qPrimerDB - qPCR Primer Database

A resource for real-time quantitative PCR primers

Version: 1.2

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
Nilaparvata lugens
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 familiaris
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
Macropus eugenii
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
Tarsius syrichta
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

Absidia glauca
Acidomyces richmondensis
Acidomyces richmondensis bfw
Acremonium chrysogenum atcc 11550
Agaricus bisporus var burnettii jb137 s8
Allomyces macrogynus atcc 38327
Alternaria alternata
Amanita muscaria koide bx008
Amphiamblys sp wsbs2006
Arthrobotrys oligospora atcc 24927
Arthroderma otae cbs 113480
Aschersonia aleyrodis rcef 2490
Ascochyta rabiei
Ascoidea rubescens dsm 1968
Ascosphaera apis arsef 7405
Ashbya gossypii
Aspergillus aculeatus atcc 16872
Aspergillus bombycis
Aspergillus brasiliensis cbs 101740
Aspergillus calidoustus
Aspergillus carbonarius item 5010
Aspergillus clavatus
Aspergillus cristatus
Aspergillus flavus
Aspergillus flavus af70
Aspergillus fumigatus
Aspergillus fumigatus var rp 2014
Aspergillus fumigatus z5
Aspergillus fumigatusa1163
Aspergillus glaucus cbs 516 65
Aspergillus lentulus
Aspergillus luchuensis
Aspergillus luchuensis cbs 106 47
Aspergillus nidulans
Aspergillus nidulans fgsc a4
Aspergillus niger
Aspergillus niger atcc 1015
Aspergillus niger gca 001515345
Aspergillus nomius nrrl 13137
Aspergillus ochraceoroseus
Aspergillus oryzae
Aspergillus oryzae 3 042
Aspergillus oryzae gca 002007945
Aspergillus parasiticus su 1
Aspergillus rambellii
Aspergillus ruber cbs 135680
Aspergillus sydowii cbs 593 65
Aspergillus terreus
Aspergillus udagawae
Aspergillus ustus
Aspergillus versicolor cbs 583 65
Aureobasidium melanogenum cbs 110374
Aureobasidium namibiae cbs 147 97
Aureobasidium pullulans exf 150
Aureobasidium subglaciale exf 2481
Baudoinia panamericana uamh 10762
Beauveria bassiana
Beauveria bassiana arsef 2860
Beauveria bassiana d1 5
Bipolaris maydis atcc 48331
Bipolaris maydis c5
Bipolaris oryzae atcc 44560
Bipolaris sorokiniana nd90pr
Bipolaris victoriae fi3
Bipolaris zeicola 26 r 13
Blastomyces dermatitidis atcc 18188
Blastomyces dermatitidis er 3
Blastomyces gilchristii slh14081
Blumeria graminis
Blumeria graminis f sp tritici 96224
Botrytis cinerea
Botrytis cinerea bcdw1
Botrytis cinerea t4
Brettanomyces bruxellensis awri1499
Byssochlamys spectabilis no 5
Candida albicans 12c
Candida albicans gc75
Candida albicans p34048
Candida albicans p37005
Candida albicans sc5314
Candida albicans sc5314 gca 000784655
Candida albicans wo 1
Candida dubliniensis cd36
Candida glabrata
Candida maltosa xu316
Candida orthopsilosis co 90 125
Candida tenuis atcc 10573
Candida tropicalis mya 3404
Capronia coronata cbs 617 96
Capronia epimyces cbs 606 96
Ceratocystis platani
Chaetomium globosum cbs 148 51
Chaetomium thermophilum var thermophilum dsm 1495
Cladophialophora bantiana cbs 173 52
Cladophialophora carrionii cbs 160 54
Cladophialophora immunda
Cladophialophora psammophila cbs 110553
Cladophialophora yegresii cbs 114405
Claviceps purpurea 20 1
Clavispora lusitaniae atcc 42720
Coccidioides immitis rmscc 2394
Coccidioides immitis rs
Coccidioides posadasii c735 delta sowgp
Coccidioides posadasii rmscc 3488
Coccidioides posadasii str silveira
Colletotrichum fioriniae pj7
Colletotrichum gloeosporioides
Colletotrichum gloeosporioides cg 14
Colletotrichum graminicola
Colletotrichum higginsianum
Colletotrichum orbiculare
Colletotrichum sublineola
Cordyceps militaris cm01
Cryptococcus neoformans
Cyphellophora europaea cbs 101466
Dactylellina haptotyla cbs 200 50
Debaryomyces hansenii cbs767
Diaporthe ampelina
Drechslerella stenobrocha 248
Emmonsia parva uamh 139
Endocarpon pusillum z07020
Eremothecium cymbalariae dbvpg 7215
Eremothecium gossypii fdag1
Erysiphe necator
Exophiala aquamarina cbs 119918
Exophiala dermatitidis nih ut8656
Exophiala mesophila
Exophiala oligosperma
Exophiala sideris
Exophiala spinifera
Exophiala xenobiotica
Fonsecaea pedrosoi cbs 271 37
Fusarium oxysporum f sp conglutinans race 2 54008
Fusarium oxysporum f sp cubense race 1
Fusarium oxysporum f sp lycopersici mn25
Fusarium oxysporum f sp melonis 26406
Fusarium oxysporum f sp pisi hdv247
Fusarium oxysporum f sp radicis lycopersici 26381
Fusarium oxysporum fo47
Fusarium oxysporum fosc 3 a
Glarea lozoyensis 74030
Kazachstania africana cbs 2517
Kazachstania naganishii cbs 8797
Kluyveromyces lactis
Komagataella phaffii cbs 7435
Kuraishia capsulata cbs 1993
Lachancea lanzarotensis
Lachancea thermotolerans cbs 6340
Lodderomyces elongisporus nrrl yb 4239
Macrophomina phaseolina ms6
Magnaporthe oryzae
Marssonina brunnea f sp multigermtubi mb m1
Metarhizium acridum cqma 102
Metarhizium album arsef 1941
Metarhizium anisopliae
Metarhizium anisopliae arsef 23
Metarhizium anisopliae arsef 549
Metarhizium anisopliae brip 53284
Metarhizium brunneum arsef 3297
Metarhizium guizhouense arsef 977
Metarhizium robertsii
Meyerozyma guilliermondii atcc 6260
Millerozyma farinosa cbs 7064
Oidiodendron maius zn
Penicillium brasilianum
Penicillium camemberti fm 013
Phialophora americana
Pseudogymnoascus sp vkm f 103
Rasamsonia emersonii cbs 393 64
Rhinocladiella mackenziei cbs 650 93
Saccharomyces arboricola h 6
Saccharomyces cerevisiae
Saccharomyces cerevisiae awri796
Saccharomyces cerevisiae cen pk113 7d
Saccharomyces cerevisiae ec1118
Saccharomyces cerevisiae fostersb
Saccharomyces cerevisiae fosterso
Saccharomyces cerevisiae kyokai no 7
Saccharomyces cerevisiae lalvin qa23
Saccharomyces cerevisiae p283
Saccharomyces cerevisiae r008
Saccharomyces cerevisiae rm11 1a
Saccharomyces cerevisiae vin13
Saccharomyces cerevisiae x saccharomyces kudriavzevii vin7
Saccharomyces cerevisiae yjm189
Saccharomyces cerevisiae yjm789
Saccharomyces kudriavzevii ifo 1802
Saccharomycetaceae sp ashbya aceri
Saitoella complicata nrrl y 17804
Scedosporium apiospermum
Scheffersomyces stipitis cbs 6054
Schizosaccharomyces pombe
Schizosaccharomyces pombe 972h
Schizosaccharomyces pombe EBC7
Sclerotinia borealis f 4128
Sclerotinia sclerotiorum
Setosphaeria turcica et28a
Sordaria macrospora
Spathaspora passalidarum nrrl y 27907
Sphaerulina musiva so2202
Sporothrix brasiliensis 5110
Sporothrix schenckii 1099 18
Sporothrix schenckii atcc 58251
Stachybotrys chartarum ibt 7711
Stachybotrys chlorohalonata ibt 40285
Talaromyces cellulolyticus
Talaromyces islandicus
Talaromyces marneffei atcc 18224
Talaromyces marneffei pm1
Talaromyces stipitatus atcc 10500
Tetrapisispora blattae cbs 6284
Tetrapisispora phaffii cbs 4417
Thermothelomyces thermophila atcc 42464
Thielavia terrestris nrrl 8126
Thielaviopsis punctulata
Torrubiella hemipterigena
Torulaspora delbrueckii
Trichoderma atroviride imi 206040
Trichoderma harzianum
Trichoderma reesei rut c 30
Trichophyton benhamiae cbs 112371
Trichophyton equinum cbs 127 97
Trichophyton interdigitale h6
Trichophyton rubrum cbs 202 88
Trichophyton rubrum d6
Trichophyton rubrum mr850
Trichophyton soudanense cbs 452 61
Trichophyton tonsurans cbs 112818
Trichophyton verrucosum hki 0517
Uncinocarpus reesii 1704
Ustilaginoidea virens
Vanderwaltozyma polyspora dsm 70294
Verruconis gallopava
Verticillium alfalfae vams 102
Wickerhamomyces ciferrii
Yarrowia lipolytica
Zygosaccharomyces bailii isa1307
Zygosaccharomyces rouxii
Zymoseptoria brevis
Zymoseptoria tritici

Microsporidia

Encephalitozoon cuniculi EC1
Encephalitozoon cuniculi EC2
Encephalitozoon cuniculi EC3
Enterocytozoon bieneusi H348
Nematocida parisii ERTm1
Nosema bombycis CQ1
Nosema ceranae BRL01
Spraguea lophii 42-110
Vittaforma corneae ATCC50505

Eudicotyledons

Aethionema arabicum
Amaranthus hypochondriacus
Anacardium occidentale
Aquilegia coerulea
Arabidopsis halleri
Arabidopsis lyrata
Arabidopsis thaliana
Arachis duranensis
Arachis ipaensis
Barbarea vulgaris
Beta vulgaris
Betula pendula
Boechera stricta
Brassica juncea
Brassica napus
Brassica nigra
Brassica oleracea capitata
Brassica oleracea italica
Brassica rapa
Calotropis gigantea
Camelina sativa
Camellia sinensis
Capsella grandiflora
Capsella rubella
Capsicum annuum Zunla
Capsicum annuum var glabriusculum
Cardamine hirsuta
Carica papaya
Castanea mollissima
Chenopodium quinoa
Cicer arietinum
Cicer reticulatum
Citrus clementina
Citrus sinensis
Coffea canephora
Cucumis melo
Cucumis sativus
Cucurbita moschata
Daucus carota
Eucalyptus camaldulensis
Eucalyptus grandis
Eutrema salsugineum
Fragaria nipponica
Fragaria nubicola
Fragaria orientalis
Fragaria vesca
Fragaria x ananassa
Glycine max
Gossypium arboreum BGI
Gossypium barbadense NAU
Gossypium hirsutum
Gossypium hirsutum BGI
Gossypium raimondii
Gossypium raimondii BGI
Helianthus annuus
Hevea brasiliensis
Hibiscus syriacus
Ipomoea batatas
Ipomoea trifida
Jatropha curcas
Kalanchoe fedtschenkoi
Kalanchoe laxiflora
Lactuca sativa
Levenworthia alabamica
Linum usitatissimum
Lotus japonicus
Malus domestica
Manihot esculenta
Medicago truncatula
Mimulus guttatus
Nicotiana benthamiana
Nicotiana sylvestris
Nicotiana tabacum
Nicotiana tomentosiformis
Olea europaea
Petunia axillaris
Petunia inflata
Phaseolus vulgaris
Populus deltoides
Populus tremula
Populus tremuloides
Populus trichocarpa
Prunus persica
Raphanus sativus
Ricinus communis
Rosa multiflora
Rubus occidentalis
Salix purpurea
Sesamum indicum
Sida fallax
Solanum lycopersicum
Solanum pennellii
Solanum tuberosum
Thellungiella parvula
Theobroma cacao
Trifolium pratense
Vigna angularis
Vigna radiata
Vigna unguiculata
Vitis vinifera

Monocotyledons

Aegilops tauschii
Ananas comosus
Asparagus officinalis
Brachypodium distachyon
Brachypodium hybridum
Brachypodium stacei
Elaeis guineensis
Hordeum vulgare
Leersia perrieri
Musa Itinerans
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
Zostera muelleri
Zoysia japonica
Zoysia matrella

Other_plants

Amborella trichopoda
Chlamydomonas reinhardtii
Cyanidioschyzon merolae
Dunaliella salina
Marchantia polymorpha
Micromonas
Micromonas pusilla
Ostreococcus lucimarinus
Physcomitrella patens
Pinus taeda
Pseudotsuga menziesii
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

               manual-1         

  • 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).

            manual-2

  • 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.

          manual_3

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.

       manual_4

  • 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).

         manual_5