Explanation of Terms Used by PlasmID

TABLE HEADER TERM
Definition
SEARCH TERM Term you searched with. if this is a recognized synonym rather than the official gene symbol then your search term will not match the gene name. Click here to learn about 'official' gene symbols.
Clone ID Internal link to information about growth conditions, insert & vector, references, and more (Clone ID is assigned by PlasmID).
Original Clone ID ID of the plasmid provided by the depositor at the time of submission.
PDB ID The Protein Data Bank (PDB) ID links to the structure of the insert within this plasmid. If a PDB ID is provided, this clone was used for structure determination.
PepcDB ID PepcDB is the Protein Expression Purification Crystallization Database. It is designed to document every step of the protein production pipeline, including reference and contact information.
Clone Type Broad category the clone falls into (e.g. cDNA insert, genomic fragment insert, no insert).
GENE ID or (ORGANISM-SPECIFIC) ID External link to NCBI's Entrez Gene record for the gene (Human, mouse, HPV-16, others) or the Organism-specific ID relevant to the clone (Yeast, Pseudomonas, others).
GENE SYMBOL Official gene symbol for the gene. Click here to learn about 'official' gene symbols.
GENE NAME Full name of the gene as given by NCBI or an organism-specific database.
Reference Sequence Sequence that the insert was INTENDED to be (for example, target sequence in a large-scale ORF cloning project). Not necessarily an exact match or same limits as the actual insert.
MUTATION Is not necessarily the final word on differences between your clone and a reference sequence! We use "mutation" to show clones that were made from a mutant allele or were intentionally engineered to have a mutation (for example, a change introduced to create a dominant negative form of a gene). Other differences can be present: see "DISCREPANCIES" and "FORMAT" (fusion v. closed) and make note that a tag/fusion protein ORF (such as GST, EGFP or Myc) might be a feature of the INSERT or of the VECTOR. Check both to be sure you have learned all you can about the clone!
DISCREPANCY Is language adopted from the Harvard Institute of Proteomics that alerts you to nucleotide differences between the reference sequence (the sequence the researcher(s) intended to clone) and the actual clone. Discrepancies may be silent or conserved substitutions, naturally occurring polymorphisms, splice variants, PCR-introduced errors, small deletions, or other difference that creates a difference between the actual clone and the reference sequence. Click on the clone sequence in the clone page and then do a conceptual translation or BLAST search to see if the clone is acceptable for your needs.
INSERT FORMAT Is language adopted from the Harvard Institute of Proteomics and distinguishes cDNA/ORFs in which the natural stop codon is present (CLOSED) from those in which the natural stop codon was purposely changed in order to create/allow C-terminal fusions (FUSION). For clones in recombinational vectors, the 'acceptor' or 'expression' vector you choose will determine what C-terminal fusion is made.
VECTOR Internal link to information about the vector, including features, properties, PDF file of map and text of sequence (when available), references, and more.
SELECTION MARKERS Resistance genes or similar present in the clone for selection (note that selection is listed for a particular host cell/organism).
DISTRIBUTION Information on any limits to distribution on the clone. The majority of clones are limited to academic and non-profit labs but additional restrictions and/or special treatment (see below) may apply.
Max Identity (%)/ Alignment Length This field refers to the alignment of the Blast input (query) sequence to its matched (subject) sequence and indicates the maximum percentage of identical nucleotides or amino acids within the noted alignment length. Click here for more information about Blast.
Max Alignment Length/ Identity (%) This field refers to the alignment of the Blast input (query) sequence to matched (subject) sequence and indicates the maximum alignment length between the input and match and the percentage identity within this length. Click here for more information about Blast.
OTHER TERMS
Definition
IS VERIFIED and VERIFICATION METHOD "Is verified" indicates whether or note the DONOR lab verified the insert/clone by some method (for example, by sequencing the insert or restriction enzyme digestion and analysis of fragments) and "verification method" tells you what method was used. This does NOT mean that we confirmed this information by any method. As is always the case, it's best to confirm the identity of the plasmid by some appropriate method before you use the clone. We welcome your feedback -- if you find a clone isn't what you thought it was, please let us know as soon as possible.
SPECIAL MTA Information on additional MTAs required for specific clones (for example, a CRE-specific MTA for CRE-containing clones).
PLASMID CLONE Defined in PlasmID as vector (required) + an insert (optional) = clone.
VECTOR The vector used in the construct. Only when we list the vector as a CLONE do we actually have the empty vector in our collection.
cDNA Partial or full-length cDNA inserts cloned directly or via PCR from a cDNA template. Please note that human clones from HIP were cloned from cDNA so they're listed as such but they contain only the open reading frame (no 5' or 3' UTR). Other cDNA clones in the collection may or may not have partial or complete UTRs.
ORF cDNA-like fragment that was cloned based on annotation of ORFs on a particular genome (for example, all of the predicted ORFs from Pseudomonas were cloned by the Harvard Institute of Proteomics -- not cDNAs -- and thus, the ORF clones may not be the same as what you'd get with a collection based on cDNAs).
 
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