How is vector name assigned?

Components used in a vector (e.g. promoters & ORFs) are automatically assigned names in most cases. These component names are then automatically assembled to produce the final vector name. Rules for assigning names are described below.

Rules for assigning names to vector components (e.g. promoters, ORFs or linkers)

  • Components from VectorBuilder's popular component collections: The component's common name is used.
    Example: CMV, EGFP, Neo

  • ORFs retrieved from VectorBuilder's gene-based databases: Gene symbol followed by RefSeq accession number or VectorBuilder ORF collection number in brackets is used as name. A species abbreviation in lower case is added in front of the gene symbol following the rules below:

    • Human, mouse and rat are assigned single-letter abbreviations “h”, “m” and “r”, respectively.
    • Many additional common species are assigned two-letter abbreviations. For example, cat is “ct”, chimpanzee is “ch”, and dog is “dg”.
    • Less common species use three-letter abbreviations of their scientific names, followed by an underscore. The first letter in the abbreviation corresponds to the first letter of the genus name, and the next two letters in the abbreviation correspond to the first two letters of the species name. For example, Drosophila melanogaster is “dme_”.
    Example of a human ORF from NCBI RefSeq collection: hRHO[NM_000539.3]
    Example of a mouse ORF from VectorBuilder ORF collection: mRho[ORF032112]
    Example of a Drosophila melanogaster ORF from NCBI RefSeq collection: dme_w[NM_057439.2]
  • Sequences pasted by user: User must define the name of their pasted sequence in order to add the sequence to the vector. User defined name will be shown in brackets. Please note that if the user pasted a sequence that has 100% sequence identity to a component in VectorBuilder’s databases, the component name will be automatically set to the official name of the VectorBuilder component.
    Example of a user pasted component: {MyGene}

  • ORF from VectorBuilder’s database that is edited by user: When an ORF retrieved from VectorBuilder’s ORF database has been edited by the user to introduce mutations, a * will be automatically added next to the official ORF name to indicate that the ORF sequence is mutated. The user can then choose to use this name or change it to a different name. If the user chooses to change the name, brackets will be added to indicate that the name is defined by the user. Please note that epitope tags added to an ORF through the Add Tag function are not considered as mutations. Example of an ORF from VectorBuilder’s database that is edited by user: hRHO[NM_000539.3]* for automatically assigned name, which can be changed by the user to another name such as {MyGene}

Rules for allowing users to change automatically assigned names

In order to ensure consistency, users cannot change automatically assigned component names under most circumstances. But there are a few exceptions as listed below:

  • When a component’s sequence is pasted by the user, the user must assign a name for it. Brackets will be added to indicate that the name is defined by the user.
  • When an ORF retrieved from VectorBuilder’s ORF database has been edited by the user to introduce mutations, a * will be automatically added next to the official ORF name. The user can choose to use this name or change it to a different name. If the user chooses to change the name, brackets will be added to indicate that the name is defined by the user.

Rules for assigning vector names

  • All vector names begin with the letter “p”.
  • Abbreviation for vector backbone is given after the letter “p”. Below are examples of commonly used backbones:
    RP: Regular plasmid
    LV: Lentivirus
    MMLV: MMLV retrovirus
    AV: Adenovirus
    AAV: Adeno-associated virus
    PB: PiggyBac transposon
    Tol2: Tol2 transposon
    ET, BAD or CS: Various bacterial expression vectors
    SC: Saccharomyces cerevisiae
    BV: Baculovirus
  • Abbreviations for biological applications, if applicable, is given in brackets after the vector backbone abbreviation. Below are examples of common biological applications:
    Exp: A vector for expressing a gene of interest
    shRNA: A vector for expressing shRNA for use in knockdown
    gRNA: A vector for expressing gRNA for use in the CRISPR system
    En: A vector for testing enhancer activity

Rules for assembling vector name as illustrated by an example

Vector name: pLV[Exp]-Hygro-CMV>FLAG/hRHO[NM_000539.3]*/10xHis:IRES:3xNLS/EGFP/HA

Interpretations:

LV: Vector backbone is lentivirus.

Exp: Biological application is mammalian gene expression.

Hygro: Marker gene is hygromycin B resistance gene.

CMV: Promoter for driving the gene of interest is CMV.

FLAG/hRHO[NM_000539.3]*/10xHis:IRES:3xNLS/EGFP/HA: The gene of interest is a polycistron containing multiple ORFs. The first ORF is hRHO[NM_000539.3], whose sequence is modified by the user (indicated by *), and is tagged with FLAG at the N terminus and 10xHis at the C terminus. It is followed by IRES, and then followed by the second ORF, which is EGFP tagged with 3xNLS at the N terminus and HA at the C terminus.