Zebrafish gene map

The Zasha Gene

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This page was originally originally published at http://zfish.uoregon.edu/zf_info/genes.html
Here's the Zasha Gene.
-Zasha.)

Vertebrate genome evolution and the zebrafish gene map. Nature Genetics 18:345-350.
John H. Postlethwait¹, Yi-Lin Yan¹, Michael A. Gates², Sally Horne³, Marc Ekker¹⁴, Angel Amores¹, Alison Brownlie⁴, Adriana Donovan⁴, Elizabeth S. Egan², Allan Force¹, Zhiyuan Gong⁵, Carole Goutel⁶, Andreas Fritz¹, Robert Kelsh⁷, Ela Knapik⁸, Eric Liao⁴, Barry Paw⁴, David Ransom⁴, Amy Singer¹, Margaret Thomson⁴, Tariq S. Abduljabbar¹³, Pam Yelick¹³, Dave Beier⁹, J.-S. Joly¹⁰, Dan Larhammar¹¹, Frederic Rosa⁶, Monte Westerfield¹, Leonard I. Zon⁴, Steve L. Johnson¹² & William S. Talbot²

¹Institute of Neuroscience, 1254 University of Oregon, Eugene, Oregon 97403-1254, USA, ²Developmental Genetics Program, Skirball Institute, New York University Medical Center, New York, New York, USA. ³Department of Biochemistry and Biophysics, University of California San Francisco, California USA. ⁴Howard Hughes Medical Institute, Children's Hospital, Boston, Massachusetts , USA. ⁵Department of Zoology, National University of Singapore, Singapore. ⁶Ecole Normale Superieure, Paris, France. ⁷Developmental Biology Programme, School of Biology and Biochemistry, University of Bath, Claverton Down, Bath, UK. ⁸Massachusetts General Hospital East, Charlestown Massachusetts, USA. ⁹Brigham and Women's Hospital Harvard Medical School, Boston, Massachusetts, USA. ¹⁰Laboratoire de Genetique des Poissons, Jouy-en-Josas, France. ¹¹Department of Medical Pharmacology, Uppsala University, Uppsala, Sweden. ¹²Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA. ¹³Department of Cytokine Biology, Forsyth Dental Center, Boston, Massachusetts,USA. ¹⁴Loeb Institute for Medical Research, Ottawa Civic Hospital, 1053 Carling Ave, Ottawa, ONT Canada, K1Y 4E9. Correspondence should be addressed to J.H.P. e-mail: jpostle@oregon.uoregon.edu.

Abstract. In chordate phylogeny, changes in the nervous system, jaws, and appendages transformed meek filter feeders into fearsome predators. Gene duplication is thought to promote such innovation. Vertebrate ancestors probably had single copies of genes now found in multiple copies in vertebrates and gene maps suggest that this occurred by polyploidization. It has been suggested that one genome duplication event occurred before, and one after the divergence of ray-finned and lobe-finned fishes. Holland et al., however, have argued that because various vertebrates have several HOX clusters, two rounds of duplication occurred before the origin of jawed fishes. Such gene-number data, however, do not distinguish between tandem duplications and polyploidization events, nor whether independent duplications occurred in different lineages. To investigate these matters, we mapped 144 zebrafish genes and compared the resulting map with mammalian maps. Comparison revealed large conserved chromosome segments. Because duplicated chromosome segments in zebrafish often correspond with specific chromosome segments in mammals, it is likely that two polyploidization events occurred prior to the divergence of fish and mammal lineages. This zebrafish gene map will facilitate molecular identification of mutated zebrafish genes, which can suggest functions for human genes known only by sequence.

Summary of mapped genes:

Table 1. Characterization of mapped zebrafish genes.

Zebrafish gene	LG	Primer sequences	Fragment (bp)	Polymorphism	Gene part	Reference	Orthologue or close mammalian homologue
activin beta b; actbb	9	F-CTCCTGCTGCATACCCACTA R-TACATTGCATAGTTCGTGCG	980	RsaI	3’UTR	Wittbrodt & Rosa X76051	INHBB 2cen-q13
activin receptor II; acvr2	9	F-TCCAGATGCAGAGGCAGAC R-GGCCATCATTTCTTGGCATA	835	DpnII	3’UTR		ACVRLK2 2q22
axial; axial	17	F-GACATACGAGCAAGTGATGCA R-GCGAAAAAAGTCCAAATAACA	454	Tsp509I	3’UTR	Strähle et al., 1993; Z22762	FKHL1 14q13 HNF3B 20p
beta-2-micro- globulin; b2m	4	F-GTCTGCTTGGCTCTCTCGAA R-CAACGCTCTTTGTGAGGTGA	905	HaeIII	intron	Ono et al., 1993; L05383	B2M 15q21-q22.2
cell division cycle 27; cdc27	3	F-GATTTGCCAATGACTCCACCGTC R-TAACAGATGGCAATCTGAAAG	287	SSCP	3’UTR	Z. Gong, unpubl. H56843	CDC27 17q12-q23.2
complement component factor b; bf	21	F-TATGGCCGACTGATTCAGATTGGT R-TCCATGCTATTTAGCCAGTCTTTT	259	SSCP	3’UTR	Seeger et al., 1996; U34662	BF 6p21.3
bone morphogenetic protein-2; bmp2	20	F-GCTCAGCCCTATCTCACTGC R-TTTCTTCCTCCAAAATAGCTCG	160	SSCP	3’UTR	Zon, L., unpubl.	BMP2 20p12
bone morphogenetic protein-4; bmp4	17	F-TAGGCTGGAACGACTGGATT R-TGTCCACGTGTGGATGTTTT	307	SSCP	3’UTR	Chin et al., 1997; U90122	BMP4 14q22-q23
brain pou domain 1.1; brn1.1	9	F-CCACGGGCAGTCCCACCAGTATC R-AGAGGGCAATATCCACGATTATCA	793	SSCP/MSPI	3’UTR	Sampath & Stuart, 1996; U43657	Brn-1 Mmu 1-22.0 (2q32)
brain pou domain 1.1; brn1.2	6	F-AAACCGCCCGCTAATCTTCTTCC R-TAGGGGGTGGGGGACATTTTACA	898	NlaIII	3’UTR	Sampath & Stuart, 1996; U43656; Matsuzaki et al., 1992; D13045	Brn-1 Mmu 1-22.0 (2q32)
vn-cadherin; cdhvn	7	F-CCTCCCACTAACTGTGTGTTT R-CATCGGCTTCCGGATATATA	626	NLAIV	3’UTR	Franklin & Sargent, 1996; U41419	CDH11 Chrom16
beta-catenin B; ctnnb	16	F-CAATCAGCTGGCCTGGTTT R-GCCAAGTCTCCAACCAACAA	829	DpnII	3’UTR	Kelly et al., 1995; U41081	CTNNB1 3p21.3
caudal homeobox-1; cad1	14	F-AGGCAAGCATGTATCACCAAGGAG R-TAATCGGGCGAGCAATAGGAAACT	271	SSCP	coding	Joly et al., 1992; X66958 S42600	CDX1 5q31-q33
collagen type II, alpha-1; col2a1	8	F-CCTAAAATCCCACGCAAGAA R-CTTGCAGCCATCCTCAAGTA	605	DpnII	intron	Yan et al., 1995; U23822	COL2A1 12q13.11-q13.2
cyclin D1; cycd1	7	F-ACGTGGACCTCTCTTGCACT R-TCAGCCTTAAACGACGGACT	979	AciI	3’UTR	Yarden et al., 1995; X87581	CCND1 11q13
cyclin E; cyce	7	F-AGAGAGCACCATCTCTTGACTT R-CAAACACTCAGAAGTTGACCAG	563	Tsp509I	3’UTR	Yarden, A. X83594	CCNE 19q12-q13
deltaA; deltaa	1	F-GAGCGGCGGGAGAAGGAC R-TGGCAGAGCAGCATGTAGAGGA	452	SSCP	5’UTR	Appel, B., unpubl.	Dll1 Mmu17-8.2
desmin; des	9	F-GCAGTGACCCATTACCGCAT R-CAGATATGACCCAACCACAC	180	SSCP	3’UTR	Gong, unpubl. U47113	DES 2q35
distal-less homeobox gene 2; dlx2	9	F-AGCCACCACTTCATCACAAT R-AGATGTTCATTCGGCTTTCA	713	Tsp509I	3’UTR	Akimenko et al., 1994. U03875	DLX2 2q32
distal-less homeobox gene 3; dlx3	12	F-AATCACTGGTACCAGCAGGG R-AATGGTTCGAGCACCACC	639	HinFI	3’UTR	Ekker et al., 1992; X65060	DLX3 17q21.3-q22
dynamo; dynamo	19	F-TGTTTTTATCCAAGCAGTTCTCAC R-CATTCTTGCCGTATTTTGCTCTCC	204	SSCP	5'UTR	S. Bruneau & F. Rosa; X99769
echidna hedgehog; ehh	6	F-CGATGCTCAAGTGGGTCAGT R-CTCCACCAATCCCTGCGT	378	MseI		Currie & Ingham, 1996; Y08426	Ihh Mmu1-38.45 (2q34-q35)
endothelin receptor B; ednrb1	1	F-CACTGTGCTGGCTTCCACTG R-ATTCTTAAAGCGCTTGCTAACCAT	340	AluI	intron	R. Kelsh, pers. comm.	EDNRB 13q22; EDNRA Chr.4
early growth response-1; egr1	14	F-GGGAGCAGTTTGATCACCTT R-GTGAAACGGCCTGTGTAAGA	820	DdeI	intron	Drummond et al., 1994; U12895	EGR1 5q23-q31
elav-related-C; elrc	3	F-TGTTGTGTAGAGAGAGAAGAA R-AGGCTTGAAGGAAGGCCTAG	220/240	size	3’UTR	Good, 1995; Kim, et al., 1996; U17601, U62018	HUC 19p13
engrailled-1; eng1	9	F-AGGAGGACAACTAGCAGAGACG R-CCAGCAAGGGAAAATACTATGG	779	HhaI	3’UTR	Ekker et al., 1992; X68445	EN1 2q13-q21
engrailled-2; eng2	7	F-GCAGCAATCGTTCGGATCT R-CATGCAAAGGCCCCAATAC	754	SSCP	3’UTR	Ekker et al., 1992; X68446	EN2 7q36
engrailled-3; eng3	2	F-ATCACGCCACAGTAACAAAG R-TGTGAGGTAACCATCCTTGC	597	HhaI	3’UTR	Ekker et al., 1992; X68447	EN1 2q13-q21
ependymin; epd	5	F-GCTGACCAGTGGAACGATGA R-CGTGAGTGGTGTCCTCAACA	851	SspI	intron	Sterrer et al., 1990; X52502	unknown
erythrocyte protein band 7.2; epb72	21	F-AAGCCCCACCCCCTAATC R-ACCAGTCCAAAATTTGGCATC	245	SSCP	3'UTR	R.Prohaska & Zon, pers. com.	EPB72 9q34.1
eukaryotic translation initiation factor 4e; eif4e	5	F-GTGCATTACTGTACTGTTGACTA R-CATGCGGTACAGGTGAATTGGG	446	MspI	intron	S.C. Fahrenkrug, unpubl.	EIF4EL1 4p15-qter; EIF4EL2 Hsa20
even-skipped-like1; eve1	3	F-CTACTGAATGGTATCGACCAAA R-ACGTTGTCTCTTGTCCTTCATT	580	Sau96I	intron	Joly et al., 1993; X71845	unknown
even-skipped homologue 2; evx2	9	F-AACGACAACACCTCCTCAAC R-CAGTCTTCCGATCTGCTCTC	850	On PAC4GC4 with hoxD cluster	intron	Herault et al., 1996; X99290	EVX2 2q24.3-q31
fibroblast growth factor-3; fgf3	7	F-CTCCATTACTAGCATGCGCA R-CTCATGAATGCGCTCCAGAA	611	Mnl1	intron	Kiefer et al., 1996; Z48714	FGF3 11q13
fibroblast growth factor receptor 4; fgfr4	21	F-CCTCCAGCTCATGCTCTTCA R-GCTGACCATTTGTCCCAGAA	1336	TaqI Tsp509I NlaIII	3’UTR	Thisse et al., 1995; U23839	FGFR4 5q35.1-qter
floating head; flh	13	F-GTACTGGCGAAAGCAGCAGTT R-GTTATGAAACGCCTTTGCAG	830/850	size	intron	Talbot et al., 1995 L48017	unknown
friend leukemia integration-1; fli1	18	F-GGGGAATTCTTACCCAAGACAGACATGACT R-CGCGGATCCCCCGCCCACCATTTTATTGCA	400	Bst XI	intron	Thompson and Zon et al., unpubl.	FLI1 11q24
fms-like tyrosine kinase-4; flt4		F-CATCCTGTATGTACCGTTAAAGGG R-AAAATATCAGTGCATACAATGGGG	243	SSCP	3'UTR	Thompson and Zon et al., unpubl.	FLT4 5q34-q35
glucose-6-phosphate dehydrogenase-like-1; g6pdl1	12	F-GAAGTGAGGAGCCGAAAAGG R-CAGTCTCAGGGTGGCATACG	244	HhaI	intron	Gong, X., unpubl.	G6PDL Hsa17
gata-binding protein 1; gata1	11	F-GGCCTTTATTTTAAACTG (SJD) F-GGCCTTTATTTTAAACTA (C32) R-CGCGGATCCATTAACCCTCACTAAAGGGAGAGCCCTTCTTGTTTCT	214	allele specific oligo	exon 5	Detrich et al., 1995; U18311	GATA1 Xp11.23
gata-binding protein 2; gata2	11	F-ACCTGACTTCCCGTGAGGCGAGC R-GGGTTAGGACAAAAGTTGGGAC	250	SSCP	intron	Detrich et al., 1995; U18312	GATA2 12q13
goosecoid; gsc	17	F-AGACAGAAAAGGTCGTCGTCA R-ACAGCCCATTCCAGAACATC	401	DdeI	3’UTR	Stachel et al., 1993; L03395	GSC 14q32.1
heat shock cognate 70-1; hsc70.1	3	F-TTCAACGGCAGAGAACTGAAC R-ATCCACCTCTTCAATGGTGGG	870	NlaIII		Graser et al., 1996; L77146	HSPA1 6p21.3
hemoglobin alpha adult-1; hbaa1	3	F-CAAGGCTGTTGTTAAGGC R-GTGAAGTCTGCAGGGAAG	600	NlaIII	intron	Chan, F.Y & Zon, L, unpubl. U50382	HBA 16pter-p13.3
hemoglobin alpha embryonic-1 minor; hbae1	12	F-CGGCCTGCTGAACCTCAG R-CATATTTGTCAGACAGAGCC DAR: AAGGTATACACTACAAACC ABO: AAGGTATACGCTACAAACC	300	allele specific oligo	intron/exon junction	Brownlie et al., unpubl.	HBB 11p15.5
hemoglobin alpha embryonic major; hbae4	3	F-CTGCCAAAGACAAAGCTGCCGTCA R-AGCATGGAGCTCACTGAGGTTCAG	350	ScrFI	3’UTR	Brownlie et al., unpubl.	HBA 16pter-p13.3
hemoglobin beta embryonic-4; hbbe3	12	F-GCTTAACTAGGTTTATGTTA R-AGTCTTATTTCTTCTAAATT	180	SSCP	3’UTR	Brownlie et al., unpubl.	HBB 11p15.5
hairy-related-1; her1	5	F-CAATCCTCTCAACCACGGAC R-ACAGCAAAGACCCCAGAACA	638	Hha I Msp I	3’UTR	Muller et al., 1996; X97329 X97623	HRY 3q28-q29
hairy-related-4; her4	23	F-AAACAACACACTCCAGCCC R-CCATCTTCGTTTAGTGCTTCC	441	BstU I	3’UTR	Muller et al., 1996; X97332	HRY 3q28-q29
hairy-related-6; her6	6	F-GCAACCGACGGACAGTTCGC R- AACGTGGAAAGATACCGCAAATA	419	SSCP	3'UTR	Von Weizsaecker; X97333
hatching gland gene 1 (cathepsin-L-like); hgg1	12	F-GCTACATCTACATGGCAAAAGAC R-GCAGGTCAAATAGATCCAGTACA	278	HaeIII	3’UTR	Thisse et al., 1994	unknown
hedge hog a; hha	9	F-CTTAACTGCAAATACGTGTGAATG R-TCTTGTTGAACCTGCTGTCG	545	MseI	3'UTR	P.Ingham
hoxa1; hoxa1	12	F-GACAGTGACAGCGACTCCAA R-TAATTGACCGGACGACAACA	693	AluI	intron	Alexandre et al., 1996; U40995	HOXA1 7p15-p14
hoxb5; hoxb5	3	F-ACACGTACACGTTTCAGTCACA R-ACAGGTCAGCTTTCTCTTTTGG	1736	DraI	inter-genic region	Njolstad et al., 1988, 1990; Molven, 1993; X68248	HOXB 17q21-q22
hoxc5; hoxc5	23	F-CATTGTCAGTTTGGTTCATCTT R-GAACTCTTTCTCCAACTCCAG	439	HhaI	intron	Ericson et al., 1993; Joly, J.S., pers. comm.; X68324	HOXC4 12q13
hox114; hoxc3	23	F-CCGTCGCATGAAGTATAAGA R-GATGTATTTCAGCTCCCGTAT	1476	MspI	3’UTR	Molven et al., 1992; X60095	unknown
hoxd4; hoxd4	9	F-CAGGTATCTAACAAGACGGCG R-CCTCGTGGTGATTTGTGAAC	469	MseI	3’UTR	Ekker, unpubl.	HOXD4 2q32
hypoxanthine guanine phosphoribosyltransferase-like; hprtl	14	F-AACGTCTTGATTGTGGAG R-TGTCTTCATCGTTTTCCC	875	SSCP	intron	Gong, X., unpubl.	HPRT1 Xq26-q27.2
islet1; isl1	5	F-AGAGTGACATCGACCAGCCT R-GGCGTTGTTCTTCCATCAGT	1110	MnlI	3’UTR	Inoue et al., 1994; Korsch, V., unpubl. D21135	ISL1 5q11
islet2; isl2	25	F-CGGGGAACATTCACTCTAGC R-TAATACTGTCCGAACACGCG	1080	NlaIII	intron	Tokumoto et al., 1995; D38453	unknown
krox20; krx20	12	F-GCGACAAAAAGAGCGAAAGT R-ATTGACCCGCGTTAGTCACT	701	MseI	3’UTR	Oxtoby & Jowett, 1993; X70322	EGR2 10q21.1
lim domain homeobox protein-1; lim1	15	F-GTGGACAGACTCGAGCC R-GACTAGGCGAGTCTCC	1330	MspI	intron	Toyama et al., 1995; L37802	LMX1 1q22-q23
lim domain homeobox protein-3; lim3	5	F- CCCGGGAGTCTCTCATATTT R-GGACAGAGCGGAATTCACAA	1011/~990	size	intron	Appel et al., 1995; U34590	LHX3 9q34.3
lim domain homeobox protein-6; lim 6	5	F-GGCGACCGAATGGAACC R-GGTGTGCTCCGTGATG	1150	RsaI	intron	Toyama & Dawid, unpubl. AF001299	unknown
lim domain only-2; lmo2	18	F-CCACAAACAAGACGGAGCCTA R-CGCACAAACGCTTCAGAGAT		HhaI	5’UTR	Thompson, T., & Zon, L., unpubl.	LMO2; 11p13
mariposa; mar	25	F-CTTGTCTCAGTCTGCAAACCA R-CTTCAAGTTTGCAATTGTAGCA	104/100	CA repeat	3’UTR	Yan, Y., & Postlethwait, J. unpubl.1	Fkh5 Mmu9-34.5 (15q22-q25)
major histocompatibility class I protein UAA; mhc1uaa	19	u10 allele F-TCCCTGAGGTACTTCTACACTGGT R-CTGTGTCTGGTTAAACCTCTCCTT n1 allele F-AACCCACAAGCTGGAAAGCCTATTAC R-TTGTGTTTGGTTGAAGCGCTCCAT	270	allele specific oligos		Takeuchi et al., 1995; Z46776	MHC-class I; 6p21.3
major histocompatibility class II protein DAB mhc2dab	8	F-TGCTGTCG(A/G)CATTTACTGGAAC R-TGCTTTATCACG(G/T)ACAGCTGA	590/570		intron	Ono et al., 1992; Sultmann et al., 1994; U08870	MHC-class II; 6p21.3
major histocompatibility class II protein DDB; mhc2ddb	8	F-AGTGAACCCATGATTTATGAC R-GAAACCAGATGCCCCCAACAG	580	allele specificoligo	intron	Sultmann et al., 1994; U08872	MHC-class II; 6p21.3
major histocompatibility class II protein DFB; mhc2dfb	8	F-CGGTGAGAGTATATGACTAACA R-AGATCTGGGGAGCATTATTTGTGCA				Sultmann et al., 1994; U08871	MHC-class II; 6p21.3
muscle segment homeobox homologue-A; msxa	14	F-GCAGACATATGCTGCCTTTTGCAC R-GTATGACACCCCATGTTTGGTGTG	186	SSCP	3’UTR	Akimenko et al., 1995; U16310	MSX2 5q34-q35
muscle segment homeobox homologue-B; msxb	1	F-TATTTAACGGACCCGTGTCC R-ACGGATAACCTCCGTGTCAG	421	MspI	3’UTR	Akimenko et al., 1995; U16311	MSX1 4p16.3-p16.1
muscle segment homeobox homologue -C; msxc	13	F-GTGTGATGCGAAAATAAACTCCTG R-GCAAAATACTCTGTGTCCCAAAAG	462	SSCP	3’UTR	Akimenko et al., 1995; U16311	MSX3 Mmu7-68.2 (10q26)
muscle segment homeobox homologue-D; msxd	21	F-CGGAACATTTTAGCTCCGTC R-GTGGTGGACATTAACTCATCCA	250/~225	size	CA repeat in 3’UTR	Ekker et al., 1992a; X65062 S40823	unknown
muscle segment homeobox homologue -E; msxe	14	F-CAGCTTTCGGGATTTCGTTT R-TTTTACAGCTCAGGCATCCC		HinfI/SSCP MGH ref. cross	3’ UTR	Ekker M., et al., unpubl; U50563	unknown
myeloblastosis oncogene; myb	23	F-CCACTTGCCTCTCCAGTTAA R-CAGCTCGTTTTCTGTTGACA	820	Rsa I	intron	Thompson and Zon et al., unpubl.	MYB 6q22
myogenic differentiation; myod	25	F- ATGAGGGATCTGTCCTGAGTG R-TTGTTCGTTTTCGTCGCTTT	750	DdeI	TTTC repeat in 3’UTR	Weinberg et al., 1996; Z36945	MYOD1 11p15.4
myogenin; myog	11	F-AGGATCTGCTGAACGACGAC R-CAAGACTGGCATTCGGAACT	485	HinFI		Weinberg et al., 1996;	MYOG 1q31-q41
nodal-related-3; ndr3	5	F-GTATAGTAGTGTGTATGAGCATCTGG R-AGCTGACCCGCTC(A/C)GGTT	126/120	CA repeat	intron	Rebagliati, M & Dawid, I, unpubl.;	nodal Mmu10-29.0
neural adhesion molecule L1.1; nadl1.1	23	F-TCAACCCCAACATGCCTC R-CAAGCACACACACGCACAT	560/570	size	3’UTR	Tongiorgi et al., 1995; X89204	L1 Xq28
NK2 transcription factor related-2; nk2.2	17	F-CACAGTTCCCAACAGCACAT R-GCCAGTGTTTATTCATGGCC	414	Mse I	3’UTR	Barth & Wilson; X85977	NKX2A 14q13
NK2 transcription factor related-5; nkx2.5	14	F-GGCTTTTACGCGAAGAACTTCC R-TCGCTGGAGCTCGTACACCTG	1400/1200	size	intron	Chen & Fishman 1996; S83517; J. Alexander & D. Stanier, pers. comm.	CSX 5q34
no tail (Brachyury); ntl	19	F- CCTCCTCAATGTACGATCCA R-TCAAAGAGCCCAACAAATACA	921	HinFI	3’UTR	Schulte-Merker et al, 1992; S57147	T 6q27
neuro-peptide Y; npy	19	F-CAGGGTGTGATTTTGTACTT R-CACCCAAAAAGTAAGATTCA	565	NlaIII	intron	D. Larhammar, unpubl.	NPY 7p15.1
orthodentical homologue-2; otx2	17	F-GCGTCCTCATGGAAACTGAA R-CACATTACCGCTCCAGACAA	1073	SSCP/NLAIII	3'UTR	Mori et al.; D26173	Otx2 14q21-q22
orthodentical homologue-3; otx3	1	F-ACCACTGGCGTCCCGTCG R-CCGCCGCAGAGCTGAAGT	450	SSCP	3'UTR	Mori et al.; D26174	Otx2 14q21-q22
patched1; ptc1	2	F-AGCAAGGAGCTACGCTACAC R-GCAGGGGAAAAGCTTATCAA	480	SSCP	3’UTR	Concordet et al., 1996; X98883	PTCH 9q22.3
paired box homeotic gene 2; pax2	13	F-TTCCCCATTTTCTCTCAATCA R-TTCTGACACGTCCGTGAGAG	149	CA repeat	3’UTR	Krauss et al., 1991; X63961	PAX2 10q25
paired box homeotic gene 9; pax9	17	F-ACATCGGTGCACTTGGTCTGGTAG R-TTTTGCCTGAATGAATGAATGCTC	453	NlaIII	3’UTR	Nornes et al., 1996; U40932	PAX9 14q12-q13
pou domain-2; pou2	21	F-GCCCTTTGATGACGAGTGTG R-TTGGAGATGGGAGAGTGCAA	796	BfaI	3’UTR	Takeda et al., 1994; D28548; Hauptmann & Gerster 1995 X84224	OCT3 6p21.3
pou domain-c; pouc	23	F-CAACCGTCGACAGACTCTGA R-ATGTCCACAGATTCCATCTGG	889	AluI		Johansen et al., 1993; X68432	Emb Mmu15-57.0 (12q12-q13)
peptide YY; pyy	3	F-ACTTCACCTTCGAGGTATCG R-GTACAGTGAAAAGAAGACATT	518	SSCP	3’UTR	D. Larhammar, unpubl.	PYY 17q21
redcone pigment; rcp	11	F-CATCATGCAGCTCTTTGGAA R-CATGGGCAGGCATCTACC	554	BsrDI	3’UTR	Robinson, J., unpubl.	RCP Xq28
retinoic acid receptor-alpha-2.A; rara2A	12	F-CAGTTGTAGCCCCTCCCTCT R-AGTCTCTGGTCATTGCAGGC	362	size	3’UTR	Stachel & Kushner, unpubl.; Joore et al., 1994; L03398	RARA 17q12
retinoic acid receptor-alpha-2.B; rara2b	3	F-GAGGGTCTGGAGGGAGGC R-GGGGGTCTCTGTGTCTTTCG	1068	DdeI	3’UTR	Stachel & Kushner, unpubl.; Joore et al., 1994; L03399	RARA 17q12
retinoic acid receptor- gamma; rarg	23	F-GGGCCATAACTCTGAAGATG R-GAACCCGTTGAAAGTACACTG	624	SSCP	3’UTR	Joore et al., 1994; S74156	RARG 12q13
ret proto-oncogene-1; ret1	13	F-GCTCTCCTATATGACGACTC R-GTAAAGACAGGGTTAGTGGC	187	RsaI	3’UTR	Bisgrove, B., unpubl.	RET 10q11.2
retinoid X receptor alpha; rxra	2	F-GACTGAAGTGTCTGGAGCATC R-CTGATTGCTGGTGACTGTTTAC	399	SSCP	3'UTR	Jones et al.; U29940
retinoid X receptor-epsilon; rxre	19	F-GACACCCCAATCGACACCTT R-AGATGCAGCAGGCCAAGAAT	722	DpnII	3’UTR	Jones et al., 1995; U29942	RXRB 6p21.3
stem-cell leukemia hematopoietic transcription factor; scl	22	F-gggATTcAgcAgcccTATc R-gcAgggcTAAAgTTggggT(Tg)	75/73	SSLP	3'UTR	E.C. Liao and L. Zon, unpubl.	SCL 1p32
sonic hedgehog; shh	7	F-ACACACACACGGAGTCGAAT R-AAAGAAACAGCTCAAGACTGCA	369	MnlI	3’UTR	Ekker, S et al., 1995;Fietz et al., 1994; Roelink et al., 1994; g1171141; Z35669; L27585	SHH 7q36
snail-1; sna1	11	F- TGTCAGGTTGGGGGTGGGTTG R- TCAGAGATGTGGCGGTCAGGG	155	size	CA repeat in 3’UTR	Thisse et al., 1993; Hammerschmidt et al., 1993; S68799, X74790	ZFP39 Hsa19
snail-2; sna2	23	F-CACTCCGAGGTGAAGAAGTACC R-GTGGAATCAAAACAGGCACC	HhaI	175	3’UTR	Thisse et al., 1995b. U24225	unknown
synaptosomal-associated protein of 25 kDa-A; snap25a	20	F-ATGCACATATCACCCGG R-AGTGCTCGTCGTATTAG	460	AluI	3’UTR	Risinger, C., 1995	SNAP25 20p11.2
synaptosomal-associated protein of 25 kDa-B; snap25b	17	F-GACATGGCTGACTCCAACAAAA R-TGGCAGGCTAAGATAAG	590	RsaI	3’UTR	Risinger, C., 1995	SNAP25 20p11.2
SRY-box containing gene-19; sox19	5	F-CGCCTCTTACACACATCTGA R-TGACTCCCCTTTTTACACAACT	815	MseI	3’UTR	Vriz & Lovell-Badge, 1995; X79821	SOX2 3q26.3-q27
seven-up-like 44; svp44	5	F-TGTTATTATCCGGGAGCAGC R-TGCACAGGCATATCATGGAT	963	HinFI	CA repeat in 3’UTR	Fjose et al., (1993); X70299	COUP-TFI 5q14
T-box-6; tbx6	7	F-AGGGTGAAGTGTTTTGGGGCATAA R-GCGCTCTGGCACACCTCTTCTAAC	318	SSCP	3'UTR	Hug et al.; U80951
type 1 serine/threonine kinase receptor taram-A; tarama	23	F-GGATGTTGAGGATCCATCCTGTGAT R-CTGCAGTACIATIGTCCTGGCCA	230	SSCP	intron	Renucci et al., 1996 X94119	ACVRLK1 12q11-q14
tenascin C; tnc	5	F-CGCCAGTAACATTCAAACAG R-CCTGCAGGGGTTGACTCT		MseI		Qiao et al., 1995; U14940	TNC 9q32-q34
tyrosine kinase with IG and EGF homology domains; tie1	6	F-GGGGAATTCAAAATTGCTGATTTT R-CGCGGATCCACTCTTGGTGGTGTA	300	Tsp509I	intron	Thompson, T., & Zon, L., unpubl.	TIE1 1p34-p33
thyroxin receptor A1; tra1	3	F-GCACCTCCAAACCACATCC R-GTCTTCCTGATTCCCCGTG	356	SSCP		Essner,J.J. & Hackett,P.B., unpubl. DRU54796	THRA1 17q11.2-q12
transferrin-A; tfa	2	F-CGATATGATTGAGAGGACCTACAA R-TCATTTCATCCCCTTTTGTGATA	167	SSCP	3’UTR	Z. Gong, unpubl.	TF 3q21
tyrosine receptor kinase-b2; trkb2	5	F-ATGGATCCACGGCACACTTCATGCGC R-GCAGGATCCCAACTTCTTTCGATGGT	425/430	size	3'UTR	Martin, S., unpubl.	NTRK2 9q22.1
tiggywinkle hedge hog; twhh		F-GATATCGAATTCGACTGCTGCTGTACATT R-GGAAAACATCCTCCTGA	450	SSCP	3’UTR	Ekker et al., 1995; U30710	SHH 7q36
dermo-1A; dermoa	9	F-TCGCCATGATGATAGTACAGG R-CATTGGATGGAAATCGAAAAA	253	RsaI	3’UTR	Riggleman, B., unpubl.	TWIST-DERMO1 2q37.3
valentino; val	23	F-CCACGAGCGACAACCCGTCCT R-GGTCCCCCTGTCGCCTCTCTC	511	RsaI	3’UTR	Moens et al., 1997;	Kreisler 2-91.0 (20q12-q13.1)
vegital RNA-1; vg1	17	F-GTCCATTCGTTTGATCCTAAA R-CAGCATCTACATGCACATTCT	266	TaqI	3’UTR	Helde & Grunewald, 1993; U00931
wilms tumor-1; wt1	25	F-GCCTAGCCTGCTGTGTTATCCTT R-CTGGTGTCGTTTTAGCTGGTCTGA	726	RsaI/SSCP	coding	Kent et al., 1995; X85734, X85735	WT1 11p13
wingless/int1 homologue-1; wnt1	23	F-TGACCAACCTGCACAACAAT R-ATCCCGAGATGAAGGGAGTT	1700/ 2200	size	intron	Molven et al., (1991); X58880 X57301	WNT1 12q12-13
wingless/int1 homologue-2; wnt2	18	F-GGGGCTACGACACATCAAGA R-CAAAACAGCGAATAAAGACGG	260	Dpn II	3’UTR	Blader et al., unpubl. U51266	WNT2 7q31
wingless/int1 homologue-4; wnt4	15	F1-ACGGAGGAGGTGGAGGTG R1-TCACAGGAACAGCCACGAGT	360	SSCP/DdeI	3'UTR	Ungar et al.; U25141
wingless/int1 homologue-8; wnt8	14	F-GCGGTCAACCTGCATAACAA R-CTGCATCCAGCATGTCTGAA	210	MwoI	intron	Kelly et al.; U10869	WNT8B 10q24
wingless/int1 homologue-10b-related; wnt10br	23	F-GCAAGGTCACAGAGTGGGTTAA R-GGCACAAGTGTTCTCCAGTCAT	826	NlaIII	3’UTR	Riggleman, B., unpubl.; Krauss et al., 1992; 263561	Wnt10b Mmu15-56.8
wingless/int1 homologue 10A; wnt10a	9	F-CAACTGTGAGAGCCTTTGCT R-CAGTGCAAGTCCAAATTCAGT	353	SSCP	3’UTR	Kelly et al., 1993; U02544	unknown
wingless/int1 homologue-11-related; wnt11r	10	F- CCGAGGCTACAACCCTTACA R-CAGAGAGGTTTTGCCGTTTCT	732	size	3’UTR	Riggleman, B., unpubl.
achaete scute homolog A; zasha	4	F-CAACTTCTGGACGAGCATGA R-TTCTGAGGGAGGCAAAACC	978	SSCP	3’UTR	Allende & Weinberg, 1994; U14587	ASCL1 12q22-q23
achaete scute homolog B; zashb	7	F-CTCCATCCGTCTCCAACG R-GTGCATGGGCTTCCTAGTGT	581			Allende & Weinberg 1994; U14590	Mash2 Mmu7-69.3
ETS-related factor1; zef1	14	F-TGTGCCAGTTGAGATGCTTC R-TCCATCTTGTGTGTGACAATCA		SSCP	3'UTR	Nimer, S., unpubl.
ETS-related factor2; zef2	1	F-TCTGGATGTCCGTCATTTCA R-TGTGAAACACAGGCAGAAGC		SSCP	3'UTR	Nimer, S., unpubl.