Eccles:QPCR reference genes: Difference between revisions

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===Hprt1===
===Hprt1===
<showhide>__HIDER__
<hide>
*PrimerBank ID 7305155a1, 142 bp, 7752 bp genomic amplicon
*PrimerBank ID 7305155a1, 142 bp, 7752 bp genomic amplicon
*GenBank Accession NM_013556
*GenBank Accession NM_013556
Line 208: Line 210:
**DGG name: AJ_Mm_Hprt1R
**DGG name: AJ_Mm_Hprt1R
**Current [stock]:
**Current [stock]:
</hide></showhide>


===Actb===
===Actb===
<showhide>__HIDER__
<hide>
*rtprimerdb ID 2848
*rtprimerdb ID 2848
*Amplicon size: 87
*Amplicon size: 87
Line 222: Line 227:
**Current [stock]:
**Current [stock]:
*Annealing Temperature: 60 ??C
*Annealing Temperature: 60 ??C
</hide></showhide>


===B2m===
===B2m===
<showhide>__HIDER__
<hide>
*rtprimerdb ID 2866
*rtprimerdb ID 2866
*Amplicon size: 194 bp
*Amplicon size: 194 bp
Line 236: Line 244:
**Current [stock]:
**Current [stock]:
*Annealing Temperature: 60 ??C
*Annealing Temperature: 60 ??C
</hide></showhide>


===<font color="red">B2m</font>===
===<font color="red">B2m</font>===
<showhide>__HIDER__
<hide>
*PrimerBank
*PrimerBank
*GenBank Accession  NM_009735
*GenBank Accession  NM_009735
Line 251: Line 262:
*Forward Primer TTCTGGTGCTTGTCTCACTGA 21 61.0 26-46 Exon 1
*Forward Primer TTCTGGTGCTTGTCTCACTGA 21 61.0 26-46 Exon 1
*Reverse Primer CAGTATGTTCGGCTTCCCATTC 22 61.0 129-108 Exon 2
*Reverse Primer CAGTATGTTCGGCTTCCCATTC 22 61.0 129-108 Exon 2
</hide></showhide>


===Gapd===
===Gapd===
<showhide>__HIDER__
<hide>
</hide></showhide>


===28S===
===28S===
<showhide>__HIDER__
<hide>
*from qpcrlist message 3097 <http://groups.yahoo.com/group/qpcrlistserver/message/3097>
*from qpcrlist message 3097 <http://groups.yahoo.com/group/qpcrlistserver/message/3097>
*Multi species
*Multi species
Line 265: Line 282:
**DGG name: 28S_R
**DGG name: 28S_R
**Current [stock]:
**Current [stock]:
</hide></showhide>


===Tbp===
===Tbp===
<showhide>__HIDER__
<hide>
*rtprimerdb ID 49
*rtprimerdb ID 49
*Forward Primer:  GGCCTCTCAGAAGCATCACTA (21 bp) Spans Exon2/3
*Forward Primer:  GGCCTCTCAGAAGCATCACTA (21 bp) Spans Exon2/3
Line 278: Line 298:
*Amplicon size: 167
*Amplicon size: 167
*Annealing Temperature: 55 ??C
*Annealing Temperature: 55 ??C
</hide></showhide>


===Rpl32===
===Rpl32===
<showhide>__HIDER__
<hide>
*PrimerBank
*PrimerBank
*GenBank Accession  NM_172086
*GenBank Accession  NM_172086
Line 298: Line 321:
**DGG name: AJ_Mm_Rpl32R
**DGG name: AJ_Mm_Rpl32R
**Current [stock]:
**Current [stock]:
</hide></showhide>


===Sdha===
===Sdha===
<showhide>__HIDER__
<hide>
*Primerbank
*Primerbank
*LocusLink ID  66945
*LocusLink ID  66945
Line 319: Line 345:
**DGG name: AJ_Mm_SdhaR
**DGG name: AJ_Mm_SdhaR
**Current [stock]:
**Current [stock]:
</hide></showhide>


===Ywhaz===
===Ywhaz===
<showhide>__HIDER__
<hide>
*PrimerBank
*PrimerBank
*GenBank Accession  NM_011740
*GenBank Accession  NM_011740
Line 339: Line 368:
**DGG name: AJ_Mm_YwhazR
**DGG name: AJ_Mm_YwhazR
**Current [stock]:
**Current [stock]:
</hide></showhide>


===Hmbs===
===Hmbs===
<showhide>__HIDER__
<hide>
*PrimerBank
*PrimerBank
*GenBank Accession  NM_013551
*GenBank Accession  NM_013551
Line 360: Line 392:
**DGG name: AJ_Mm_HmbsR
**DGG name: AJ_Mm_HmbsR
**Current [stock]:
**Current [stock]:
</hide></showhide>


===<font color="red">Hspca</font>===
===<font color="red">Hspca</font>===
<showhide>__HIDER__
<hide>
*PrimerBank
*PrimerBank
*GenBank Accession  M36830
*GenBank Accession  M36830
Line 375: Line 410:
*Forward Primer AATTGCCCAGTTAATGTCCTTGA 23 60.2 60-82
*Forward Primer AATTGCCCAGTTAATGTCCTTGA 23 60.2 60-82
*Reverse Primer TCGTAACGGATTTTATCCAGAGC 23 60.2 170-148
*Reverse Primer TCGTAACGGATTTTATCCAGAGC 23 60.2 170-148
</hide></showhide>

Revision as of 14:12, 18 July 2006

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

<showhide>__HIDER__ <hide>

  • 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

</hide></showhide>

HPRT1: hypoxanthine phosphoribosyltransferase 1 (Lesch-Nyhan syndrome)

<showhide>__HIDER__ <hide>

  • 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

</hide></showhide>

UBC: ubiquitin C

<showhide>__HIDER__ <hide>

  • 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

</hide></showhide>

YWHAZ: tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide

<showhide>__HIDER__ <hide>

  • 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

</hide></showhide>

HMBS: hydroxymethylbilane synthase

<showhide>__HIDER__ <hide>

  • 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

</hide></showhide>

RPL13A: ribosomal protein L13a

<showhide>__HIDER__ <hide>

  • 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

</hide></showhide>

SDHA: succinate dehydrogenase complex, subunit A, flavoprotein (Fp)

<showhide>__HIDER__ <hide>

  • 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

</hide></showhide>

TBP: TATA box binding protein

<showhide>__HIDER__ <hide>

  • 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

</hide></showhide>

GAPDH

<showhide>__HIDER__ <hide> </hide></showhide>

B2M

<showhide>__HIDER__ <hide> </hide></showhide>

28S

<showhide>__HIDER__ <hide>

</hide></showhide>

PPIB

<showhide>__HIDER__ <hide> </hide></showhide>

Mouse

Mouse reference genes for Sybr Green QPCR

Hprt1

<showhide>__HIDER__ <hide>

  • 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]:

</hide></showhide>

Actb

<showhide>__HIDER__ <hide>

  • 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

</hide></showhide>

B2m

<showhide>__HIDER__ <hide>

  • 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

</hide></showhide>

B2m

<showhide>__HIDER__ <hide>

  • 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

</hide></showhide>

Gapd

<showhide>__HIDER__ <hide> </hide></showhide>

28S

<showhide>__HIDER__ <hide>

</hide></showhide>

Tbp

<showhide>__HIDER__ <hide>

  • 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

</hide></showhide>

Rpl32

<showhide>__HIDER__ <hide>

  • 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]:

</hide></showhide>

Sdha

<showhide>__HIDER__ <hide>

  • 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]:

</hide></showhide>

Ywhaz

<showhide>__HIDER__ <hide>

  • 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]:

</hide></showhide>

Hmbs

<showhide>__HIDER__ <hide>

  • 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]:

</hide></showhide>

Hspca

<showhide>__HIDER__ <hide>

  • 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

</hide></showhide>

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