Housekeeping gene

A housekeeping gene is typically a constitutive gene that is required for the maintenance of basic cellular function, and are found in all cells of an organism. Although some housekeeping genes are expressed at relatively constant levels (such as HSP90 and Beta-actin), other housekeeping genes may vary depending on experimental conditions. The origin of the term "housekeeping gene" remains obscure. Literature from 1976 used the term to describe specifically tRNA and rRNA. Interpreting gene expression data can be problematic, with most human genes registering 5-10 copies per cell (possibly representing error). Housekeeping genes are expressed in at least 25 copies per cell and sometimes number in the thousands.

[[Image:Biological cell.svg|thumb|400px|Diagram of a typical [[animalia|animal]] (eukaryotic) cell, showing subcellular components.

Organelles: (1) nucleolus (2) nucleus (3) ribosome (4) vesicle (5) rough endoplasmic reticulum (ER) (6) Golgi apparatus (7) Cytoskeleton (8) smooth endoplasmic reticulum (9) mitochondria (10) vacuole (11) cytoplasm (12) lysosome (13) centrioles within centrosome]]

Transcription Factors



 * ATF4 Activating transcription factor 4
 * BTF3
 * E2F4
 * ERH (gene) Enhancer of rudimentary homolog of drosophila (which in turn is the first enzymatic step in pyrimidine synthesis.  Regulated by MITF)
 * HMGB1 High mobility group box binds DNA
 * ILF2
 * IER2 formerly ETR101 Immediate Early Protein
 * JUND
 * LTBP4
 * LMO1 Rhombotin 1
 * MYC also considered an oncogene when mutated regulates transcription of 15% of all genes
 * PAX8
 * PHF1 Plant homology domain
 * PTTG1IP
 * SREBF1 Sterol Regulatory Element Binding Protein Smith Magenis
 * TBP aka TATA-binding protein or GTF2D or TFIID
 * TCEB2 Elongin
 * TCOF1 interacts with UBF to translate rRNA

Repressors

 * ANF91, HPF7, HTF10 Kruppel Associated Box domain
 * ID3 (gene) inhibits DNA binding
 * PUF60
 * NFKBIA Suppresses NF-kappa
 * RING1

RNA Splicing

 * ADAR
 * BAT1
 * FBL Fibrillarin
 * HNRPD
 * HNRPK
 * PTBP1
 * PABPN1
 * SFRS3
 * SFRS9
 * SFNRPA
 * SNRPB
 * SNRPD
 * SNRPD2
 * SNRPG

Translation Factors

 * EIF1 aka SUI1
 * EIF3C formerly EIF3S8
 * EIF3D formerly EIF3S4
 * EIF3F formerly EIF3S5
 * EIF3I formerly EIF3S2
 * EIF3G formerly EIF3S7
 * EIF4A2
 * EIF4G2
 * TUFM Tu translational elongation factor mitochondrial

tRNA Synthetases

 * IARS
 * KARS
 * RARS
 * SARS
 * VARS2
 * YARS

RNA Binding Protein

 * PABPC1 PolyA Binding Protein
 * ELAVL3

Ribosomal Proteins

 * RPL3
 * RPL5
 * RPL8
 * RPL9
 * RPL10
 * RPL11
 * RPL12
 * RPL13
 * RPL13A Introns contain genes for small nucleolar RNAs U32, U33, U34, and U35
 * RPL14
 * RPL15
 * RPL17
 * RPL18
 * RPL19
 * RPL25
 * RPL27
 * RPL29
 * RPL30
 * RPL32
 * RPL34
 * RPL35
 * RPL36
 * RPL37
 * RPL38
 * RPL40 transcribed with ubiquitin (see FAU (gene))
 * RPLP1
 * RPLP2
 * RPS2
 * RPS5
 * RPS9
 * RPS10
 * RPS11
 * RPS12
 * RPS13
 * RPS14
 * RPS15
 * RPS16
 * RPS18
 * RPS19
 * RPS20
 * RPS23
 * RPS24
 * RPS25
 * RPS26
 * RPS27 transcribed with ubiquitin (see FAU (gene))
 * RPS28
 * RPS30 transcribed with ubiquitin as the FAU (gene)


 * RPN1 Ribophorin anchors the ribosome to rough endoplasmic reticulum


 * MRPL9

RNA Polymerase

 * POLR2A
 * POLR2E
 * POLR2J
 * POLR2L

Protein Processing

 * Cyclophilin A Serine-threonine phosphatase inhibitor involved in protein folding
 * CANX Folding of glycoproteins within endoplasmic reticulum
 * CAPNS1 Calpain protease
 * NACA Nascent polypeptide associated complex alpha polypeptide
 * PFDN1 Prefoldin 1
 * PFDN5 Prefoldin 5
 * SNX3 Sorting nexin
 * SNX17
 * SNX27
 * SSR2 Protein translocation in ER
 * SUMO2 Protein targeting

Heat Shock Proteins

 * HSPA8
 * HSP90AB1
 * HSBP1

Histone

 * CDH4 Nucleosome remodeling
 * HIST1H2BC
 * H2AFY Histone 2 Subfamily
 * H2AFZ essential for embryogenesis
 * H3F3A H3 Histone Famiy

Cell Cycle

 * ARHGAP1
 * ARHGDIA
 * CENPB Centromere protein B
 * CTBP1
 * cyclophilin
 * CCND3
 * GAS1 Blocks entry into S phase
 * PPP2CB Negative regulator of growth and cell division
 * PPP2R1A Negative regulator of growth and cell division
 * RAD9
 * KIAA0174 or IST1 homolog (locates to central dividing line of dividing cells)

Apoptosis

 * DAD1 Defender against cell death
 * DAP (gene)
 * DAXX Death Associated Protein 6

Oncogenes

 * ARAF
 * MAZ (gene)
 * MYC also considered a transcription factor
 * SAFB
 * RAB1A

DNA Repair/Replication

 * Ku80 aka XRCC5
 * MCM3AP possibly a primase

Metabolism

 * PRKAG1 Senses energy level and inactivates HMGCoA reductase and Acetyl CoA Carboxylase

Carbohydrate Metabolism

 * PRKCSH Glucosidase 2, subunit beta (activated by PKC)
 * B4GALT2
 * GUSB Beta Glucuronidase Sly syndrome
 * Chitinase
 * Phosphogluconate dehydrogenase
 * GSK3A
 * hexokinase rate limiting step? no reference
 * H6PD
 * Glucose-6-phosphate isomerase
 * Phosphofructokinase 1
 * Aldolase A
 * Aldolase C
 * Triosephosphate isomerase
 * GAPDH
 * Phosphoglycerate kinase
 * Phosphoglycerate mutase
 * Enolase
 * PKM2 Pyruvate kinase, muscle
 * Lactate dehydrogenase
 * LDHB Lactate dehydrogenase
 * TALDO1 Transaldolase in pentose shunt
 * Transketolase
 * TSTA3 Mannose metabolism

Citric Acid Cycle

 * SDHA Succinate Dehydrogenase subunit A
 * MDH1 Malate dehydrogenase

Lipid Metabolism

 * GM2A not highly expressed constitutively
 * HADHA Trifunctional protein subunit alpha
 * HADHB Trifunctional protein subunit beta

Amino Acid Metabolism

 * COMT Catechol-O-methyl transferase
 * GGTLA1 Gamma glutamyl transferase-like 1
 * PHGDH Phosphoglycerate dehydrogenase (first and rate-limiting step of serine biosynthesis)
 * ODC1
 * TPMT

Nucleotide Synthesis

 * IMPDH2 Guanine Nucleotide biosynthesis

NADH Dehydrogenase

 * NDUFA1
 * NDUFA2
 * NDUFA7
 * NDUFB7
 * NDUFC1
 * NDUFS5
 * NDUFV2
 * DIA1

Cytochrome C Oxidase
(Note that COX1, COX2, and COX3 are mitochondrially encoded)
 * COX4I1
 * COX5A
 * COX5B
 * COX6A1
 * COX6B1
 * COX7A2L
 * COX7C
 * COX8
 * CYC1
 * UQCRC1
 * UQCRH
 * UQCRQ see Cytochrome C1

Mitochondrial

 * ATP5A1
 * ATP5D
 * ATP5G1
 * ATP5G3
 * ATP5H
 * ATP5I
 * ATP5J2
 * ATP5O

Lysosomal

 * ATP6IP1 ?
 * ATP6V0B
 * ATP6V0C
 * ATP6VE1
 * ATP6V1F
 * ATP6V1G1

Lysosome

 * CTSD can degrade insulin in hepatocytes
 * Cystatin B May protect cell from leaking lysosomes
 * LAMP1
 * Mannose 6-phosphate receptor
 * SGSH Mutations can cause Sanfilippo syndrome

Proteosome

 * PSMB1
 * PSMB2
 * PSMB4
 * PSMB6
 * PSMA7
 * PSMB7
 * PSMD8
 * PSMD11
 * PSME2
 * UBA1
 * Ubiquitin B
 * UBE2I
 * UBE2D2
 * UBE2M
 * USP11

Ribonuclease

 * RNH Ribonuclease inhibitor

Oxidase/Reductase

 * TXN Thioreductase

Cytoskeletal

 * Actinin alpha 4
 * ACTG1 gamma actin
 * ADD1
 * ANXA6
 * ARPC4 Actin-related protein 2/3 complex
 * Beta-actin
 * CAPZB
 * COL6A1
 * DNCL1 Cytoplasmic Dynein
 * EZR Ezrin (anchors actin to plasma membrane)
 * KIFC3 kinesin
 * Moesin
 * MYH9 Myosin chain 9
 * RHOA also implicated in regulation of cell cycle
 * SEPT1 homologus to CDC10 in S. cerevesiae
 * SEPT2
 * SLC9A3R2 Links SLC9A3 to cytoskeleton
 * TAGLN
 * TAGLN2
 * TMSB10 Thymosin beta 10
 * TUBB Tubulin, beta polypeptide
 * TUBB4
 * WDR1 actin dissassembly?

Organelle Synthesis
A specialized form of cell signaling
 * BLOC1S1
 * AP2M1
 * ANXA2
 * ANXA6
 * ANXA7
 * AP1B1 Coated vessicles
 * CLTA Clathrin A (vessicles)
 * CLTB Clathrin B (vessicles)
 * GP2 (gene) enzymatic secretory granules (hugely upregulated in pancreas)
 * KDELR1 Lys-Asp-Glu-Leu tag that targets to endoplasmic reticulum

Mitochondrion

 * MTX1

Surface

 * AP2S1
 * CD81
 * GPAA1
 * LGALS9
 * MGAT1
 * VAMP3

Cell Adhesion

 * ADAM15
 * Beta-catenin
 * CNTN1 Contactin
 * Delta-catenin

Channels and Transporters

 * ABCG2 formerly BCRP1 xenobiotic transporter (not expressed in great amounts in most tissues)
 * CALM1 Calmodulin grasps calcium ions
 * CALM2 Calmodulin grasps calcium ions
 * HPCAL1 also grasps calcium; upregulated in retina
 * GRIK5
 * MFSD10 aka TETRAN or tetracycline transporter-like protein
 * TFRC Transferrin receptor
 * FOLR1 Folate receptor
 * SLC25A11 mitochondrial oxoglutarate/malate carrier

Receptors

 * ACVRL1 TGF Beta receptor family Rendu-Osler-Weber syndrome
 * CD23A FCER2 low affinity IgE receptor (lectin)
 * GRM4 Metabotropic glutamate receptor
 * JAG1 NOTCH2 Receptor associated with Alagille syndrome
 * MC2R Melanocortin receptor type 2 (similar to ACTH receptor)
 * SSTR5 Somatostatin receptor tends to inhibit other hormones

HLA/Immunoglobulin/Cell recognition

 * BAT1
 * BSG Basigin Immunoglobulin Superfamily, extracelluar metalloproteinase
 * B2M Beta-2 microglobulin
 * HLAC
 * HLAG
 * MIF macrophage migration inhibitory factor
 * TAPBP

Kinases/Signalling

 * ADRBK1 can downregulate response to epinephrine
 * AGPAT1 acyl 3 phosphoglycerol acyl transferase
 * ARF1
 * ARF3
 * ARF4
 * ARF5
 * ARL2 RAS Superfamily
 * CSF1 Colony stimulating factor not highly expressed constitutively at 5-12
 * C-src tyrosine kinase
 * DCT dopachrome tautomerase
 * EFNA3
 * FKBP1A
 * GDI1 GDP Dissociation inhibitor (Rab family)
 * GNAS1 ubiquitously expressed, but differentially imprinted
 * GNAI2
 * HAX1 associated with tyrosine kinases
 * ILK Integrin linked kinase
 * MAPKAPK2
 * MAP2K2
 * MAP3K11
 * PITPNM Phosphatidylinositol transfer protein
 * RAC1 Ro GTPase involved with many signaling pathways
 * RAP1B GTPase involved with cell adhesion
 * RAGA Ras-related GTP Binding
 * STK19
 * STK24 Serine/Threonine Kinase
 * STK25
 * YWHAB Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, beta polypeptide
 * YWHAH Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, h polypeptide
 * YWHAQ Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide
 * YWHAZ Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide

Growth Factors

 * AIF1
 * HDGF Hepatoma derived growth factor (translocates to nucleus)
 * HGS
 * LTBP4
 * VEGFB
 * ZFP36L1

Tissue Necrosis Factor

 * CD40 formerly TNFRSF5

Casein Kinase

 * CSNK1E
 * CSNK2B

Miscellaneous
tetratricopeptide''
 * ALAS1 Aminolevulinic Acid Synthase type 1 (type 2 is erythroid and associated with porphyria)
 * ARHGEF2 Rho guanine nucleotide exchange factor
 * ARMET Mesencephalic astrocyte-derived neurotrophic factor
 * AES amino terminal enhancer of split
 * BECN1 involved in autophagy and partners with PI3K
 * BUD31 formerly Maternal G10 transcript
 * Creatine kinase CKB (ATP reservoir)
 * Cytidine deaminase questionable: not present in very high levels at all
 * CPNE1
 * ENSA (gene)
 * FTH1 Heavy chain of Ferritin
 * GDI2 rab/ras vessicular trafficking
 * GUK1 Guanylate kinase transfers phosphate from ATP to GMP
 * HPRT Hypoxanthine-guanine phosphoribosyltransferase
 * IFITM1 Induced by interferon, transmembrane protein
 * JTB (gene) Jumping translocation breakpoint
 * MMPL2
 * NME2 (formerly NM23B) Nucleoside diphosphate kinase
 * NONO
 * P4HB
 * PRDX1 peroxiredoxin (reduces peroxides)
 * PTMA Prothymosin
 * RPA2 Binds DNA during replication to keep it straightened out
 * SULT1A3 Sulfate conjugation (note: SULT1C is cited in earlier literature as being ubiquitous but this may be an example of different tags being used to refer to a common area of 2 closely related genes. If the tag is too short, then it may not be specific enough to truly specify one member of a gene family from another)
 * SYNGR2 Synaptogyrin (may participate in vessicle translocation)
 * Tetratricopeptide, TTC1 ''small glutamine rich

Open_reading_frame

 * C11Orf13
 * C14orf2
 * C21orf33

Sperm/Testis
Although this page is devoted to genes that should be ubiquitously expressed, this section is for genes whose current name reflects their relative upregulation in testes
 * SPAG7
 * SRM Spermidine synthase
 * TEGT Bax-1 inhibitor
 * DAZAP2 Deleted in azoospermia
 * MEA1 Male enhanced antigen