Whole-genome screening indicates a possible burst of formation of processed pseudogenes and Alu repeats by particular L1 subfamilies in ancestral primates

Table 1 Processed pseudogene content of the human genome

Annotated genes^†
Gene class*	Genes that generated PPs	PPs
Enzymes
Kinase	24	37
Dehydrogenase	16	80
Transferase	15	25
Peptidase	10	15
Phosphatase	9	13
Synthase	8	20
Synthetase	5	23
Translocase	4	7
Protease	4	4
Reductase	3	3
Phospholipase	2	5
RNA polymerase	2	3
Others	46	63
Total	148	298
Structural proteins
Ribosomal proteins	31	416
Actin-related proteins	9	23
Keratin	5	57
Ribosomal proteins (mitochondrial)	4	7
Tubulin	4	6
Histone	2	5
Myosin	2	4
Dynein	2	3
Kinesin	1	1
Total	60	522
Others
Ligand-binding proteins^‡	30	56
Transcription factor^‡	11	23
RNA-binding proteins^‡	11	15
Translation initiation/termination	9	21
Proteasome	9	19
Heat-shock protein	8	29
Solute carrier	7	14
Zinc finger protein^‡	7	11
Ring finger protein^‡	7	10
Nuclear ribonucleoprotein^‡	6	19
Autoantigen	6	12
Receptor	6	8
Splicing factor^‡	5	7
DEAD/H box polypeptide	4	4
Carcinoma-associated antigen	4	4
Channel	3	11
Thioredoxin	3	5
Others	295	464
Total	431	732
Total annotated genes	639	1,552
Hypothetical genes ^§	660	2,112
Grand total	1,299	3,664

*The functional annotation of NCBI Reference Sequence (RefSeq) collection (v2003.01.06) was used for this classification [61]. Respective genes were classified into only one category. ^†Ensembl gene transcripts (v1.1.0) which are correspond to the RefSeq collection (v2003.01.06). ^‡These seven gene classes were classified as 'Ligand binding' in Figure 1a,b for simplicity. ^§Ensembl gene transcripts (v1.1.0) that do not correspond to the RefSeq collection (v2003.01.06).

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