Eccles:QPCR reference genes: Difference between revisions
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==Human== | ==Human== | ||
===ACTB: actin, beta=== | ===ACTB: actin, beta=== | ||
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*Genomic amplicon: 226bp | *Genomic amplicon: 226bp | ||
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===B2M=== | ===B2M=== |
Latest revision as of 14:28, 20 April 2010
Eccles Lab > DGG Oligos > QPCR > reference genes (Sybr)
A red heading indicates candidate reference gene primers that have not been ordered.
Human
ACTB: actin, beta
- RTPrimerDB ID: 2219
- Organism: Homo sapiens (Hs, Human)
- Forward Primer: TCCCTGGAGAAGAGCTACG (19 bp) exon 3
- DGG ID: 2769
- DGG name: Hs_ACTB_F
- Current [stock]: 64.4 uM
- Reverse Primer: GTAGTTTCGTGGATGCCACA (20 bp) exon 4
- DGG ID: 2770
- DGG name: Hs_ACTB_R
- Current [stock]: 91.6 uM
- Annealing Temperature: 60 °C
- 131 bp
- Genomic amplicon: 226bp
B2M
GAPDH
- RTPrimerDB ID: 3
- GAPD: glyceraldehyde-3-phosphate dehydrogenase
- Alias Symbol(s): G3PD, GAPDH, 3' end
- Organism: Homo sapiens (Hs, Human)
- Entrez Gene ID: 2597
- Ensembl Gene ID: ENSG00000111640
- This primer pair amplifies part of the following transcript:
- ENST00000229239 (Exons: 9, Transcript length: 1310 bp, Translation length: 335 residues)(length: 87 bp)
- Forward Primer: TGCACCACCAACTGCTTAGC (20 bp) exon 7
- DGG ID:
- DGG name: Hs_GAPDH_F
- Current [stock]: 131 uM
- Reverse Primer: GGCATGGACTGTGGTCATGAG (21 bp) exon 7/8
- DGG ID:
- DGG name: Hs_GAPDH_R
- Current [stock]: 113 uM
- Annealing Temperature: 60 °C
- Publication PubMed ID 12184808, Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe A, Speleman F
Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes
Genome Biol. 2002 Jun 18;3(7):RESEARCH0034. Epub 2002 Jun 18GNB2L1
- F: CACAACGGGCACCACCAC
- Current [stock]: 142 uM
- R: CACACACCCAGGGTATTCCAT
- Current [stock]: 103 uM
HMBS: hydroxymethylbilane synthase
- RTPrimerDB ID: 4
- Alias Symbol(s): AIP, UPS, PBGD
- Organism: Homo sapiens (Hs, Human)
- This primer pair amplifies part of the following transcript:
- ENST00000278715 (Exons: 14, Transcript length: 1501 bp, Translation length: 361 residues)(length: 64 bp)
- Genomic amplicon: 3252bp
- Forward Primer: GGCAATGCGGCTGCAA (16 bp) Exon 1
- DGG ID: 2777
- DGG name: Hs_HMBS_F
- Current [stock]: 100.3 uM
- Reverse Primer: GGGTACCCACGCGAATCAC (19 bp) Exon 2
- DGG ID: 2778
- DGG name: Hs_HMBS_R
- Current [stock]: 49.9 uM
- Annealing Temperature: 60 °C
HPRT1: hypoxanthine phosphoribosyltransferase 1 (Lesch-Nyhan syndrome)
- RTPrimerDB ID: 5
- Alias Symbol(s): HPRT, HGPRT
- Organism: Homo sapiens (Hs, Human)
- (length: 94 bp)
- Genomic Amplicon: 4893bp
- Forward Primer: TGACACTGGCAAAACAATGCA (21 bp) Exon 6
- DGG ID: 2771
- DGG name: Hs_HPRT1_F
- Current [stock]: 81.7 uM
- Reverse Primer: GGTCCTTTTCACCAGCAAGCT (21 bp) Exon 6/7
- DGG ID: 2772
- DGG name: Hs_HPRT1_R
- Current [stock]: 80.3 uM
- Annealing Temperature: 60 °C
PPIB
- F: ATGATCCAGGGCGGAGACTT
- Current [stock]: 92 uM
- R: CAGGCCCGTAGTGCTTCAG
- Current [stock]: 88 uM
RPL13A: ribosomal protein L13a
- RTPrimerDB ID: 6
- Organism: Homo sapiens (Hs, Human)
- This primer pair amplifies part of the following transcript:
- ENST00000270634 (Exons: 8, Transcript length: 1125 bp, Translation length: 203 residues)(length: 126 bp)
- Forward Primer: CCTGGAGGAGAAGAGGAAAGAGA (23 bp)
- DGG ID: 2779
- DGG name: Hs_RPL13A_F
- Current [stock]: 61.9 uM
- Reverse Primer: TTGAGGACCTCTGTGTATTTGTCAA (25 bp)
- DGG ID: 2780
- DGG name: Hs_RPL13A_R
- Current [stock]: 52.8 uM
- Annealing Temperature: 60 °C
SDHA: succinate dehydrogenase complex, subunit A, flavoprotein (Fp)
- RTPrimerDB ID: 7
- Alias Symbol(s): FP, SDH2, SDHF
- Organism: Homo sapiens (Hs, Human)
- This primer pair amplifies part of the following transcripts:
- ENST00000264932 (Exons: 15, Transcript length: 2280 bp, Translation length: 664 residues)(length: 86 bp)
- ENST00000327872 (Exons: 13, Transcript length: 1880 bp, Translation length: 517 residues)(length: 86 bp)
- Forward Primer: TGGGAACAAGAGGGCATCTG (20 bp)
- DGG ID: 2781
- DGG name: Hs_SDHA_F
- Current [stock]: 83.9 uM
- Reverse Primer: CCACCACTGCATCAAATTCATG (22 bp)
- DGG ID: 2782
- DGG name: Hs_SDHA_R
- Current [stock]: 83 uM
- Annealing Temperature: 60 °C
TBP: TATA box binding protein
- RTPrimerDB ID: 2627
- Alias Symbol(s): GTF2D, SCA17, TFIID, GTF2D1
- Organism: Homo sapiens (Hs, Human)
- This primer pair amplifies part of the following transcript:
- ENST00000230354 (Exons: 8, Transcript length: 1845 bp, Translation length: 339 residues)(length: 132 bp)
- Forward Primer: TGCACAGGAGCCAAGAGTGAA (21 bp)
- DGG ID: 2783
- DGG name: Hs_TBP_F
- Current [stock]: 77.9 uM
- Reverse Primer: CACATCACAGCTCCCCACCA (20 bp)
- DGG ID: 2784
- DGG name: Hs_TBP_R
- Current [stock]: 73.6 uM
- Annealing Temperature: 60 °C
UBC: ubiquitin C
- RTPrimerDB ID: 8
- Alias Symbol(s): HMG20
- Organism: Homo sapiens (Hs, Human)
- (length: 133 bp)
- Forward Primer: ATTTGGGTCGCGGTTCTTG (19 bp)
- DGG ID: 2773
- DGG name: Hs_UBC_F
- Current [stock]: 65.9 uM
- Reverse Primer: TGCCTTGACATTCTCGATGGT (21 bp)
- DGG ID: 2774
- DGG name: Hs_UBC_R
- Current [stock]: 60.5 uM
- Annealing Temperature: 60 °C
YWHAZ: tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide
- RTPrimerDB ID: 9
- Alias Symbol(s): KCIP-1
- Organism: Homo sapiens (Hs, Human)
- (length: 94 bp)
- Forward Primer: ACTTTTGGTACATTGTGGCTTCAA (24 bp)
- DGG ID: 2775
- DGG name: Hs_YWHAZ_F
- Current [stock]: 47.1 uM
- Reverse Primer: CCGCCAGGACAAACCAGTAT (20 bp)
- DGG ID: 2776
- DGG name: Hs_YWHAZ_R
- Current [stock]: 85.4 uM
- Annealing Temperature: 60 °C
- Not intron-spanning
28S
- 28S, from qpcrlist message 3097 <http://groups.yahoo.com/group/qpcrlistserver/message/3097>
- Multi species
- F tcatcagaccccagaaaagg
- DGG ID: 2785
- DGG name: 28S_F
- Current [stock]: 86.6 uM
- R gattcggcaggtgagttgtt
- DGG ID: 2786
- DGG name: 28S_R
- Current [stock]: 98 uM
Mouse
Mouse reference genes for Sybr Green QPCR
Hprt1
- PrimerBank ID 7305155a1, 142 bp, 7752 bp genomic amplicon
- GenBank Accession NM_013556
- NCBI Protein Accession NP_038584
- Species Mouse
- Coding DNA Length 657
- Gene Description hypoxanthine guanine phosphoribosyl transferase [Mus musculus].
- Primer Pair Descriptions:
- PrimerBank ID 7305155a1
- Amplicon Size 142
- Genomic size 7752
Sequence (5' -> 3') Length Tm Location
- Forward Primer TCAGTCAACGGGGGACATAAA 21 60.8 324-344 Exon 4
- DGG ID: 2661
- DGG name: AJ_Mm_Hprt1F
- Current [stock]:
- Reverse Primer GGGGCTGTACTGCTTAACCAG 21 62.4 465-445 Exon 6
- DGG ID: 2662
- DGG name: AJ_Mm_Hprt1R
- Current [stock]:
Actb
- rtprimerdb ID 2848
- Amplicon size: 87
- Genomic size: 174
- Forward Primer: ATGCTCCCCGGGCTGTAT (18 bp) Exon 2
- DGG ID: 2663
- DGG name: AJ_Mm_ActbF
- Current [stock]:
- Reverse Primer: CATAGGAGTCCTTCTGACCCATTC (24 bp) Exon 3
- DGG ID: 2664
- DGG name: AJ_Mm_ActbR
- Current [stock]:
- Annealing Temperature: 60 ??C
B2m
- rtprimerdb ID 2866
- Amplicon size: 194 bp
- Genomic size: 1663
- Forward Primer: ATTCACCCCCACTGAGACTG (20 bp) Exon 2
- DGG ID: 2665
- DGG name: AJ_Mm_B2mF
- Current [stock]:
- Reverse Primer: TGCTATTTCTTTCTGCGTGC (20 bp) Exon 4 (UTR)
- DGG ID: 2666
- DGG name: AJ_Mm_B2mR
- Current [stock]:
- Annealing Temperature: 60 ??C
B2m
- PrimerBank
- GenBank Accession NM_009735
- NCBI Protein Accession NP_033865
- Species Mouse
- Coding DNA Length 360
- Gene Description beta-2 microglobulin; beta 2 microglobulin; beta2-microglobulin [Mus musculus].
- Primer Pair Descriptions:
- PrimerBank ID 31981890a1
- Amplicon Size 104
- Genomic Size 3172
Sequence (5' -> 3') Length Tm Location
- Forward Primer TTCTGGTGCTTGTCTCACTGA 21 61.0 26-46 Exon 1
- Reverse Primer CAGTATGTTCGGCTTCCCATTC 22 61.0 129-108 Exon 2
Gapd
28S
- from qpcrlist message 3097 <http://groups.yahoo.com/group/qpcrlistserver/message/3097>
- Multi species
- F tcatcagaccccagaaaagg
- DGG ID: 2785
- DGG name: 28S_F
- Current [stock]:
- R gattcggcaggtgagttgtt
- DGG ID: 2786
- DGG name: 28S_R
- Current [stock]:
Tbp
- rtprimerdb ID 49
- Forward Primer: GGCCTCTCAGAAGCATCACTA (21 bp) Spans Exon2/3
- DGG ID: 2667
- DGG name: AJ_Mm_TbpF
- Current [stock]:
- Reverse Primer: GCCAAGCCCTGAGCATAA (18 bp) Exon 3
- DGG ID: 2668
- DGG name: AJ_Mm_TbpR
- Current [stock]:
- Amplicon size: 167
- Annealing Temperature: 55 ??C
Rpl32
- PrimerBank
- GenBank Accession NM_172086
- NCBI Protein Accession NP_742083
- Species Mouse
- Coding DNA Length 408
- Gene Description ribosomal protein L32 [Mus musculus].
- PrimerBank ID 25742730a1
- Amplicon Size 100
- Genomic size 734
Sequence (5' -> 3') Length Tm Location
- Forward Primer TTAAGCGAAACTGGCGGAAAC 21 61.4 92-112 Spans exon 2/exon 3
- DGG ID: 2669
- DGG name: AJ_Mm_Rpl32F
- Current [stock]:
- Reverse Primer TTGTTGCTCCCATAACCGATG 21 60.4 191-171 Exon 3
- DGG ID: 2670
- DGG name: AJ_Mm_Rpl32R
- Current [stock]:
Sdha
- Primerbank
- LocusLink ID 66945
- GenBank Accession BC011301
- NCBI Protein Accession AAH11301
- Species Mouse
- Coding DNA Length 1987
- Gene Description Sdha protein [Mus musculus].
- PrimerBank ID 15030102a1
- Amplicon Size 106
- Genomic size 1458
Sequence (5' -> 3') Length Tm Location
- Forward Primer GGAACACTCCAAAAACAGACCT 22 60.4 62-83 Exon 2
- DGG ID: 2671
- DGG name: AJ_Mm_SdhaF
- Current [stock]:
- Reverse Primer CCACCACTGGGTATTGAGTAGAA 23 61.1 167-145 Exon 3
- DGG ID: 2672
- DGG name: AJ_Mm_SdhaR
- Current [stock]:
Ywhaz
- PrimerBank
- GenBank Accession NM_011740
- NCBI Protein Accession NP_035870
- Species Mouse
- Coding DNA Length 738
- Gene Description tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide [Mus musculus].
- Primer Pair Descriptions:
- PrimerBank ID 6756041a3
- Amplicon Size 120
Sequence (5' -> 3') Length Tm Location
- Forward Primer AACAGCTTTCGATGAAGCCAT 21 60.3 579-599 Spans exon 5/6
- DGG ID: 2673
- DGG name: AJ_Mm_YwhazF
- Current [stock]:
- Reverse Primer TGGGTATCCGATGTCCACAAT 21 60.7 698-678 Exon 6/7
- DGG ID: 2674
- DGG name: AJ_Mm_YwhazR
- Current [stock]:
Hmbs
- PrimerBank
- GenBank Accession NM_013551
- NCBI Protein Accession NP_038579
- Species Mouse
- Coding DNA Length 1086
- Gene Description hydroxymethylbilane synthase; porphobilinogen deaminase [Mus musculus].
- Primer Pair Descriptions:
- PrimerBank ID 30794512a2
- Amplicon Size 101
- Genomic size 285
Sequence (5' -> 3') Length Tm Location
- Forward Primer ACTCTGCTTCGCTGCATTG 19 60.8 727-745 Exon 11
- DGG ID: 2675
- DGG name: AJ_Mm_HmbsF
- Current [stock]:
- Reverse Primer AGTTGCCCATCTTTCATCACTG 22 60.6 827-806 Spans exon 12/13
- DGG ID: 2676
- DGG name: AJ_Mm_HmbsR
- Current [stock]:
Hspca
- PrimerBank
- GenBank Accession M36830
- NCBI Protein Accession AAA37868
- Species Mouse
- Coding DNA Length 1041
- Gene Description heat-shock protein hsp86.
- Primer Pair Descriptions:
- PrimerBank ID 194033a2
- Amplicon Size 111
- Genomic size 211
Sequence (5' -> 3') Length Tm Location
- Forward Primer AATTGCCCAGTTAATGTCCTTGA 23 60.2 60-82
- Reverse Primer TCGTAACGGATTTTATCCAGAGC 23 60.2 170-148