| 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 |