A Simple Solution for Oligonucleotide Design

Click here for a list of viruses in the database


Two search options:
1. Search by virus name and/or primer data
2. Search by PMID, VirOligoID, or taxonomy ID;

Virus name:

Oligo Sequence:

Tm:
°C± °C
Oligo length:
bp± bp



PMID:

Common Data ID:

Taxonomy ID:

GI Number:

CommonData ID: BM1351Publication date: 03/02
PMID: 11939332GI: 9049956 Taxonomy ID: 11099
Virus Name: pestivirus type 1; Bovine viral diarrhea virus genotype 2Product size (PCR):
bp
MgCl2: 12.5 mMdNTPs: mMType: RT-PCR
Temp (PCR cycle):50C 30min>95C 15min>(94C 1min>55C 1min>72C 2min)*40>72C 7min
Buffer: 1x RT-PCR buffer (One Step RT-PCR kit; Qiagen), 1x TaqMan buffer A (Applied Biosystems), 0.08U/microL RNase inhibitor, 1microL enzyme mix (Qiagen)
Polymerase: HotStart Taq poly (Qiagen)Cycler:
Note: Universal PCR. Primers amplify the following bovine viral diarrhea viruses:
pestivirus type 1 [Taxonomy:11099]
genotype 2 [Taxonomy:54315]

RT-PCR is performed in a single step.
Total RT-PCR volume is 25microL containing 5microL RNA, 0.5microM each primer, and 0.3microM probe.
Article mentions 12.5mM MgCl2 being used in PCR and is contained in the buffer.
Enzyme mix contains Omniscript RTase, Sensiscript RTase, and HotStart Taq polymerase.
Forward(PB00933) primer
Oligo type: Degeneracy: 8
Target: 186-205Tm: Max Tm 78.2 C Min Tm 74.1 C at salt 1000.0mMLength:
Sequence: GGG(A/C/G/T)AGTCGTCA(A/G)TGGTTCG
(0 other experimental conditions)
Note:
Reverse(PB00934) primer
Oligo type: Degeneracy: 2
Target: 385-363Tm: 74.5 C at salt 1000.0mMLength:
Sequence: GTGCCATGTACAGCAGAG(A/T)TTTT
(0 other experimental conditions)
Note:
Forward(PB00935) primer
Oligo type: Degeneracy: 4
Target: 233-252Tm: Max Tm 82.3 C Min Tm 78.2 C at salt 1000.0mMLength:
Sequence: CCA(C/T)GTGGACGAGGGCA(C/T)GC
(0 other experimental conditions)
Note: 5'labelled with 6-caroxy-fluorescein and 3'labelled with 6-carboxy-tetra-methyl-rhodamine.
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