Remodeling Cildb, a popular database for cilia and links for ciliopathies

Arnaiz, Olivier; Cohen, Jean; Tassin, Anne-Marie; Koll, France

doi:10.1186/2046-2530-3-9

Cilia

Table 2 Evolutionary conservation of centrosomal proteins viewed through CildbV3.0

From: Remodeling Cildb, a popular database for cilia and links for ciliopathies

	Protein ID	Synonyms	Mus	Rattus	Danio	Apis	Drosophila	Class
1	ENSP00000380378	PAFAH1B1,LIS1,LIS2,MDCR	yes	yes	yes	yes	yes	1 (yyyyy)
2	ENSP00000364691	CROCC,ROLT,ROLT,rootletin	yes	yes	yes	yes	yes	1 (yyyyy)
3	ENSP00000309591	PRKACA,PKACA,PKACa	yes	yes	yes	yes	yes	1 (yyyyy)
4	ENSP00000263710	CLASP1,MAST1	yes	yes	yes	yes	yes	1 (yyyyy)
5	ENSP00000263811	DYNC1I2,DNCI2,IC2	yes	yes	yes	yes	yes	1 (yyyyy)
6	ENSP00000216911	AURKA,AIK,ARK1,AURA,AURORA2	yes	yes	yes	yes	yes	1 (yyyyy)
7	ENSP00000364721	MAPRE1,EB1,EB1	yes	yes	yes	yes	yes	1 (yyyyy)
8	ENSP00000265563	PRKAR2A,PKR2,PRKAR2	yes	yes	yes	yes	yes	1 (yyyyy)
9	ENSP00000355966	NEK2,HsPK21,NEK2A,NLK1	yes	yes	yes	yes	yes	1 (yyyyy)
10	ENSP00000261965	TUBGCP3,GCP3,SPBC98	yes	yes	yes	yes	yes	1 (yyyyy)
11	ENSP00000252936	TUBGCP2,GCP2,Grip103,h103p	yes	yes	yes	yes	yes	1 (yyyyy)
12	ENSP00000251413	TUBG1,CDCBM4,GCP-1	yes	yes	yes	yes	yes	1 (yyyyy)
13	ENSP00000456648	TUBGCP4,76P,GCP-4,GCP4	yes	yes	yes	yes	yes	1 (yyyyy)
14	ENSP00000323302	POC1B,PIX1,TUWD12,WDR51B	yes	yes	yes	yes	yes	1 (yyyyy)
15	ENSP00000324464	CSNK1D,ASPS,CKIdelta,FASPS2,HCKID	yes	yes	yes	yes	yes	1 (yyyyy)
16	ENSP00000270861	PLK4,SAK,STK18,Sak	yes	yes	yes	yes	yes	1 (yyyyy)
17	ENSP00000356785	NME7,MN23H7,NDK7	yes	yes	yes	yes	yes	1 (yyyyy)
18	ENSP00000273130	DYNC1LI1,DNCLI1,LIC1	yes	yes	yes	yes	yes	1 (yyyyy)
19	ENSP00000359300	CETN2,CALT,CEN2	yes	yes	yes	yes	yes	1 (yyyyy)
20	ENSP00000287380	TBC1D31,Gm85,WDR67	yes	yes	yes	yes	yes	1 (yyyyy)
21	ENSP00000287482	SASS6,SAS-6,SAS6	yes	yes	yes	yes	yes	1 (yyyyy)
22	ENSP00000300093	PLK1,PLK,STPK13	yes	yes	yes	yes	yes	1 (yyyyy)
23	ENSP00000257287	CEP135,CEP4,MCPH8	yes	yes	yes	yes	yes	1 (yyyyy)
24	ENSP00000439376	DCTN2,DCTN50,DYNAMITIN,RBP50	yes	yes	yes	yes	yes	1 (yyyyy)
25	ENSP00000395302	CKAP5,ch-TOG,CHTOG,MSPS	yes	yes	yes	yes	yes	1 (yyyyy)
26	ENSP00000342510	CEP97,LRRIQ2	yes	yes	yes	yes	yes	1 (yyyyy)
27	ENSP00000348965	DYNC1H1,DHC1,DHC1a	yes	yes	yes	yes	yes	1 (yyyyy)
28	ENSP00000469720	CETN2,CALT,CEN2	yes	yes	yes	yes	yes	1 (yyyyy)
29	ENSP00000317156	CEP192,PPP1R62	yes	yes	yes	yes	no	2 (yyyyn)
30	ENSP00000270708	WRAP73,WDR8	yes	yes	yes	yes	no	2 (yyyyn)
31	ENSP00000248846	TUBGCP6,GCP-6,GCP6,MCCRP,MCPHCR	yes	yes	yes	yes	no	2 (yyyyn)
32	ENSP00000393583	AZI1,AZ1,Cep131,ZA1	yes	yes	yes	yes	no	2 (yyyyn)
33	ENSP00000283645	TUBGCP5,GCP5	yes	yes	yes	yes	no	2 (yyyyn)
34	ENSP00000303058	CEP120,CCDC100	yes	yes	yes	yes	no	2 (yyyyn)
35	ENSP00000313752	SSNA1,N14,NA-14	yes	yes	yes	yes	no	2 (yyyyn)
36	ENSP00000355812	FGFR1OP,FOP	yes	yes	yes	yes	no	2 (yyyyn)
37	ENSP00000343818	CDK5RAP2,C48,Cep215,MCPH3	yes	yes	yes	no	yes	3 (yyyny)
38	ENSP00000344314	OFD1,CXorf5,JBTS10,RP23	yes	yes	yes	no	no	4 (yyynn)
39	ENSP00000317144	PIBF1,C13orf24,CEP90	yes	yes	yes	no	no	4 (yyynn)
40	ENSP00000204726	GOLGA3,GCP170,MEA-2,golgin-160	yes	yes	yes	no	no	4 (yyynn)
41	ENSP00000206474	HAUS4,C14orf94	yes	yes	yes	no	no	4 (yyynn)
42	ENSP00000281129	CEP128,C14orf145,C14orf61,LEDP/132	yes	yes	yes	no	no	4 (yyynn)
43	ENSP00000262127	CEP76,C18orf9,HsT1705	yes	yes	yes	no	no	4 (yyynn)
44	ENSP00000370803	CCP110,Cep110,CP110	yes	yes	yes	no	no	4 (yyynn)
45	ENSP00000263284	CCDC61	yes	yes	yes	no	no	4 (yyynn)
46	ENSP00000223208	CEP41,JBTS15,TSGA14	yes	yes	yes	no	no	4 (yyynn)
47	ENSP00000303769	AKNA	yes	yes	yes	no	no	4 (yyynn)
48	ENSP00000302537	MDM1	yes	yes	yes	no	no	4 (yyynn)
49	ENSP00000264935	CEP72,FLJ10565	yes	yes	yes	no	no	4 (yyynn)
50	ENSP00000419231	CEP70,BITE	yes	yes	yes	no	no	4 (yyynn)
51	ENSP00000306105	CEP89,CCDC123	yes	yes	yes	no	no	4 (yyynn)
52	ENSP00000380661	CEP250,C-NAP1,CEP2,CNAP1	yes	yes	yes	no	no	4 (yyynn)
53	ENSP00000356579	CEP350,CAP350,GM133	yes	yes	yes	no	no	4 (yyynn)
54	ENSP00000260372	HAUS2,C15orf25,CEP27,HsT17025	yes	yes	yes	no	no	4 (yyynn)
55	ENSP00000360540	CEP55,C10orf3,CT111,URCC6	yes	yes	yes	no	no	4 (yyynn)
56	ENSP00000355500	CEP170,FAM68A,KAB	yes	yes	yes	no	no	4 (yyynn)
57	ENSP00000369871	HAUS6,Dgt6,FAM29A	yes	yes	yes	no	no	4 (yyynn)
58	ENSP00000371308	CENPJ,BM032,CENP-J,CPAP,LAP,LIP1,MCPH6,Sas-4	yes	yes	yes	no	no	4 (yyynn)
59	ENSP00000282058	HAUS1,CCDC5,HEI-C,HEIC	yes	yes	yes	no	no	4 (yyynn)
60	ENSP00000283122	CETN3,CDC31,CEN3	yes	yes	yes	no	no	4 (yyynn)
61	ENSP00000352572	PCNT,KEN,MOPD2,PCN,PCNT2,PCNTB	yes	yes	yes	no	no	4 (yyynn)
62	ENSP00000295872	SPICE1,CCDC52,SPICE	yes	yes	yes	no	no	4 (yyynn)
63	ENSP00000317902	CEP57,MVA2,PIG8,TSP57	yes	yes	yes	no	no	4 (yyynn)
64	ENSP00000426129	CEP63	yes	yes	yes	no	no	4 (yyynn)
65	ENSP00000308021	CEP290,BBS14,JBTS5,LCA10,MKS4,NPHP6,POC3,rd16,SLSN6	yes	yes	yes	no	no	4 (yyynn)
66	ENSP00000439056	HAUS5,dgt5	yes	yes	yes	no	no	4 (yyynn)
67	ENSP00000462740	CEP41,JBTS15,TSGA14	yes	yes	yes	no	no	4 (yyynn)
68	ENSP00000265717	PRKAR2B,PRKAR2,RII-BETA	yes	yes	no	yes	yes	5 (yynyy)
69	ENSP00000345892	NDE1,HOM-TES-87,LIS4,NDE,NUDE	yes	yes	no	yes	yes	5 (yynyy)
70	ENSP00000358921	ACTR1A,ARP1,CTRN1	yes	yes	no	yes	yes	5 (yynyy)
71	ENSP00000447907	DYNLL1,DLC1,DLC8,DNCL1,DNCLC1,hdlc1,LC8	yes	yes	no	no	no	6 (yynnn)
72	ENSP00000278935	CEP164,NPHP15	yes	yes	no	no	no	6 (yynnn)
73	ENSP00000264448	ALMS1,ALSS	yes	yes	no	no	no	6 (yynnn)
74	ENSP00000316681	KIAA1731	yes	yes	no	no	no	6 (yynnn)
75	ENSP00000456335	CNTROB,LIP8,PP1221	yes	yes	no	no	no	6 (yynnn)
76	ENSP00000348573	AKAP9,AKAP350,AKAP450,CG-NAP,HYPERION,LQT11	yes	no	no	no	no	7 (ynnnn)
77	ENSP00000384844	DCTN1,DAP-150,P135	no	no	yes	yes	yes	8 (nnyyy)

This table presents the list of 77 human proteins obtained from a BioMartsearch described in the text. The output gives a total of 133 proteinsencoded by 77 genes, due to the presence of splice variants. For clarity,only one protein ID per gene has been presented in the table, afterverification that all the splice variants of each gene displays the sameorthology relationships with the species presented here. This tableillustrates evolutionary conservation where a “yes” indicatesthat the human protein has an Inparalog in Cildb and a “no” thatno Inparanoid orthology was found. The column ‘class’ serves toorder the output genes in the table (from 5× ‘yes’ at thetop to much fewer ‘yes’ at the bottom, along criteria of certainspecies being closer to each other than others, whereby the order from leftto right goes human-mouse-rat (mammals), then fish (vertebrate), then beeand fly (insects). All instances of lacking orthology (“no”)were individually verified by BLAST searches using the Cildb BLAST. TheBLAST results were consistent with the absence of orthologs in the species,and only three exceptions contradict the Inparanoid results, highlighted asbold characters in the table.
1- Human Azi1 (ENSP00000393583) has no inparalog in Drosophilaalthough an ortholog called dilatory exists. BLAST search on theDrosophila genome indeed light up dilatory, with ascore very close to the one found for the Apis inparalogs by BLAST.The difference between these different outputs may result from the value ofdefault thresholds taken by the Inparanoid program and the different lengthsof the proteins.
2- Human cdk5rap2 (ENSP00000343818) has no Inparalog in Apis,although homologs are found by BLAST. Inparanoid relationships of the topthree Apis proteins in the list (XP_006563202.1, XP_006563201.1,XP_392107.3) appear to be Inparalogs of Drosophila centrosomin(cnn, cdk5rap2) for which 8 of 12 splice variant proteins display humanInparalogs. However, no direct Inparanoid relationships exist between theApis proteins and any human protein.
3- Human dynactin/dctn1 (ENSP00000384844) has surprisingly no Inparalogs inmouse and rat whereas some are found in fish, bee and fly. However, mouseand rat homologs are easily found by BLAST search. After carefulexamination, it appears that the only ENSP00000384844 dynactin protein foundcommon to the three human centrosomal studies, is one of the splice variantsexcluded from Inparalog groups. Indeed, the 16 splice variants for the humandynactin gene ENSG00000204843 and the seven splice variants for itsmouse counterpart ENSMUSG00000031865 are related by Inparanoidorthology through three groups, hsap_mmus.17187 (one human and onemouse gene), hsap_mmus.1073 (four human and one mouse gene) andhsap_mmus.977 (one human and two mouse genes). The remaining tenhuman protein variants (among which is ENSP00000384844) and three mouseprotein variants encoded by these genes are not included in the orthologygroups, probably because their exon composition was too different from theother protein variants.
These three examples represent the limits of Inparanoid orthologyprediction, highlighting the fact that reciprocal BLAST searches cannot beavoided, and thus represent an important complementary approach, for theanalysis of individual proteins.

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ISSN: 2046-2530

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