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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-independent NTPase essential for DNA replication. There are 4 ts-mutants. D5 has also been implicated in recombination.
  VACWR111 D6R    late late   70kDa small subunit of early gene transcription factor VETF
  VACWR112 D7R    early early Lee-Chen 1988a (E) DNA-dependent RNA polymerase subunit rpo18
  VACWR113 D8L    late     IMV membrane protein binds cell surface chondroitin; may effect viral entry
  VACWR114 D9R    early early Lee-Chen 1988a (E) contains mutT-like motif of NTP-phosphohydrolase for DNA repair
  VACWR115 D10R    late late   contains mutT-like motif of NTP-phosphohydrolase for DNA repair
  VACWR116 D11L    late late   ATPase, nucleoside triphosphate phosphohydrolase-I, NPH-I; transcription elongation, termination, release factor
  VACWR117 D12L    early/late early Lee-Chen 1988a (E) small subunit of mRNA capping enzyme; transcription termination factor VTF
  VACWR118 D13L    late late   rifampicin target associates with inner surface immature virus membrane
  VACWR119 A1L    early/late intermediate Keck 1990(I) late gene transcription factor VLTF-2
  VACWR120 A2L    late intermediate Keck 1990(I) late gene transcription factor VLTF-3
  VACWR121 A2.5L    late late   S-S bond formation pathway; CxxxC links SH-oxidase E10R and thioredoxin G4L
  VACWR122 A3L    late late   p4b precursor of core protein 4b
  VACWR123 A4L    late late   39kDa core protein complexes with core protein p4a/4a
  VACWR124 A5R    early/late early Ahn 1992 (E) DNA-dependent RNA polymerase subunit rpo19
  VACWR125 A6L    early/late     unknown
  VACWR126 A7L    late late   82kDa large subunit of early gene transcription factor VETF
  VACWR127 A8R    early early Sanz 1999 (E) 32kDa small subunit of transcription factor VITF-3 used for intermediate gene expression
  VACWR128 A9L    late late   IMV membrane protein required for morphogenesis
  VACWR129 A10L    late late   precursor p4a of core protein 4a, complexes with A4L
  VACWR130 A11R    late late   unknown
  VACWR131 A12L    late     core protein
  VACWR132 A13L    late late   IMV membrane protein
  VACWR133 A14L    late late   Repression of 90 aa A14 membrane phosphoprotein arrests virion assembly prior to/at crescent formation; interacts with A17; F10 and H1 substrate
  VACWR134 A14.5L    early/late     nonessential hydrophobic IV and IMV membrane protein; deletion attenuates virus virulence
  VACWR135 A15L    late     unknown
  VACWR136 A16L          soluble myristylprotein
  VACWR137 A17L    late late   IMV membrane protein required for morphogenesis
  VACWR138 A18R    early/late early/late Pacha 1990 (E,L) DNA helicase; effects elongation and termination of postreplicative viral transcription
  VACWR139 A19L    late     unknown
  VACWR140 A21L    late late   Component of the poxvirus multiprotein entry-fusion complex
  VACWR141 A20R    early/late early McDonald 1997 (E) stoichiometric component of the DNA polymerase processivity factor
  VACWR142 A22R    early/late late   A late protein essential for concatemer resolution. An E. coli RuvC-like protein with holliday junction resolvase activity.
  VACWR143 A23R    early/late early Sanz 1999 (E) 45kDa large subunit of intermediate gene transcription factor VITF-3
  VACWR144 A24R    early/late early/late Patel 1989 (E,L) DNA-dependent RNA polymerase subunit rpo132
7 VACWR145 A25L    pseudogene     gene fragment, cowpox A-type inclusion protein
7 VACWR146 no ortholog    pseudogene     gene fragment, cowpox A-type inclusion protein
7 VACWR147 no ortholog    pseudogene     gene fragment, cowpox A-type inclusion protein
7 VACWR148 no ortholog    late     gene fragment, cowpox A-type inclusion protein
  VACWR149 A26L    late     MV protein required for incorporating MV into A-type inclusion body; involved in MV attachement to cell surface (PMID: 18842719).
  VACWR150 A27L    late late   IMV surface protein; roles in IMV-cell attachment, fusion, and microtubule transport
  VACWR151 A28L    late late   unknown, putative signal peptide
  VACWR152 A29L    early/late early Amegadzie 1991a (E) DNA-dependent RNA polymerase rpo35
  VACWR153 A30L    late late   Vaccinia core protein component of the seven protein complex required for virosomal uptake by viral crescents
  VACWR153.5 A30.5L    late      
  VACWR154 A31R    early     unknown
  VACWR155 A32L    late late   putative ATPase involved in DNA packaging
  VACWR156 A33R    late     EEV membrane phosphoglycoprotein associates with A36R; involved in CEV-cell adherence and actin tail formation
  VACWR157 A34R    early/late late   EEV glycoprotein involved in CEV cell adherence and actin tail formation
  VACWR158 A35R    early/late     unknown
  VACWR159 A36R    early/late early/late Parkinson 1994 (E) ,  Grosenbach 2000(L) IEV transmembrane phosphoprotein interacts with A33R and used in actin tail formation
  VACWR160 A37R    early     unknown
  VACWR161 pseudogene    pseudogene     unknown
  VACWR162 A38L    early/late     CD47-like putative membrane protein
8 VACWR163 A39R    late     gene fragment, semaphorin-like; intact protein proinflammatory in VAC-mouse skin lesion model; host defense modulator
8 VACWR164 A39R          gene fragment, semaphorin-like; intact protein proinflammatory in VAC-mouse skin lesion model; host defense modulator
  VACWR165 A40R    early early Wilcock 1999 (E) C-type lectin-like type-II membrane protein; deletion attenuates intradermal lesion in VAC-mouse model; host defense modulator
  VACWR166 A41L    early/late early Gardner 2001 (E) secreted glycoprotein; deletion causes more severe lesion and enhanced viral clearance in VAC-mouse skin model; host defense modulator
  VACWR167 A42R    early/late late   profilin-like
  VACWR168 A43R    early/late     putative type-I membrane glycoprotein
  VACWR169 268    early/late     unknown
  VACWR170 A44L    early early Moore 1992 (E) hydroxysteroid dehydrogenase; deletion attenuates intradermal lesion in VAC-mouse model; host defense modulator
  VACWR171 A45R    late late   inactive Cu-Zn superoxide dismutase-like in virion
  VACWR172 A46R    early/late     Toll/IL1-receptor [TIR]-like; suppresses TIR-dependent signal transduction; host defense modulator
  VACWR173 A47L    early/late     unknown
  VACWR174 A48R    early/late early Smith 1989b (E) thymidylate kinase
  VACWR175 A49R    early/late     unknown
  VACWR176 A50R    early/late early Smith 1989a (E) ATP-dependent DNA ligase
  VACWR177 A51R    early/late     unknown
  VACWR178 A52R    early/late     Toll/IL1-receptor [TIR]-like suppresses TIR-dependent signal transduction; host defense modulator
  pseudogene A54L    pseudogene     A54L; putative; Hypothetical protein
  VACWR179 A53R    early/late     gene fragment, secreted TNF-receptor-like protein; CrmC, intact in some VAC strains; host defense modulator
  VACWR180 A55R    early/late     kelch-like
  VACWR181 A56R    early/late early/late Brown 1991 (E,L) hemagglutinin; EEV; type-I membrane glycoprotein; inhibits cell fusion
9 VACWR181.5 269    early/late     5` fragment of CPXV-GRI:A59R
9 VACWR182 A57R    pseudogene     guanylate kinase
  VACWR183 B1R    early/late early Banham 1992 (E) B1 is an early ser/thr kinase needed for ongoing viral DNA replication capable of phosphorylating the viral H5 and cellular ribosomal proteins.
10 VACWR184 B2R    early/late     unknown
10 VACWR185 B3R    pseudogene     unknown
  VACWR186 B4R    early/late     ankyrin-like
  VACWR187 B5R    early/late early/late Engelstad 1992 (E,L) EEV type-I membrane glycoprotein; required for trans-Golgi/endosomal membrane-wrapping of IMV
  VACWR188 B6R    early/late     ankyrin-like
  VACWR189 B7R    late     21kDa precursor protein processed to 18kDa membrane protein; deletion reduces lesion in VAC-mouse skin model; host defense modulator
  VACWR190 B8R    early/late early Symons 2002 (E) soluble interferon-gamma receptor-like; host defense modulator
  VACWR191 B9R    early     6kDa intracellular viral protein has N-terminal signal sequence
  VACWR192 B10R    pseudogene     unknown
  VACWR193 B11R    early/late     unknown
  VACWR194 B12R    early early Banham 1993 (E) ser/thr protein kinase-like
11 VACWR195 B13R    early early Kettle 1995 (E) SPI-2/CrmA inhibits Fas-mediated apoptosis, IL-1 convertase, lipoxygenase pathway
11 VACWR195 B14R    early early Kettle 1995 (E) SPI-2/CrmA inhibits Fas-mediated apoptosis, IL-1 convertase, lipoxygenase pathway
  VACWR196 B15R    early/late     unknown
12 VACWR197 270    late     IL-1-beta-inhibitor [VACWR-B15R]; prevents febrile response in VAC-mouse intranasal model; host defense modulator
12 VACWR197 B16R    late     IL-1-beta-inhibitor [VACWR-B15R]; prevents febrile response in VAC-mouse intranasal model; host defense modulator
  VACWR198 B17L    early/late     unknown
  VACWR199 B18R    early/late     ankyrin-like
  VACWR200 B19R    early early Ueda 1990 (E) IFN-alpha/beta-receptor-like secreted glycoprotein; host defense modulator [VACWR-B18R]
  VACWR201 pseudogene    pseudogene     unknown
13 VACWR202 B20R          ankyrin-like
13 VACWR203 B20R          unknown
  VACWR204 no ortholog    pseudogene     kelch-like fragment; unknown
  VACWR204.5 264    late      
  VACWR205 C12L    early/late early Kettle 1995 (E) serine protease inhibitor-like SPI-1; host defense modulator
  no ortholog 271    early     5` fragment of CPXV-GRI:B22R
14 VACWR206 C14L    early/late     unknown
14 VACWR206 C13L    early/late     unknown
  VACWR207 no ortholog VACWR012 no ortholog pseudogene     [ITR] gene fragment, zinc finger-like; apoptosis; host defense modulator
  VACWR208 no ortholog VACWR011 no ortholog early/late     [ITR] gene fragment, zinc finger-like; apoptosis; host defense modulator
  VACWR209 no ortholog VACWR010 C10L early     [ITR] unknown
  VACWR210 no ortholog VACWR009 C11R early/late     [ITR] secreted epidermal growth factor-like; binds EGF receptor
  no ortholog B21R no ortholog C15L       B21R; putative; Hypothetical protein
  no ortholog B22R no ortholog C16L early/late     B22R; putative; Hypothetical protein
  no ortholog B23R no ortholog C17L       B23R; putative; host range polypeptide
  no ortholog B24R no ortholog C18L pseudogene     B24R; putative; host range protein
15 VACWR211 B25R VACWR008 C19L early     [ITR] gene fragment, ankyrin-like
15 pseudogene B26R pseudogene C20L pseudogene     B26R; putative; Hypothetical protein
15 VACWR212 no ortholog VACWR007 no ortholog pseudogene     [ITR] unknown
15 VACWR213 B27R VACWR006 C21L pseudogene     [ITR] gene fragment, ankyrin-like
15 VACWR214 pseudogene VACWR005 pseudogene pseudogene     [ITR] gene fragment, ankyrin-like
16 VACWR215 B28R VACWR004 C22L late     [ITR] gene fragment, TNF-alpha-receptor-like; host defense modulator
  VACWR216 no ortholog VACWR003 no ortholog pseudogene     [ITR] unknown
16 VACWR217 pseudogene VACWR002 pseudogene pseudogene     [ITR] gene fragment, TNF-alpha-receptor-like; host defense modulator
  VACWR218 B29R VACWR001 C23L early/late     [ITR] chemokine-binding protein; host defense modulator

Notes

NoteComment
1 CPXV-GRI:D2L is fragmented into two ORFs in both VACV-WR (002 & 004) and VACV-COP (C22L and an unannotated ORF). WR:004 and C22L preserved the 5'UTR of the CPXV-GRI:D2L, while WR004 and the unannotated COP ORF come from the 3' end of the CPXV-GRI gene, and are not predicted to have transcriptional promoters. The non-coding ORF VACWR003 is on the other strand is not another fragment of this gene.
2 CPXV-GRI:D3L is fragmented differently in VACV-WR (005-008) and VACV-COP (C19-"C21.5"). Only WR008 and C19L conserve the transcriptional promoters in the 5' UTR.
3 CPXV-GRI:D4L is fragmented in VACV-COP (C18L, C17L), but has no ortholog in VACV-WR.
4 CPXV-GRI:C7R is fragmented in VACV-WR (WR011, WR012) but has no ortholog in VACV-COP.
5 CPXV-GRI:C9L is fragmented in VACV-WR (WR014, WR016, WR015, WR016, WR017) but has no ortholog in VACV-COP.
6 CPXV-GRI:M5L is fragmented in three pieces in both VACV-WR (WR038, WR037, WR036) and VACV-COP (K6L, L5L and an unannotated ORF) Only WR038 and K6L conserve the transcriptional promoter in the 5' UTR.
7 CPXV-GRI:A26L (ATI repeat) is fragmented differently in VACV-WR (WR148-145) and VACV-COP (A25L and A26L). Strictly speaking, WR145 is the ortholog of COP:A25L, but in the literature, WR148 is referred to as "A25L" (Chung et al. 2006, Journal of Virology; PMID 16474121).
8 CPXV-GRI:A41R is conserved in VACV-COP (A39R) and fragmented in VACV-WR (WR163, WR164). WR164 does not conserve the 5' UTR, and lacks putative transcriptional promoters.
9 CPXV-GRI:A59R is fragmented in both VACV-COP and VACV-WR into a very short, previously un-annotated, fragment of the 5' end, which conserves the CPXV 5' UTR and promoters (WR181.5 and COP:269), while the larger 3'-proximal fragments (WR182 and COP:A57R) are not predicted to have any transcriptional promoters in their 5' UTR.
10 CPXV-GRI:B2R is similarly fragmented in both VACV-COP and VACV-WR. Only the upstream fragment conserves the 5' UTR and its promoters. The downstream fragment is not predicted to be expressed.
11 CPXV-GRI:B12R is conserved in VACV-WR (WR195) but fragmented in VACV-COP (B13R and B14R).
12 CPXV-GRI:B14R is conserved in VACV-WR (WR197) but fragmented in VACV-COP (unannotated ORF and B16R).
13 CPXV-GRI:B17R is conserved in VACV-COP (B20R) but is fragmented into two fragments, neither of which conserves the 5' UTR in VACV-WR (WR202 and WR203).
14 CPXV-GRI:B21R is conserved in VACV-WR (WR206) but fragmented in VACV-COP ( C14L and C13L).
15 CPXV-GRI:I3R, like its ITR partner CPXV-GRI:D3L, is multiply fragmented in VACV-WR and VACV-COP. Only WR211 and COP:B25R conserve the 5' UTR and are predicted to be transcribed.
16 CPXV-GRI:I4R, like its ITR partner CPXV-GRI:D2L, is fragmented into two ORFs in both VACV-WR (WR215 and WR217) and VACV-COP (B28R and an unannotated ORF). WR215 and B28R preserved the 5'UTR of the CPXV-GRI:I4R, while WR217 and the unannotated COP ORF come from the 3' end of the CPXV-GRI gene, and are not predicted to have transcriptional promoters. The non-coding ORF VACWR216 is on the other strand, and is not another fragment of this gene.

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