| DNA ligase 3 (EC 6.5.1.1) (DNA ligase III) (Polydeoxyribonucleotide synthase [ATP] 3) | Lig3 | P97386 | 3 |
| DNA methyltransferase 1-associated protein 1 (DNMAP1) (DNMT1-associated protein 1) (MAT1-mediated transcriptional repressor) | Dmap1 Mmtr | Q9JI44 | 3 |
| DNA polymerase alpha catalytic subunit (EC 2.7.7.7) (DNA polymerase alpha catalytic subunit p180) | Pola1 Pola | P33609 | 3 |
| DNA segment, Chr 6, Wayne State University 176, expressed, isoform CRA_f (Protein FAM3C) | Fam3c D6Wsu176e mCG_9383 | G5E911 | 3 |
| DNA topoisomerase 3-beta-1 (EC 5.99.1.2) (DNA topoisomerase III beta-1) | Top3b Top3b1 | Q9Z321 | 3 |
| DNA-binding protein RFX2 (Regulatory factor X 2) | Rfx2 | P48379 | 3 |
| DNA-directed RNA polymerase I subunit RPA1 (RNA polymerase I subunit A1) (EC 2.7.7.6) (DNA-directed RNA polymerase I largest subunit) (DNA-directed RNA polymerase I subunit A) (RNA polymerase I 194 kDa subunit) (RPA194) | Polr1a Rpa1 Rpo1-4 | O35134 | 3 |
| DNA-directed RNA polymerase I subunit RPA2 (RNA polymerase I subunit 2) (EC 2.7.7.6) (DNA-directed RNA polymerase I 135 kDa polypeptide) (RPA135) | Polr1b Rpa2 Rpo1-2 | P70700 | 3 |
| DNA-directed RNA polymerase I subunit RPA43 (Twist neighbor protein) | Twistnb | Q78WZ7 | 3 |
| DNA-directed RNA polymerase III subunit RPC3 (RNA polymerase III subunit C3) (DNA-directed RNA polymerase III subunit C) | Polr3c | Q9D483 | 3 |
| Dolichol-phosphate mannosyltransferase subunit 3 (Dolichol-phosphate mannose synthase subunit 3) (DPM synthase subunit 3) (Dolichyl-phosphate beta-D-mannosyltransferase subunit 3) (Mannose-P-dolichol synthase subunit 3) (MPD synthase subunit 3) | Dpm3 | Q9D1Q4 | 3 |
| Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3B (Oligosaccharyl transferase subunit STT3B) (STT3-B) (EC 2.4.99.18) (B6dom1 antigen) (Source of immunodominant MHC-associated peptides) | Stt3b Simp | Q3TDQ1 | 3 |
| Double-strand break repair protein MRE11 (Double-strand break repair protein MRE11A) (MmMRE11A) (Meiotic recombination 11 homolog 1) (MRE11 homolog 1) (Meiotic recombination 11 homolog A) (MRE11 homolog A) | Mre11 Mre11a | Q61216 | 3 |
| Double-stranded RNA-binding protein Staufen homolog 1 | Stau1 | A2A5R8 | 3 |
| Dual specificity mitogen-activated protein kinase kinase 2 (MAP kinase kinase 2) (MAPKK 2) (EC 2.7.12.2) (ERK activator kinase 2) (MAPK/ERK kinase 2) (MEK 2) | Map2k2 Mek2 Mkk2 Prkmk2 | Q63932 | 3 |
| Dual specificity mitogen-activated protein kinase kinase 7 (MAP kinase kinase 7) (MAPKK 7) (EC 2.7.12.2) (JNK-activating kinase 2) (MAPK/ERK kinase 7) (MEK 7) (c-Jun N-terminal kinase kinase 2) (JNK kinase 2) (JNKK 2) | Map2k7 Mkk7 | Q8CE90 | 3 |
| Dynactin-associated protein (MCG9249) (Putative uncharacterized protein) | Dynap mCG_9249 | Q9D7M5 | 3 |
| Dynamin-2 | Dnm2 | F8WIV5 | 3 |
| Dynein heavy chain 2, axonemal (Axonemal beta dynein heavy chain 2) (Ciliary dynein heavy chain 2) | Dnah2 Dnahc2 | P0C6F1 | 3 |
| Dynein intermediate chain 2, axonemal (Axonemal dynein intermediate chain 2) | Dnai2 Dnaic2 | A2AC93 | 3 |
| Dyslexia-associated protein KIAA0319-like protein (Adeno-associated virus receptor) (AAVR) | Kiaa0319l Aavr | Q8K135 | 3 |
| Dystonin | Dst | S4R1P5 | 3 |
| Dystrophin | Dmd | P11531 | 3 |
| E3 ISG15--protein ligase Herc6 (EC 2.3.2.-) | Herc6 | F2Z461 | 3 |
| E3 ubiquitin-protein ligase (EC 2.3.2.26) | Nedd4l mCG_131856 | G3X9H8 | 3 |
| E3 ubiquitin-protein ligase BRE1B (BRE1-B) (EC 2.3.2.27) (RING finger protein 40) (RING-type E3 ubiquitin transferase BRE1B) | Rnf40 Bre1b Kiaa0661 | Q3U319 | 3 |
| E3 ubiquitin-protein ligase CBL (EC 2.3.2.27) (Casitas B-lineage lymphoma proto-oncogene) (Proto-oncogene c-Cbl) (RING-type E3 ubiquitin transferase CBL) (Signal transduction protein CBL) | Cbl | P22682 | 3 |
| E3 ubiquitin-protein ligase DTX3L (EC 2.3.2.27) (Protein deltex-3-like) (RING-type E3 ubiquitin transferase DTX3L) | Dtx3l Bbap | Q3UIR3 | 3 |
| E3 ubiquitin-protein ligase HECTD1 | Hectd1 | F8WIE5 | 3 |
| E3 ubiquitin-protein ligase RING1 (EC 2.3.2.27) (Polycomb complex protein RING1) (RING finger protein 1) (RING-type E3 ubiquitin transferase RING1) (Transcription repressor Ring1A) | Ring1 Ring1A Rnf1 | O35730 | 3 |
| E3 ubiquitin-protein ligase RNF126 (EC 2.3.2.27) (RING finger protein 126) | Rnf126 | Q91YL2 | 3 |
| E3 ubiquitin-protein ligase RNF130 | Rnf130 | Q5SVR5 | 3 |
| E3 ubiquitin-protein ligase RNF19A (EC 2.3.2.-) (Double ring-finger protein) (Dorfin) (Gametogenesis-expressed protein GEG-154) (RING finger protein 19A) (UBCM4-interacting protein 117) (UIP117) (XY body protein) (XYbp) | Rnf19a Geg-154 Rnf19 Xybp | P50636 | 3 |
| E3 ubiquitin-protein ligase SMURF1 | Smurf1 | E9Q4K9 | 3 |
| E3 ubiquitin-protein ligase TRAF7 | Traf7 | F8WJF7 | 3 |
| E3 ubiquitin-protein ligase TRIM23 (EC 2.3.2.27) (ADP-ribosylation factor domain-containing protein 1) (GTP-binding protein ARD-1) (RING-type E3 ubiquitin transferase TRIM23) (Tripartite motif-containing protein 23) | Trim23 Arfd1 | Q8BGX0 | 3 |
| E3 ubiquitin-protein ligase UHRF1 (EC 2.3.2.27) (Nuclear protein 95) (Nuclear zinc finger protein Np95) (RING-type E3 ubiquitin transferase UHRF1) (Ubiquitin-like PHD and RING finger domain-containing protein 1) (mUhrf1) (Ubiquitin-like-containing PHD and RING finger domains protein 1) | Uhrf1 Np95 | Q8VDF2 | 3 |
| EF-hand calcium-binding domain-containing protein 3 | Efcab3 | Q80X60 | 3 |
| EH domain-binding protein 1-like protein 1 | Ehbp1l1 | E9QP49 | 3 |
| ELKS/Rab6-interacting/CAST family member 1 (ERC-1) (CAZ-associated structural protein 2) (CAST2) (Rab6-interacting protein 2) | Erc1 Cast2 Kiaa1081 Rab6ip2 | Q99MI1 | 3 |
| ELKS/Rab6-interacting/CAST family member 1 (Rab6 interacting protein 2, isoform CRA_b) | Erc1 Rab6ip2 mCG_131716 | V9GXP8 | 3 |
| Elongation factor 1-delta (Fragment) | Eef1d | F6ZFU0 | 3 |
| Elongation factor 1-delta (Putative uncharacterized protein) | Eef1d | Q80T06 | 3 |
| Endoglin | Eng | F7A1B4 | 3 |
| Endoglin (Putative uncharacterized protein) | Eng | Q3UAM9 | 3 |
| Endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase (EC 3.2.1.113) (ER alpha-1,2-mannosidase) (ER mannosidase 1) (ERMan1) (Man9GlcNAc2-specific-processing alpha-mannosidase) (Mannosidase alpha class 1B member 1) | Man1b1 | A2AJ15 | 3 |
| Endoplasmic reticulum metallopeptidase 1 (EC 3.4.-.-) (Felix-ina) | Ermp1 D19Wsu12e Fxna Kiaa1815 | Q3UVK0 | 3 |
| Enoyl-CoA delta isomerase 2, mitochondrial (EC 5.3.3.8) (Delta(3),delta(2)-enoyl-CoA isomerase) (D3,D2-enoyl-CoA isomerase) (Dodecenoyl-CoA isomerase) (Peroxisomal 3,2-trans-enoyl-CoA isomerase) (pECI) | Eci2 Peci | Q9WUR2 | 3 |
| Env polypeptide (Fragment) | 0 | Q61975 | 3 |
| Ephrin type-A receptor 3 (EC 2.7.10.1) (EPH-like kinase 4) (EK4) (mEK4) (Tyrosine-protein kinase TYRO4) (Tyrosine-protein kinase receptor ETK1) | Epha3 Etk1 Mek4 Tyro4 | P29319 | 3 |
| Ephrin type-A receptor 5 (EC 2.7.10.1) (Brain-specific kinase) (CEK-7) (EPH homology kinase 1) (EHK-1) | Epha5 Bsk Ehk1 | Q60629 | 3 |
| Ephrin type-A receptor 6 (EC 2.7.10.1) (EPH homology kinase 2) (EHK-2) | Epha6 Ehk-2 Ehk2 | Q62413 | 3 |
| Ephrin type-A receptor 8 (EC 2.7.10.1) (EPH- and ELK-related kinase) (Tyrosine-protein kinase receptor EEK) | Epha8 Eek | O09127 | 3 |
| Epidermal growth factor receptor pathway substrate 15 isoform B (Epidermal growth factor receptor substrate 15) | Eps15 | Q5JC28 | 3 |
| Epsilon-sarcoglycan | Sgce | F6R6P2 | 3 |
| ER degradation-enhancing alpha-mannosidase-like protein 3 (EC 3.2.1.113) (Alpha-1,2-mannosidase EDEM3) | Edem3 | Q2HXL6 | 3 |
| Erythrocyte membrane protein band 4.2 (Erythrocyte protein 4.2) (P4.2) | Epb42 Epb4.2 | P49222 | 3 |
| Ester hydrolase C11orf54 homolog (EC 3.1.-.-) | 0 | Q91V76 | 3 |
| Ethanolamine-phosphate cytidylyltransferase (EC 2.7.7.14) (CTP:phosphoethanolamine cytidylyltransferase) (Phosphorylethanolamine transferase) | Pcyt2 | Q922E4 | 3 |
| Eukaryotic elongation factor 2 kinase (eEF-2 kinase) (eEF-2K) (EC 2.7.11.20) (Calcium/calmodulin-dependent eukaryotic elongation factor 2 kinase) | Eef2k | O08796 | 3 |
| Eukaryotic translation initiation factor 3 subunit B (eIF3b) (Eukaryotic translation initiation factor 3 subunit 9) (eIF-3-eta) | Eif3b EIF3B EIF3S9 Eif3s9 | Q8CIJ3 | 3 |
| Eukaryotic translation initiation factor 3 subunit J-B (eIF3j-B) (Eukaryotic translation initiation factor 3 subunit 1-B) (eIF-3-alpha-B) (eIF3 p35) | Eif3j2 Eif3s1-2 Gm9781 | Q66JS6 | 3 |
| Eukaryotic translation initiation factor 4 gamma 2 | Eif4g2 | F7CBP1 | 3 |
| Eukaryotic translation initiation factor 5A (eIF-5A) (Fragment) | Eif5a | A0A0A0MQM0 | 3 |
| Exocyst complex component 1 | Exoc1 Sec3l1 | Q5PPR2 | 3 |
| Exosome complex component RRP4 (Exosome component 2) (Ribosomal RNA-processing protein 4) | Exosc2 Rrp4 | Q8VBV3 | 3 |
| Exosome complex component RRP40 (EC 3.1.13.-) (Exosome component 3) (Ribosomal RNA-processing protein 40) | Exosc3 Rrp40 | Q7TQK4 | 3 |
| Exosome complex component RRP45 (Autoantigen PM/Scl 1) (Exosome component 9) (P75 polymyositis-scleroderma overlap syndrome-associated autoantigen) (Polymyositis/scleroderma autoantigen 1) (Polymyositis/scleroderma autoantigen 75 kDa) (PM/Scl-75) | Exosc9 Pmscl1 | Q9JHI7 | 3 |
| Expressed sequence AU040320 | AU040320 | Z4YK56 | 3 |
| Extracellular sulfatase Sulf-1 (mSulf-1) (EC 3.1.6.-) | Sulf1 Kiaa1077 | Q8K007 | 3 |
| F-box only protein 22 | Fbxo22 Fbx22 | Q78JE5 | 3 |
| FACT complex subunit SSRP1 (Fragment) | Ssrp1 | A2AW05 | 3 |
| Fanconi anemia group I protein homolog (Protein FACI) | Fanci | Q8K368 | 3 |
| Fc fragment of IgG-binding protein | Fcgbp | E9Q0B5 | 3 |
| FERM domain-containing protein 4A | Frmd4a Frmd4 Kiaa1294 | Q8BIE6 | 3 |
| FERM domain-containing protein 6 | Frmd6 | Q8C0V9 | 3 |
| Ferric-chelate reductase 1 | Frrs1 | A0A0G2JFP4 | 3 |
| Fibroleukin (Cytotoxic T-lymphocyte-specific protein) (Fibrinogen-like protein 2) (Prothrombinase) | Fgl2 Fiblp | P12804 | 3 |
| Filamin-binding LIM protein 1 (FBLP-1) (CSX-associated LIM) | Fblim1 Cal | Q71FD7 | 3 |
| FK506-binding protein 15 (FKBP-15) (133 kDa FK506-binding protein) (133 kDa FKBP) (FKBP-133) (WASP and FKBP-like) (WAFL) | Fkbp15 Fkbp133 Kiaa0674 | Q6P9Q6 | 3 |
| Focadhesin | Focad Kiaa1797 | A2AKG8 | 3 |
| Forkhead box protein K1 (Myocyte nuclear factor) (MNF) | Foxk1 Mnf | P42128 | 3 |
| Four and a half LIM domains protein 2 (FHL-2) (Skeletal muscle LIM-protein 3) (SLIM-3) | Fhl2 | O70433 | 3 |
| Four and a half LIM domains protein 3 (FHL-3) (Skeletal muscle LIM-protein 2) (SLIM-2) | Fhl3 | Q9R059 | 3 |
| Fractalkine (C-X3-C motif chemokine 1) (CX3C membrane-anchored chemokine) (Neurotactin) (Small-inducible cytokine D1) [Cleaved into: Processed fractalkine] | Cx3cl1 Cx3c Fkn Scyd1 | O35188 | 3 |
| Fukutin-related protein (EC 2.-.-.-) | Fkrp | Q8CG64 | 3 |
| FXYD domain-containing ion transport regulator 6 (PLM-like protein) (Phosphohippolin) | Fxyd6 Plp | Q9D164 | 3 |
| FYN-binding protein (Adhesion and degranulation promoting adaptor protein) (ADAP) (FYB-120/130) (p120/p130) (FYN-T-binding protein) (SLAP-130) (SLP-76-associated phosphoprotein) | Fyb | O35601 | 3 |
| G-protein-signaling modulator 1 (Activator of G-protein signaling 3) | Gpsm1 Ags3 C10a | Q6IR34 | 3 |
| GA-binding protein alpha chain (GABP subunit alpha) | Gabpa E4tf1a | Q00422 | 3 |
| Gag-Pol polyprotein | Mela gag-pol | P70355 | 3 |
| Gag-pro-pol polyprotein | 0 | Q1KYM2 | 3 |
| Galectin | Pick1 | E9QAC6 | 3 |
| Gamma-aminobutyric acid receptor-associated protein | Gabarap | B1AR50 | 3 |
| Gamma-aminobutyric acid receptor-associated protein (GABA(A) receptor-associated protein) | Gabarap | Q9DCD6 | 3 |
| Gamma-parvin | Parvg | Q9ERD8 | 3 |
| Ganglioside-induced differentiation-associated protein 1 (GDAP1) | Gdap1 | O88741 | 3 |
| Gap junction beta-2 protein (Connexin-26) (Cx26) | Gjb2 Cxn-26 | Q00977 | 3 |
| Gap junction beta-3 protein (Connexin-31) (Cx31) | Gjb3 Cxn-31 | P28231 | 3 |
| GAS2-like protein 3 | Gas2l3 | A0A0R4J1A6 | 3 |