| Table S4. Primers and clones |
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| adapted from
Akiyama-Oda and Oda, Sci. Adv. 6, eaba7261 (2020) |
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| under a Creative Commons
Attribution License 4.0 (CC BY 4.0) |
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| Genes
identified in the Pt-hh and Pt-ptc pRNAi, RNA-seq, and differential expression analysis |
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| aug3 gene model |
Gene name |
Isolation |
Accession number |
cDNA clone |
Primer 1 |
Primer 2 |
Primer 3 |
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| aug3.g9172 |
Pt-otd (oc2) |
Akiyama-Oda
& Oda (2003) |
AB096074 |
pZL-km.otd#8-1 |
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| aug3.g5611 |
Pt-fgf8 |
EST |
FY381077 |
eS7_SB_042_E12 |
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| aug3.g12202 |
Pt-opa |
Kanayama et al.
(2011) |
AB605264 |
At_eW_022_A24 |
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| aug3.g8250 |
Pt-BarH1 |
PCR |
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pCRII-aug3.g8250(f1-r1)#5 |
ACTCCACAAGCAAATGCCAC |
AGATGACGCTGAAGATGAGG |
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| aug3.g9493 |
Pt-latrophilin-B |
PCR |
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pCRII-aug3.g9493(f1-r1)#6 |
GCCTTTGTATGCGGATGATC |
CGGTAGTCCAAGTTAGTCCT |
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| aug3.g12543 |
Pt-fam132B |
EST |
FY222963 |
At_eW_021_C06 |
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| aug3.g7954 |
Pt-lab-A |
Akiyama-Oda
& Oda (2010) |
AB433903 |
pCRII-km.lab1-5RACE#9 |
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| aug3.g11337 |
Pt-prd1
(pax3/7A) |
EST |
LC379632 |
eS6_d1_51_D04 |
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| aug3.g11865 |
Pt-h15-1
(Pt-tbx20-C) |
cDNA library
screening |
AB177874 |
pBS-Tb#6(p2-2)s |
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| aug3.g5391 |
Pt-naked cuticle |
PCR |
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pCRII-aug3.g5391(F,R)#6 |
ATGGAGGTCACATGCAGTGT |
ACGAGATGTGCTTGGTGACA |
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| aug3.g8856 |
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EST |
FY218738 |
At_eW_006_P01 |
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| aug3.g416 |
Pt-snail |
Yamazaki et al.
(2005) |
AB167392 |
pZL-km.snail#7-1-1 |
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| aug3.g12734 |
Pt-Delta2 |
PCR |
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pCRII-aug3.g12734(F,R)#4 |
GGAATCAGATTACAGCTCTC |
GATGTGCTCATCATATCTGG |
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| aug3.g14027 |
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PCR |
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pCRII-aug3.g14027(f2-r2)#1 |
CATCCACTCCTTGCCTACCG |
CCAGGCACTGTATAACTTGG |
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| aug3.g7547 |
Pt-ets1 |
RACE |
LC379613 |
pCRII-km.Ets-5Race#2 |
CCACTTCGTCCGGGTCGGTGAGCTTGA |
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| aug3.g11833 |
Pt-glypican6-B |
EST |
FY220493 |
At_eW_012_M09 |
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| aug3.g14296 |
Pt-znf423 |
PCR |
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pCRII-aug3.g14296(f1-r1)#1 |
TGCACATCGTGCAATGTTGC |
GCAATCATAACTCGGACACC |
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| aug3.g5177 |
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EST |
FY374464 |
eS6_d1_33_F05 |
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| aug3.g13867 |
Pt-hth1 |
EST |
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S7_d1_48_G06 |
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| aug3.g15983 |
Pt-inv1 |
PCR |
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pCRII-aug3.g15983(f1-r1)#5 |
GAGTCCGATGGTACTTGATG |
ATGCGCCATTAATTTCAGCG |
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| aug3.g2279 |
Pt-UBE2QL |
EST |
FY381410 |
eS7_SB_046_B10 |
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| aug3.g12690 |
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PCR |
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pCRII-aug3.g12690(f1-r1)#4 |
CGCAACAACACGCATCATGA |
CCATGTGTGCCATTTCGTGT |
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| aug3.g4 |
Pt-FBXL7-A |
EST |
FY371327 |
S7_d1_36_G03 |
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| aug3.g1241 |
Pt-proximal to
raf |
PCR |
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pCRII-aug3.g1241(f1-r1)#1 |
TCAATGCCAGGATCGAGCAG |
GGATGCAGGCAATCCATTCG |
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| aug3.g8837 |
Pt-tbx20-A |
EST |
FY368741 |
S7_d1_06_F05 |
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| aug3.g27747 |
Pt-exd2 |
PCR |
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pCRII-aug3.g27747(F,R)#1 |
GTGAGGCATGGACGATCCAC |
GCAGCGTATAGGTTGGCTTC |
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| aug3.g19033 |
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EST |
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eS6_d1_96_D10 |
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| aug3.g4396 |
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PCR |
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pCRII-aug3.g4396(F,R)#1 |
TTAGTCGAAGGTGTGGAAGA |
ATCCAATGATTGCGGCAGAG |
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| aug3.g2762 |
Pt-runx-B |
PCR |
FY223076 |
pCRII-km.runt-1 |
CTTCTCATTGGGACCTATTTC |
TAATGTCTTGGTTGATCTCCA |
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| aug3.g10461 |
Pt-bruchpilot-B |
PCR |
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pCRII-aug3.g10461_9(f4-r4)#4 |
TCAAGTGGACATGGCACGTG |
TTGTTCTAGGTGGAGCTTCC |
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| aug3.g14054 |
Pt-rps12 |
EST |
FY224341 |
At_eW_024_O06 |
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| aug3.g11119 |
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PCR |
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pCRII-aug3.g11119(f2-r2)#1 |
AGATTGCCACAGTCACCTCT |
TCCAAACAACACAATCGCGT |
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| aug3.g10830 |
Pt-esrp |
PCR |
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pCRII-aug3.g10830(F,R)#2 |
GTCACCGCTGGTCTGCAAGA |
TCTCTGTGTTTCTGCAGAGC |
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| aug3.g20669 |
Pt-bab-A |
EST |
FY225142 |
At_eW_027_B10 |
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| aug3.g15189 |
Pt-msx1 |
EST |
FY222578 |
At_eW_020_B15 |
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| aug3.g9575 |
Pt-gas1 |
EST |
FY223857 |
At_eW_023_I22 |
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| aug3.g26043 |
Pt-bcl11 |
EST |
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eS6_d1_82_G07 |
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| aug3.g23531 |
Pt-AP2-A |
EST |
FY374387 |
eS6_d1_32_G05 |
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| aug3.g27568 |
Pr-shifted |
PCR |
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pCRII-aug3.g27568(f1-r1)#1 |
CCTCTGGTGACCACAAGTAT |
TCGCTTATTGCACCTGTTGC |
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| aug3.g17640 |
Pt-Scr-B |
RACE |
LC379624 |
pCRII-km.Scr2-3Race#2 |
GAAGGCGGATTGAGATTGCCCATGC |
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| aug3.g12644 |
(serine
protease) |
EST |
FY373933 |
eS6_d1_27_C12 |
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| aug3.g16493 |
(homeodomain
protein) |
PCR |
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pCRII-aug3.g16493(f1-r1)#2 |
CGAGGTTCGCGTAGAATCAG |
TCTGTGGTGCATAGGTTTGC |
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| aug3.g3273 |
Pt-basonuclin-A |
EST |
FY223376 |
At_eW_022_D23 |
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| aug3.g13321 |
Pt-ci |
Kanayama et al.
(2011) |
AB605263 |
pCRII-km.ci5RACE#1 |
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| aug3.g13939 |
Pt-nrarp-B |
EST |
FY221701 |
At_eW_017_H20 |
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| aug3.g10604 |
Pt-echinoid (ed) |
EST |
FY225122 |
At_eW_027_A14 |
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| aug3.g22741 |
Pt-RTP-B |
RACE-nested PCR |
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pCRII-aug3.g22741-5n(r2)#2 |
GATACCACATGGCTGCTTCA |
GTCCAACCGTGTCCGCATTCCTCGC |
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| aug3.g27670 |
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EST |
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S7_d1_70_G12 |
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| aug3.g13591 |
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EST |
FY218778 |
At_eW_007_A22 |
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| aug3.g5060 |
Pt-winged eye-B |
EST |
FY219253 |
At_eW_008_I13 |
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| aug3.g9517 |
Pt-dipeptidyl
peptidase2 |
EST |
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eS6_d1_86_B11 |
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| aug3.g9057 |
Pt-mob2 |
PCR |
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pCRII-aug3.g9057(f1-r2)#6 |
GGAATGTAGTGTTCCTGAAAC |
GAACTTTAAGGGTGAGGAAC |
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| aug3.g5160 |
Pt-zswim6 |
PCR |
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pCRII-aug3.g5160(f1-r1)#1 |
GCTGGCATCTTGATGAAGAAC |
AAGAGCTAAGGTACGAGCAC |
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| aug3.g12989 |
|
RACE-nested PCR |
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pCRII-aug3.g12989-5n2(r2)#1 |
CCTGTCTCTTTGCATCAGAT |
GGCGTTTGCCGAGCTATTTGCGTGCA |
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| aug3.g12367 |
Pt-4-hydroxyphenylpyruvate-dioxygenase |
EST |
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S7_d1_67_A07 |
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| aug3.g26944 |
Pt-grhpr-B |
PCR |
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pCRII-aug3.g26944(F,R)#1 |
GCCTAGTGTTCCGAAAGAAG |
CGTGAGGTAGAAGAGCGATG |
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| aug3.g12961 |
Pt-zfp236 |
EST |
FY369220 |
S7_d1_11_H11 |
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| aug3.g11765 |
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EST |
FY221740 |
At_eW_017_K07 |
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| aug3.g9827 |
Pt-frizzled4 |
RACE |
LC379618 |
pCRII-Fz4-5Race#3 |
GCGATGGTTTTGACAGCAGGGACGAAC |
GTTCGTCCCTGCTGTCAAAACCATCGC |
GTAATGAATGGAGTAGATGCTGATG |
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| aug3.g1487 |
Pt-TET2 |
RACE-nested PCR |
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pCRII-aug3.g1485-3n(f2)#2 |
GGGATCGAACATTTGCCTAG3 |
CTGTGCATCATGACGTTCGC |
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| aug3.g4121 |
Pt-rnf220 |
EST |
FY379695 |
eS7_SB_025_F04 |
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| aug3.g16317 |
Pt-laminin-alpha-1 |
EST |
FY373247 |
eS6_d1_18_F12 |
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| aug3.g6466 |
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PCR |
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pCRII-aug3.g6466(F,R)#1 |
GGTTCAAGCATCCAAGACGA |
ACAGAAGGTGATGGACTACG |
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| aug3.g1352 |
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PCR |
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pCRII-aug3.g1352(F,R)#2 |
AGACATGACAGGACTATGCA |
TAACAACGAGATGTCTGGAC |
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| aug3.g11246 |
Pt-cyclinD-1 |
EST |
FY222941 |
At_eW_021_B07 |
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| aug3.g4220 |
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EST |
FY381549 |
eS7_SB_047_G05 |
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| aug3.g18899 |
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EST |
FY369865 |
S7_d1_19_B10 |
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| aug3.g9270 |
Pt-Notum |
EST |
FY371093 |
S7_d1_34_B10 |
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| aug3.g4876 |
Pt-Secreted
frizzled-related protein |
PCR |
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pCRII-aug3.g4876(f1-r2)#1 |
GTTATCAAGACCAAGATCCG |
CAGTAAACCCTCATGAACGT |
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| aug3.g8295 |
Pt-mirr4 |
EST |
FY370739 |
S7_d1_29_C06 |
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| aug3.g13482 |
Pt-rhomboid |
cDNA library
screening |
LC379651 |
pBS-rhomboid |
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| aug3.g4413 |
Pt-NDNF |
EST |
FY373185 |
eS6_d1_18_A06 |
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| aug3.g21549 |
Pt-odd-skipped
related-B (osr-B) |
PCR |
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pCRII-aug3.g21549(f1-r1)#1 |
CTCTCACTCCCACCAGTCCA |
TGGTCCTCCTGAGGTCGCAG |
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| aug3.g26688 |
|
PCR |
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pCRII-aug3.g26688(f1-r1)#1 |
CATGGTGACGACTTATCAGA |
ACTAATGTCACGAGACCAAC |
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| aug3.g19340 |
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EST |
FY375558 |
eS6_d1_46_H12 |
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| aug3.g17638 |
|
RACE-nested PCR |
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pCRII-aug3.g17638_3n-1#1 |
CTAACTATCCTTGGTCTTGGTGCAG |
CAACGGGATGTTCCTTCGTTCCAAG |
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| aug3.g12585 |
Pt-uninflatable-A |
PCR |
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pCRII-aug3.g12585(f1-r1)#1 |
ATGCAGCTGTGGCTGGTACA |
ACTGCATAGTTCTTCCGAGC |
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| aug3.g5781 |
Pt-magu |
EST |
FY373859 |
eS6_d1_26_E01 |
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| aug3.g362 |
Pt-maob-1 |
EST |
FY375784 |
eS6_d1_50_C03 |
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| aug3.g2333 |
Pt-sp6-9 |
EST |
FY380736 |
eS7_SB_038_H11 |
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| aug3.g17729 |
Pt-noggin-D |
PCR |
|
pCRII-aug3.g17729(f1-r1)#2 |
GACGATTCTAGGCAACTTCC |
GAACTTTAACCCAGGAACAG |
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| aug3.g10793 |
|
EST |
FY370360 |
S7_d1_24_F07 |
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| aug3.g3879 |
Pt-eph |
EST |
FY225184 |
At_eW_027_D06 |
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| aug3.g9731 |
|
PCR |
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pCRII-aug3.g9731(f1-r1)#3 |
TGGTCAACTCTACTCCTTCT |
CCACCTCCAGTCTCCATTTC |
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| aug3.g12797 |
Pt-Argonaute-C |
PCR |
|
pCRII-aug3.g12797(F,R)#1 |
TGCAGAAAAGAGCTGAGCGA |
TGTTGCCAATCGTAGTCTTG |
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| aug3.g26574 |
Pt-Filamin |
PCR |
|
pCRII-aug3.g26574(f1-r1)#1 |
TAGGCTATAAGCCCACTGAG |
GCCATACACAGAACAGAAGA |
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| aug3.g15186 |
Pt-Myotubularin-related
protein 14-B |
PCR |
|
pCRII-aug3.g15186(F,R)#2 |
GGAAGTTGATTGTTCTGTCG |
GGCTGTGCAATCGAAGTGCT |
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| aug3.g26155 |
Pt-piopio |
PCR |
|
pCRII-aug3.g26155(F,R)#1 |
CCAGTCATGACATTGAGGGA |
CGGAGTAGATGGATGATCCT |
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| aug3.g14946 |
|
EST |
FY368371 |
S7_d1_02_E10 |
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|
| aug3.g11541 |
|
PCR |
|
pCRII-aug3.g11541(F,R)#2 |
TCTGTTTCAGCTGTTTAGTC |
GCAGTAGAAGAGACAGTAGG |
|
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| aug3.g4422 |
|
PCR |
|
pCRII-aug3.g4422(f1-r1)#1 |
TCAGTTGGAGCATTCATAGC |
CCTTCGTCTTTACGGCATCT |
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| aug3.g13802 |
Pt-mif |
EST |
FY380519 |
eS7_SB_036_E03 |
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| aug3.g4245 |
|
PCR |
|
pCRII-aug3.g4245(f1-r1)#2 |
GGATGGATACTTCTGCCTGA |
CAAGTCCCAACTCACATATG |
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|
| aug3.g2915 |
Pt-seven-up-A |
PCR |
|
pCRII-aug3.g2915(f1-r1)#2 |
ACCCTACGACGACTGTGGTC |
GGACAACAGCATGTCCCGT |
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| aug3.g19649 |
Pt-slu7-C |
EST |
FY223883 |
At_eW_023_K01 |
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| aug3.g25707 |
|
EST |
FY216693 |
At_eW_001_A16 |
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| aug3.g7019 |
|
EST |
FY378006 |
eS7_SB_005_C07 |
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| aug3.g15841 |
|
PCR |
|
pCRII-aug3.g15841(F,R)#2 |
CACCGGCGATTTCAGAGGCT |
AGAGTGATCCGTCATTTGAC |
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| Genes
identified in the Pt-msx1 pRNAi, RNA-seq, and differential expression analysis |
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| aug3 gene model |
Gene name |
Isolation |
Accession number |
cDNA clone |
Primer 1 |
Primer 2 |
|
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|
|
| aug3.g18397 |
Pt-prd2
(pax3/7B) |
RACE |
LC379633 |
pBS-km.pax3/7b-3RACE#2-1 |
TAGAATTGGCCGCAGCCGGTGTCCGTC |
|
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| aug3.g5047 |
Pt-asl-H |
EST |
FY37438 |
eS6_d1_32_G02 |
|
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|
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| aug3.g3963 |
Pt-ets21c |
EST |
FY375900 |
eS6_d1_51_E01 |
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| aug3.g9318 |
Pt-krüppel-1 (krü-1) |
PCR |
|
pCRII-aug3.g9318(f1,r1)#2 |
AAGTCAATGGATCTATGTCG |
CTAAGCGAAGGTGAGAATGG |
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|
| aug3.g16372 |
Pt-GCH1 |
PCR |
|
pCRII-aug3.g16372(f1,r1)#6 |
GCAAACTGTTGCACGTTCTTC |
CAGCATCGTGCTCGTAATCG |
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| aug3.g11688 |
Pt-pax6-A |
PCR |
|
pCRII-aug3.g11688(F,R)#3 |
TGTTCAGAGATTTGAGTGCC |
ATGACGTGAGGTTGAGCCGT |
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| aug3.g19819 |
|
EST |
FY225095 |
At_eW_026_P10 |
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| aug3.g1120 |
|
EST |
|
eS6_d1_71_C09 |
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| aug3.g25735 |
Pt-Na/Ca
exchange protein-A |
PCR |
|
pCRII-aug3.g25735(F,R)#1 |
GAAGAGCTTCGACAGGTTGT |
ATAGCGGCAATGGACCAAGC |
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| aug3.g11206 |
|
PCR |
|
pCRII-aug3.g11206(F,R)#4 |
CCGCTCCAAGTAACAACAGA |
CCAAGTCCAAAGGCAAATCG |
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| aug3.g16171 |
|
PCR |
|
pCRII-aug3.g16171(F2,R)#4 |
CAGAATAACAGAAGCAGGAG |
CTTGGACGCCTAACAGAAGA |
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| aug3.g297 |
|
PCR |
|
pCRII-aug3.g297(F,R)#1 |
CCAATGAGACTCTTAAGACC |
AGCAGGATCTTGTTCAGTTG |
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| aug3.g18316 |
|
EST |
FY371371 |
S7_d1_37_C02 |
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| aug3.g17399 |
Pt-histone H2A-2
(H2A-2) |
PCR |
|
pCRII-aug3.g17399(F,R)#2 |
GTGAATATGTCTGGACGTGG |
CGGGGATGCTAGAAGACAGT |
|
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| aug3.g1123 |
|
PCR |
|
pCRII-aug3.g1123(F2,R2)#2 |
GCTCCATCTACCGCTCTACA |
ACTCAGAGCACAGTTTGCTC |
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| aug3.g8877 |
|
PCR |
|
pCRII-aug3.g8877(F,R)#1 |
TGAACACAGACATCGAGAAG |
ATCACCACACCGATAGCTGG |
|
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| aug3.g11448 |
|
EST |
FY370181 |
S7_d1_22_F05 |
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| aug3.g14989 |
|
EST |
FY373321 |
eS6_d1_19_E08 |
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|
| aug3.g19451 |
Pt-pax6-B |
PCR |
|
pCRII-aug3.g19451(F2,R2)#5 |
GCCACTGCCAGATTCCACAC |
CGCGGGTGATGTTCCGTGAG |
|
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|
| aug3.g23620 |
|
PCR |
|
pCRII-aug3.g23620(f1,r1)#3 |
TTGCCTTCCTCATACCATCA |
GAACTAGTGCCAACTTTAGC |
|
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| aug3.g3346 |
Pt-zfp36-A |
PCR |
|
pCRII-aug3.g3346(f1-r1)#2 |
GGAAAGACAGCTTAATGGAC |
CGATTGATATCGACAGCAAC |
|
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| aug3.g27619 |
Pt-CG8312-B |
EST |
FY219817 |
At_eW_010_F17 |
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|
| aug3.g3231 |
Pt-Dipeptidyl-peptidase
1-A |
EST |
FY379275 |
eS7_SB_020_E12 |
|
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| aug3.g3735 |
|
EST |
FY368601 |
S7_d1_05_B05 |
|
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|
|
| aug3.g2550 |
Pt-caspase-B |
PCR |
|
pCRII-aug3.g2550(F,R)#1 |
ATGGCTTCTTCTAGGACTAC |
CTGTACATCTCAGGTGAAGC |
|
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|
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|
| aug3.g15606 |
Pt-Scr-A |
RACE |
LC379634 |
pCRII-km.scr1-3RACE#1 |
CGCATGCGCTCTGTCTATCAGAACGA |
|
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|
| aug3.g25079 |
|
PCR |
|
pCRII-aug3.g25079(F,R)#1 |
CGTCGTAGCAGCAACTTACT |
TGCGAACTCCATTGGAGACA |
|
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|
| aug3.g11061 |
Pt-sox2-A |
EST |
FY371175 |
S7_d1_35_A11 |
|
|
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|
|
|
|
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|
|
| aug3.g4957 |
Pt-BDH1 |
EST |
FY376318 |
eS6_d1_56_B11 |
|
|
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|
|
|
|
|
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|
|
| aug3.g4586 |
Pt-fd102C |
EST |
FY374807 |
eS6_d1_38_A10 |
|
|
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|
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|
|
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|
| aug3.g20968 |
Pt-hairy-D |
EST |
FY370178 |
S7_d1_22_F02 |
|
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| Other genes |
|
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|
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|
|
|
| aug3 gene model |
Gene name |
Isolation |
Accession number |
cDNA clone |
Primer 1 |
Primer 2 |
|
|
|
|
|
|
|
|
|
|
| aug3.g12643 |
Pt-caudal (cad) |
Akiyama-Oda
& Oda (2003) |
AB096075 |
pBS-km.caudal |
|
|
|
|
|
|
|
|
|
|
|
|
| aug3.g25248 |
Pt-Delta |
Oda et al.
(2007) |
AB287420 |
pZL-km.Delta-dT#10-1 |
|
|
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|
|
|
|
|
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|
|
| aug3.g4322 |
Pt-hedgehog (hh) |
Oda et al.
(2007) |
AB125742 |
pZL-km.hh#10-2 |
|
|
|
|
|
|
|
|
|
|
|
|
| aug3.g14374 |
Pt-patched (ptc) |
Akiyama-Oda
& Oda (2010) |
AB433900 |
pCRII-km.ptc5RACE#7 |
|
|
|
|
|
|
|
|
|
|
|
|
| aug3.g15608 |
Pt-Dfd-A |
Akiyama-Oda
& Oda (2010) |
AB433904 |
At_eW_016_B10 |
|
|
|
|
|
|
|
|
|
|
|
|
| aug3.g26989 |
Pt-fascin |
Akiyama-Oda
& Oda (2010) |
AB433905 |
At_eW_022_p10 |
|
|
|
|
|
|
|
|
|
|
|
|
| aug3.g15243 |
Pt-noto1 |
Hemmi et al.
(2018) |
LC350092 |
pBS-km.not2#2-1-1 |
|
|
|
|
|
|
|
|
|
|
|
|
| aug3.g15600 |
Pt-antp-A |
RACE |
NM_001323821 |
pCRII-km.antp2-3RACE#6 |
GACGCGTCGGCGTCGGATCGAGATC |
|
|
|
|
|
|
|
|
|
|
|
| aug3.g17585 |
Pt-eve |
RACE |
LC379064 |
pCRII-km3RACE-eve-long |
TGGCGAGACTTGAGAAAGAGTTCTGCCG |
|
|
|
|
|
|
|
|
|
|
|
| aug3.g4026 |
Pt-hairy |
cDNA library
screening |
AB125743 |
pBS-km.hairy-RIRV |
|
|
|
|
|
|
|
|
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