Fluorescent Protein Guide: Subcellular Localization
Background
The subcellular localization of a protein is often tied to its function, so it's important to determine where your protein of interest resides. There are a variety of methods for determining subcellular localization. One of the most common is to use fluorescence microscopy to compare the localization of your protein of interest with known markers.
Addgene has assembled a collection of fluorescent fusion proteins that are targeted to various organelles or subcellular structures. You should fuse your protein of interest with a fluorescent protein that has a different emission wavelength. For example, if the marker protein is fused to GFP, you may want to fuse your protein to a red fluorescent protein (see this fusion protein guide to find the appropriate backbone). Then, by examining the overlap between your fusion protein and the marker fusion protein using fluorescence microscopy, you can assess whether your protein is targeted to the same structures as these well-characterized proteins.
General Structures
Browse or search the table below to find markers of general cellular organelles and structures.
Plasmid | Structure | Targeting Gene/Signal | Fluorescent Protein | PI | |
---|---|---|---|---|---|
H2B-mCherry | Chromatin | H2B | mCherry | Benezra | |
H2B-GFP | Chromatin | H2B | GFP | Wahl | |
pCAG-mGFP | Membrane | palmitoylation sequence from GAP43 | EGFP | Cepko | |
pPalmitoyl-mTurquoise2 | Membrane | palmitoylation sequence from p63 | mTurquoise2 | Gadella | |
pmTurquoise2-Mito | Mitochondria | COX8A(1-29) | mTurquoise2 | Gadella | |
pEBFP2-Nuc | Nucleus | NLS | EBFP2 | Campbell | |
pmTurquoise2-H2A | Nucleus | H2A | mTurquoise2 | Gadella | |
CAV1-mCherry | Caveolae | Cav1 | mCherry | Helenius | |
pABCb10-GFP | Mitochondria | ABCb10 | GFP | Shirihai | |
mCherry-Mito-7 | Mitochondria | Mitochondrialtargeting sequence(COX8A) | mCherry* | Davidson | |
mito-BFP | Mitochondria | mitochondrial targeting signal (COX4) | TagBFP | Voeltz | |
pmTurquoise2-NES | Non-nucleus | Nuclear Export Sequence | mTurquoise2 | Gadella | |
pQC NLS mCherry IX | Nucleus | NLS | mCherry | Cepko | |
pmTurquoise2-Peroxi | Peroxisomes | Peroxisomal Targeting Sequence | mTurquoise2 | Gadella | |
GFP-Mff | Mitochondria-Outer Membrane | Mff | acGFP1 | Voeltz | |
mCherry-LaminB1-10 | Nuclear Envelope | LaminB1 | mCherry* | Davidson | |
mCherry-LaminA-C-18 | Nuclear Envelope | LaminA1 | mCherry* | Davidson | |
pEGFP-C1-Fibrillarin | Nucleolus | Fibrillarin | EGFP | Huang | |
pmKalama1-Nuc | Nucleus | NLS | mKamala1 | Campbell | |
pQC NLS YFP IX | Nucleus | NLS | YFP | Cepko | |
pcDNA3.1-kappa-myc-dL5-2xG4S-TMst | Cell surface (mammalian) | PDGFR-derived | dL5 FAP (fluorogen activating protein); mCerulean3 fusion | Bruchez | |
pH2B-miRFP703 | Chromatin | H2B | miRFP703 | Verkhusha | |
pcDNA3.1-KozATG-dL5-2XG4S-mCer3 | Cytosol, nucleoplasm | None | dL5 FAP (fluorogen activating protein); mCerulean3 fusion | Bruchez | |
cfSGFP2-N | Extracellular milieu | cfSGFP2-N | EGFP | Wada | |
Lck-GFP | Membrane | palmitoylation sequence from Lck | EGFP | Green | |
pcDNA3.1-COXIV-COX8-dL5-2XG4S-mCer3 | Mitochondria | COX IV-derived (1-22 aa) import sequence and COX VIII signal peptide | dL5 FAP (fluorogen activating protein); mCerulean3 fusion | Bruchez | |
pMito-miRFP703 | Mitochondria | COX8A | miRFP703 | Verkhusha | |
mCherry-TOMM20-N-10 | Mitochondria-Outer Membrane | TOMM20 | mCherry* | Davidson | |
pmScarlet-i_NES_C1 | Non-nucleus | Nuclear Export Sequence | mScarlet-I | Gadella | |
pmScarlet-H_NES_C1 | Non-nucleus | Nuclear Export Sequence | mScarlet-H | Gadella | |
pmScarlet_NES_C1 | Non-nucleus | Nuclear Export Sequence | mScarlet | Gadella | |
pcDNA3.1-NLS-myc-dL5-2xG4S-mCer3 | Nucleus | NLS (from Mak16p protein) | dL5 FAP (fluorogen activating protein); mCerulean3 fusion | Bruchez | |
pmScarlet-i_H2A_C1 | Nucleus | H2A | mScarlet-I | Gadella | |
pmScarlet-H_H2A_C1 | Nucleus | H2A | mScarlet-H | Gadella | |
pmScarlet_H2A_C1 | Nucleus | H2A | mScarlet | Gadella | |
pTDpelB-C_sfYFPTwinStrep | Periplasmic space | PelB signal sequence | YFP | Dammeyer | |
pmScarlet-I_peroxisome_C1 | Peroxisome | SRL | mScarlet-I | Gadella | |
pmScarlet-H_peroxisome_C1 | Peroxisome | SRL | mScarlet-H | Gadella | |
pmScarlet_peroxisome_C1 | Peroxisome | SRL | mScarlet | Gadella | |
mCherry-Peroxisomes-2 | Peroxisomes | Peroximal Targeting Signal 1 (PTS1) | mCherry* | Davidson | |
pcDNA3.1-KozATG-myc-dL5-2XG4S-mCer3-SKL | Peroxisomes | SKL tripeptide, peroxisome transport signal | dL5 FAP (fluorogen activating protein); mCerulean3 fusion | Bruchez |
*Fusions to other FPs can be found by searching the complete Michael Davidson Fluorescent Protein Collection.
Cytoskeletal Elements
Browse or search the table below to find markers of cytoskeletal elements.
Plasmid | Structure | Targeting Gene/Signal | Fluorescent Protein | PI | |
---|---|---|---|---|---|
pCAG-mGFP-Actin | Actin Filaments | beta-actin | EGFP | Yasuda | |
pLifeAct-mTurquoise2 | Actin Filaments | LifeAct | mTurquoise2 | Gadella | |
GFP-UtrCH | Actin Filaments | utrophin (aa# 1-261) | GFP | Bement | |
pIRESneo-EGFP-alpha Tubulin | Microtubules | alpha-tubulin | EGFP | Wadsworth | |
pmTurquoise2-Tubulin | Microtubules | alpha-tubulin | mTurquoise2 | Gadella | |
mCh-alpha-tubulin | Microtubules | alpha-tubulin | mCherry | Voeltz | |
pPAmCherry-b-actin | Actin Filaments | beta-actin | PAmCherry1 | Verkhusha | |
mCherry-Lifeact-7 | Actin Filaments | LifeAct | mCherry* | Davidson | |
pDEST/LIfeAct-mCherry-N1 | Actin Filaments | LifeAct | mCherry | Shaw | |
pEGFP Centrin2 | Centrioles (dependent on cell cycle) | Centrin-2 | EGFP | Nigg | |
pPAmCherry-a-tubulin | Microtubules | alpha-tubulin | PAmCherry | Verkhusha | |
EMTB-3XGFP | Microtubules | ensconsin | GFP | Bement | |
EMTB-mCherry | Microtubules | ensconsin | mCherry | Bement | |
pLifeAct_mScarlet_N1 | Actin Filaments | LifeAct | mScarlet | Gadella | |
pEGFP PICH | Centromeres (dependent on cell cycle) | PICH | EGFP | Nigg | |
pEGFP-mNFM | Intermediate Filaments (neuronal) | Nefm | EGFP | Brown | |
pLifeAct-miRFP703 | Actin Filaments | LifeAct | miRFP703 | Verkhusha | |
pLifeAct_mScarlet-i_N1 | Actin Filaments | LifeAct | mScarlet-I | Gadella | |
pLifeAct_mScarlet-H_N1 | Actin Filaments | LifeAct | mScarlet-H | Gadella | |
pEGFP Cep170 C-term | Centrioles (dependent on cell cycle) | Cep170 | EGFP | Nigg | |
mEmerald-PLK1-N-16 | Centrosome | Plk1 | mEmerald* | Davidson | |
pVimentin-miRFP703 | Intermediate Filaments (vimentin) | vimentin | miRFP703 | Verkhusha | |
pKeratin-miRFP703 | Intermediate Filaments (epithelial) | Keratin | miRFP703 | Verkhusha | |
mCherry-Tubulin-C-18 | Microtubules | alpha-tubulin | mCherry* | Davidson | |
pDEST/N1-hEB1-GFP | Microtubules | EB1 | GFP | Shaw | |
pmiRFP703-Tubulin | Microtubules | alpha-tubulin | miRFP703 | Verkhusha | |
pEB3-miRFP703 | Microtubules | EB3 | miRFP703 | Verkhusha | |
pmScarlet-i_alphaTubulin_C1 | Microtubules | alpha-tubulin | mScarlet-I | Gadella | |
pmScarlet-H_alphaTubulin_C1 | Microtubules | alpha-tubulin | mScarlet-H | Gadella | |
pmScarlet_alphaTubulin_C1 | Microtubules | alpha-tubulin | mScarlet | Gadella | |
pEGFP-rNFM | Intermediate Filaments (neuronal) | Nefm | EGFP | Brown |
*Fusions to other FPs can be found by searching the complete Michael Davidson Fluorescent Protein Collection.
Cell Junctions
Browse or search the table below to find markers of cellular junctions.
Plasmid | Structure | Targeting Gene/Signal | Fluorescent Protein | PI | |
---|---|---|---|---|---|
pDEST/hCx43-EGFP-N1 | Gap Junctions | Connexin 43 | EGFP | Shaw | |
pDEST-mCherry-GJA1-20k-N1 | Gap Junctions | Connexin 43 / GJA1-20k | mCherry | Shaw | |
mCherry-Cx43-7 | Gap Junctions | Connexin 43 / GJA1-20k | mCherry* | Davidson | |
E-cadherin-GFP | Adherens junctions | E-cadherin | GFP | Stow | |
Paxillin-pEGFP | Focal adhesions | paxillin | GFP | Horwitz | |
pPaxillin-PSmOrange | Focal adhesions | paxillin | PSmOrange | Verkhusha | |
mEmerald-Paxillin-22 | Focal Adhesions | paxillin | mEmerald* | Davidson | |
mApple-VE-Cadherin-N-10 | Tight Junctions | VE-Cadherin | mApple | Davidson | |
pZyxin-miRFP703 | Focal adhesions | Zyxin | miRFP703 | Verkhusha |
*Fusions to other FPs can be found by searching the complete Michael Davidson Fluorescent Protein Collection.
Secretory Pathway
Browse or search the table below to find markers of secretory pathway components.
Plasmid | Structure | Targeting Gene/Signal | Fluorescent Protein | PI | |
---|---|---|---|---|---|
pEF.myc.ER-E2-Crimson | Endoplasmic Reticulum | ER retention signal | E2-Crimson | Glick | |
pmTurquoise2-ER | Endoplasmic Reticulum | ER retention signal | mTurquoise2 | Gadella | |
mCh-Sec61 beta | Endoplasmic Reticulum | Sec61 | mCherry | Voeltz | |
BFP-Sec61 beta | Endoplasmic Reticulum | Sec61 | BFP | Voeltz | |
BFP-KDEL | Endoplasmic Reticulum | BiP ER signal sequence | BFP | Voeltz | |
Rtn4a-GFP | Endoplasmic Reticulum | Rtn4a | AcGFP | Voeltz | |
ERoxBFP | Endoplasmic Reticulum | ER retention signal | oxBFP | Snapp | |
ERmoxGFP | Endoplasmic Reticulum | ER retention signal | moxGFP | Snapp | |
GolgiCFP | Golgi | eNOS(1-33) | CFP | Newton | |
pmTurquoise2-Golgi | Golgi | B4GALT1(1-61) | mTurquoise2 | Gadella | |
GalToxBFP | Golgi | GalT signal anchor transmembrane domain | oxBFP | Snapp | |
Clathrin-LCa-EYFP | Clathrin-coated vesicles | Clathrin, light polypeptide | EYFP | Zhuang | |
mRFP-Clc | Clathrin-coated vesicles | Clathrin, light polypeptide | mRFP | Helenius | |
mEmerald-Clathrin-15 | Clathrin-coated vesicles | Clathrin | mEmerald* | Davidson | |
DsRed-Rab5 WT | Early endosomes | RAB5A | DsRed2 | Pagano | |
mRFP-Rab5 | Early endosomes | RAB5A | mRFP | Helenius | |
mCh-Rab5 | Early endosomes | Rab5 | mCherry | Voeltz | |
BFP-Rab5 | Early endosomes | Rab5 | BFP | Voeltz | |
GFP-Rab5B | Early endosomes | Rab5B | AcGFP | Voeltz | |
GFP-Rab4B | Early endosomes | Rab4B | AcGFP | Voeltz | |
GFP-rab7 WT | Late endosomes | RAB7 | GFP | Pagano | |
DsRed-rab7 WT | Late endosomes | RAB7 | DsRed | Pagano | |
mCh-Rab7A | Late endosomes | Rab7a | mCherry | Voeltz | |
GFP-Rab7A | Late endosomes | Rab7a | AcGFP | Voeltz | |
GFP-rab11 WT | Recycling endosomes | RAB11A | GFP | Pagano | |
DsRed-rab11 WT | Recycling endosomes | RAB11A | DsRed | Pagano | |
Lamp1-YFP | Lysosomes | Lamp-1 | YFP | Mothes | |
Lamp1-RFP | Lysosomes | Lamp-1 | RFP | Mothes | |
mCherry-Lysosomes-20 | Lysosomes | LAMP1 | mCherry* | Davidson | |
pCMB-AUTr | Autophagosome | LC3(ATG8) | mCherry | Harrison | |
pEGFP-LC3 (human) | Autophagosome | LC3 | EGFP | Finkel | |
pLAMP1-miRFP703 | Lysosomes | LAMP1 | miRFP703 | Verkhusha | |
pmiRFP703-Clathrin | Clathrin-coated vesicles | Clathrin | miRFP703 | Verkhusha | |
pmScarlet-i_Giantin_C1 | Golgi apparatus | Giantin | mScarlet-I | Gadella | |
pmScarlet-H_Giantin_C1 | Golgi apparatus | Giantin | mScarlet-H | Gadella | |
pmScarlet_Giantin_C1 | Golgi apparatus | Giantin | mScarlet | Gadella | |
pCytERM_mScarlet-i_N1 | ER | CytERM | mScarlet-I | Gadella | |
pCytERM_mScarlet-H_N1 | ER | CytERM | mScarlet-H | Gadella | |
pCytERM_mScarlet_N1 | ER | CytERM | mScarlet | Gadella | |
pTag-RFP-C-h-Rab11a-c-Myc | Recycling endosomes | Rab11a | TagRFP | Johnson | |
pTag-BFP-C-h-Rab11a-c-Myc | Recycling endosomes | Rab11a | TagBFP | Johnson | |
pTag-RFP-C-h-Rab7-c-Myc | Late endosomes | Rab7 | TagRFP | Johnson | |
pTag-BFP-C-h-Rab7-c-Myc | Late endosomes | Rab7 | TagBFP | Johnson | |
pTag-RFP-C-h-Rab5a-c-Myc | Early endosomes | Rab5a | TagRFP | Johnson | |
pTag-BFP-C-h-Rab5a-c-Myc | Early endosomes | Rab5a | TagBFP | Johnson | |
pTag-RFP-C-h-Rab4a-c-Myc | Recycling endosomes | Rab4a | TagRFP | Johnson | |
pTag-BFP-C-h-Rab4a-c-Myc | Recycling endosomes | Rab4a | TagBFP | Johnson | |
pcDNA3.1-kappa-myc-dL5-2XG4S-mCer3-KDEL | Endoplasmic reticulum (ER) | KDEL | dL5 FAP (fluorogen activating protein); mCerulean3 fusion | Bruchez |
*Fusions to other FPs can be found by searching the complete Michael Davidson Fluorescent Protein Collection.

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