qPrimerDB - qPCR Primer Database

A resource for real-time quantitative PCR primers

Version: 1.1

Birds_and_Reptiles

Anas platyrhynchos
Gallus gallus
Meleagris gallopavo
Pelodiscus sinensis
Taeniopygia guttata

Fish

Astyanax mexicanus
Danio rerio
Gadus morhua
Gasterosteus aculeatus
Latimeria chalumnae
Lepisosteus oculatus
Oreochromis niloticus
Oryzias latipes
Petromyzon marinus
Poecilia formosa
Takifugu rubripes
Xiphophorus maculatus

Insecta

Acromyrmex echinatior
Aedes aegypti
Anopheles coluzzii
Anopheles stephensi
Apis dorsata
Apis florea
Apis mellifera
Athalia rosae
Bactrocera cucurbitae
Bactrocera dorsalis
Bombus terrestris
Bombyx mori
Camponotus floridanus
Cerapachys biroi
Ceratitis capitata
Chilo suppressalis
Danaus plexippus
Diaphorina citri
Drosophila ananassae
Drosophila erecta
Drosophila grimshawi
Drosophila melanogaster
Drosophila mojavensis
Drosophila sechellia
Drosophila simulans
Drosophila virilis
Drosophila willistoni
Drosophila yakuba
Fopius arisanus
Harpegnathos saltator
Heliconius melpomene
Linepithema humile
Macrocentrus cingulum
Megachile rotundata
Megaselia scalaris
Melitaea cinxia
Microplitis demolitor
Musca domestica
Nasonia vitripennis
Pediculus humanus
Plutella xylostella
Pogonomyrmex barbatus
Rhodnius prolixus
Solenopsis invicta
Tribolium castaneum
Vollenhovia emeryi
Wasmannia auropunctata
Zootermopsis nevadensis

Mammalia

Ailuropoda melanoleuca
Bos taurus
Callithrix jacchus
Canis lupus familiaris
Carlito syrichta
Cavia porcellus
Chlorocebus sabaeus
Choloepus hoffmanni
Dasypus novemcinctus
Dipodomys ordii
Echinops telfairi
Equus caballus
Erinaceus europaeus
Felis catus
Gorilla gorilla
Homo sapiens
Ictidomys tridecemlineatus
Loxodonta africana
Macaca mulatta
Microcebus murinus
Monodelphis domestica
Mus musculus
Myotis lucifugus
Nomascus leucogenys
Ornithorhynchus anatinus
Oryctolagus cuniculus
Otolemur garnettii
Ovis aries
Pan troglodytes
Papio anubis
Pongo abelii
Procavia capensis
Pteropus vampyrus
Rattus norvegicus
Sarcophilus harrisii
Sus scrofa
Tupaia belangeri
Tursiops truncatus
Vicugna pacos

Other_animals

Anolis carolinensis
Caenorhabditis briggsae
Caenorhabditis elegans
Ciona intestinalis
Ciona savignyi
Ixodes scapularis
Lottia gigantea
Mnemiopsis leidyi
Octopus bimaculoides
Sarcoptes scabiei
Strongylocentrotus purpuratus
Strongyloides ratti
Tetranychus urticae
Xenopus tropicalis

Fungi

Saccharomyces cerevisiae

Eudicotyledons

Aethionema arabicum
Amaranthus hypochondriacus
Arabidopsis halleri
Arabidopsis lyrata
Arabidopsis thaliana
Arachis duranensis
Arachis ipaensis
Beta vulgaris ssp. vulgaris
Boechera stricta
Brassica napus
Brassica oleracea capitata
Brassica oleracea italica
Brassica rapa
Camellia sinensis
Capsella grandiflora
Capsella rubella
Carica papaya
Chenopodium quinoa
Cicer arietinum
Citrus clementina
Citrus sinensis
Coffea canephora
Cucumis melo
Cucumis sativus
Cucurbita moschata
Daucus carota
Eucalyptus grandis
Eutrema salsugineum
Fragaria vesca
Glycine max
Gossypium hirsutum
Gossypium raimondii
Kalanchoe fedtschenkoi
Kalanchoe laxiflora
Linum usitatissimum
Lotus japonicus
Malus domestica
Manihot esculenta
Medicago truncatula
Mimulus guttatus
Nicotiana tabacum
Phaseolus vulgaris
Populus deltoides
Populus trichocarpa
Prunus persica
Ricinus communis
Salix purpurea
Sida fallax
Solanum lycopersicum
Solanum tuberosum
Thellungiella parvula
Theobroma cacao
Trifolium pratense
Vigna angularis
Vigna radiata
Vitis vinifera

Monocotyledons

Aegilops tauschii
Ananas comosus
Brachypodium distachyon
Brachypodium stacei
Hordeum vulgare
Leersia perrieri
Musa acuminata
Oropetium thomaeum
Oryza barthii
Oryza brachyantha
Oryza glaberrima
Oryza glumaepatula
Oryza longistaminata
Oryza meridionalis
Oryza punctata
Oryza rufipogon
Oryza sativa Indica
Oryza sativa Japonica
Panicum hallii
Setaria italica
Setaria viridis
Sorghum bicolor
Spirodela polyrhiza
Triticum aestivum
Triticum urartu
Zea mays
Zostera marina

Other_plants

Amborella trichopoda
Chlamydomonas reinhardtii
Cyanidioschyzon merolae
Marchantia polymorpha
Micromonas pusilla CCMP1545
Micromonas sp. RCC299
Ostreococcus lucimarinus
Physcomitrella patens
Selaginella moellendorffii
Volvox carteri

Manual

Overview

  • Home: Introduction of qPrimerDB; What's New; Search content in the qPrimerDB;  Search primers for interested genes; Browse; Statistics of the qPrimerDB; Links to Browse, Tools, Downloads, Documents, Help and BioDB.
  • Browse: Favorite organism; Plants; Animals; Others; Sorting by alphabets.
  • Tools: qPrimerDB BLAST for conversion of gene ID; Design request and Result feedback form; 
  • Downloads: Download best primers and all primers.
  • Document: Manual; Pipeline; Statistics; Resource.
  • Help: FAQ; Contact us.
  • BioDB: Link to Biological Database platform (BioDB).

Homepage

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  • Browse: users can browse interested organisms by choosing their classification and scientific name. Fox example, users could browse the primers of Arabidopsis thaliana by sequentially clicking "Plants", "Eudicotyledons" and "Arabidopsis thaliana" (corresponding to "1", "2" and "3" in the red rectangle) as the following figure. Primers of target organism then could be viewed. More detailed information can be accessed for each gene via the hyperlink in the blue rectangle in the primer ID ("4" in the red rectangle) and gene ID ("5" in the red rectangle) columns. For example, users can view the detailed information for best primer of AT1G72390 by clicking the hyperlink of primer ID A.thaliana.005900.v1, including gene description, primer pair description, hyperlink for ‘All primers for AT1G72390’, and amplicon and template sequences. The table of all primers for AT1G72390 could be viewed by clicking the hyperlinks ‘AT1G72390’ ("5" in the red rectangle) in ‘Best Primers for Arabidopsis thaliana’ page or ‘All primers for AT1G72390’ ("6" in the red rectangle) in ‘Details for primer A.thaliana.005900.v1’ page. Then, detailed information for each of all primers could be viewed by clicking the primer ID of interest ("7" in the red rectangle).

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  • Search and export primers for interested genes:  users can search primers by choosing the name(s) of the target organism(s) and inputting keywords (Gene or transcript ID: "ENST00000161863.8"; Primer ID: "H.sapiens.000100v1"; keywords: "YTH domain containing 2"). There are three steps from searching to result export. Taking ENST00000260810.9 and ENST00000161863.8 as an example, users should choose the organism name by sequentially clicking "Organisms" (1a) and "Homo sapiens" (1b) as the following figure in step 1. Then, the keywords for search query need to be entered in the search query box, such as "ENST00000260810.9 ENST00000161863.8" (2a). After clicking the "search" button (2b), the results will be returned immediately in step 2. For results export in step 3, users just need to click the check boxes (3a) before target genes, finally, click the button "Export to XLS" or "Export to JSON" (3b) to obtain searching results. Users could enter multiple keywords separated by space to retrieve primers of multiple target genes simultaneously.

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Browse

  • Browse by different group of organisms: browse by Favorites, Plants (Eudicotyledons, Monocotyledons, Other plants), Animals (Birds and Reptiles, Fish, Insecta, Mammalia, Other animals), Other eukaryotes (fungi) and Sorting by alphabets.
  • Favorites: the following organisms were included (Animals: Apis mellifera, Bombyx mori, Danio rerio, Drosophila melanogaster, Homo sapiens, Mus musculus, Nasonia vitripennis; Plants: Arabidopsis thaliana, Glycine max, Oryza sativa, Physcomitrella patens, Solanum lycopersicum, Solanum tuberosum, Zea mays; Other eukaryotes: Saccharomyces cerevisiae)
  • By alphabets: All the scientific names of 148 organisms were listed in alphabetical order.

Tools

  • qPrimerDB BLAST: a set of tools built with NCBI-BLAST+, and used for searching homologous genes or converting gene IDs between different databases, retrieving gene-specific qPCR primers of target genes subsequently. It supports aligning aginst multiple databases. For example, if we would like to retrieve gene-specific qPCR primer for a gene with a different name in other databases, like "AtCDC5" gene in Arabidopsis thaliana. We could get the gene ID in the qPrimerDB using qPrimerDB BLAST as follows. In step 1, we need to choose the database by click "Database" (1a) and  "Arabidopsis thaliana" (1b), select the output format (table is necessary for getting qPCR primer) and hit number (1c), and enter the sequence in FASTA format or qPrimerDB identifiers each with a prefix "ID:" (1d). After clicking the submit button (1e), we could get the BLAST result in table format (1f). Finally, all the information (primer ID, gene ID, primer sequence, etc.) about query gene will be returned by clicking the subject name, which is marked in a blue rectangle.

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  • Design request: If the qPrimerDB doesn't cover the organism of your interest, users can send a feedback form to us and we will add the gene-specific qPCR primer pairs for you. But, please check the update news to confirm whether the primer design has already been planned for your interested organisms.
  • Result feedback: users can submit the qPCR detection results to us (melting curve and/or gel electrophoresis), especially the specificity of primer pairs used, which will be included and displayed in the next version of qPrimerDB.

Downloads

  • Primers: users can get the best primer and all primer of 148 organisms through choosing target organism (1-2) and clicking the download icon (3).

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