Biology Reference
In-Depth Information
Table 2
(continued)
HCMV ORF
US22
593
NE
+
+
+
+
+
+
+
+
US23
592
A
+
+
+
+
+
+
+
+
US24
500
A
+
+
+
+
+
+
+
+
US25
179
NE
nr
+
+
+
+
+
−−
US26
603
A
+
+
+
+
+
+
+
+
US27
362
NE
+
+
+
+
+
+
+
−
US28
323
NE
+
+
+
+
+
+
+
5
US29
462
NE
nr
+
+
+
+
+
+
+
US30
349
NE
+
+
+
+
+
+
+
+
US31
197
NE
nr
+
+
+
+
+
+
+
US32
183
NE
nr
+
+
+
+
+
+
+
US33
137
NE
nr
+
+
+
+
+
+
−
US34
163
NE
nr
+
+
+
+
+
+
−
−
−
−−
US34a
65
nt
nr
+
++
US35
109
nt
nr
−
−
+
−−−−
−−−−
TRS1 788 A + + + + + + + +
a
Open reading frame length in amino acids (aa) is listed using FIX as the reference strain except
where sequence was deleted due to the insertion of the bacterial artificial chromosome. In those
regions, the Merlin sequence was used to determine ORF size. Light grey boxes denoting the
number of amino acids indicate that more than one HCMV strain lacks a methionine within 80
amino acids from the stop codon
b
Fibroblast phenotypes of mutant viruses as determined by Yu et al. (2003) are listed. The pheno-
types described are nonessential (NE), essential (E), augmenting (A) or not tested (nt)
c
Reported expression of the ORF was determined if the ORF has been reported to have a growth
phenotype when mutated or if confirmed by Western blot or mass spectroscopy. (+) designates that
the ORF has been confirmed to be expressed or to have a functional impact on viral replication
and (nr) designates no report of expression or functional impact
d
For each of the seven indicated cytomegaloviruses, BlastP analysis of the translation of all ORFs
>80 amino acids against a database of previously identified HCMV ORFS was utilized to deter-
mine conservation of the ORF. All translations that had a blast expect value of <10
-5
was consid-
ered a match. Matches are designated by (+) in a white box and nonmatches by (-) in a dark grey
box. Light grey boxes with a (+) designate ORFs that lack a methionine within 80 amino acids of
the stop codon. A number in the box designates that two neighboring ORFs contain translated
peptides that match a single predicted ORF thereby suggesting a frame shift mutation. In strains
where a different but highly related ORF is present in place of the listed ORF, the ORF name is
listed as is the case with UL154 in place of RL12 in FIX BAC and UL153 in place of RL13/14
and UL152 in place of UL146 in FIX BAC and PH BAC. BAC designates where the bacterial
artificial chromosome sequence was inserted in the HCMV genome
US36
110
nt
nr
−
−
+
either been directly shown to encode proteins or to influence viral replication when
they are mutated (Table 2). Perhaps the more intriguing set of ORFs are the 59
ORFs present in all HCMVs, but not in CCMV (Fig. 2, white arrows). Some of
these are likely to be spurious. For example, many of the ORFs extending from
RL2* through RL9* may not encode proteins. Analysis with a gene-finding algo-
rithm indicated that seven out of nine ORFs tested in this region have low coding
