. 2016 Jun 15;1(3):e00081-15. doi: 10.1128/mSphere.00081-15

TABLE 1 .

Gene content and major features of the complete 205,896-bp EEHV4(Baylor) genome^h,ⁱ

Gene name and orientation	Protein name	Type	Family or status	Position coordinates	% GC content	Protein size (aa)	% amino acid identity (% length matched) to:				Note or comment
Gene name and orientation	Protein name	Type	Family or status	Position coordinates	% GC content	Protein size (aa)	EEHV1A Kimba	EEHV1A Raman	EEHV1B Emelia	EEHV5 Vijay	Note or comment
TR	3.5× 22-bp			340–420			Related to multimerized 17-bp repeats in TR of EEHV1A/1B/5
TR	Regulatory motifs			1070–1410			All have a cluster of 6–9× palindromic (8-bp) CREB-binding sites
Nil	vFUT9		Novel				E47	EE63	EE63	EE63	Absent in EEHV4^a
Nil		7xTM	Novel				Nil	Nil	Nil	EE62B	Unique to EEHV5
Nil			IgFam				Nil	Nil	Nil	EE62A	Unique to EEHV5
Nil	vGPCR7	7xTM	E3fam				E48	EE62	Nil	EE62	Absent in EEHV4
Nil			E49fam				E49	EE61	Nil	Frag	Absent in EEHV4
Nil	vIgF1		Novel				E50	EE60	Nil	Nil	Absent in EEHV4, -5 outside the probosciviruses
Nil	vGPCR8	7xTM	E3fam				Frag	Frag	EE59	Nil	Absent in EEHV4
Nil			E49fam				E51	EE58	EE58	Nil	Absent in EEHV4
Nil	vIgF2		IgFam				E52	EE57	Frag	Nil	Absent in EEHB4
Nil			E49fam				Nil	Nil	EE56	Nil	Absent in EEHV4
Nil			IgFam				Nil	Nil	EE55	Nil	Absent in EEHV4
Nil			IgFam				Nil	Nil	EE54	Nil	Absent in EEHV4
Nil	vIgF2.4		IgFam				Frag	EE53	EE53	Nil	Absent in EEHV4
Nil	vIgF2.5		IgFam				E53	EE52	EE52	EE52	Absent in EEHV4
Nil	vOX2-1		Novel				E54	EE51	EE51	EE51	Absent in EEHV4
Nil	vIgF3		IgFam				E55	EE50	EE50	EE50	Absent in EEHV4
Nil	vCD48		IgFam				Nil	Nil	Nil	EE49D	Unique to EEHV5
Nil			IgFam				Nil	Nil	Nil	EE49C	Unique to EEHV5
Nil	vCD48		IgFam				Nil	Nil	Nil	EE49B	Unique to EEHV5
Nil			IgFam				Nil	Nil	Nil	EE49A	Unique to EEHV5
E1, F		7xTM	E3fam	2061–3608	69	515	25 (45)	EE49	EE49	EE49	N-term S/T extended
Nil	Cys-rich	7xTM	E3fam				E2	EE48	EE48	EE48	Absent in EEHV4
E3, F	vGPCR6	7xTM	E3fam	3981–4928	68	315	30 (70)	EE47	EE47	EE47	Match to RAIP3 or C-5-Afam
E3.1, F	vGPCR6.1	7xTM	E3fam	4991–6169	62	392	28 (60)	EE45	EE45	EE45	Unique to EEHV4
E3.2, F	vGPCR6.2	7xTM	E3fam	6747–7727	67	328	30 (45)	EE45	EE45	EE45	Unique to EEHV4
E2A, F		7xTM	Novel	8015–9295	58	426	Nil	Nil	Nil	Nil	Unique to EEHV4; S/T dom
E3.3, F	vGPCR6.3	7xTM	E3fam	9714–10721	50	335	34 (41)	EE45	EE45	EE45	Unique to EEHV4
E3.4, F	vGPCR6.4	7xTM	E3fam	11637–12674	56	345	38 (69)	EE45	EE45	EE45	Unique to EEHV4
E4, F	vGCNT1	AcTransf	Novel	13026–14642	63	538	61 (68)	EE46	EE46	EE46	—^b
Nil	vGPCR5	7xTM	E3fam				E5	EE45	EE45	EE45	Absent in EEHV4
Nil			Novel				E5A	EE44	EE44	Nil	Short, memb, absent EEHV4
Nil	vCD48		IgFam				Nil	Nil	Nil	EE44A	Unique to EEHV5
E4A, F			Novel	15171–15653	44	160	Nil	Nil	Nil	Nil	Unique to EEHV4
E4B, F			Novel	15712–16578	56	288	Nil	Nil	Nil	Nil	Unique to EEHV4
E4C, F			Novel	16779–17234	54	151	Nil	Nil	Nil	Nil	Unique to EEHV4
E6A, C	E27ex1		Novel	17811–17398	57	137	E27	EE20	Nil	EE20	35% (44%) match to E27
E6B, F			Novel	17978–18256	49	92	Nil	Nil	Nil	Nil	Unique to EEHV4
E6, C		7xTM	E6fam	19679–18855	60	274	33 (89)	EE43	EE43	EE43
Nil, C	vCXCL2?		E7A					Nil	Nil	Nil	Absent in EEHV1B/4/5
E7, C		7xTM	E6fam	20663–19956	55	235	32 (84)	EE42	EE42	EE42
E7B, C		7xTM	Novel	21647–20871	26	258	Nil	Nil	Nil	Nil	Unique to EEHV4
Nil		7xTM	E6fam				E8	EE41	EE41	EE41	Absent in EEHV4
E9, C		7xTM	E6fam	22653–21757	27	298	34 (18)	EE40	Frag	EE40	Match to C-term EE40 only (esp EEHV5)
E9A, F	vOGT	AcTransf	Novel	22993–24237	42	414	Nil	Nil	Nil	Nil	Unique to EEHV4^c
E9B, C	(Truncated)		Novel	24664–24281	23	127	Nil	Nil	Nil	EE39/40	Match to EEHV5 N-term16-aa EE39/40 only
E9C, C			Novel	25233–24718	27	171	Nil	Nil	Nil	Nil	Unique to EEHV4
E10A, C		7xTM	E6fam	26078–25197	61		Nil	Nil	Nil	25 (46)	Matches central EE40(EEHV5) only
Nil		7xTM	E6fam				E10	EE39	EE39	EE39	Absent in EEHV4
E11, C		7xTM	E6fam	27127–26363	61	254	36 (96)	EE38	EE38	EE38
E12, C		7xTM	E6fam	28314–27457	60	285	34 (77)	EE37	EE37	EE37
E12A, C			Novel	28547–28281	60	88	Nil	Nil	Nil	Nil	Unique to EEHV4
E13, C		7xTM	E6fam	29780–28965	58	271	52 (88)	EE36	EE36	EE36
E14.1, C		7xTM	E14fam	31024–30215	59	269	27 (91)	Nil	Nil	Nil	Duplication of E14
E14.2, C		7xTM	E14fam	32191–31280	52	303	24 (77)	Nil	Nil	Nil	Duplication of E14
E14, C		7xTM	E14fam	33228–32419	57	269	26 (79)	EE35	EE35	EE35
E15, C	vGPCR4	7xTM	E15fam	34435–33425	58	336	34 (86)	EE34	EE34	EE34	26% (49%) match to Lox C-5-C
E16, C		7xTM	E14fam	35571–34768	57	267	40 (97)	EE33	EE33	EE33
Nil			Novel				E16C	Nil	Nil	Nil	Conserved in EEHV1 and EEHV5
Nil			Novel				E16A/B	Nil	Nil	Nil	Spliced; unique to EEHV1A/B
E16D, C	vECTL		Novel	36141–35584	45	185	Nil	Nil	Nil	Nil
E17, F	E27ex1		Novel	36491–36826	45	111	37 (99)	EE32	EE32	EE32	Match to E27, 30% (50%)
E17A, F			Novel	36944–37252	63	102	Nil	Nil	Nil	Nil	Unique to EEHV4
Nil			Novel				Nil	Nil	Nil	EE32A	Unique to EEHV5
E18, F		7xTM	E18fam	37215–38018	57	267	32 (70)	EE31	EE31	EE31	Related to E28 by 30% (51%)
Nil			Novel				E18B	EE30A	EE30A	EE30A	Absent in EEHV4
Nil			Novel				E18A	EE30	EE30	EE30	Absent in EEHV4
E18C, F			Novel	38433–38720	59	94	Nil	Nil	Nil	Nil	Unique to EEHV4
E19, F	ORF-F2		U54.5fam	39303–41042	68	579	52 (89)	EE29	EE29	EE29	25% (77%) to ORF-F1
E20, C	vGPCR4A	7xTM	E15fam	43188–42154	57	344	46 (84)	EE28	EE28	EE28	23% (67%) match to Lox RAIP3
E20B, C			Novel	45323–44904	65	139	Nil	Nil	Nil	Nil	Unique to EEHV4
E20A, F			Novel	45338–45664	61	108	43 (33)	EE27	EE27	EE27
E21, C	vGPCR4B	7xTM	E15fam	46925–45810	59	371	35 (76)	EE26	EE26	EE26	27% (35%) match to Lox RAIP3
E22, F			Novel	47646–47921	49	91	48 (96)	EE25	EE25	EE25
E22A, F			Novel	48621–48730	53	79	46 (48)	EE24	EE24	EE24
E23B, C			Novel	48993–49325	57	110	Nil	Nil	Nil	Nil	Unique to EEHV4
E24B, C	vOX2-Bex2		Novel	49596–49250	56	132	E54	EE51	EE51	EE51
	vOX2-Bex1		Novel	50001–49950							Short first exon
Nil	vOX2-3						E24	EE23	EE23	EE23	Absent in EEHV4
Nil	vOX2-V (E23A)						Nil	Nil	Nil	EE22A	Unique to EEHV5
Nil	vOX2-2						E25	EE22	EE22	EE22	Absent in EEHV4
E26, C	vGPCR3	7xTM	E3fam	51287–50418	50	289	42 (92)	EE21	EE21	EE21	Match to ChemR C-5-C
E27, F	E27ex1	E27	Novel	52138–52606	55	245	57 (58)	EE20ex1	EE20ex1	EE20ex1	Related to E6A, E17
	E27ex2		Novel	52785–53053	59		Nil	Nil	Nil	Nil	Unrelated to EE20ex2
E28, F		7xTM	E18fam	53115–53861	54	248	44 (90)	EE19	EE19	EE19	Related to E18 by 30% (51%)
E29, F		7xTM	Novel	54092–54781	55	229	42 (91)	EE18	EE18	EE18
E30, C			Novel	55453–54911	55	180	<15	EE17	EE17	EE17	Acidic similarity only
E30A, C	E30Aex2		Novel	55883–55534	42	133	Nil	Nil	Nil	Nil	Unique to EEHV4
	E30Aex1		Novel	56146–56095	40		Nil	Nil	Nil	Nil	Unique to EEHV4
Nil							E31	EE16	EE16	EE16	Absent in EEHV4
E31A, C			Novel	56923–56321	56	200	35 (46)	EE15	EE15	EE15	Only N-term cons
E31B, C			Novel	57113–56610			Nil	Nil	Nil	Nil	Unique to EEHV4
E31C, C	E31Cex		Novel	57646–57182	61	136	65 (12)	EE14	EE14	EE14	No ATG, splice to E32?
E32, C	U14.5		βδ?	60473–57717	60	918	45 (82)	EE13	EE13	EE13
Nil, F							E33	EE12A	Frag	Nil	Unique to EEHV1A
E33A			Novel	60991–61236	50	81	37 (59)	EE12	EE12	EE12
U14, C	U14		βδ	63078–61408	59	556	37 (75)	U14	U14	U14
U13.5, C	U13.5		βδ	64742–63444	52	432	76 (54)	UL34	UL34	UL34
U12, C	vGPCR2ex2	7xTM	βδ	67327–65060	57	783	50 (53)	U12	U12	U12
	vGPCR2ex1			67537–67454			56 (100)	U12	U12	U12	Short first exon
E34, F	ORF-C		Novel	68025–74276	59	2,083	42 (16)	U11	U11	U11	Only N-term cons in EEHV1, and -5
U4, F	U4	U4	βδ	74389–76053	61	554	58 (94)	U4	U4	U4	24% (38%) HHV6 U4
U4.5, F	ORF-B	U4	βδ	76687–78444	63	585	59 (93)	EE11	EE11	EE11	24% (30%) U4
E35, F	ORF-A		Novel	79137–81659	63	840	51 (46)	EE10	EE10	EE10
U44, C	U44		Core	82518–83729	55	403	77 (23)	U44	U44	U44	Only C-term cons in EEHV1 and -5
U43, F	PRI		Core	83629–87234	59	1,201	51 (84)	U43	U43	U43	Primase subunit
U42, F	MTAex1			87495–87627			65 (51)	U42	U42	U42	Short first exon
	MTAex2		Core	87948–92020	64	1,401	52 (24)	U42	U42	U42	Posttranscriptional regulator
Ori-Lyt				92346–93325							—^d
U41, F	MDBP		Core	93861–97376	61	1,171	63 (99)	U41	U41	U41	SS DNA binding protein
U40, F	TER2		Core	97498–99591	59	697	73 (98)	U40	U40	U40
U39, F	gB		Core	99533–102121	57	862	64 (94)	U39	U39	U39	Env glycoprotein B
U38, F	POL		Core	102273–105527	62	1,084	65 (99)	U38	U38	U38	DNA polymerase
U37, C	DOC		Core	106545–105740	59	268	64 (97)	U37	U37	U37	Docking protein
U36, C			Core	108154–106538	63	538	69 (89)	U36	U36	U36
U35, F			Core	108266–108553	48	95	69 (98)	U35	U35	U35
U34, F			Core	108717–109619	53	300	63 (99)	U34	U34	U34
U33, F	CRP		βγδ	109914–111518	64	534	49 (91)	U33	U33	U33	Cys-rich protein
U32, F	SCP		Core	111409–111672	58	87	46 (67)	U32	U32	U32	Small capsid protein
U31, C	TEG-L		Core	118856–111873	65	2,321	44 (89)	U31	U31	U31	Large tegument
U30, C	TEG-S		Core	124420–119289	61	1,713	45 (53)	U30	U30	U30	Small tegument
U29, F	TRI1		Core	124423–125313	60	296	60 (98)	U29	U29	U29	Capsid triplex 1
U28, F	RRA		Core	125563–128073	61	836	68 (66)	U28	U28	U28	Ribonucleotide reductase A
U27.5, F	RRB (ORF-H)		αγδ	128212–129117	53	301	75 (99)	EE9	EE9	EE9	Ribonucleotide reductase B
U27, F	PPF		Core	129702–131023	64	437	52 (65)	U27	U27	U27	Pol processivity factor
U45.7, F	ORF-J		Novel	131035–131784	58	216	44 (33)	EE8	EE8	EE8
U46, F	gN		Core	131800–132105	49	101	63 (53)	U46	U46	U46	Env glycoprotein N
U47, C	gO (ORF-D)		Βδ	132837–132187	52	216	34 (94)	U47	U47	U47	Env glycoprotein O
U48, C	gH		Core	135086–132816	49	756	47 (96)	U48	U48	U48	Env glycoprotein H
U48.5, C	TK (ORF-E)		αγδ	136101–135052	56	349	50 (87)	EE7	EE7	EE7	Thymidine kinase
U49, F			Core	136100–136801	57	233	48 (85)	U49	U49	U49
U50, F	PAC2		Core	136620–138347	57	575	64 (99)	U50	U50	U50	Packaging
U51, F	vGPCR1	7xTM	βδ	138430–139647	56	405	42 (95)	U51	U51	U51	—^e
U52, C			Core	140605–139832	53	257	65 (98)	U52	U52	U52
U53, F	SCA/PRO		Core	140698–142485	60	595	49 (91)	U53	U53	U53	Scaffold protease
U54.5, C	ORF-F1		U54.5fam	144154–142715	61	479	38 (99)	U54	U54	U54	27% (95%) match to ORF-F2
U56, C	TRI2		Core	145344–144445	59	299	68 (99)	U56	U56	U56	Capsid triplex 2
U5, C	MCP		Core	149563–145511	63	1,350	71 (99)	U57	U57	U57	Major capsid protein
U58, F	vTBP		βγδ	150117–153134	61	1,005	63 (87)	U58	U58	U58	TATA-binding protein
U59, F			βγδ	152794–154152	62	452	48 (79)	U59	U59	U59
U60, C	TERex3		Core	155504–154377	57	660	92 (99)	U60	U60	U60	Terminase subunit 1
U62, F			βγδ	155733–156005	54	90	57 (97)	U62	U62	U62
U63, F			βγδ	155944–156546	51	200	67 (72)	U63	U63	U63
U64, F	PAC1		Core	156527–158552	64	541	48 (63)	U64	U64	U64	Packaging
U65, F			Core	158055–159071	59	338	48 (98)	U65	U65	U65
U66, C	TERex2		Novel	159272–159153			90 (100)	U66	U66	U66	Terminase subunit 1
	TERex1		Core	160224–159490	53		89 (99)	U66	U66	U66	Terminase subunit 1
U67, F			βγδ	160612–161742	58	376	61 (98)	U67	U67	U67
U68, F			Core	161739–162104	51	121	66 (98)	U68	U68	U68
U69, F	CPK		Core	162613–164232	59	539	57 (96)	U69	U69	U69	Conserved protein kinase
U70, F	EXO		Core	164529–166094	61	521	53 (97)	U70	U70	U70	Exonuclease
U71, F	MyrTeg		Core	166031–166342	56	103	41 (67)	U71	U71	U71	Myristylated tegument
U72, C	gM		Core	167655–166537	55	372	66 (93)	U72	U72	U72	Envelope glycoprotein M
U73, F	OBP (ORF-G)		αδ	168094–171645	61	1,183	65 (68)	U73	U73	U73	Origin-binding protein
U74, F	PAF		Core	171659–173830	63	723	61 (91)	U74	U74	U74	Pol-associated factor
U75, C			Core	174625–173813	63	270	54 (84)	U75	U75	U75
U76, C	POR		Core	176750–174579	63	723	74 (78)	U76	U76	U76	Portal protein
U77, F	HEL		Core	176701–179574	63	957	79 (79)	U77	U77	U77	Helicase subunit
E36, F	ORF-M		Novel	180833–183805	65	990	62 (19)	U79	U79	U79	Env glycoprotein M (only N-term cons)
Nil	ORF-N, vCXCL1		Novel				E36A	EE6	Nil	EE6	Chemokine-like, absent in 1B, 4
U81, C	UDG		Core	185284–184277	63	335	68 (68)	U81	U81	U81	Uracil DNA glycosylase
U82, C	gL		Core	186080–185253	48	275	37 (94)	U82	U82	U82	Env glycoprotein L
E37, C	ORF-Oex3		Novel	186570–186007	41	709	37 (95)	EE5	EE5	EE5
	ORF-Oex2		Novel	186897–186677	40		<15	EE5	EE5	EE5
	ORF-Oex1		Novel	188411–187067	41		<15	EE5	EE5	EE5
Nil	ORF-Pex2		Novel				E38	EE4	EE4	EE4	Absent in EEHV4
	ORF-Pex1		Novel				E38	EE4	EE4	EE4	Absent in EEHV4
Nil	ORF-Qex2		Novel				E39	EE3	EE3	Nil	Absent in EEHV2, -4, -5
	ORF-Qex1		Novel				E39	EE3	EE3	Nil	Absent in EEHV2, -4, -5
E39A, C	ORF-Rex2		Novel	189482–188506	40	367	Nil	Nil	Nil	Nil	Unique to EEHV4
	ORF-Rex1		Novel	189690–189564	32		Nil	Nil	Nil	Nil	Unique to EEHV4
E40, C	ORF-K		Novel	194372–189975	66	1,465	72 (16)	EE2	EE2	EE2	Only C-term cons
E44A, C	ORF-S		Novel	200795–199809	64	328	36 (84)	EE1A	EE1A	EE1A	Overlaps ORF-L
E44, C	ORF-L IE-like		Novel	201282–195226	65	2,018	52 (11)	EE1	EE1	EE1	Transcriptional regulator
TR	Palindrome			202971–203014							45-bp hairpin
TR	Packaging motifs			205612–205665							—^f
TR	Packaging motifs			205784–205896							—^g

Fucosyl transferase 9 = EC 2.4.1.152.

Acetylglucosamine transferase 1 = EC 2.4.1.1.

UDP-β-Gal N-acetylglucosamine transferase 3, also known as O-linked N-acetylglucosamine transferase = EC 2.4.1.255.

Complex dyad symmetry. Resemblance to alphaherpesvirus Ori-L and Ori-S as well as HHV6 Ori-Lyt, but not to cytomegalovirus Ori-Lyt, much larger than EEHV1 and EEHV5 versions, 3× 90-bp and other dyad symmetry elements with 5× OBP-binding site motifs plus 35× 20-bp AT-rich tandem repeats.

No matches to other betaherpesvirus vGPCRs.

83% DNA match over 54 bp to terminal repeat motifs at 2852 to 2905 and 180311 to 180358 in EEHV1B(Emelia).

72% DNA match over 112 bp to terminal repeat motifs present in all three copies of the “a” sequence of HSV-1(KOS).

The six clusters of genes or exons with unusually low GC content are shown in bold.

ⁱ

Abbreviations: TR, tandem repeat; N-term, N terminal; dom, domain; memb, membrane; C term, C terminal; esp, especially; cons, conservation; SS, single stranded; UDG, uracil DNA glycosylase; Frag, fragmented; F, forward strand; C, complementary strand.