miRNA Naming Standards
miRNA (microRNA) is a genome encoded non-coding RNA molecule containing about 20~23 nucleotides, which functions in degradation of RNA-induced silencing complex (RISC) or inhibits its translation via base-pairing with target mRNA.
miRNA (microRNA) is evolutionarily conserved, which implies that the miRNA (microRNA) found in plants, animals and some viruses mostly expresses in the specific tissue and development stage. The tissue specificity and time sequence of miRNA (microRNA) decide the function specificity for tissues and cells, which indicates that miRNA plays various roles in the regulating process for cell growth and development.
miRBase sequence database is one of the leading public databases to store miRNA information, providing published miRNA (microRNA) sequences and annotations. Currently, the total amount of miRNAs recorded in miRBase (Release 21.0) has already exceeded 35,000.
①For miRNA (microRNA) found before naming convention, keep the original name, such as has-let-7;
②Mature miRNA (microRNA) is abbreviated as miR. Based on the species name and discovery orders, add Arabic numbers, such as has-miR-122;
③For the highly homologous miRNA (microRNA), add lower-alpha (a, b, c,…) behind its numbers, such as has-miR-34a, hsa-miR-34b, hsa-miR-34c, etc;
④For miRNA (microRNA) with same mature sequence transcribed from DNA sequences on various chromosomes, add Arabic numbers in the end for differentiation, such as hsa-miR-199a-1and hsa-miR-199a-2;
⑤Generally, the precursor length for a miRNA (microRNA) is about 70~80nt, which might respectively produce miRNA (microRNA) by two arms.
Traditional Method: No need to add any symbol for the miRNA (microRNA) with higher expression level and add * for the ones with lower expression level, such as rno-miR-9*. Sometimes, miRNA (microRNA) with * will never appear.
However, if there are no obvious expression differences, then respectively name after “-5p” and “-3p”. For example, hsa-miR-26b-5p and hsa-miR-26b-3p respectively indicate they are processed from 5’end and 3’end of precursor has-mir-26b.
For the previous naming convention, sometimes, “-s” and “-as” will be used, which has already been canceled now.
Note: miRBase 18.0 has made large modifications to the mature miRNA (microRNA). Most of miRNAs (microRNA) with * are changed to “-5p” or “-3p”. Surely, new name will still correspond to its original name.
Case Studies: http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000442
2) miRNA Reference Number and Name (eg. animal miRNA)
miRBase records the precursor sequence and mature sequence for miRNA (microRNA), of which:
① Precursor miRNA (microRNA)
The precursor transcript of hairpin structural miRNA (microRNA) will be named after “mir” and its reference number will be with “MI”, such as the precursor ID for human miRNA122 is hsa-mir-122 with Accession MI0000442.
② Mature miRNA (microRNA)
Mature miRNA (microRNA) with 20~23nt will be named after “miR” and its reference number will be with “MIMAT”. Human miR-122 has two mature bodies, which one of their IDs is hsa-miR-122-5p with Accession MIMAT0000421 and the other one is hsa-miR-122-3p with Accession MIMAT000 4590.
Case Studies: http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000442
①Animal:
Precursor miRNA (microRNA): abbreviation for animal species +“-”+ mir+“-”+ as naming sequence, such as hsa-mir-122;
Mature miRNA (microRNA): abbreviation for animal species +“-”+ miR+“-”+ as naming sequence, such as hsa-miR-122-5p;
②Plant:
Precursor miRNA (microRNA): abbreviation for plant species +“-”+ MIR+ as naming sequence, such as ath-MIR156a. Note: MIR are upper case and no “-“ between naming sequence;
Mature miRNA (microRNA): abbreviation for plant species +“-”+ miR+ as naming sequence, such as ath-miR156a. Note: miR are lower case and no “-“ between naming sequence;
③ Virus:
Precursor miRNA (microRNA): abbreviation for virus species +“-”+ mir+ as naming sequence, such as bhv1-mir-B1;
Mature miRNA (microRNA): abbreviation for virus species +“-”+ miR+ as naming sequence, such as hv1-miR-B1.

1) Most of miRNAs (microRNA) genes are transcribed by RNA polymerases II, generating longer stem loop structure which is called primary miRNA (primary miRNA, pri-miRNA).
2) Under the function of Drosha-DGCR8 complex, Pri-miRNA will form into hairpin RNA with 60-70 nucleotides and become precursor miRNA (precursor miRNA, pre-miRNA).
3) Subsequently, under the influence of Exprotin-5 complex [2], pre-miRNA will be transferred out of nucleus, and becomes the miRNA (microRNA) complex by cleavage of Dicer in cytoplasm. miRNA (microRNA) complex (RNA-induced silencing complex, RISC) will be connected with miRNA 3’UTR into P-body (processing body) of cytoplasm.
4) Mode of action is related to matching level:
①If miRNA (microRNA) is complete matching with target mRNA, then mRNA will be degraded by this complex;
②If both sequences are partial matching, especially the called seed sequence for miRNA (microRNA) 5’ end 2-8 nucleotides are complete matching with target mRNA, then inhibit target mRNA translation to silence specific genes;
③Some reports show that partial miRNAs can regulate the epigenetics alterations by matching with DNA;
④In addition, some miRNAs (microRNA), such as miRNA-16 that can specifically combine with AU rich element (AU rich element, ARE) contained in 3’UTR of some genes, guide Ago proteins in RISC region to bond to TTP to further change the corresponding half-life for mRNA and accelerate target mRNA degradation.