Table 3 Most common Gene Ontology (GO) functional terms for different sets of sequences *

All genes (Total = 33930)

retropseudogenes (Total = 2493)

All PRs (Total = 631)

PRs formed since divergence from dog lineage (Total = 211) **

GO:0005515, protein binding (2360)

GO:0003735, structural constituent of ribosome (203)

GO:0008270, zinc ion binding (49)

GO:0003735, structural constituent of ribosome (11)

GO:0008270, zinc-ion binding (2069)

GO:0008270, zinc ion binding (189)

GO:0006355, regulation of transcription, DNA-dependent (35)

GO:0003677, DNA binding (10)

GO:0006355, regulation of transcription, DNA-dependent (2029)

GO:0006355, regulation of transcription, DNA-dependent (166)

GO:0005509, calcium ion binding (25)

GO:0006355, regulation of transcription, DNA-dependent (9)

GO:0005524, ATP-binding (1687)

GO:0003676, nucleic acid binding (132)

GO:0005525, GTP binding (21)

GO:0005525, GTP binding (5)

GO:0003677, DNA binding (1339)

GO:0003723, RNA binding (126)

GO:0005515, protein binding (21)

GO:0003823, antigen binding (5)

GO:0007165, signal transduction (1264)

GO:0005515, protein binding (114)

GO:0004842, ubiquitin-protein ligase activity (21)

GO:0003676, nucleic acid binding (5)

GO:0016740, transferase activity (1263)

GO:0003677, DNA binding (110)

GO:0003677, DNA binding (20)

GO:0030145, manganese ion binding (4)

GO:0004872, receptor activity (1242)

GO:0005524, ATP binding (93)

GO:0003676, nucleic acid binding (20)

GO:0020037, heme binding (4)

GO:0016787, hydrolase activity (1171)

GO:0046872, metal ion binding (63)

GO:0003735, structural component of the ribosome (16)

GO:0016757, transferase activity, transferring glycosyl groups (4)

GO:0003700, transcription factor activity (1052)

GO:0000166, nucleotide binding (57)

GO:0003723, RNA binding (13)

GO:0005509, calcium ion binding (4)

Mouse

All genes (Total = 32442)

Retropseudogenes (Total = 2969)

PRs (Total = 663)

PRs formed since divergence from dog lineage (Total = 298) **

GO:0005515, protein binding (2502)

GO:0003676, nucleic acid binding (273)

GO:0005515, protein-binding (17)

GO:0003735, structural constituent of ribosome (16)

GO:0004872, receptor activity (1923)

GO:0051287, NAD binding (243)

GO:0003735, structural constituent of ribosome (16)

GO:0005524, ATP binding (8)

GO:0006355, regulation of transcription, DNA-dependent (1571)

GO:0008943, glyceraldehyde-3-phosphate dehydrogenase activity (243)

GO:0008270, zinc ion binding (12)

GO:0005515, protein-binding (7)

GO:0008270, zinc ion binding (1481)

GO:0004365, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) activity (243)

GO:0006355, regulation of transcription, DNA-dependent (12)

GO:0016740, transferase activity (6)

GO:0005524, ATP binding (1252)

GO:0008270, zinc ion binding (235)

GO:0005524, ATP binding (12)

GO:0016491, oxidoreductase activity (6)

GO:0016740, transferase activity (1036)

GO:0003735, structural constituent of ribosome (201)

GO:0005509, calcium ion binding (12)

GO:0006355, regulation of transcription, DNA-dependent (6)

GO:0003677, DNA binding (1017)

GO:0005515, protein-binding (101)

GO:0016740, transferase activity (10)

GO:0016853, isomerase activity (5)

GO:0016787, hydrolase activity (911)

GO:0016491, oxidoreductase activity (94)

GO:0016787, hydrolase activity (9)

GO:0016787, hydrolase activity (5)

GO:0000166, nucleotide binding (873)

GO:0005524, ATP binding (78)

GO:0003677, DNA binding (9)

GO:0003677, DNA binding (5)

GO:0003676, nucleic acid binding (872)

GO:0004190, aspartic-type endopeptidase activity (77)

GO:0003676, nucleic acid binding (9)

GO:0016874, ligase activity (3)