Eccles:QPCR reference genes: Difference between revisions

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Line 27: Line 27:
**DGG ID: 2771
**DGG ID: 2771
**DGG name: Hs_HPRT1_F
**DGG name: Hs_HPRT1_F
**Current [stock]:
*Reverse Primer: GGTCCTTTTCACCAGCAAGCT (21 bp) Exon 6/7
*Reverse Primer: GGTCCTTTTCACCAGCAAGCT (21 bp) Exon 6/7
**DGG ID: 2772
**DGG ID: 2772
**DGG name: Hs_HPRT1_R
**DGG name: Hs_HPRT1_R
**Current [stock]:
*Annealing Temperature: 60 °C
*Annealing Temperature: 60 °C


Line 40: Line 42:
**DGG ID: 2773
**DGG ID: 2773
**DGG name: Hs_UBC_F
**DGG name: Hs_UBC_F
**Current [stock]:
*Reverse Primer: TGCCTTGACATTCTCGATGGT (21 bp)
*Reverse Primer: TGCCTTGACATTCTCGATGGT (21 bp)
**DGG ID: 2774
**DGG ID: 2774
**DGG name: Hs_UBC_R
**DGG name: Hs_UBC_R
**Current [stock]:
*Annealing Temperature: 60 °C
*Annealing Temperature: 60 °C


Line 53: Line 57:
**DGG ID: 2775
**DGG ID: 2775
**DGG name: Hs_YWHAZ_F
**DGG name: Hs_YWHAZ_F
**Current [stock]:
*Reverse Primer: CCGCCAGGACAAACCAGTAT (20 bp)
*Reverse Primer: CCGCCAGGACAAACCAGTAT (20 bp)
**DGG ID: 2776
**DGG ID: 2776
**DGG name: Hs_YWHAZ_R
**DGG name: Hs_YWHAZ_R
**Current [stock]:
*Annealing Temperature: 60 °C
*Annealing Temperature: 60 °C


Line 68: Line 74:
**DGG ID: 2777
**DGG ID: 2777
**DGG name: Hs_HMBS_F
**DGG name: Hs_HMBS_F
**Current [stock]:
*Reverse Primer: GGGTACCCACGCGAATCAC (19 bp) Exon 2
*Reverse Primer: GGGTACCCACGCGAATCAC (19 bp) Exon 2
**DGG ID: 2778
**DGG ID: 2778
**DGG name: Hs_HMBS_R
**DGG name: Hs_HMBS_R
**Current [stock]:
*Annealing Temperature: 60 °C
*Annealing Temperature: 60 °C


Line 81: Line 89:
**DGG ID: 2779
**DGG ID: 2779
**DGG name: Hs_RPL13A_F
**DGG name: Hs_RPL13A_F
**Current [stock]:
*Reverse Primer: TTGAGGACCTCTGTGTATTTGTCAA (25 bp)
*Reverse Primer: TTGAGGACCTCTGTGTATTTGTCAA (25 bp)
**DGG ID: 2780
**DGG ID: 2780
**DGG name: Hs_RPL13A_R
**DGG name: Hs_RPL13A_R
**Current [stock]:
*Annealing Temperature: 60 °C
*Annealing Temperature: 60 °C


Line 96: Line 106:
**DGG ID: 2781
**DGG ID: 2781
**DGG name: Hs_SDHA_F
**DGG name: Hs_SDHA_F
**Current [stock]:
*Reverse Primer: CCACCACTGCATCAAATTCATG (22 bp)
*Reverse Primer: CCACCACTGCATCAAATTCATG (22 bp)
**DGG ID: 2782
**DGG ID: 2782
**DGG name: Hs_SDHA_R
**DGG name: Hs_SDHA_R
**Current [stock]:
*Annealing Temperature: 60 °C
*Annealing Temperature: 60 °C


Line 110: Line 122:
**DGG ID: 2783
**DGG ID: 2783
**DGG name: Hs_TBP_F
**DGG name: Hs_TBP_F
**Current [stock]:
*Reverse Primer: CACATCACAGCTCCCCACCA (20 bp)
*Reverse Primer: CACATCACAGCTCCCCACCA (20 bp)
*DGG ID: 2784
**DGG ID: 2784
**DGG name: Hs_TBP_R
**DGG name: Hs_TBP_R
**Current [stock]:
*Annealing Temperature: 60 °C
*Annealing Temperature: 60 °C


Line 125: Line 139:
**DGG ID: 2785
**DGG ID: 2785
**DGG name: 28S_F
**DGG name: 28S_F
**Current [stock]:
*R gattcggcaggtgagttgtt  
*R gattcggcaggtgagttgtt  
**DGG ID: 2786
**DGG ID: 2786
**DGG name: 28S_R
**DGG name: 28S_R
**Current [stock]:
===PPIB===
===PPIB===


==Mouse==
==Mouse==

Revision as of 14:41, 17 July 2006

Eccles Lab > DGG Oligos > QPCR > reference genes (Sybr)


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]:
  • Reverse Primer: GTAGTTTCGTGGATGCCACA (20 bp) exon 4
    • DGG ID: 2770
    • DGG name: Hs_ACTB_R
    • Current [stock]:
  • Annealing Temperature: 60 °C
  • 131 bp
  • Genomic amplicon: 226bp

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]:
  • Reverse Primer: GGTCCTTTTCACCAGCAAGCT (21 bp) Exon 6/7
    • DGG ID: 2772
    • DGG name: Hs_HPRT1_R
    • Current [stock]:
  • 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]:
  • Reverse Primer: TGCCTTGACATTCTCGATGGT (21 bp)
    • DGG ID: 2774
    • DGG name: Hs_UBC_R
    • Current [stock]:
  • 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]:
  • Reverse Primer: CCGCCAGGACAAACCAGTAT (20 bp)
    • DGG ID: 2776
    • DGG name: Hs_YWHAZ_R
    • Current [stock]:
  • Annealing Temperature: 60 °C

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]:
  • Reverse Primer: GGGTACCCACGCGAATCAC (19 bp) Exon 2
    • DGG ID: 2778
    • DGG name: Hs_HMBS_R
    • Current [stock]:
  • Annealing Temperature: 60 °C

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]:
  • Reverse Primer: TTGAGGACCTCTGTGTATTTGTCAA (25 bp)
    • DGG ID: 2780
    • DGG name: Hs_RPL13A_R
    • Current [stock]:
  • 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]:
  • Reverse Primer: CCACCACTGCATCAAATTCATG (22 bp)
    • DGG ID: 2782
    • DGG name: Hs_SDHA_R
    • Current [stock]:
  • 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]:
  • Reverse Primer: CACATCACAGCTCCCCACCA (20 bp)
    • DGG ID: 2784
    • DGG name: Hs_TBP_R
    • Current [stock]:
  • Annealing Temperature: 60 °C

GAPDH

B2M

28S

PPIB

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
  • Reverse Primer GGGGCTGTACTGCTTAACCAG 21 62.4 465-445 Exon 6

Actb

rtprimerdb ID 2848 Amplicon size: 87 Genomic size: 174 Forward Primer: ATGCTCCCCGGGCTGTAT (18 bp) Exon 2 Reverse Primer: CATAGGAGTCCTTCTGACCCATTC (24 bp) Exon 3 Annealing Temperature: 60 ??C

B2m

rtprimerdb ID 2866 Amplicon size: 194 bp Genomic size: 1663 Forward Primer: ATTCACCCCCACTGAGACTG (20 bp) Exon 2 Reverse Primer: TGCTATTTCTTTCTGCGTGC (20 bp) Exon 4 (UTR) 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 R gattcggcaggtgagttgtt

Tbp

rtprimerdb ID 49 Forward Primer: GGCCTCTCAGAAGCATCACTA (21 bp) Spans Exon2/3 Reverse Primer: GCCAAGCCCTGAGCATAA (18 bp) Exon 3 Amplicon size: 167 Annealing Temperature: 55 ??C

Actg1

Ubc

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 Reverse Primer TTGTTGCTCCCATAACCGATG 21 60.4 191-171 Exon 3

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 Reverse Primer CCACCACTGGGTATTGAGTAGAA 23 61.1 167-145 Exon 3

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 Reverse Primer TGGGTATCCGATGTCCACAAT 21 60.7 698-678 Exon 6/7

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 Reverse Primer AGTTGCCCATCTTTCATCACTG 22 60.6 827-806 Spans exon 12/13

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

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