Molecular Vision: Shimauchi-Matsukawa, Mol Vis 2008; 14:358-369. Table 3

Table 3. Identified cone genes

GI	Identification [gene symbol]	Sp	Length (bases)	Lowest Expected value	Start - End (position of a base)	Signal Intensity	Frq	ISH
	Other genes
37589638	N-myc downstream regulated gene 1, like [ndrg1l]	Dr	1712	0.E+00	55 - 733	5.3	4	c1
18858260	Aryl hydrocarbon receptor 2 [ahr2]	Dr	7126	4.E-30	5574 - 5680	2.3	4	c2
46249950	zgc:85611/Acyl-coemzyme A binding domain containing [zgc:85611]	Dr	1745	6.E-48	442 - 630	2.5	1	c3
42542723	14-3-3 theta polypeptide/ ywhaq [ywhaq]	Dr	1943	1.E-87	1055 - 1467	1.5	1	c4
28279778	SET translocation (myeloid leukemia-associated) A [seta]	Dr	1715	0.E+00	315 - 847	3.1	1	c5
62132940	wu:fa20e05/ Spectrin alpha chain, brain [wu:fa20e05]	Dr	1795	0.E+00	761 - 1186	5.1	1	c6
68360189	Similar to Kruppel-like factor 9 [LOC565869]	Dr	987	3.E-73	739 - 985	3.0	1	c7
34784092	Opposite strand transcription unit to Stag3 [gats]	Dr	2295	4.E-27	2005 - 2113	5.7	1	c8
28278872	Cyclin L1 [ccnl1]	Dr	1967	5.E-10	1489- 573	5.3	1	c9
39645455	Prosaposin [psap]	Dr	2390	4.E-73	999 - 1329	2.1	1
19068029	Growth hormone protein gene [gh]	Cal	11576	2.E-16	3370 - 3453	12.1	1
39645429	Poly A binding protein, cytoplasmic 1 b [pabpc1b]	Dr	2794	5.E-111	1043 - 1416	3.2	1
	Housekeeping genes
55071759	ATPase 6 gene [mt-atp6]	Cc	668	8.E-99	87 - 271	3.0	3
85720010	Eukaryotic translation initiation factor 5 [eif5]	Ip	759	1.E-75	197 - 599	1.7	1
	Hit with genomic sequence
111153896	Zebrafish DNA sequence from clone DKEYP-10C7 in linkage group 23	Dr	171155	1.E-14	20126 - 20236	3.2	1
52421057	Zebrafish DNA sequence from clone DKEY-19E4 in linkage group 6	Dr	209866	1.E-20	200719 - 200809	3.0	1

The results of homology search analysis are summarized. Candidate genes preferentially expressed in cones were searched in our differential array screening (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 cone cDNA relative to that of rod 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: Cal, Catla catla; Cc, Cyprinus carpio; Dr, Danio rerio; Ip, Ictalurus punctatus.