Table 3 Primary Non Function (PNF) miRNA interactions with the mitochondrial proteome. The table summarizes PNF miRNA interactions with identified transcripts of open reading frames (ORF), Ensembl gene identification (ENSG), location of ORF, number of nucleotides (nt), homolog protein product of ORF and ontological biological process associated with protein as identified by the Protein Database. miRDB target score range 50–100, the higher the score the more likely that a given miRNA targets given gene. Further details of protein class, protein evidence and subcellular localization from Protein Atlas are also associated with identified ORF protein. If ORF protein is recognized by Mitocarta2.0 to be a mitochondrial protein (IMPI > 0.7) it is marked as “yes” (Y) and any ascribed function is summarized.

From: An in silico argument for mitochondrial microRNA as a determinant of primary non function in liver transplantation

PNF miRNA

Gene Target

Homolog protein

Gene Ontology Biological Process

Protein class

Subcellular localization

Evidence at Protein Level

MitoCarta

miR-107

miR-103a-3p

C7orf55

UPF0562 family FMC1 (Formation of mitochondrial complex V assembly factor 1)

negative regulation of lipid catabolic process

Intracellular Protein

Mitochondrial Matrix

Y

Y mt biogenesis

ENSG00000164898

7q34

342nt

miRDB target score 61

IMPI 1

miR-23b

C5orf63

Glutaredoxin-like protein

oxidation-reduction, contains phosphorylation and O-glycosylation sites

Intracellular Protein

Mitochondrial

Transcript

—

ENSG00000164241

5q23.2

417nt

miRDB target score 64

IMPI 0.8

C2orf69

UPF0565 family UDP-glucose: NAD+ 6-oxidoreductase

oxidoreductases, specifically those acting on the CH-OH group of donor with NAD+ or NADP+ as acceptor.

Secreted protein

Mitochondrial Matrix

Y

Y

ENSG00000178074

2q33.1

1158nt

miRDB target score 99

IMPI 0.72

C15orf40

UPF0235 family

uncharacterized

Intracellular Protein

Mito and Nucleus

Y

—

ENSG00000169609

15q25.2

462nt

miRDB target score 55

IMPI 0.79

miR-194–5p

C14orf159

UPF0317 family

uncharacterized

Intracellular Protein

Mitochondrial Matrix

UPF0317 family

—

ENSG00000133943

14q32.11

1851nt

miRDB target score 61

IMPI 1

miR-296–3p

C8orf82

UPF0598 family

Redox signal transduction

Intracellular Protein

Mitochondrial Matrix and Nucleus

Y

Y mt biogenesis

ENSG00000213563

8q24.3

651nt

miRDB target score 69

IMPI 0.72

miR-940

C19orf12

Family not named Ankyrin motif

In response to oxidative stress, relocates to the cytosol forming aggregates that partially co-localize with mitochondria, apoptosis, calcium balance role, lipid metabolism.

Plasma membrane

Mitochondrial and endoplasmic reticulum

Y

—

ENSG00000131943

19q12

459nt

mIRDB target score 72

IMPI 1

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