QPCR

The Davidson laboratory at Caltech generated a panel of quantitative PCR primers useful for measuring mRNA abundance of genes involved in early development, particularly those in the endomesoderm gene regulatory network. Below is the table of primer sequences.

Note that the gene names listed in the table have been updated according to nomenclature guidelines and may have changed on the gene pages in Echinobase, however, they are listed as synonyms and the gene pages can be found by searching for the name listed in the table.

qPCR Primer Table

GENE	Full Name	Contributor	Primer seq (Forward)	Primer seq (Reverse)	Primer Length	Tm	Product size	Comments from Q-PCR	Source for seq. info
18S	18 S ribosomal RNA	AR	CAGGGTTCGATTCCGTAGAG	CCTCCAGTGGATCCTCGTTA	20/20	59.7/60.1	185 bp	works well; clean disassociation curve	Turbeville et al 1994; NCBI: L28055
Alx		PO	CAGTGCAGCTTTACGTGGAC	TTAAGTCTCGGCACGACAAA
Apo L	Apolipophorin	JR	AGAAGAGCATCGTGCAATGA	CAGCCATGGTGTTAGCAATG	20/20	59.55/60.13	154	works well; clean disassociation curve	Cdna
APOBEC	cytidine deaminase	JR	ACCCAGTTTCACCCTCCTCT	AGGCACTCAGCTGCAAAGTT	20/20	59.97/60.20	162	ok	Bra screen
Blimp1a	SpKrox	JS	GACCGAGGTCGATTACCAGA	CCGCGTACCTTTTGGTATGT	20/20		175	The efficiency of this primer has been confirmed by CY. The previous Otx-alpha primer has been removed from this data base because it does not work well.
Blimp1b	Spkrox early form	JS	TCGCTATGCGGGATCTCTAC	GGGGTCCTTGACCTCGTAA	20/19	56.1/56.3	206	The efficiency of this primer has been confirmed by CY. The previous Otx-alpha primer has been removed from this data base because it does not work well.
BMP2/4	Ligand	JN	CCAGCAAGGTCGAAGAACTC	CTCTACCCGACGACGATGAT	20/20	~60/~60	126bp	works well; clean disassociation curve
BRA	Brachyury	CL	ACACATCGACCCATCATCAA	CATGGTGTCGTATCTTGGAAAG	20/22	59.77/59.49	139	works well; clean disassociation curve
Brn1-2-4 (UI)	Brn1-2-4 (novel POU domain transcription factor)	CY	GTCGCATTAAGCTCGGCTAC	CAGCGGCTTCAGTTTACACA
CAPK	SMC	JR	ccaagtacgcaggaggaaga	gagagcatcggctattgtca	20/20	60.39/58.98	100bp	OK	Endoderm/Ectoderm diff. Scr. Larval Cdna
CAT	CAT REPORTER		TCCGGCCTTTATTCACATTC	CGGTGTAACAAGGGTGAACA	20/20	53.9/55.1
Cyclophillin	PMCspecific	GA	CCAAAGTGATGGAGGTGCTT	ACAATCGTGTATGGGCAAAT	20/20	60.1/57.8	161 bp	works well, clean dissociation curve	cDNA from 40h lyb
CyIIIa		PO	ACGCTGCAGGATTTGTAATG	TGCCAATGACAATCCCTATG	20/20	58.80/59.36	146BP	not tested, ordered
cyIIIa - UTR	cyIIIa mRNA, against 3' UTR	TB	GAAGAACAAAAATAAAACGCATCTG	ATTGTTTGTATTGCATTCTCCAATC	25/25	60/60	60	The efficiency of this primer has been confirmed by CY. The previous Otx-alpha primer has been removed from this data base because it does not work well.
cyIIIa int1	cyIIIa intron probe	TB	TGAACAAAACTGTGAAATGTGAAA	GGGCAGGGATAAAGTACCATC	24/21	60/60	108	The efficiency of this primer has been confirmed by CY. The previous Otx-alpha primer has been removed from this data base because it does not work well.
Dec	Decorin	CC	TTTATCTAGTTACACTTTTGCTGGTGA	ATAGATTGAGATTATCAAAGCCTCCT	27/26	59.7/59.1	300bp	works well, clean dissociation curve	cDNA from 20 hrs arrayed lib.
Dec II	Decorin	CC	GTCCAGGTGGAACACCAGAT	TGCTCCTAATGGTACGTTGACA	20/22	59.82/60.55	158bp	works well, clean dissociation curve	cDNA from 20 hrs arrayed lib.
DELTA		PO	ACGGAGCTACATGCCTGAAC	TCACAATGGACCGAATCAGA	20/20	60.29/60.05	151bp	works well, clean dissociation curve	H.Sweet cDNA
Dop T	Dopamine tautomerase	JR	CGAGTTCGCGTACAGCATAG	GAATCCTTCGGGAAACTGCT	20/20	59.66/60.58	143	works well; clean disassociation curve	Cdna
Dri	PMCs 15-20h; Oral Ectod after25h	GA	GGTTTCCCTAGGCAAGGAAC	GACAAGATGCTGCTGTTGGA	20/20	58.9/59.4	147bp	works well, clean dissociation curve	cDNA from 40harrayed lyb
E(spl)-1	Enhancer of split-1	CC	AGTCACAGTTCCCCAGCAAC	GTGACTGTGGTGGTGTCAGG	20/20	60.16/60.05	200	works well, clean dissociation curve	partial seq from Posakony's lab
ECM3	ECM protein (see Ettensohn)	AR	AGGGCAGTGATGTTGCCTAC	GTTTGCAGCAGGGTCGTATT	20/20	60.1/60.1	161 bp	works well; clean disassociation curve	cDNA clone from 12 hr arrayed lib.
Ef1	Elongation factor 1a	CA-M	CTTGGAAAGGGATCGTTCAA	GCCTGTGAGGTTCCAGTGAT				OK	Endoderm/Ectoderm diff. Scr. Larval Cdna
ENDO 16	Calcium Binding Protein	CL	GACCGAACGCCGATATAAGA	GCCATCGTCCCTTTAGTTCA	20/20	60.06/60.07	198bp	works well; clean disassociation curve	NCBI: L34680
Erg	Mesoderm ets factor	QT	AACGAGAGCCACATCTGGAG	TTTCGCTACGCTACAATCCA			150bp
EVE	Even Skipped	AR	CACAGACCCTGGACTTTCGT	GACAAACGGTCATCCCACTT	20/20	60.2/59.8	175 bp	works well; clean disassociation curve	cDNA clone from 12/15hr arrayed lib.
Ferr	Ferritin	CA-M	GCCTCGAGGAAGTCAGTCAT	ACCAACGTGGAGGTAGCATC				OK	Endoderm/Ectoderm diff. Scr. Larval Cdna
FGF	Ligand	JN	CTCTTTGCCACCCTCATCAT	CCCTCGACTTGATGCTTTTC	20/20	~60/~60	172bp	works well; clean disassociation curve
Ficolin	fibrinogen-domain protein	JR	GATGGACAAAGAGGGCTACG	TGAACCAGTCCGTCACTTCA	20/20	59.69/60.29	197		CDNA
Fkh1/FoxB	SpFkh1	PO	AAGCCATCCACAACCAAATC	CATATCCGTCGAACGAGTCA	20/20	59.80/59.67	147bp	works well, clean dissociation curve	David,E.S. et Al (1999) NCBI:AF149706
FMO	Flavin-containing monooxygenase	CC	GTCGGTGGACAATCACCTCT	ACGAGGACATTCTTGCCATT	20/20	59.97/59.56	199	works well, clean dissociation curve	cDNA from 20 hrs arrayed lib.
FoxA	(=HNF3beta) TF	PO	CCAACCGACTCCGTATCATC	CGTAGCTGCTCATGCTGTGT	20/20	60.34/60.23	160bp	works well, clean dissociation curve	Coding from BAC clone
FoxN2/3	PMC TF		TTCATGTCGATAGAGGACTGC	TTCGGAAGCACTTGTTGAGA
FoxY	Forkead class gene FoxY	AR	TGCACTGCACTGACTCTGC	CTTTCCATTCCGTGGTGAAG	19/20			works well; clean disassociation curve	cDNA clone from 12 hr arrayed lib.
GAPDH	Phosphate DeHydrogenase internal standard	Garry Wessel	AGGCTTCTTCAGACGGACAG	TGCTAAGGCTGTTGGAAAGG	20/20	59.6/90.38	120	The efficiency of this primer has been confirmed by CY. The previous Otx-alpha primer has been removed from this data base because it does not work well.
GATA c	TF	PO	CAGGGACATCATGTGCAAAC	CCGTGTTTGAATGCCTTCTT	20/20	59.97/60.11	155bp	works well, clean dissociation curve	cDNA clone from 20hr arrayed lib.
GATA e	Gata 4/5/6 factor	CL	ATGCATGCGGTCTCTACCA	CGCCACAGTGTTGTAGTGCT	19/20			works well; clean disassociation curve	NCBI: AF077675
GATA e (2)	TF	PO	CTGGCTCAAGACGAGAAGGA	CCTCTTCCGAGTCTGAATGC	20/20	60.67/59.95	176bp	works well, clean dissociation curve	cDNA clone from 20hr arrayed lib.
GCM	Glial Cells Missing	AR	CGACTGATAACCACGCTCAA	TTAACGACGTCGGTCGATTC	20/20	59.9/61.0	178 bp	works well; clean disassociation curve	cDNA clone from 12 hr arrayed lib.
Gelsolin	gelsolin-domain protein	JR	CTCCATCGACGAGAGGAGAA	CCTTCTGCTACGACCGAAAC	20/20
GFP		PO	AGGGCTATGTGCAGGAGAGA	CTTGTGGCCGAGAATGTTTC	20/20	59.97/60.64	152bp	works well, clean dissociation curve	Cathy seq on EpGFP
Hedghog	Ligand	PO	ggcttcgattgggtcaacta	GTTGACCACGGCTACCTCAT	20/20	~60/~60	~150bp	works well; clean disassociation curve
HES	Hairy	JR	TCTCAGGATTGGCAGCAAGT	CGTTAATCCTCGCTCGTCTT	20/20	60.94/59.48	175		Cdna
HesC	Repressor of micromeres		ccagaacagggcgaatctaa	CGAAGACGGGTTTCAATGTC	20/20	~60/~60
Hex (TF 263)	PMC and SMC TF	MH	TTCTTGTGGAACCCGTTCAT	CGGGGAGAGGTATTTCTGGT
Hmx	SpHmx	CL	TCGTCGTTTGAAGGTTGAAGT	TGATAGACGCATCTTGCTCG	21/20	59.77/60.12	152	works well; clean disassociation curve	NCBI: D85079
HNF3beta	HNF3 beta (same gene as FOXa)	AR	CATTGATCGTATCCGTGCTG	TTGCCACCGTTGTTGATTT	20/19	60.1/60.0	190 bp	works well; clean disassociation curve	cDNA clone from 15 hr arrayed lib.
HNF-6	Hepatocyte Nuclear Factor 6	OO	TGCAGCTTCTCTGCATACCA	ACTCCAACATGCCTCCAAAC	20/20	51.8/51.8	152bp	works well, clean dissociation curve	cDNA clone from 7/20/40hr arrayed lib.
Hox11/13B	TF Hox cluster	PO	CACAGGCTCTCGACCTAACC	GGTGGATGAGGTGGTAGATGA	20/21	59.87/59.79	155bp	works well, clean dissociation curve	Dobias et al(1998) NCBI:AF042652
Hsp70	Heat sock protein	CA-M	CACTTGGGTGGTGAGGACTT	TACCCTCAAACAGGGAATCG				OK	Endoderm/Ectoderm diff. Scr. Larval Cdna
ISP1	nontrans poly A mRNA	AR	TGTGTTTCATTCCGTGGCTAT	GCCAACCCTTCTGATCAACT	21/19	60.4/59.1	180 bp	works well; clean disassociation curve	Calzone et al 1988; NCBI: Y00216
KAKAPO	actin binding	JR	GTGGCATTTATGAGCGGTCT	CGGCCCAGTACTTCAAGGAGA	20/20	60.10/59.28	177	OK	Bra screen
Krl	The original information has been deleted by someone, unknown reason.	TM (originally contributed by CBL)	CACGAACTCTTCGCAATCAA	CCAAGGGACAGGAGTGAAGA
Lefty	Lefty, Nodal inhibitor	JN	CGTAGTCGCCACATCAGAGA	CAGATACATCATGGGCAACG	20/20	~60/~60	132bp	works well; clean disassociation curve
LIM	Lim-HD	PO	GTATCCGATCCGTTGACGAC	TAGCCTTGCATTCACAGCAC	20/20	60.35/60.02	153bp	works well, clean dissociation curve	cDNA clone from 15hr arrayed lib.
Lys	Lysosomal associated protein	CA-M	TACCCGACAACCACTGTGTC	GCTCCCTCTCTGCGAAATAA				OK	Endoderm/Ectoderm diff. Scr. Larval Cdna
Msp130	PMCspecific	GA	agagcaacgctcattctggt	ctccgaattgcattttgtca	20/20	60/59.7	149bp	seems ok: ask me for dissociation peak
Nk1	Nkx1 homeobox TF	JR	GACCATGCATGTGCGTAAAC	TCTGTGACTGCCACTCATCC	20/20	60.00/59.83	175	works well; clean disassociation curve	Cdna
NKX 2.1	Apical plate from 24h on	GA	CGTGAGAGCTTCCCTACCTG	GAAGCTCCCTAGCTCGATGA	20/20	59.5/60.0	201bp	works well, clean dissociation curve	Peterson et al., umpublished data
Nodal	nodal, OE activator	JN	GACAACCCAAGCAACCACG	CGCACTCCTGTACGATCATG	19/20	~60/~60	178bp	works well with Sp, Lv, and Pl Nodal; clean disassociation curve
Not	SpNot	CL	GAGCGACTTGAGCAGGAGTT	GGACCTGCTGTTTCTCGAAG	20/20	58.75/59.99	159	works well; clean disassociation curve	NCBI: AF109903
Notch		CC	ACGGAGCCAAGCCTAAGAA	TCGTCACAGGCAACGAATAA	19/20	59.9/60.2	207	works well, clean dissociation curve
nrl	neuralized-like Zn fing; Ubq Ligase	JR	ATAGGTGCCCTGCACATAGG	ATCCAGCTTCCGAGGGTAAC	20/20	59.98/60.46	148	works well; clean disassociation curve	Cdna
OrCT	Endomeso diff gene	JR	GAC TTC AGA CGC GTT GGT CT	TTA TCA CTG TCG GGG AGT TTG
Otx-alpha new	SpOtx-alpha (exon6)	CL/CY	CCTTACCAGCACCTGATCG	CTGGTCCTGCTGAACAAGGT	19/20	57.0/57.2	192	The efficiency of this primer has been confirmed by CY. The previous Otx-alpha primer has been removed from this data base because it does not work well.
Otx-beta1	This primer recognize both SpOtx-beta1and beta2 (exon 3 and 5)	CL/CY	GTTTAGGAACGTCGCTGGAA	TGAAGGTGGTGGTGATGTTG	20/20	55.15/55.15	487/187	The efficiency of this primer has been confirmed by CY. The previous Otx-beta primer has been removed from this data base because it does not work well.
Otx-beta2	Recognize exclusively SpOtx-beta1 (exon 4)	CL/CY	TGAATAACAGCCCTAGAAGAGCA	CTGCTCTACCGTCACCGATT	23/20	55.74/56.23	130	The efficiency of this primer has been confirmed by CY. The previous Otx-beta primer has been removed from this data base because it does not work well.
Otx-beta3	This primer recognize SpOtx-beta3 (exon 1 and 2)	CL/CY	CCACTCCACCGCTTCTACAC	CTTCAAGGTGCCGATAATTGA	20/21	59.25/53.42	150	The efficiency of this primer has been confirmed by CY. The previous Otx-beta primer has been removed from this data base because it does not work well.
Otx-beta4	This primer recognize SpOtx-beta1, beta2 and beta3 (exon 5)	CY	TGGATCATTCTGCCTTGACA	ACATAGCGGGATGCATGAG	20/19	54/54.9	189	The efficiency of this primer has been confirmed by CY. The previous Otx-alpha primer has been removed from this data base because it does not work well.
Pitx2	TF	MH	ACATTTCACCAGCCAGCAAC	TCAAGTTACACCACGCACAGA			104
PKS	polyketide synthase	JR	ATCGTTGGATCCTCAACAGC	GACACACTGTGCGCAATACC	20/20	60.08/60.19	195	works well; clean disassociation curve	Cdna
Pm27	PMCspecific	GA	cgaaagtggtctgctgatga	ctcgctctctctttccaacg	20/20	59.98/60.27	149bp	works well, clean dissociation curve
Pmar1	Sp Hbox 12 Homeodomain TF	PO	GCGTTCAACGACAACCAGTA	GGTTGATGAGCAGAGCTTGA	20/20	59.76/59.12	152bp	works well, clean dissociation curve	cDNA clone from 9.5hr phage lib.
Prox1	SMC TF		AGGTACCGGAGGGCTTCTT	ATGGTCTTCTTCCAGGATGG
RFP	RFP (I got RFP clone from Mr. Damle)	JN	ATGAGGCTGAAGCTGAAGGA	TGGTGTAGTCCTCGTTGTGG	20/20	~60/~60	142bp	works well; clean disassociation curve
S403		CC	CTGCGGTGAGAGCAAGTTTA	GAGAGCGTTGCCTGAACAAC	20/20	59.2/60.99	199bp	works well, clean dissociation curve	cDNA from 20 hrs arrayed lib.
Six1/2	Aboral SMC TF	SM	TGAAACACCGTCAAAACAAGG	TGCTCTGGATGAAGATGAAGG
SM30	Spicule Matrix protein	OO	GTTCTCCGGTAGGCAAACA	ACATTTTGGGGCAAATGAAA	19/20	59.4/59.9	196bp	works well, clean dissociation curve	Akasaka,K. ET AL.,1994.NCBI U05962
SM50-LC	SM50	LC	tagcctttgctacgggtcaa	ctgaggcgacgaaactgaa	20/19	60.4/60.16
Snail	EMT TF expressed in SMC	SM	AAGGAGTACTCGACGTTCGG	TCCTGATGTGCATTTTGAGG			136bp
Sox B1	SpSox B1	CL	ATTCTGTGAACGTCATGGCA	TTGTCCTCTTGACCACACCA	20/20	60.12/60.13	184	bad dissossiation curve	NCBI: AF157389
Sox E	Sp SoxE	MH	CGGGAAGAGAAAACCTCACA	TTTTCCCAGGGTCTTGCTC			130bp
SoxC	Wave TF	MH	CATGGTTTGGTCACAAATCG	TACGGAGATTTCGCCACTTC
Sp cbf-a	CCAAT-binding factor, A (Ubq expression)	TB	ACCCATCGCTAATGTTGCTC	CACTGGCTTCGCTTGTGATA	20/20	60/60	131	The efficiency of this primer has been confirmed by CY. The previous Otx-alpha primer has been removed from this data base because it does not work well.
Sp cbf-b	CCAAT-binding factor, B (Ubq expresion)	TB	GGATTCCCAAGGAGAGAAGG	ATAGAGGGCGAAGGGATCAT	20/20	60/60	130	The efficiency of this primer has been confirmed by CY. The previous Otx-alpha primer has been removed from this data base because it does not work well.
Sp cbf-c	CCAAT-binding factor, C (Ubq expression)	TB	TCCTCTTATTCTCTTCTGTATGTAGCC	ATAAGTGCTGAAGCCCCAGT	27/20	60/60	100	The efficiency of this primer has been confirmed by CY. The previous Otx-alpha primer has been removed from this data base because it does not work well.
Sp gcf-1	GCF1, general activator	TB	ACCAGACCTTCTCCCACCTT	TCTCTTGCGGTTGTTCTCCT	20/20	60/60		The efficiency of this primer has been confirmed by CY. The previous Otx-alpha primer has been removed from this data base because it does not work well.
Sp myb	myb (cyIIIa repressor)	TB	AACCATTCACAAGCCACTCC	TGGTCCTCCTGCCTTCTCTA	20/20	60/60	147	The efficiency of this primer has been confirmed by CY. The previous Otx-alpha primer has been removed from this data base because it does not work well.
Sp oct-1	oct-1, cyIIIa activator	TB	CACAGGGTGATGTTGGTCTG	GGAGAGGTTTGAGCTTGCAC	20/20	60/60	123	The efficiency of this primer has been confirmed by CY. The previous Otx-alpha primer has been removed from this data base because it does not work well.
Sp P3A2	P3A2, OE repressor of cyIIIa	TB	AGCATCATGGAAGGGATGAC	GTGTACCACAGCATGGGATG	20/20	60/60	104	The efficiency of this primer has been confirmed by CY. The previous Otx-alpha primer has been removed from this data base because it does not work well.
Sp runt	runt (cyIIIa activator, ubiq)	TB	CGGTACGGAGGAACAACCTA	AGGGCTCTCTGTCTTCACCA	20/20	60/60	149	The efficiency of this primer has been confirmed by CY. The previous Otx-alpha primer has been removed from this data base because it does not work well.
Sp tef-1	TEF-1/scalloped, cyIIIa activator	TB	GGCCACTGCCTTACAAGAAC	AGGGTCATGAGATGGTCCTG	20/20	60/60	146	The efficiency of this primer has been confirmed by CY. The previous Otx-alpha primer has been removed from this data base because it does not work well.
Sp tondu	tondu/vestigial, TEF-1 co-factor	TB	ACTCCGGTGATTTGGACAAG	CAGTGAGCGGCTAAAATGTTC	20.21	60/60	50	The efficiency of this primer has been confirmed by CY.
The previous Otx-alpha primer has been removed from this data base because it does not work well.
SpDlx	Aboral Ectoderm TF	EL	CCAGCTTACAACTCCAACAGC	TTACCTGAGTTTGAGTGAGTCCA
SPEC 1	aboral ectoderm	GA	GCGCATGCTCAGATTGTATC	CAAGGAGTGGTAAGGGTGGA	20/20	58.6/59.0	164 bp	works well, clean dissociation curve	Hardin,S.H.,1985 NCBI X03287
Spec2a	SpSpec2a	PYL	GGACGGTAAAATCTGCCTTG	AGACGATTATGTCACCCTCTCC				The efficiency of this primer has been confirmed by PYL.
SpElk	Ets TF	Inna	ATCATGGTCGCTAGTCCTCTCCT	TGACAAGAGAACAGTCGGTGTGA
SpEts	TF	PO	GCACTGGTCCATCAAGGAGT	GATGTGCTCCCAGAGGATGT	20/20	60.12/60.08	145bb	works well, clean dissociation curve	Rao and Childs(1993) NCBI:L19541
SpEts4	TF Ets4	PO	CTCCAGCCCAACTCCTACAG	GATGGAGCGAGAGAGCTTGT	20/20	60		works well, checked by Paola
SpGsc	Homeodomain TF	PO	GCGACACGCTCCCTATCTAC	CGATGTCGCCTCTTTCTCTT	20/20	59.87-59.57	147bp	works well, clean dissociation curve	Angerer(2001)-NCBI: AF315231
SpIrxA	Aboral Ectoderm TF	EL	TATGGAATGGACCTGAACGG	TATGATCTTTTCGCCCTTGG
SpLox	A gene that is expresed in the endoderm at 45 h	Ina Arnone	GTGCGACGGACTCCCTATAA	TTCAGACGCCATGGTGTAAA	20/20	56.2/54.4		works well, clean dissociation curve
SpMSP130like	PMC differentiation gene	JR	TTC TTG GTC GCC TGG ATT AC	ACC TTG GCA TCG CAT AGA AG
SpNK2.2	Aboral Ectoderm TF	EL	ACACTTGGCGAGCATTATCC	CGGAGAAGGTAACGGATTCA
SpTbx2/3	Aboral Ectoderm TF	EL	ACTGCCGGTACAAGTTCCAC	GACACATTTCTGCATCCATTG
SpZ12-1	TF	PO	AGTCGTCCAGCCATGTCTTT	AAGCACACCTCGCACCTATC	20/20	59.73/60.29	151bp	works well, clean dissociation curve	Wang D. et Al (1995) NCBI:U19831
Su(H)	Suppressor of hairless	CC	GCTCCATCGTTGATGATCTCT	GGACGCTGATGATCCAGTCT	21/20	59.26/60.23	156	works well, clean dissociation curve	partial seq from Posakony's lab
SuTx	sulfotransferase	CC	AATTCATGCCAGAGCCATTG	CCGAGAACTCGACCTTCAAC	20/20	61/59.84	204	works well, clean dissociation curve	cDNA from 20 hrs arrayed lib.
TBR	T-brain	JR	GAAACATTCGCCTTCCTTGT	GAAGGCGTCGGTTTACCTCT	20/20	59.17/60.63	98	primers reversed, and 3' primer bridges exon1 and exon2, making this pair unsuitable for genomic DNA quantitation	Cdna
Tel	Maternal + Zygotic mesoderm TF	QT	TGTTAGCTTCTGCCCCTGTT	CGACGAGAGAGGGTCTTCAG			162 bp
Tgif (ark 43)	PMC and Endoderm TF	MH	GCTCTACCTATCTCGCTTGGC	TGGTGAACTTGTCAGGGTCT
UBQ	Ubiquitin	CL	CACAGGCAAGACCATCACAC	GAGAGAGTGCGACCATCCTC	20/20	60.16/59.95	147bp	works well; clean disassociation curve
VegFR	VegF Receptor	JR	AGGGCAGGTCAACAGTTCAG	GGCAACCAATTTGACATCCT
Wnt 5a	Wnt 5a	PYL	TGCTGTGGAAGAGGCTACAA	TTCTGCACTTCCGACACTTG	20/20			works well, clean dissociation curve
WNT 8 (2)		PO	TGTCGTTCATTCAAGCCATC	TATCACTCGCCATTCGTTCA	20/20	59.65/60.22	183bp	works well, clean dissociation curve