Table 1.

Representative examples of protein, RNA and DNA motifs

Motif type	Example motif	Consensus sequencea	Function
Protein short linear motifs
Ligand - promote complex formation	SH3 ligand	PxxPx[KR]	Complex formation with SH3 domains [195]
	Nuclear receptor box	LxxLL	Complex formation with Nuclear receptors [196]
	LD motif	[LV][DE]x[LM][LM]xxL	Complex formation with FAT domains [197]
	LxCxE motif	[IL]xCxE	Complex formation with Rb [198]
	RGD motif	RGD	Complex formation with Integrin family members [199]
Localisation - recruit targeting and transport pathways to control protein localisation	Nuclear Export Signal (NES)	ΦxxΦxxxΦxxΦxΦ	Translocation from the nucleus to the cytoplasm [200]
	KDEL ER retrieval signal	[KH]DEL-COOH	Translocation from the Golgi to the endoplasmatic reticulum (ER) [201]
	Ciliary targeting signal	RVxP	Transport to the plasma membrane of the cilia [202]
	Peroxisomal targeting signal	[KRH]xxΦ$ or [KRH]Φ$	Import into the peroxisomal lumen [203]
	Tyrosine endocytic signal	YxxΦ	Directs endocytosis of membrane proteins [204]
Enzyme recruitment - recruit enzymes to the protein/complex to modify/demodify a site distinct from the bound motif	Cyclin docking motif	[RK]xLx{0,1}[LF]	Recruitment of the Cyclin-Cdk holoenzyme [205]
	PP1 docking motif	RVxF	Recruitment of the PP1 phosphotase holoenzyme [206]
	Tankyrase docking motif	Rxx[PGAV][DEIP]G	Recruitment of the Tankyrase poly-(ADP-ribose) polymerase [207]
	USP7 docking motif	PxxS	Recruitment of the USP7 deubiquitylating enzyme [208]
	NEDD4 docking motif	PPxY	Recruitment of the NEDD4 ubiquitylating enzyme [209]
Stability - recruit E3 ubiquitin ligases and promote substrate polyubiquitylation to control protein stability	APC/C D box degron	RxxLxxΦ	APC/C E3 ubiquitin ligase [210]
	PIP degron	Φ[ST]D[FY][FY]xxx[KR]	Recruitment of the Cdt2 CRL4 E3 ubiquitin ligase [211]
	Fbw7 degron	pTPxxp[ST]	Recruitment of the Fbw7 SCF E3 ubiquitin ligase [212]
	Oxygen dependent VHL degron	[IL]AoPx{6,8}ΦxΦ	Recruitment of von Hippel-Lindau protein (pVHL) containing E3 ubiquitin ligase [213]
	MDM2 degron	FxxxWxxΦ	Recruitment of the MDM2 ubiquitin ligase [214]
Modification - act as sites of moiety attachment/removal, isomerisation or cleavage	PIKK phosphorylation site	([ST])Q	Phosphorylation by PIKK family kinases [215]
	Pin1 isomerisation site	p[ST](P)	Isomerisation by the Pin1 phosphorylation-dependent prolyl isomerase [216]
	N-Glycosylation site	Nx([ST])	Glycosylation by Oligosaccharyltransferase [217]
	Caspase-3 and −7 cleavage motif	[DE]xxD|[AGS]	Cleavage by Caspase family proteases [218]
	Myristoylation site	NH2-M(G)xxx[AGSTCN]	Myristoylation by Myristoyl-CoA:protein N-myristoyltransferase [219]
RNA motifs
Stability	Adenosine and uridine (AU)-rich elements (ARE)	AUUUA	Recruits positive and negative regulators of mRNA stability [13]
Splicing	5′ splice junction	AG/GURAGU	Recruits splice site recognising U1 snRNA component of the spliceosome [14]
Modification	Polyadenylation signal	AUUAAA	Recruits cleavage and polyadenylation specificity factor (CPSF) to cleave and polyadenylate 3′-UTRs [15]
Localisation	Muscleblind binding motifs	YGCUKY	Targets mRNAs to membranes [16]
miRNA recruitment	miR-125b miRNA response element	CUCAGGG	Regulates expression of mutiple proteins [17]
DNA regulatory elements
Basal machinery recruitment	TATA box	TATAAAA	Recruitment of the basal transcription machinery to the core gene promoter required for initiation of transcription [9]
Promoters/Enhancers	CCAAT/enhancer binding protein (C/EBP) site	CCAAT	Promotion of gene expression [10]
Silencers/Insulators	CCCTC-binding factor (CTCF) binding site	CCGCGNGGNGGCAG	Diverse functions including acting as a transcriptional repressor and insulator [11]
Endonucleases	EcoRI restriction site	G|AATTC	Sequence specific cleavage of DNA [12]

^aPatterns are representative and roughly define the specificity of the motif binding partner. Pattern syntax for proteins: letters denote a specific amino acid; “x” denotes any amino acid; square brackets denote a subset of allowed amino acids; curly brackets denote length variability; round brackets indicate a position targeted for post-translational modification after motif recognition; “_p” denotes a phosphorylation site required for binding; “_o” denotes a hydroxylation site required for binding; “|” denotes a cleavage site; “Φ” (phi) denotes a aliphatic residue; “_NH2-” indicates the amino-terminus of the protein; “_-COOH” indicates the carboxyl-terminus of the protein. Pattern syntax for DNA and RNA: “/” denotes a splice site. “K” denotes a guanine or a uracil; “Y” denotes an adenine or a cytosine; “R” denotes an adenine or a guanine; “N” denotes any base; “|” denotes a cleavage site