Molecular Vision: Shimauchi-Matsukawa, Mol Vis 2008; 14:358-369. Table 2

Table 2. Identified rod genes

GI	Identification [gene symbol]	Sp	Length (bases)	Lowest Expected value	Start - End (position of a base)	Signal Intensity	Frq	ISH
	Known as rod specific genes
27542822	Cyclic nucleotide gated channel [gfCNG3]	Ca	2654	0.E+00	1658 - 2397	29.4	44	r1
34785175	Guanine nucleotide binding protein (G protein), beta 1 subunit [gnb1]	Dr	3230	1.E-36	2155 - 2255	5.2	8
765276	Rhodopsin [rhodopsin]	Cc	1584	0.E+00	579 - 1181	5.9	2
12862624	G protein-coupled receptor kinase 1A-1a [GRK1A-1a]	Cc	3777	1.E-98	2036 - 2289	11.2	2
83955365	G protein-coupled receptor kinase 1A-1b [GRK1A-1b]	Cc	3565	1.E-98	2667 - 3040	16.9	1
37748508	Guanine nucleotide binding protein (G protein), gamma 1 subunit [gngt1]	Dr	704	9.E-39	166 - 310	29.6	1
	Other genes
68356047	Similar to aspartate beta-hydroxylase isoform b [asph]	Dr	3592	1.E-17	3106 - 3179	19.8	5	r2
29436543	zgc:56703/ DnaJ (Hsp40) homolog, subfamily C, member 5 [zgc:56703]	Dr	2556	3.E-18	1684 - 1845	5.7	4	r3
56967377	O-GlcNAc transferase [OGT]	Dr	3111	0.E+00	778 - 1376	3.5	1	r4
89886286	Facilitated glucose transporter 1 [slc2a1]	Dr	1696	4.E-102	1167 - 1521	4.0	1	r5
68356301	Hypothetical protein LOC554424/ Polo-like kinase 3 [LOC554424]	Dr	3289	5.E-74	294 - 513	28.4	1
42794004	ADP-ribosylation factor 2 [arf2]	Dr	2660	6.E-15	1878 - 1970	6.6	1
50368934	l-isoaspartyl protein carboxyl methyltransferase [pcmt]	Dr	2740	1.E-17	2625 - 2723	15.8	1
28278430	Profilin 2 like [pfn21]	Dr	2020	2.E-53	1309 - 1497	3.3	1
41055366	zgc:56668/ Signal recognition particle 9 kDa protein [srp9]	Dr	757	2.E-78	96 - 422	13.0	1
68392381	Nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor-like 1 [nfbbil1]	Dr	7291	1.E-47	7101 - 7223	1.9	1
18147599	Carbonic anhydrase 2 [Car2]	Th	1976	1.E-25	1259 - 1452	10.4	1
	Hit with genomic sequence
62868299	Zebrafish DNA sequence from clone DKEY-31K5 in linkage group 8	Dr	87522	3.E-34	78867- 78956	11.9	2
40353178	Zebrafish DNA sequence from clone CH211-235E18 in linkage group 2	Dr	196642	2.E-60	177487 - 177740	2.0	1
54606605	Zebrafish DNA sequence from clone CH211-194G1 in linkage group 5	Dr	197143	5.E-102	100810 - 101064	7.0	1
54606605	Zebrafish DNA sequence from clone CH211-194G1 in linkage group 5	Dr	197143	1.E-63	99403 - 99645	10.4	1
73853724	Zebrafish DNA sequence from clone CH211-103A8 in linkage group 3	Dr	165773	4.E-11	91117 - 91175	3.0	1
40994808	Zebrafish DNA sequence from clone CH211-206I14 in linkage group 7	Dr	173867	9.E-40	112044 - 112153	1.7	1
50724681	Zebrafish DNA sequence from clone DKEY-100E19 in linkage group 14	Dr	262038	8.E-21	228195 - 228365	4.6	1
55818874	Zebrafish DNA sequence from clone DKEY-158P11 in linkage group 4	Dr	92140	3.E-12	15398 - 15466	24.5	1
42517023	Zebrafish DNA sequence from clone DKEY-208P1 in linkage group 17	Dr	188037	4.E-94	92142 - 92399	12.1	1
51127565	Zebrafish DNA sequence from clone DKEY-95O3 in linkage group 15	Dr	155540	2.E-13	73341 - 73448	4.5	1

The results of homology search analysis are summarized. Candidate genes preferentially expressed in rods were searched in our differential array screening (similar study as shown in Figure 3), and the sequence of a clone obtained in our study was compared with those of the known genes in the database. The gene that showed the highest homology to our clone is listed with its gene identification number (GI), the name of identified gene (Identification [gene symbol]), animal species of the gene (Sp), and the length of the gene (Length). The region of our clone in the gene identified is shown as the position of a base in the gene (Start-End) together with an index to show the degree of homology (Lowest expected value). Also shown are a signal intensity (a mean of 2 independent studies) of rod cDNA relative to that of cone cDNA (Signal Intensity), the number of clones we identified (Frq), and the label of the in situ hybridization study shown in Table 4 (ISH). Species are: Ca, Carassius auratus; Cc, Cyprinus carpio; Dr, Danio rerio; Th, Tribolodon hakonesis.