Primer Pairs

The MGI report PRB_PrimerSeq.rpt provides associations between MGI genetic markers and primer pairs (probes¹).

To read this report using the key "primers", use the following code:

# To read all records (more than 45,000), use `read_report("primers")`.
(assoc_primers <- read_report(report_key = "primers", n_max = 30L))

## # A tibble: 30 × 10
##    marker_id   marker_symbol marker_name    chromosome genetic_map_pos primer_id
##    <chr>       <chr>         <chr>          <fct>                <dbl> <chr>    
##  1 MGI:1336996 10S           DNA segment, … 17                      NA MGI:1339…
##  2 MGI:1337121 10T           DNA segment, … 17                      NA MGI:1339…
##  3 MGI:1923536 1110006E14Rik RIKEN cDNA 11… 12                      NA MGI:5633…
##  4 MGI:1923536 1110006E14Rik RIKEN cDNA 11… 12                      NA MGI:5633…
##  5 MGI:1923536 1110006E14Rik RIKEN cDNA 11… 12                      NA MGI:5633…
##  6 MGI:2388983 116J6.1       DNA segment, … 7                       NA MGI:2389…
##  7 MGI:1337061 11S           DNA segment, … 17                      NA MGI:1339…
##  8 MGI:1337057 11T           DNA segment, … 17                      NA MGI:1339…
##  9 MGI:1337123 12T           DNA segment, … 17                      NA MGI:1339…
## 10 MGI:1337037 138017-Sp6    DNA segment, … 17                      NA MGI:1338…
## # ℹ 20 more rows
## # ℹ 4 more variables: primer_name <chr>, primer_fwd_seq <chr>,
## #   primer_rev_seq <chr>, primer_amplimer_size <chr>

Primer variables

All primer related variables are scoped with the prefix primer_. The primer_id variable is the key for a primer pair, which is also a genetic marker, so it follows the same format as values of marker_id.

Example: MGI:1923536

The primer pairs associated with marker MGI:1923536 are:

assoc_primers |>
  dplyr::filter(marker_id == "MGI:1923536") |>
  dplyr::select("marker_id", dplyr::starts_with("primer_"))

## # A tibble: 3 × 6
##   marker_id   primer_id   primer_name primer_fwd_seq      primer_rev_seq      
##   <chr>       <chr>       <chr>       <chr>               <chr>               
## 1 MGI:1923536 MGI:5633749 F1, R1      GTCGGTTGGAAAGGAGTGT TTGTGAAATAGCAGGCATCT
## 2 MGI:1923536 MGI:5633748 F3, R3      GAAAGAGGAGAAATTGGG  GTTTTCAGCACATAGTAGG 
## 3 MGI:1923536 MGI:5633746 F2, R2      TCACATCTCAATGCCACTC CCTGTACCAGACGAAATCA 
## # ℹ 1 more variable: primer_amplimer_size <chr>

Variables

marker_id

marker_id: MGI accession identifier. A unique alphanumeric character string that is used to unambiguously identify a particular record in the Mouse Genome Informatics database. The format is MGI:nnnnnn, where n is a digit.

marker_symbol

marker_symbol: marker symbol is a unique abbreviation of the marker name.

marker_name

marker_name: marker name is a word or phrase that uniquely identifies the genetic marker, e.g. a gene or allele name.

chromosome

chromosome: mouse chromosome name. Possible values are names for the autosomal, sexual or mitochondrial chromosomes.

genetic_map_pos

genetic_map_pos: genetic map position in centiMorgan (cM): a unit of length in a genetic map. Two loci are 1 cM apart if recombination is detected between them in 1% of meioses.

primer_id

primer_id: an MGI accession identifier standing for a PCR primer. A unique alphanumeric character string that is used to unambiguously identify a particular record in the Mouse Genome Informatics database. The format is MGI:nnnnnn, where n is a digit.

primer_name

primer_name: PCR primer pair name.

primer_fwd_seq

primer_fwd_seq: PCR primer forward sequence.

primer_rev_seq

primer_rev_seq: PCR primer reverse sequence.

primer_amplimer_size

primer_amplimer_size: PCR primer amplimer size, as a character vector.