Evolution of Class I cytokine receptors

Liongue, Clifford; Ward, Alister C

doi:10.1186/1471-2148-7-120

BMC Ecology and Evolution

Table 1 Homology and expression analysis of Class I cytokine receptor genes from sea squirt and zebrafish¹

From: Evolution of Class I cytokine receptors

				Related tetraodon sequence		Putative human homology				Expression
		Receptor Sequence	Accession Number							RT-PCR
				Receptor Sequence	Accession Number	Most similar	Percent Similarity (Identity)	Topology	Synteny	24 hpf	72 hpf	EST coverage of coding sequence (aa)
Sea Squrit		clf-3	BN000968	tnCRFA2	AAR25665	clf-3	30.5	clf-3	N/A	N/A	N/A	1–463
		gp130-like	BN000969	tnCRFA26	AAR25689	gp130	28.0	gp130	N/A	N/A	N/A	662–1124
Zebrafish	Group 1	clf-3	AM233512	tnCRFA2	AAR25665	CLF-3	66.4	CLF-3	CLF-3	+	+	1–444
		epor	BN000857	tnCRFA9	AAR25672	EPOR	25.3	EPOR	EPOR	+	+	353–464
		tpor	BN000861	tnCRFA22	AAR25685	TPOR	17.5	TPOR	-	-	+	67–244
		ghr.a	BN000777	tnCRFA5	AAR25668	GHR	29.0	GHR	GHR	+	+	1–554
		ghr.b	BN000776	tnCRFA6	AAR25669	GHR	33.1	GHR	-	+	+	1–436, 467–570
		prlr.a	AY375318	tnCRFA7	AAR25670	PRLR	24.8	PRLR	PRLR^	+	+	312–602
		prlr.b	BN000805	tnCRFA8	AAR25671	PRLR	33.3	PRLR	-	+	+	36–144
		crfa4	BN000914	tnCRFA4	AAR25667	GHR	(35.1)	GHR/PRLR	-	+	+	1–117, 205–364
	Group 2	obr	BN000731	tnCRFA30	AAR25693	OBR	22.4	OBR	OBR	+	+	245–444, 943–1100
		gcsfr	AM157796	-	-	GCSFR	25.6	GCSFR	GCSFR^^	+	+	-
		gp130	BN000730	tnCRFA26	AAR25689	GP130	31	GP130	GP130	+	+	-
		lifr.a	BN000768	tnCRFA29	AAR25692	OSMR	23	OSMR	LIFR	+	+	1–173, 246–425
		lifr.b	BN000769	tnCRFA29	AAR25692	OSMR	20.6	OSMR	LIFR	+	+	1–182, 452–956
		osmr	BN001082	tnCRFA28	AAR25691	LIFR	((32.2))	OSMR	OSMR	+	+	-
		il-12rβ2.a	BN000858	tnCRFA25	AAR25688	IL-12Rβ2	21.5	IL-12Rβ2	IL-12Rβ2	+	+	-
		il-12rβ2.b	BN000972	tnCRFA25	AAR25688	IL-12Rβ2	17.4	IL-12Rβ2	-	-	-	1–146, 445–549
		il-23r	BN000859	tnCRFA24	AAR25687	IL-23R	15.1	IL-12Rβ2	IL-23R	-	+	-
	Group 3	il-6rα	BN000832	tnCRFA21	AAR25684	IL-6Rα	17.3	IL-6Rα	IL-6Rα	+	+	463–580
		il-11rα	BN000772	tnCRFA17	AAR25680	IL-11Rα	26.9	IL-11Rα	-	+	+	1–248, 276–402
		il-27rβ	BN000734	tnCRFA3	AAR25666	IL-27Rβ	23.4	IL-27Rβ	-	+	+	1–302
		cntfr	BN000926	tnCRFA16	AAR25679	CNTFR	49.3	CNTFR	-	+	+	1–357
		clf-1.a	BN000719	tnCRFA1	AAR25664	CLF-1	61.7	CLF-1	-	+	+	1–287, 322–389
		clf-1.b	BN000970	tnCRFA1	AAR25664	CLF-1	54.7	CLF-1	CLF-1	+	+	1–270
		il-12p40.a	BN000854	tnCRFA14	AAR25677	IL-12p40	21.4	IL-12p40	IL-12p40	-	+	1–231
		il-12p40.b	BN000860	tnCRFA15	AAR25678	IL-12p40	20.7	IL-12p40	IL-12p40	-	+	72–281
	Group 4	il-2rβ	BN000818	tnCRFA12	AAR25675	IL-2Rβ	21.7	Group 4	IL-2Rβ(?)	-	+	1–138, 390–501
		il-4rα	BN000884	-	-	IL-4Rα	13.3	IL-4Rα	IL-4Rα	+	+	1–314, 356–624
		il-7rα	BN000775	tnCRFA11	AAR25674	IL-7Rα	20.5	IL-7Rα	IL-7Rα	-	+	1–372
		il-21rα.a	BN000773	tnCRFA13	AAR25676	IL-21Rα	23.8	IL-21Rα	-	+	+	1–508
		il-21rα.b	BN000971	tnCRFA20	AAR25683	IL-21Rα	(19.5)	-	-	-	-	-
		il-3rβc	BN000973	tnCRFA23	AAR25686	IL-3Rβc	14.1	IL-3Rβc	IL-3Rβc	-	-	1–193
	Group 5	il-2rγ c.a	BN000831	tnCRFA10	AAR25673	IL-2Rγ c	21.6	IL-2Rγ c	-	-	+	1–211, 314–362
		il-2rγ c.b	BN000817	tnCRFA10	AAR25673	IL-2Rγ c	18.0	IL-2Rγ c	IL-2Rγ c	+	+	-
		tslpr	-	-	-	TSLPR iso2	17.6	-	TSLPR	+	+	-
		il-13rα1	BN000774	tnCRFA19	AAR25682	IL-13Rα1	16.7	Group 5	IL-13Rα1	+	+	1–411
		il-13rα2	BN000679	tnCRFA18	AAR25681	IL-13Rα2	30.2	IL-13Rα2	IL-13Rα2	+	+	1–405

¹Class I receptor chains are listed (and ordered by structural groups in the case of zebrafish) along with their Accession Number of the nucleotides (zebrafish) or protein (T. nigroviridis), closest human homologue based on percentage identity of the full-length protein, topology (Figure 1), synteny (Additional file 3) and expression status. Expression of zebrafish receptor chains was analyzed by RT-PCR on RNA extracted from either 24 hpf or 72 hpf, with the presence of an appropriately sized product following agarose gel electrophoresis indicated with a plus (+), or its absence with a minus (-). The existence of corresponding EST(s) is indicated for all sequences, including those from sea squirt. The numbers indicates amino acid coverage; bolded numbers represent either coverage of the start or stop codons, and absence with a minus (-). Brackets indicate sequences for which full-length sequence was unavailable, and so the CHD only was used, with double brackets indicating availability of only a partial CHD sequence. ^ indicates synteny with T. nigroviridis and ^^ indicates synteny with T. rubripes. Two additional receptors were omitted from the table and the final tally of receptors because these sequence was partial (tpor (GenBank accession no. BN001083)), have silent and missense mutations (il-4rα (GenBank accession no. BN000885)).

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