Nr.	UCR cluster span	Nr UCRs	Gene Symbol	Gene Description	InterPro domain(s)	Evidence for involvement in embryonic development? (PubMed reference in brackets)
1.	chr15:32.7M-36.2M	84	MEIS2	Meis1, myeloid ecotropic viral integration site 1 homolog 2	Homeobox	YES [12880965]
2.	chr2:143.5M-147.8M	81	ZFHX1B	zinc finger homeobox 1b	Homeobox Zn-finger, C2H2 type	YES [15006694]
3.	chr19:34.8M-37.8M	80	ZNF536	KIAA0390 gene product (zinc finger)	Znf_C2H2, NLS_BP	YES [10819330]
4.	chr10:129.6M-132.1M	79	EBF3	COE3 (Early B-cell factor 3, EBF-3)		YES [14732407]
5.	chr10:76.5M-79.1M	77	ZNF503	zinc finger protein 503	Znf_PHD Znf_C2H2 Eggshell	YES [14983057]
6.	chr16:52.9M-55.6M	64	IRX-3 IRX-5 IRX-6	Iroquis-class protein IRX-3 Iroquis-class protein IRX-5 Iroquis-class protein IRX-6	Homeobox Homeobox Homeobox	YES [12100884]
7.	chr9:121.2M-123.3M	62	PBX3	pre-B-cell leukemia transcription factor 3	PBX Homeobox	YES [15466398]
8.	chr5:90.6M-94.4M	62	NR2F1	nuclear receptor subfamily 2, group F, member 1	Hormone_rec_lig Stdhrmn_receptor Str_ncl_receptor Znf_C4steroid	YES [11784326]
9.	chr7:112.9M-115.4M	60	FOXP2 ; TFEC	forkhead box P2 (immune tolerance development) ; Similar to transcription factor EC	Involucrin_rpt TF_Fork_head Znf_C2H2 ------- HLH_basic	YES [12876151]
10.	chr13:70.2M-72.5M	52	DACH	dachshund homolog (Drosophila)	Transform_Ski	YES [10767315]
11.	chr10:102.1M-104.6M	52	PAX2	paired box gene 2 (kidney, differentiation, eyes, CNS)	Paired_box Homeobox	YES [15242798]
12.	chr3:69.5M-71.7M	52	FOXP1	forkhead box P1	TF_Fork_head Znf_C2H2	YES [12687690]
13.	chr2:58.3M-61.2M	48	BCL11A	B-cell lymphoma/leukemia 11A (COUP-TF interacting protein 1)	Znf_C2H2	YES [12711548]
14.	chr5:1.7M-5.1M	46	IRX-4; IRX-2; IRX-1	Homeobox protein IRX-4; Homeobox protein IRX-2; Homeobox protein IRX-1	Homeobox   Homeobox   Homeobox	YES [11335133], [11455441]
15.	chr2:175.7M-178.0M	46	ATF-2; EVX-2; HOX-D*	activating transcription factor 2 (brain) ; Homeobox even-skipped homolog protein 2 (EVX-2) ; HOX-D cluster	Znf_C2H2 TF_bZIP -------------------- Homeobox Antifreeze_1 HTH_lambrepressr CytC_heme_bind -------------------- Homeobox HTH_lambrepressr	YES [8978698]
16.	chr2:155.9M-158.3M	41	NR4A2	nuclear receptor subfamily 4, group A, member 2 (brain)	Znf_C4steroid Hormone_rec_lig NURR_receptor Nucorph_receptor Stdhrmn_receptor Rtnoid_receptor VitD_receptor	YES [15009684]
17.	chr1:62.3M-63.6M	39	FOXD3	forkhead, box D3	TF_Fork_head	YES [11262245]
18.	chr1:89.5M-91.1M	38	LMO4 ; KIAA1221	LIM domain only 4; KIAA1221 (brain-specific zinc finger protein)	LIM ----------- Znf_C2H2	YES [12619132]
19.	chr18:71.7M-74.1M	38	ZNF407	zinc finger protein 407	Znf_C2H2	NO
20.	chr2:65.6M-67.9M	35	MEIS1	Meis1, myeloid ecotropic viral integration site 1 homolog (mouse)	Homeobox	YES [12183364]
21.	chr8:105.2M-106.9M	35	ZFPM2	zinc finger protein, multitype 2 ((FOG-2) (Friend of GATA-2)	Znf_C2H2	YES [12213678]
22.	chr16:50.2M-52.9M	35	TNRC9	trinucleotide repeat containing 9 (HMG box DNA binding protein)	Highmoblty_12 HMG-box HMG_12_box	NO
23.	chr8:76.2M-78.3M	33	ZFH4	zinc finger homeodomain 4	AMP-bind Homeobox Somatotropin Znf_C2H2 Znf_U1	NO
24.	chr11:14.9M-17.0M	32	SOX6	SRY (sex determining region Y)-box 6	HMG_12_box ATP_GTP_A NLS_BP	YES [12571105]
25.	chr9:15.5M-17.8M	31	BNC2	Basonuclin 2	CytC_heme_BS Znf_C2H2	NO
26.	chr5:765M-779M	31	OTP	orthopedia homolog	Homeobox Homeo_OAR HTH_lambrepressr	YES [11071765]
27.	chr10:114.0M-115.5M	30	TCF7L2	transcription factor 7-like 2 (T-cell specific, HMG-box)	HMG-box	YES [11845287]
28.	chr18:74.9M-76.9M	30	SALL3	Sal-like protein 3 (Zinc finger protein SALL3) (hSALL3)	Znf_C2H2	YES [10610715]
29.	chr10:124.4M-125.7M	27	BUB3	Mitotic checkpoint protein BUB3	WD40	YES [10995385]
30.	chr6:8.1M-10.9M	26	TFAP2A	Transcription factor AP-2 alpha (AP2-alpha)	TF_AP2 TF_AP2_alpha	YES [14534133]
31.	chr4:84.6M-86.2M	26	NKX6-1	Homeobox protein NKX-6.1	Homeobox HTH_lambrepressr PRO_rich	YES [15456722]
32.	chr1:9.8M-11.0M	25	FLJ20321	Hypothetical protein FLJ20321 (zinc finger)	Znf_C2H2 ATP_GTP_A NLS_BP	NO
33.	chr8:64.5M-66.4M	25	BHLHB5	Basic helix-loop-helix domain containing, class B, 5	HLH_basic	YES [14643684]
34.	chr20:20.4M-21.9M	25	NKX-2.2	Homeobox protein NKX-2.2	Homeobox ------------- Paired_box	YES [8575293]
35.	chr16:71.5M-74.1M	25	ATBF1	Alpha-fetoprotein enhancer binding protein (AT motif-binding factor)	Homeobox Znf_C2H2	YES [12926016]
36.	chr1:86.6M-88.5M	22	LMO4	LIM domain transcription factor LMO4 (LIM-only protein 4) (LMO-4)	LIM	YES [12619132]
37.	chr7:68.5M-69.9M	22	AUTS2	Autism susceptibility candidate (unknown function)	P_rich_extensn NLS_BP	YES [12160723]
38.	chr6:97.3M-100.5M	22	POU3F2	Nervous-system specific octamer-binding transcr. factor N-Oct-3	Homeobox POU_domain POU_homeo	YES [10064882]
39.	chr10:118.4M-120.8M	21	EMX2	Homeobox protein EMX2 (empty spiracles homolog 2 (Drosophila))	Homeobox	YES [15501221]
40.	chr18:22.1M-23.2M	21	EHZF	Early hematopoietic zinc finger (LYST-interacting protein LIP3)	Znf_C2H2	NO
41.	chr11:7.8M-8.8M	20	LMO1	LIM domain only 1 (rhombotin 1) (expressed mainly in CNS)	LIM	YES [1507224]
42.	chr3:158.6M-159.9M	20	SHOX2	Short stature homeobox protein 2 (Homeobox protein Og12X)	Homeobox Homeo_OAR HTH_lambrepressr Paired_homeo	YES [14769946]
43.	chr4:111.5M-113.5M	19	PITX2	Pituitary homeobox 2 (ALL1 responsive protein ARP1)	Homeo_OAR Homeobox Paired_homeo	YES [14975719]
44.	chr4:79.9M-81.2M	18		NOT DETERMINED		NO
45.	chr2:173.8M-175.4M	18	SP3	Transcription factor Sp3 (SPR-2).	Znf_C2H2	NO
46.	chr15:64.3M-66.1M	18	MADH3	Mothers against decapentaplegic homolog 3 (SMAD 3)	Dwarfin Dwarfin_A SMAD_FHA	YES [15183723]
47.	chr9:91.1M-92.2M	18	PTCH	Patched protein homolog 1 (PTC1)	Patched family Patched transmembrane receptor Sterol-sensing 5TM box	YES [12917290]
48.	chr4:147.2M-148.9M	18	POU4F2	POU domain, class 4, transcription factor 2 (Brn-3B).	Homeobox POU_domain POU_homeo	YES [14973295]
49.	chr2:164.0M-165.4M	17	-	weakly similar to GC-rich sequence DNA-binding factor (GCF) [Homo sapiens]		NO
50.	chr17:34.3M-35.7M	17	LHX1	LIM homeobox 1	Homeobox LIM LIM_homeo	YES [12799141]