Table 2.

Predicted CRX target genes

Ranking	RefSeq ID	Chromosome	Gene name	EMSAa	ChIP	Transfection
1b	NM_001708	chr7	Opsin 1 (cone pigments), short-wave-sensitive (OPN1SW)
2	NM_001297	chr16	Cyclic nucleotide-gated channel beta 1 (CNGB1)
3	NM_000541	chr2	S-Antigen; retina and pineal gland (arrestin) (SAG)
4c	NM_033028	chr15	Bardet–Biedl syndrome 4 (BBS4)	+
5	NM_000326	chr15	Retinaldehyde binding protein 1 (RLBP1)
6	NM_000283	chr4	Phosphodiesterase 6B, rod, beta (PDE6B)
7	NM_012265	chr22	Chromosome 22 open reading frame 3 (C22orf3)
8	NM_000180	chr17	Guanylate cyclase 2D, membrane (retina-specific) (GUCY2D)	+	+	+
9	NM_000539	chr3	Rhodopsin (opsin 2, rod pigment) (RHO)
10	NM_000330	chrX	Retinoschisis (X-linked, juvenile) 1 (RS1)
11	NM_001604	chr11	Paired box gene 6 (aniridia, keratitis) (PAX6)
12	NM_002900	chr10	Retinol binding protein 3, interstitial (RBP3)
13	NM_006269	chr8	Retinitis pigmentosa 1 (autosomal dominant) (RP1)	+	+	+
14d	NM_000440	chr5	Phosphodiesterase 6A, cGMP-specific, rod, alpha (PDE6A)
15	NM_000350	chr1	ATP-binding cassette, sub-family A (ABC1), member 4 (ABCA4)	+	+	+
16	NM_004312	chrX	Arrestin 3, retinal (X-arrestin) (ARR3)	+	+
17	NM_014848	chr15	Synaptic vesicle protein 2B homolog (SV2B)
18	NM_007123	chr1	Usher syndrome 2A (autosomal recessive, mild) (USH2A)
19	NM_006493	chr13	Ceroid-lipofuscinosis, neuronal 5 (CLN5)
20	NM_022567	chrX	Nyctalopin (NYX)
21	NM_005272	chr1	Guanine nucleotide binding protein (G protein), (GNAT2)
22	NM_002574	chr1	Peroxiredoxin 1 (PRDX1)
23	NM_005316	chr11	General transcription factor IIH, polypeptide 1 (GTF2H1)
24	NM_000253	chr4	Microsomal triglyceride transfer protein (MTP)
25	NM_000409	chr6	Guanylate cyclase activator 1A (retina) (GUCA1A)

^aPositive results from each experiment are marked with ‘+’.

^bThe positive controls are highlighted by italics.

^cThe genes selected for experimental validation are in bold font.

^dThis gene was not selected as positive control in our analysis, but has been found to be CRX target recently (52).