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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)
  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.