. 2005 Mar;15(3):343–351. doi: 10.1101/gr.3266405

Table 1.

Primate-specific duplications of metazoan single-copy genes

Chrom. band	Copy number^a	Mouse pairwise score	Gene name	Protein AC	Description
1p36.33	2	L	ATAD3B	NP_114127	AAA-ATPase TOB3
1q23.2	2	H	VANGL1	NP_620409	Vang-like protein
1p13.1	2	H	VANGL1	NP_620409	Vang-like protein
2p23.1	2	H	XDHA	NP_000370	Xanthine oxidoreductase
2q33.1	2	H	XDHA	NP_000370	Xanthine oxidoreductase
2q12.3	6	H	RANBP2	NP_006258	RanBP2
3p12.3	3	L	SB153	BAC086025	SB153 protein, isoform 1
3q22.1	3	L	SB153	BAC086025	SB153 protein, isoform 1
3q21.1	2	H	EAF2	NP_060926	ELL associated factor 2
3p25.1	2	H	EAF2	NP_060926	ELL associated factor 2
5q13.2	3	L^*	SMN1	NP_000335	Survival motor neuron 1
5q13.2	3	L^*	GTF2H2	NP_001506	Transcription factor IIH
5q35.2	2	L	THOC3	NP_115737	THO complex subunit 3
5q35.3	2	L	THOC3	NP_115737	THO complex subunit 3
6p12.3	3	H	TFAP2A	NP_003211	Transcription factor AP-2 α
6p24.3	3	H	TFAP2A	NP_003211	Transcription factor AP-2 α
7p22.1	2	L^*	C7orf28A	NP_056437	CGI-43 protein
7q22.1	4	L	POLR2J2	NP_116580	RNA polymerase II subunit 11
7p13	4	L	POLR2J2	NP_116580	RNA polymerase II subunit 11
7q11.3	3	H	WBSCR20A	NP_060514	Williams Beuren syndrome-associated gene
8p21.2	2	H	DPYS	NP_001376	Dihydropyrimidinase
8p22.3	2	H	DPYS	NP_001376	Dihydropyrimidinase
12p11.1	2	L	ALG10	NP_116223	Glucosyltransferase
12p12	2	L	ALG10	NP_116223	Glucosyltransferase
12q24.13	2	H	PTPN11	NP_002825	Protein tyrosine phosphatase
12p13.31	2	H	PTPN11	NP_002825	Protein tyrosine phosphatase
15q24.1	3	H	COMMD4	NP_060298	COMM domain containing 4
15q24.2
15q24.3
16p12.1	2	L^*	EIF3S8	NP_003743	Translation initiation factor 3
16p13.11	3	L	PM5	NP_055102	pM5 protein
16p13.3	3	L	PM5	NP_055102	pM5 protein
16q22.3	2	H	PDRD	NP_060460	Pyruvate dehydrogenase phosphatase
17q23.2	2	H	USP32	NP_115971	Ubiquitin-specific hydrolase 32
17p13.2	2	H	USP32	NP_115971	Ubiquitin-specific hydrolase 32
17q23.3	2	H	TLK2	NP_006843	Tousled-like kinase 2
17q11.2	2	H	TLK2	NP_006843	Tousled-like kinase 2

The database accession number of the longest of the human paralogs is reported. The phylogenetic relationship between the human copies has been assessed on the basis of the global score of their pairwise alignment (see text). H indicates that the global alignment of one of the human copies was scoring better with the mouse ortholog than with the other paralogs; L indicates the opposite, L^* indicates that the human copies were almost identical (>99% sequence identity). Note that, because of the specific constraints used, this list reports only a subset of primate-specific genes, namely, the ones with single-copy orthologs in other metazoans and with duplications in primates. For a full list of primate-specific genes, see Long et al. (2003) and references therein.

This refers to the number of gene copies annotated in Ensembl at the time of analysis (see Methods), In the case of RanBP2, six genes were annotated in Ensembl, but we collected expression evidence for nine genes (RanBP2 and eight related genes). Moreover, five out of the six Ensembl genes appear to be fragments (the encoded predicted proteins are 46, 156, and 905 residues long).