The ribosomal protein genes and Minute loci of Drosophila melanogaster

Marygold, Steven J; Roote, John; Reuter, Gunter; Lambertsson, Andrew; Ashburner, Michael; Millburn, Gillian H; Harrison, Paul M; Yu, Zhan; Kenmochi, Naoya; Kaufman, Thomas C; Leevers, Sally J; Cook, Kevin R

doi:10.1186/gb-2007-8-10-r216

Table 3 Analysis of duplicate CRP genes and CRP-like genes

From: The ribosomal protein genes and Minute loci of Drosophila melanogaster

	Gene			K _A /K _S ^b		cDNA clones
	Symbol^a	Location	Comments	Pair-wise^c	Branch-specific^d	Total^e	% testis^f	% Amino acid identity^g
RpS5	RpS5a	X: 15E5-7	-	0.07	0.09	133	1	78
	*RpS5b*	3R: 88D6	-		0.09	60	7
RpS6	RpS6	X: 7C2	-	NA	NA	150	5	33^h
	*CG11386*	X: 7C2	CG11386 and CG33222 are tandem repeats of the third exon and flanking regions of RpS6		NA	0	0
	*CG33222*	X: 7C2			NA	3	0
RpS10	*RpS10a*	3R: 98A14	Lacks introns; likely retrogene	0.10	0.15	1	0	73
	RpS10b	X: 18D3	-		0.01	156	0
RpS14	RpS14a	X: 7C6-7	RpS14a and RpS14b share identical gene structures	NA	NA	154	2	100
	*RpS14b*	X: 7C8			NA	12	0
RpS15A	RpS15Aa	X: 11E11-12	-	0.16	0.00	150	1	98
	*RpS15Ab*	2R: 47C1	Lacks introns; likely retrogene		NA	67	1
RpS19	RpS19a	X: 14F4	-	0.09	0.01	134	1	65
	*RpS19b*	3R: 95C13	-		0.08	1	100
RpS28	*RpS28a*	3R: 99D2	Lacks introns; likely retrogene	0.05	0.06	0	0	82
	RpS28b	X: 8E7	-		0.00	131	1
	*RpS28-like*	2L: 30B3	-	NAⁱ	NA	1	0	36/37^j
RpLP0	RpLP0	3L: 79B2	-	NA	NA	157	2	18
	*RpLP0-like*	2R: 46E5-6	Present in all eukaryotes		NA	11	0
RpL7	RpL7	2L: 31B1	-	NA	NA	168	4	30
	*RpL7-like*	2L: 33C1	-		NA	32	0
RpL10A	*RpL10Aa*	3R: 88D10	Lacks introns; likely retrogene	0.05	0.06	7	71	64
	RpL10Ab	3L: 68E1	-		0.02	160	4
RpL22	RpL22	X: 1C4	-	NA	NA	145	2	38
	*RpL22-like*	2R: 59D3	-		NA	5	60
RpL24	RpL24	2L: 34B10	-	NA	NA	162	3	23
	*RpL24-like*	3R: 86E5	Present in all eukaryotes		NA	34	3
RpL34	*RpL34a*	3R: 96F10	RpL34a and RpL34b share identical gene structures	0.04	0.09	56	4	78
	RpL34b	3R: 85D15			0.04	132	2
RpL37	RpL37a	X: 13B1	-	0.01	NA	158	3	72
	*RpL37b*	2R: 59C4	Lacks introns; likely retrogene		0.04	3	0^k

^aBold font indicates CRP-like genes, putative pseudogenic fragments (CG11386 and CG33222) or the member of a duplicate gene pair that is expressed in a small number of tissues and/or at relatively low levels. ^bK_A/K_Scalculations are not applicable (NA) to highly diverged sequences or cases where the numbers of both synonymous and nonsynonymous substitutions are very small (<5). ^cCalculated for each D. melanogaster CRP gene pair using maximum likelihood analysis. Values for pairwise comparisons are shown on the first row of each pair. ^dBranch-specific score in a three-way maximum likelihood tree including D. pseudoobscura orthologs. A four-way tree was used for RpS19 sequences. ^eTotal number of cDNA clones (excluding those from cultured cell lines) given in FlyBase [60] (April 2007). RpS28-like cDNA evidence from L Crosby (personal communication). ^fPercentage of cDNA clones from adult testis cDNA libraries (AT, UT and BS), rounded to the nearest integer. ^gIdentity between proteins across their whole length. Values for pairwise comparisons are shown on the first row of each pair. ^hIdentity between RpS6 and the CG11386 or CG33222 protein. If CG11386 or CG33222 were used as alternative third exons of RpS6, the protein encoded would be 60% identical to the conventional RpS6 (see text for details). ⁱRpS28-like is too highly diverged from both RpS28a and RpS28b for a pair-wise K_A/K_Scalculation to be applicable. ^jIdentity between the RpS28-like protein and RpS28a/RpS28b. ^kThere is experimental evidence that RpL37b expression is enriched in adult testis [79].

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