chart

Notes Genome ITR Paralogs Temporal Expression Description
WR COP WR COP Predicted Known References
  VACWR001 C23L VACWR218 B29R early/late early/late Venkatesan 1982 (E,L) [ITR] chemokine-binding protein; host defense modulator
1 VACWR002 pseudogene VACWR217 pseudogene pseudogene     [ITR] gene fragment, TNF-alpha-receptor-like; host defense modulator
  VACWR003 no ortholog VACWR216 no ortholog pseudogene     [ITR] unknown
1 VACWR004 C22L VACWR215 B28R late     [ITR] gene fragment, TNF-alpha-receptor-like; host defense modulator
2 VACWR005 pseudogene VACWR214 pseudogene pseudogene     [ITR] gene fragment, ankyrin-like
2 VACWR006 C21L VACWR213 B27R pseudogene     [ITR] gene fragment, ankyrin-like
2 VACWR007 no ortholog VACWR212 no ortholog pseudogene     [ITR] unknown
2 pseudogene C20L pseudogene B26R pseudogene     putative C20L
2 VACWR008 C19L VACWR211 B25R early     [ITR] gene fragment, ankyrin-like
3 no ortholog C18L no ortholog B24R pseudogene     putative C18L; host range protein
3 no ortholog C17L no ortholog B23R       putative C17L; host range polypeptide; 5` fragment of CPXV-GRI:D4L, including predicted upstream promoter
  no ortholog C16L no ortholog B22R early/late     putative C16L
  no ortholog C15L no ortholog B21R       putative C15L
  VACWR009 C11R VACWR210 no ortholog early/late early Cooper 1981 (E) [ITR] secreted epidermal growth factor-like; binds EGF receptor
  VACWR010 C10L VACWR209 no ortholog early early Cooper 1981 (E) [ITR] unknown
4 VACWR011 no ortholog VACWR208 no ortholog early/late early Cooper 1981 (E) [ITR] gene fragment, zinc finger-like; apoptosis; host defense modulator
4 VACWR012 no ortholog VACWR207 no ortholog pseudogene     [ITR] gene fragment, zinc finger-like; apoptosis; host defense modulator
  VACWR013 no ortholog    early/late early Cooper 1981 (E) interleukin-18-binding protein; host defense modulator; absent from VACCP
5 VACWR014 no ortholog    pseudogene     gene fragment, ankyrin-like, 77kDa cowpox host-range
5 VACWR015 no ortholog    pseudogene     gene fragment, ankyrin-like 77kDa cowpox host-range
5 VACWR016 no ortholog    pseudogene     gene fragment, ankyrin-like 77kDa cowpox host-range
5 VACWR017 no ortholog    early/late     gene fragment, ankyrin-like 77kDa cowpox host-range
  VACWR018 no ortholog    early/late early Cooper 1981 (E) unknown
  VACWR019 C9L    early early Cooper 1981 (E) ankyrin-like
  VACWR020 C8L    late late   unknown
  VACWR021 C7L    early/late     host-range; possible host defense modulator
  VACWR022 C6L    early/late     unknown
  VACWR023 C5L    early     unknown
  VACWR024 C4L    early/late     unknown
  VACWR025 C3L    late     secreted complement binding [C3b/C4b]; host defense modulator
  VACWR026 C2L    early/late     kelch-like
  VACWR027 C1L    early/late     unknown
  VACWR028 N1L    early/late early/late Kotwal 1989 (E,L) virokine; host defense modulator
  VACWR029 N2L    early/late early Morgan 1984 (E) alpha-amanitin target
  VACWR030 M1L    early/late early Morgan 1984 (E) ankyrin-like
  VACWR031 M2L    early/late early Xiang 1998 (E) unknown
  VACWR032 K1L    early/late early Morgan 1984 (E) K1L is a host range gene needed for viral replication in rabbit cells and is capable of complementing for C7L function in human cells.
  VACWR033 K2L    early/late early Turner 1995 (E) serine protease inhibitor-like; SPI-3, prevents syncytia; host range determinant; host defense modulator
  VACWR034 K3L    early/late early Morgan 1984 (E) interferon resistance; host defense modulator
  VACWR035 K4L    early/late     phospholipase-D-like
6 VACWR036 pseudogene    pseudogene     gene fragment, putative monoglyceride lipase
6 VACWR037 K5L    pseudogene     gene fragment, putative monoglyceride lipase
6 VACWR038 K6L    early/late     gene fragment, putative monoglyceride lipase
  VACWR039 K7R    early/late     unknown
  VACWR040 F1L    early early Roseman 1990 (E) unknown
  VACWR041 F2L    early/late early Roseman 1990 (E) dUTPase, expressed early, non-essential in tissue culture, involved in nucleotide metabolism
  VACWR042 F3L    late late   kelch-like
  VACWR043 F4L    early early Roseman 1990 (E) ribonucleotide reductase small subunit
  VACWR044 F5L    early/late early Roseman 1990 (E) putative F5L; putative major membrane protein
  VACWR045 F6L    early/late early Roseman 1990 (E) unknown
  VACWR046 F7L    early early Roseman 1990 (E) putative F7L
  VACWR047 F8L    early/late late   protein with iActA-like proline repeats; not required for actin tails formation
  VACWR048 F9L    early/late late   S-S bond formation pathway; thiol substrate
  VACWR049 F10L    late late   ser/thr kinase
  VACWR050 F11L    early     unknown
  VACWR051 F12L    early/late early Zhang 2000 (E) involved in plaque and EEV formation; on IEV, not CEV, IV or IMV
  VACWR052 F13L    late late   palmytilated EEV membrane protein; phospholipase motif, required for IEV formation
  VACWR053 F14L    early/late     unknown
  VACWR053.5 F14.5L    early/late      
  VACWR054 F15L    early/late     unknown
  VACWR055 F16L    early/late     unknown
  VACWR056 F17R    early/late late   putative DNA-binding phosphoprotein in virus core
  VACWR057 E1L    late     poly-A polymerase catalytic subunit VP55
  VACWR058 E2L    early/late     unknown
  VACWR059 E3L    early/late early Murcia-Nicolas 1999 (E) double-stranded RNA binding protein; inhibits antiviral activities of interferon; host-range determinant; host defense modulator
  VACWR060 E4L    early/late early Murcia-Nicolas 1999 (E) DNA-dependent RNA polymerase subunit rpo30, intermediate-gene transcription factor VITF1; TFIIS-like
  VACWR061 E5R    early/late early Murcia-Nicolas 1999 (E) abundant component of virosome
  VACWR062 E6R    early/late     unknown
  VACWR063 E7R    early/late     soluble, myristylprotein has N-myristyltransferase target MGxxxS/T/A
  VACWR064 E8R    early/late early/late Doglio 2002 (E,L) membrane protein may help wrap virosome; associates with IV/IMV and cores; F10L kinase substrate
  VACWR065 E9L    early/late early Earl 1986 (E) DNA polymerase
  VACWR066 E10R    early/late late   S-S bond formation pathway; sulfhydryl oxidase, substrates L1R/F9L
  VACWR067 E11L    late late   virion core protein
  VACWR068 O1L    early/late     unknown
  VACWR069 O2L    late late   nonessential glutaredoxin; not part of E10R-G4L S-S bond formation pathway
  VACWR069.5 266    late     hypothetical protein
  VACWR070 I1L    late late   DNA-binding core protein
  VACWR071 I2L    late late   unknown
  VACWR072 I3L    early/late early/intermediate/late Schmitt 1988 (E,L) ,  Vos 1988(I) ssDNA-binding phosphoprotein
  VACWR073 I4L    early/late early Schmitt 1988 (E) ribonucleotide reductase large subunit
  VACWR074 I5L    early/late late   Minor membrane component of the virion
  VACWR075 I6L    early/late     unknown
  VACWR076 I7L    late late   viral core cysteine proteinase
  VACWR077 I8R    late early/intermediate Pacha 1990 (E) ,  Vos 1988(I) An encapsidated 72kDa protein, with NTPase and RNA helicase activity. Essential for early transcription.
  VACWR078 G1L    early/late late   insulin metalloproteinase-like has ENE and HLLEH inverse of HXXEX sites
  VACWR079 G3L    late late   unknown
  VACWR080 G2R    early/late     late transcription elongation factor
  VACWR081 G4L    late late   S-S bond formation pathway; thioredoxin-like
  VACWR082 G5R    early early da Fonseca 2004 (E) unknown
  VACWR083 G5.5R    early early Amegadzie 1992 (E) DNA-dependent RNA polymerase subunit rpo7
  VACWR084 G6R    late     unknown
  VACWR085 G7L    late late   Vaccinia core protein component of the seven protein complex required for virosomal uptake by viral crescents
  VACWR086 G8R    late intermediate Keck 1990(I) late gene transcription VLTF-1
  VACWR087 G9R    late late   myristylprotein
  VACWR088 L1R    late late   IMV membrane protein target of neutralizing antibody; S-S bond formation pathway thiol substrate; myristylprotein
  VACWR089 L2R    early/late     unknown
  VACWR090 L3L    late     unknown
  VACWR091 L4R    late late   ssDNA/ssRNA binding protein involved in early mRNA regulation
  VACWR092 L5R    late late   Component of the poxvirus multiprotein entry-fusion complex
  VACWR093 J1R    late late   Vaccinia core protein component of the seven protein complex required for virosomal uptake by viral crescents
  VACWR094 J2R    early early Weir 1987 (E) thymidine kinase
  VACWR095 J3R    early/late early Plucienniczak 1985 (E) multifunctional poly-A polymerase subunit, cap methyltransferase, and transcription elongation factor
  VACWR096 J4R    early early Hooda-Dhingra 1989 (E) DNA-dependent RNA polymerase subunit rpo22
  VACWR097 J5L    early/late     late 16kDa putative membrane protein
  VACWR098 J6R    early early/late Broyles 1986 (E,L) DNA-dependent RNA polymerase subunit rpo147
  VACWR099 H1L    late late   tyr/ser protein phosphatase
  VACWR100 H2R    late late   Component of the poxvirus multiprotein entry-fusion complex
  VACWR101 H3L    early/late late   IMV heparin binding surface protein involved in IMV maturation
  VACWR102 H4L    early/late late   RAP94; tightly associated with DNA-dependent RNA polymerase, aids early-stage transcription preinitiation and termination
  VACWR103 H5R    early/late early/late Rosel 1986 (E,L) Morphogenesis-related, substrate of B1R kinase, late gene transcription factor VLTF-4
  VACWR104 H6R    late     topoisomerase type IB
  VACWR105 H7R    late late   unknown
  VACWR106 D1R    early/late early Lee-Chen 1988a (E) large subunit of mRNA capping enzyme; transcription termination factor VTF
  VACWR107 D2L    late late   virion core protein
  VACWR108 D3R    late late   virion core protein
  VACWR109 D4R    early early Lee-Chen 1988a (E) essential, expressed early. Interacts with A20 (component of the DNA polymerase processivity factor).
  VACWR110 D5R    early/late early/late Lee-Chen 1988a (E) ,  Roseman 1987(L) A DNA-