Housekeeping gene

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This article is about the general topic of housekeeping genes. For a list of housekeeping genes that should be used as reference standard, see reference genes.

In molecular biology, housekeeping genes are typically constitutive genes that are required for the maintenance of basic cellular function, and are expressed in all cells of an organism under normal and patho-physiological conditions.[1][2][3][4] Although some housekeeping genes are expressed at relatively constant rates in most non-pathological situations, the expression of other housekeeping genes may vary depending on experimental conditions.[1][5]

The origin of the term "housekeeping gene" remains obscure. Literature from 1976 used the term to describe specifically tRNA and rRNA.[6] For experimental purposes, the expression of one or multiple housekeeping genes is used as a reference point for the analysis of expression levels of other genes. The key criterion for the use of a housekeeping gene in this manner is that the chosen housekeeping gene is uniformly expressed with low variance under both control and experimental conditions. Validation of housekeeping genes should be performed before their use in gene expression experiments such as RT-PCR. Recently a web-based database of human and mouse housekeeping genes and reference genes/transcripts, named Housekeeping and Reference Transcript Atlas (HRT Atlas), was developed to offer updated list of housekeeping genes and reliable candidate reference genes/transcripts for RT-qPCR data normalization.[1] This database can be accessed at http://www.housekeeping.unicamp.br.

Housekeeping gene regulation[]

Housekeeping genes account for majority of the active genes in the genome, and their expression is obviously vital to survival. The housekeeping gene expression levels are fine-tuned to meet the metabolic requirements in various tissues. Biochemical studies on transcription initiation of the housekeeping gene promoters have been difficult, partly due to the less-characterized promoter motifs and transcription initiation process.

Human housekeeping gene promoters are generally depleted of TATA-box, have high GC content and high incidence of CpG Islands.[7] In Drosophila, where promoter specific CpG Islands are absent, housekeeping gene promoters contain DNA elements like DRE, E-box or DPE.[8] Transcription start sites of housekeeping genes can span over a region of around 100 bp whereas transcription start sites of developmentally regulated genes are usually focused in a narrow region.[9][10][11] Little is known about how the dispersed transcription initiation of housekeeping gene is established. There are transcription factors that are specifically enriched on and regulate housekeeping gene promoters.[12][13] Furthermore, housekeeping promoters are regulated by housekeeping enhancers but not developmentally regulated enhancers.[14]

Common housekeeping genes in humans[]

The following is a partial list of "housekeeping genes." For a more complete and updated list, see HRT Atlas database compiled by Bidossessi W. Hounkpe et al.[1] The database was constructed by mining more than 12000 human and mouse RNA-seq datasets.[1]

Gene expression[]

Transcription factors[]

Sterol Regulatory Element Binding Protein
  • ATF1 NM_005171
  • ATF2 NM_001880
  • ATF4[2][15] Activating transcription factor 4 NM_001675
  • ATF6 NM_007348
  • ATF7 NM_001206682
  • ATF7IP NM_018179
  • BTF3[2][15] NM_001207 Homo sapiens basic transcription factor 3
  • E2F4[2] Homo sapiens E2F transcription factor 4, p107/p130-binding (E2F4), mRNA
  • ERH (gene)[2][15] Enhancer of rudimentary homolog of drosophila (which in turn is the first enzymatic step in pyrimidine synthesis. Regulated by MITF)
  • HMGB1[2][15] High mobility group box binds DNA
  • ILF2[2] Homo sapiens interleukin enhancer binding factor 2, 45kDa (ILF2), mRNA
  • [2] formerly ETR101 Immediate Early Protein?
  • JUND[2][15] Homo sapiens jun D proto-oncogene (JUND), mRNA
  • TCEB2[2][15] Elongin Matheo er rar
Repressors[]
  • PUF60[2][15] Homo sapiens fuse-binding protein-interacting repressor (SIAHBP1), transcript

RNA splicing[]

Small nuclear ribonucleoprotein-associated proteins B and B'
  • BAT1[15] aka
  • HNRPD[2][15] Homo sapiens heterogeneous nuclear ribonucleoprotein D (AU-rich element RNA
  • HNRPK[2][15] Homo sapiens heterogeneous nuclear ribonucleoprotein K (HNRPK), transcript
  • PABPN1[2] poly(A) binding protein, nuclear 1
  • [15] splicing factor, arginine/serine-rich

Translation factors[]

tRNA synthesis[]
  • AARS NM_001605 alanyl-tRNA synthetase
  • AARS2 NM_020745 alanyl-tRNA synthetase 2, mitochondrial
  • NM_001261434 alanyl-tRNA synthetase domain containing 1
  • NM_001751 cysteinyl-tRNA synthetase
  • NM_024537 cysteinyl-tRNA synthetase 2, mitochondrial (putative)
  • DARS NM_001349 aspartyl-tRNA synthetase
  • NM_018122 aspartyl-tRNA synthetase 2, mitochondrial
  • NM_001083614 glutamyl-tRNA synthetase 2, mitochondrial
  • FARS2 NM_006567 phenylalanyl-tRNA synthetase 2, mitochondrial
  • FARSA NM_004461 phenylalanyl-tRNA synthetase, alpha subunit
  • FARSB NM_005687 phenylalanyl-tRNA synthetase, beta subunit
  • GARS NM_002047 glycyl-tRNA synthetase
  • HARS NM_002109 histidyl-tRNA synthetase
  • HARS2 NM_012208 histidyl-tRNA synthetase 2, mitochondrial
  • IARS NM_002161 isoleucyl-tRNA synthetase
  • NM_018060 isoleucyl-tRNA synthetase 2, mitochondrial
  • KARS NM_005548 Homo sapiens lysyl-tRNA synthetase (KARS), mRNA
  • LARS2 NM_015340 isoleucyl-tRNA synthetase 2, mitochondrial
  • MARS NM_004990 methionyl-tRNA synthetase
  • NM_138395 methionyl-tRNA synthetase 2, mitochondrial
  • NARS NM_004539 asparaginyl-tRNA synthetase
  • NM_024678 asparaginyl-tRNA synthetase 2, mitochondrial (putative)
  • QARS NM_005051 glutaminyl-tRNA synthetase
  • RARS NM_002884 arginyl-tRNA synthetase
  • NM_020320 arginyl-tRNA synthetase 2, mitochondrial
  • SARS NM_006513 Homo sapiens seryl-tRNA synthetase (SARS), mRNA
  • TARS NM_152295 threonyl-tRNA synthetase
  • VARS2 NM_020442 valyl-tRNA synthetase 2, mitochondrial
  • WARS2 NM_015836 tryptophanyl tRNA synthetase 2, mitochondrial
  • YARS NM_003680 Homo sapiens tyrosyl-tRNA synthetase (YARS), mRNA
  • NM_001040436 Homo sapiens tyrosyl-tRNA synthetase (YARS), mRNA mitochondrial
RNA binding protein[]

Ribosomal proteins[]

RPS19BP1

Mitochondrial ribosomal proteins[]

RNA polymerase[]

Protein processing[]

  • PPID Peptidyl-prolyl cis-trans isomerase D
  • PPIE Peptidyl-prolyl cis-trans isomerase E
  • PPIF Peptidyl-prolyl cis-trans isomerase F
  • PPIG Peptidyl-prolyl cis-trans isomerase G
  • PPIH[17] Cyclophilin H
  • CANX[2][15] Calnexin. Folding of glycoproteins within endoplasmic reticulum
  • CAPN1 Calpain subunit
  • CAPNS1[2][15] Calpain protease subunit
  • NACA[2][15] Nascent polypeptide associated complex alpha polypeptide
  • PFDN2 Prefoldin 2
  • PFDN4 Prefoldin 4
  • PFDN5 Prefoldin 5
  • PFDN6 Prefoldin 6
  • SNX2 Sorting nexin 2
  • SNX3[2] Sorting nexin 3
  • SNX4 Sorting nexin 4
  • SNX5 Sorting nexin 5
  • SNX6 Sorting nexin 6
  • SNX9 Sorting nexin 9
  • Sorting nexin 12
  • SNX13 Sorting nexin 13
  • SNX17[15] Sorting nexin 17
  • SNX18 Sorting nexin 18
  • Sorting nexin 19
  • Sorting nexin 25
  • SSR1 Translocon-associated protein TRAPA. Protein translocation in ER
  • SSR2[2] Translocon-associated protein TRAPB. Protein translocation in ER
  • Translocon-associated protein TRAPG. Protein translocation in ER
  • SUMO1 Protein targeting
  • SUMO3 Protein targeting

Heat shock proteins[]

Histone[]

Cell cycle[]

There is significant overlap in function with regards to some of these proteins. In particular, the Rho-related genes are important in nuclear trafficking (i.e.: mitosis) as well as with mobility along the cytoskeleton in general. These genes of particular interest in cancer research.

  • ARHGAP5
  • ARHGDIA[2][15]
  • Rho guanine nucleotide exchange factor 10L
  • ARHGEF11 Rho guanine nucleotide exchange factor 11
  • Rho guanine nucleotide exchange factor 40
  • ARHGEF7 Rho guanine nucleotide exchange factor 7
  • RAB10 NM_016131 The small GTPases Rab are key regulators of intracellular membrane trafficking, from the formation of transport vesicles to their fusion with membranes
  • RAB11A NM_004663
  • RAB11B NM_004218
  • RAB14 NM_016322
  • RAB18 NM_021252
  • RAB1A NM_004161 Homo sapiens RAB1A, member RAS oncogene family (RAB1A), mRNA
  • RAB1B NM_030981
  • RAB21 NM_014999
  • RAB22A NM_020673
  • RAB2A NM_002858
  • RAB2B NM_001163380
  • RAB3GAP1 NM_012233
  • RAB3GAP2 NM_012414
  • NM_021168
  • RAB4A NM_004578
  • RAB5A NM_004162
  • RAB5B NM_002865
  • RAB5C NM_004583
  • RAB6A NM_002868
  • RAB7A NM_004637
  • RAB9A NM_004251
  • RABEP1 NM_004703
  • RABEPK NM_005833
  • RABGEF1 NM_014504
  • NM_004581
  • NM_004582
  • CENPB[2] Centromere protein B
  • CTBP1[2][15] Centromere protein T
  • CCNB1IP1 NM_021178 E3 ubiquitin-protein ligase. Modulates cyclin B levels and participates in the regulation of cell cycle progression through the G2 phase
  • CCNDBP1 NM_012142 May negatively regulate cell cycle progression
  • CCNG1 NM_004060 May play a role in growth regulation
  • CCNH NM_001239 Involved in cell cycle control and in RNA transcription by RNA polymerase II. Its expression and activity are constant throughout the cell cycle
  • CCNK NM_001099402 Regulatory subunit of cyclin-dependent kinases that mediates phosphorylation of the large subunit of RNA polymerase II
  • CCNL1 NM_020307 Transcriptional regulator which participates in regulating the pre-mRNA splicing process
  • CCNL2 NM_030937 Transcriptional regulator which participates in regulating the pre-mRNA splicing process. Also modulates the expression of critical apoptotic factor, leading to cell apoptosis.
  • CCNY NM_145012 Positive regulatory subunit of the cyclin-dependent kinases CDK14/PFTK1 and CDK16. Acts as a cell-cycle regulator of Wnt signaling pathway during G2/M phase
  • PPP1CA NM_002708 Protein phosphatase that associates with over 200 regulatory proteins to form highly specific holoenzymes which dephosphorylate hundreds of biological targets
  • PPP1CC NM_002710
  • PPP1R10 NM_002714
  • PPP1R11 NM_021959 Homo sapiens protein phosphatase 1, regulatory (inhibitor) subunit 11 (PPP1R11),
  • NM_032833
  • NM_019121
  • PPP1R7 NM_002712
  • PPP1R8 NM_002713
  • PPP2CA NM_002715
  • PPP2CB NM_001009552
  • PPP2R1A NM_014225 [15] Negative regulator of growth and cell divisionHomo sapiens protein phosphatase 2 (formerly 2A), regulatory subunit A (PR 65),
  • PPP2R2A NM_002717
  • PPP2R2D NM_018461
  • PPP2R3C NM_017917
  • PPP2R4 NM_021131
  • PPP2R5A NM_006243
  • PPP2R5B NM_006244
  • PPP2R5C NM_002719
  • PPP2R5D NM_006245
  • PPP2R5E NM_006246
  • PPP4C NM_002720
  • PPP4R1 NM_005134
  • NM_174907
  • PPP5C NM_006247
  • PPP6C NM_002721
  • NM_014678
  • PPP6R3 NM_018312
  • RAD1Homo sapiens ribonuclease/angiogenin inhibitor (RNH), mRNA
  • RAD17 NM_002869 Essential for sustained cell growth, maintenance of chromosomal stability, and ATR-dependent checkpoint activation upon DNA damage
  • RAD23B NM_002873
  • RAD50 NM_005732
  • RAD51C NM_002874
  • [2][15] (locates to central dividing line of dividing cells)

Apoptosis[]

  • DAD1[2][15] Defender against cell death
  • DAP3[2] Involved in mediating interferon-gamma-induced cell death.
  • DAXX[2] Death Associated Protein 6

Oncogenes[]

DNA repair/replication[]

  • MCM3AP[2] possibly a primase
  • XRCC5 NM_021141 Ku80[2]
  • XRCC6 NM_001469 Homo sapiens thyroid autoantigen: Single-stranded DNA-dependent ATP-dependent helicase. Has a role in chromosome translocation.

Metabolism[]

  • PRKAG1[2] Senses energy level and inactivates HMGCoA reductase and Acetyl CoA Carboxylase
  • PRKAA1 NM_006251 Catalytic subunit of AMP-activated protein kinase (AMPK), an energy sensor protein kinase that plays a key role in regulating cellular energy metabolism
  • PRKAB1 NM_006253 Non-catalytic subunit of AMP-activated protein kinase (AMPK), an energy sensor protein kinase that plays a key role in regulating cellular energy metabolism
  • PRKACA NM_002730 Phosphorylates a large number of substrates in the cytoplasm and the nucleus.
  • PRKAG1 NM_002733 Homo sapiens protein kinase, AMP-activated, gamma 1 non-catalytic subunit (PRKAG1), mRNA
  • PRKAR1A NM_002734 Regulatory subunit of the cAMP-dependent protein kinases involved in cAMP signaling in cells
  • NM_024653 Binds double-stranded RNA. Inhibits EIF2AK2 kinase activity (By similarity).

Carbohydrate metabolism[]

[15]

Citric Acid Cycle[]

  • SDHA[2] NM_004168 Succinate Dehydrogenase subunit A
  • SDHAF2 NM_017841
  • SDHB NM_002973 Iron-sulfur protein (IP) subunit of succinate dehydrogenase (SDH) that is involved in complex II of the mitochondrial electron transport chain and is responsible for transferring electrons from succinate to ubiquinone (coenzyme Q)
  • SDHC NM_003000 Membrane-anchoring subunit of succinate dehydrogenase (SDH) that is involved in complex II of the mitochondrial electron transport chain and is responsible for transferring electrons from succinate to ubiquinone (coenzyme Q).
  • SDHD NM_003001

Lipid metabolism[]

  • HADHA[2] Trifunctional protein subunit alpha

Amino acid metabolism[]

  • COMT[2] Catechol-O-methyl transferase)

NADH dehydrogenase[]

  • NDUFA2NM_002488[2]
  • NDUFA3 NM_004542
  • NDUFA4 NM_002489
  • NDUFA5 NM_005000
  • NDUFA6 NM_002490
  • NDUFA7[2] NM_005001 Homo sapiens NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 7, 14.5kDa
  • NDUFA8 NM_014222
  • NDUFA9 NM_005002
  • NDUFA10 NM_004544
  • NDUFA11 NM_175614
  • NDUFA12 NM_018838
  • NDUFA13 NM_015965
  • NDUFAF2 NM_174889
  • NDUFAF3 NM_199069
  • NDUFAF4 NM_014165
  • NDUFB2 NM_004546
  • NDUFB3 NM_002491
  • NDUFB4 NM_004547
  • NDUFB5 NM_002492
  • NDUFB6 NM_002493
  • NDUFB7[2] NM_004146 Homo sapiens NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 7, 18kDa
  • NDUFB10 NM_004548
  • NDUFB11 NM_019056
  • NDUFB8 NM_005004
  • NDUFB9 NM_005005
  • NDUFC1[2] NM_002494Homo sapiens NADH dehydrogenase (ubiquinone) 1, subcomplex unknown, 1, 6kDa
  • NDUFC2 NM_004549
  • NM_001203260
  • NDUFS5[2]
  • NDUFV2[2]
  • NDUFS2 NM_004550
  • NDUFS3 NM_004551
  • NDUFS4 NM_002495
  • NDUFS5 NM_004552 Homo sapiens NADH dehydrogenase (ubiquinone) Fe-S protein 5, 15kDa
  • NDUFS6 NM_004553
  • NDUFS7 NM_024407
  • NDUFS8 NM_002496
  • NDUFV1 NM_007103 Homo sapiens NADH dehydrogenase (ubiquinone) flavoprotein 1, 51kDa (NDUFV1),
  • NDUFV2 NM_021074 Homo sapiens NADH dehydrogenase (ubiquinone) flavoprotein 2, 24kDa (NDUFV2),

Cytochrome C oxidase[]

(Note that COX1, COX2, and COX3 are mitochondrially encoded)

  • COX4I1[2] 001861
  • COX5B[2][15] NM_001862
  • COX6B1[2][15] NM_001863
  • COX6C NM_004374
  • COX7A2 NM_001865 Homo sapiens cytochrome c oxidase subunit VIIa polypeptide 2 (liver) (COX7A2),
  • COX7A2L[2] NM_004718
  • COX7C[2] NM_001867
  • [2]
  • COX8A NM_004074 Homo sapiens cytochrome c oxidase subunit VIII (COX8), nuclear gene encoding
  • NM_004375
  • COX14 NM_032901
  • COX15 NM_004376
  • NM_016468
  • NM_001031617
  • COX20 NM_198076
  • CYC1[2] Homo sapiens cytochrome c-1 (CYC1)
  • UQCC NM_018244 Required for the assembly of the ubiquinol-cytochrome c reductase complex (mitochondrial respiratory chain complex III or cytochrome b-c1 complex)
  • NM_013387
  • UQCR11 NM_006830 Homo sapiens ubiquinol-cytochrome c reductase (6.4kD) subunit (UQCR), mRNA
  • UQCRB NM_006294
  • UQCRC1 NM_003365 Homo sapiens ubiquinol-cytochrome c reductase core protein I (UQCRC1), mRNA
  • UQCRC2 NM_003366
  • NM_001089591
  • UQCRQ NM_014402 Homo sapiens low molecular mass ubiquinone-binding protein (9.5kD) (QP-C), mRNA

ATPase[]

  • ATP2C1 NM_014382
  • ATP5A1 NM_004046 Homo sapiens ATP synthase, H+ transporting, mitochondrial F1 complex, alpha
  • ATP5B NM_001686
  • ATP5C1 NM_005174
  • ATP5D NM_001687 Homo sapiens ATP synthase, H+ transporting, mitochondrial F1 complex, delta
  • ATP5F1 NM_001688
  • ATP5G2 NM_005176
  • ATP5G3 NM_001689 Homo sapiens ATP synthase, H+ transporting, mitochondrial F0 complex, subunit c
  • ATP5H NM_006356 Homo sapiens ATP synthase, H+ transporting, mitochondrial F0 complex, subunit d
  • ATP5J NM_001685
  • ATP5J2 NM_004889 Homo sapiens ATP synthase, H+ transporting, mitochondrial F0 complex, subunit f,
  • NM_001198879
  • ATP5L NM_006476
  • ATP5O NM_001697 Homo sapiens ATP synthase, H+ transporting, mitochondrial F1 complex, O subunit
  • ATP5S NM_015684
  • ATP5SL NM_018035
  • ATP6AP1 NM_001183 Homo sapiens ATPase, H+ transporting, lysosomal interacting protein 1 (ATP6IP1),
  • ATP6V0A2 NM_012463
  • ATP6V0B NM_004047 Homo sapiens ATPase, H+ transporting, lysosomal 21kDa, V0 subunit c (ATP6V0B),
  • ATP6V0C NM_001694 Homo sapiens ATPase, H+ transporting, lysosomal 16kDa, V0 subunit c (ATP6V0C),
  • ATP6V0D1 NM_004691
  • ATP6V0E1 NM_003945
  • ATP6V1C1 NM_001695
  • ATP6V1D NM_015994
  • ATP6V1E1 NM_001696 Homo sapiens ATPase, H+ transporting, lysosomal 31kDa, V1 subunit E isoform 1
  • ATP6V1F NM_004231 Homo sapiens ATPase, H+ transporting, lysosomal 14kDa, V1 subunit F (ATP6V1F),
  • ATP6V1G1 NM_004888 Homo sapiens ATPase, H+ transporting, lysosomal 13kDa, V1 subunit G isoform 1
  • ATP6V1H NM_015941
  • ATPAF2 NM_145691
  • ATPIF1 NM_016311

Lysosome[]

  • CTSD[2][15] can degrade insulin in hepatocytes
  • CSTB[2] May protect cell from leaking lysosomes
  • LAMP1[2][15]
  • LAMP2
  • M6PR[2][15]

Proteasome[]

  • PSMA1 NM_002786
  • PSMA2 NM_002787
  • PSMA3 NM_002788
  • PSMA4 NM_002789
  • PSMA5 NM_002790
  • PSMA6 NM_002791
  • PSMA7 NM_002792 Homo sapiens proteasome (prosome, macropain) subunit, alpha type, 7 (PSMA7),
  • PSMB1 NM_002793 Homo sapiens proteasome (prosome, macropain) subunit, beta type, 1 (PSMB1), mRNA
  • PSMB2 NM_002794 Homo sapiens proteasome (prosome, macropain) subunit, beta type, 2 (PSMB2), mRNA
  • PSMB3 NM_002795
  • PSMB4 NM_002796 Homo sapiens proteasome (prosome, macropain) subunit, beta type, 4 (PSMB4), mRNA
  • PSMB5 NM_002797
  • PSMB6 NM_002798
  • PSMB7 NM_002799 Homo sapiens proteasome (prosome, macropain) subunit, beta type, 7 (PSMB7), mRNA
  • PSMC2 NM_002803
  • PSMC3 NM_002804
  • PSMC4 NM_006503
  • PSMC5 NM_002805
  • PSMC6 NM_002806
  • PSMD1 NM_002807
  • PSMD10 NM_002814
  • PSMD11 NM_002815 Homo sapiens proteasome (prosome, macropain) 26S subunit, non-ATPase, 11
  • PSMD12 NM_002816
  • PSMD13 NM_002817
  • PSMD14 NM_005805
  • PSMD2 NM_002808
  • PSMD3 NM_002809
  • PSMD4 NM_002810
  • PSMD5 NM_005047
  • PSMD6 NM_014814
  • PSMD7 NM_002811
  • PSMD8 NM_002812 Homo sapiens proteasome (prosome, macropain) 26S subunit, non-ATPase, 8 (PSMD8),
  • PSMD9 NM_002813
  • PSME2 NM_002818 Homo sapiens proteasome (prosome, macropain) activator subunit 2 (PA28 beta)
  • PSME3 NM_005789
  • PSMF1 NM_006814
  • NM_020232
  • NM_032302
  • NM_001128591
  • UBA1 NM_003334 Homo sapiens ubiquitin-activating enzyme E1 (A1S9T and BN75 temperature
  • UBA2 NM_005499
  • NM_003968
  • UBA5 NM_024818
  • UBA52 NM_003333
  • NM_177967
  • NM_145253
  • UBAP1 NM_016525
  • UBAP2L NM_014847
  • UBB NM_018955 Homo sapiens ubiquitin B (UBB), mRNA
  • UBC NM_021009 Homo sapiens ubiquitin C (UBC), mRNA
  • UBE2A NM_003336
  • UBE2B NM_003337
  • UBE2D2 NM_003339 Homo sapiens ubiquitin-conjugating enzyme E2D 2 (UBC4/5 homolog, yeast)
  • UBE2D3 NM_003340
  • NM_015983
  • UBE2E1 NM_003341
  • UBE2E2 NM_152653
  • UBE2E3 NM_006357
  • NM_080678
  • UBE2G2 NM_003343
  • UBE2H NM_003344
  • UBE2I NM_003345 Homo sapiens ubiquitin-conjugating enzyme E2I (UBC9 homolog, yeast) (UBE2I),
  • UBE2J1 NM_016021
  • NM_058167
  • NM_005339
  • UBE2L3 NM_003347
  • UBE2M NM_003969 Homo sapiens ubiquitin-conjugating enzyme E2M (UBC12 homolog, yeast) (UBE2M),
  • UBE2N NM_003348
  • NM_001012989
  • NM_017582
  • UBE2R2 NM_017811
  • UBE2V1 NM_021988
  • UBE2V2 NM_003350
  • NM_018299
  • UBE2Z NM_023079
  • UBE3A NM_000462
  • NM_130466
  • UBE3C NM_014671
  • UBE4A NM_004788
  • UBE4B NM_006048
  • USP10 NM_005153
  • USP14 NM_005151
  • USP16 NM_006447
  • USP19 NM_006677
  • USP22 NM_015276
  • USP25 NM_013396
  • USP27X NM_001145073
  • USP33 NM_015017
  • NM_032557
  • USP39 NM_006590
  • USP4 NM_003363
  • USP47 NM_017944
  • USP5 NM_003481
  • USP7 NM_003470
  • USP8 NM_005154
  • USP9X NM_001039590

Ribonuclease[]

Thioreductase[]

Structural[]

Cytoskeletal[]

[2][17] [18]

  • ANXA6[2]
  • ANXA7
  • ARPC1A Actin-related peptide
  • ARPC2
  • CAPZA2
  • CAPZB[2][15]
  • RHOA[2][15] also implicated in regulation of cell cycle
  • RHOB
  • RHOT1 mitochondrial trafficking
  • RHOT2
  • TUBB[2][15] Tubulin, beta polypeptide
  • WDR1[2][15] actin disassembly?

Organelle synthesis[]

A specialized form of cell signaling

  • BLOC1S1[2][15]
  • BLOC1S2NM_173809
  • NM_212550
  • NM_018366
  • NM_012388
  • AP1G1 NM_001128
  • AP1M1 NM_032493
  • AP2A1 NM_014203
  • AP2A2 NM_012305
  • AP2M1[2]
  • AP2S1 NM_004069
  • AP3B1 NM_003664
  • AP3D1 NM_003938
  • AP3M1 NM_012095
  • AP3S1 NM_001284
  • AP3S2 NM_005829
  • AP4B1 NM_006594
  • NM_018229
  • ANXA6[2] Annexin 6
  • ANXA7[15] Annexin 7
  • AP1B1[2][15] Coated vesicles
  • CLTA[2] Clathrin A (vesicles)
  • CLTB[2][15] Clathrin B (vesicles)
  • CLTC

Mitochondrion[]

Surface[]

Cell adhesion[]

  • CTNNA1 NM_001903
  • CTNNB1[2]
  • CTNNBIP1 NM_020248
  • CTNNBL1 NM_030877
  • CTNND1 NM_001085458 delta catenin[15]

Channels and transporters[]

  • NM_012089
  • ABCB7 NM_004299
  • ABCD3 NM_002857
  • ABCE1 NM_002939
  • ABCF1 NM_001090
  • ABCF2 NM_005692
  • NM_018358
  • CALM1[2][15] Calmodulin grasps calcium ions
  • NM_024311 similar to MSFD10 aka TETRAN or tetracycline transporter-like protein[2]
  • NM_174983
  • NM_138431
  • NM_032889
  • SLC15A4 NM_145648
  • SLC20A1 NM_005415
  • SLC25A11[2] mitochondrial oxoglutarate/malate carrier
  • NM_173471
  • NM_031212
  • SLC25A3 NM_002635
  • NM_030780
  • SLC25A38 NM_017875
  • SLC25A39 NM_016016
  • NM_014655
  • SLC25A46 NM_138773
  • SLC25A5 NM_001152
  • SLC27A4 NM_005094
  • SLC30A1 NM_021194
  • NM_022902
  • NM_006345
  • SLC35A2 NM_005660
  • NM_080670
  • NM_005827
  • SLC35B2 NM_178148
  • SLC35C2 NM_015945
  • NM_024881
  • NM_018656
  • NM_025181
  • SLC38A2 NM_018976
  • SLC39A1 NM_014437
  • SLC39A3 NM_144564
  • SLC39A7 NM_006979
  • SLC41A3 NM_017836
  • SLC46A3 NM_181785
  • NM_017842

Receptors[]

  • ACVR1 NM_001105 similar to ACVRL1 TGF Beta receptor family Rendu-Osler-Weber syndrome
  • ACVR1B NM_004302
  • CD23[2] FCER2 low affinity IgE receptor (lectin)

HLA/immunoglobulin/cell recognition[]

  • BAT1[2] aka DDX39B which is involved in RNA splicing
  • BSG[2] Basigin Immunoglobulin Superfamily, extracelluar metalloproteinase
  • MIF[2][15] macrophage migration inhibitory factor
  • TAPBP[2]

Kinases/signalling[]

  • ADRBK1[2] can downregulate response to epinephrine
  • AGPAT1[2][15] acyl 3 phosphoglycerol acyl transferase
  • ARF1[2][15]
  • ARF3[2]
  • ARF4[2]
  • ARF5[2][15]
  • ARL2[2][15] RAS Superfamily
  • CSF1[2] Colony stimulating factor not highly expressed constitutively at 5-12
  • CSK C-src tyrosine kinase[2]
  • DCT[2][15] dopachrome tautomerase
  • EFNA3[2]
  • FKBP1A[2][15]
  • GDI1[2] GDP Dissociation inhibitor (Rab family)
  • GNAS1[2] ubiquitously expressed, but differentially imprinted
  • GNAI2[2][15]
  • HAX1[2][15] associated with tyrosine kinases
  • ILK[2] Integrin linked kinase
  • MAPKAPK2[2]
  • MAP2K2[2][15]
  • MAP3K11[2]
  • [2] Phosphatidylinositol transfer protein
  • RAC1[2][15] Ro GTPase involved with many signaling pathways
  • RAP1B[2][15] GTPase involved with cell adhesion
  • [2][15] Ras-related GTP Binding
  • STK19[2]
  • STK24[2] Serine/Threonine Kinase
  • STK25[15]
  • YWHAB[2][15] Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, beta polypeptide
  • YWHAH[2][15] Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, h polypeptide
  • YWHAQ[2][15] Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide
  • YWHAZ[2][15] Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide

Growth factors[]

Tissue necrosis factor[]

  • CD40[2] formerly TNFRSF5

Casein kinase[]

Miscellaneous[]

  • ALAS1 Aminolevulinic Acid Synthase type 1 (type 2 is erythroid and associated with porphyria)
  • ARHGEF2[2] Rho guanine nucleotide exchange factor
  • ARMET[2][15] Mesencephalic astrocyte-derived neurotrophic factor
  • [2][15] amino terminal enhancer of split
  • BECN1[2] involved in autophagy and partners with PI3K
  • [2] formerly Maternal G10 transcript
  • Creatine kinase[2] CKB (ATP reservoir)
  • Cytidine deaminase[2] questionable: not present in very high levels at all
  • CPNE1[2]
  • ENSA (gene)[2]
  • FTH1[2] Heavy chain of Ferritin
  • GDI2[2] rab/ras vesicular trafficking
  • GUK1[2][15] Guanylate kinase transfers phosphate from ATP to GMP
  • HPRT[2][17][18] Hypoxanthine-guanine phosphoribosyltransferase
  • IFITM1[2] Induced by interferon, transmembrane protein
  • JTB (gene)[2][15] Jumping translocation breakpoint
  • [2]
  • NME2[2][15] (formerly NM23B) Nucleoside diphosphate kinase
  • NONO[2][17]
  • P4HB[2][15]
  • PRDX1[2] peroxiredoxin (reduces peroxides)
  • PTMA[2] Prothymosin
  • RPA2[2] Binds DNA during replication to keep it straightened out
  • SULT1A3[2] Sulfate conjugation (note: SULT1C is cited in earlier literature as being ubiquitous [15] 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)
  • [2][15] Synaptogyrin (may participate in vesicle translocation)
  • Tetratricopeptide, TTC1[2] small glutamine rich tetratricopeptide

Open_reading_frame[]

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

See also[]

References[]

  1. ^ a b c d e Hounkpe, Bidossessi Wilfried; Chenou, Francine; de-Lima, Franciele; De-Paula, Erich Vinicius (2020-07-14). "HRT Atlas v1.0 database: redefining human and mouse housekeeping genes and candidate reference transcripts by mining massive RNA-seq datasets". Nucleic Acids Research: gkaa609. doi:10.1093/nar/gkaa609. ISSN 0305-1048. PMC 7778946.
  2. ^ a b c d e f g h i j k l m n o p q r s t u v w x y z aa ab ac ad ae af ag ah ai aj ak al am an ao ap aq ar as at au av aw ax ay az ba bb bc bd be bf bg bh bi bj bk bl bm bn bo bp bq br bs bt bu bv bw bx by bz ca cb cc cd ce cf cg ch ci cj ck cl cm cn co cp cq cr cs ct cu cv cw cx cy cz da db dc dd de df dg dh di dj dk dl dm dn do dp dq dr ds dt du dv dw dx dy dz ea eb ec ed ee ef eg eh ei ej ek el em en eo ep eq er es et eu ev ew ex ey ez fa fb fc fd fe ff fg fh fi fj fk fl fm fn fo fp fq fr fs ft fu fv fw Eisenberg E, Levanon EY (July 2003). "Human housekeeping genes are compact". Trends in Genetics. 19 (7): 362–5. arXiv:q-bio/0309020. doi:10.1016/S0168-9525(03)00140-9. PMID 12850439.
  3. ^ Butte AJ, Dzau VJ, Glueck SB (December 2001). "Further defining housekeeping, or "maintenance," genes Focus on "A compendium of gene expression in normal human tissues"". Physiological Genomics. 7 (2): 95–6. doi:10.1152/physiolgenomics.2001.7.2.95. PMID 11773595.
  4. ^ Zhu J, He F, Hu S, Yu J (October 2008). "On the nature of human housekeeping genes". Trends in Genetics. 24 (10): 481–4. doi:10.1016/j.tig.2008.08.004. PMID 18786740.
  5. ^ Greer S, Honeywell R, Geletu M, Arulanandam R, Raptis L (April 2010). "Housekeeping genes; expression levels may change with density of cultured cells". Journal of Immunological Methods. 355 (1–2): 76–9. doi:10.1016/j.jim.2010.02.006. PMID 20171969.
  6. ^ Rifkind RA, Marks PA, Bank A, Terada M, Maniatis GM, Reuben R, Fibach E (Nov–Dec 1976). "Erythroid differentiation and the cell cycle: some implications from murine foetal and erythroleukemic cells". Annales d'Immunologie. 127 (6): 887–93. PMID 1070288.
  7. ^ Smale ST, Kadonaga JT (2003). "The RNA polymerase II core promoter". Annual Review of Biochemistry. 72: 449–79. doi:10.1146/annurev.biochem.72.121801.161520. PMID 12651739.
  8. ^ Rach EA, Winter DR, Benjamin AM, Corcoran DL, Ni T, Zhu J, Ohler U (January 2011). "Transcription initiation patterns indicate divergent strategies for gene regulation at the chromatin level". PLoS Genetics. 7 (1): e1001274. doi:10.1371/journal.pgen.1001274. PMC 3020932. PMID 21249180.
  9. ^ Ni T, Corcoran DL, Rach EA, Song S, Spana EP, Gao Y, Ohler U, Zhu J (July 2010). "A paired-end sequencing strategy to map the complex landscape of transcription initiation". Nature Methods. 7 (7): 521–7. doi:10.1038/nmeth.1464. PMC 3197272. PMID 20495556.
  10. ^ Carninci P, Sandelin A, Lenhard B, Katayama S, Shimokawa K, Ponjavic J, et al. (June 2006). "Genome-wide analysis of mammalian promoter architecture and evolution". Nature Genetics. 38 (6): 626–35. doi:10.1038/ng1789. PMID 16645617.
  11. ^ Hoskins RA, Landolin JM, Brown JB, Sandler JE, Takahashi H, Lassmann T, et al. (February 2011). "Genome-wide analysis of promoter architecture in Drosophila melanogaster". Genome Research. 21 (2): 182–92. doi:10.1101/gr.112466.110. PMC 3032922. PMID 21177961.
  12. ^ Lam KC, Mühlpfordt F, Vaquerizas JM, Raja SJ, Holz H, Luscombe NM, et al. (2012). "The NSL complex regulates housekeeping genes in Drosophila". PLoS Genetics. 8 (6): e1002736. doi:10.1371/journal.pgen.1002736. PMC 3375229. PMID 22723752.
  13. ^ Lam KC, Chung HR, Semplicio G, Iyer SS, Gaub A, Bhardwaj V, et al. (February 2019). "The NSL complex-mediated nucleosome landscape is required to maintain transcription fidelity and suppression of transcription noise". Genes & Development. 33 (7–8): 452–465. doi:10.1101/gad.321489.118. PMC 6446542. PMID 30819819.
  14. ^ Zabidi MA, Arnold CD, Schernhuber K, Pagani M, Rath M, Frank O, Stark A (February 2015). "Enhancer-core-promoter specificity separates developmental and housekeeping gene regulation". Nature. 518 (7540): 556–9. doi:10.1038/nature13994. PMC 6795551. PMID 25517091.
  15. ^ a b c d e f g h i j k l m n o p q r s t u v w x y z aa ab ac ad ae af ag ah ai aj ak al am an ao ap aq ar as at au av aw ax ay az ba bb bc bd be bf bg bh bi bj bk bl bm bn bo bp bq br bs bt bu bv bw bx by bz ca cb cc cd ce cf cg ch ci cj ck cl cm cn co Velculescu VE, Madden SL, Zhang L, Lash AE, Yu J, Rago C, Lal A, Wang CJ, Beaudry GA, Ciriello KM, Cook BP, Dufault MR, Ferguson AT, Gao Y, He TC, Hermeking H, Hiraldo SK, Hwang PM, Lopez MA, Luderer HF, Mathews B, Petroziello JM, Polyak K, Zawel L, Kinzler KW (December 1999). "Analysis of human transcriptomes". Nature Genetics. 23 (4): 387–8. doi:10.1038/70487. PMID 10581018.
  16. ^ Hsiao LL, Dangond F, Yoshida T, Hong R, Jensen RV, Misra J, et al. (December 2001). "A compendium of gene expression in normal human tissues". Physiological Genomics. 7 (2): 97–104. CiteSeerX 10.1.1.333.2656. doi:10.1152/physiolgenomics.00040.2001. PMID 11773596.
  17. ^ a b c d e f Quiagen. "RT2 Profiler PCR Array (96-Well Format and 384-Well Format". Qiagen Catalog No. 330231 PAHS-00ZA.
  18. ^ a b c Caradec J, Sirab N, Keumeugni C, Moutereau S, Chimingqi M, Matar C, Revaud D, Bah M, Manivet P, Conti M, Loric S (March 2010). "'Desperate house genes': the dramatic example of hypoxia". British Journal of Cancer. 102 (6): 1037–43. doi:10.1038/sj.bjc.6605573. PMC 2844028. PMID 20179706.

External links[]

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