Evaluation and classification of RING-finger domains encoded by the Arabidopsis genome

Kosarev, Peter; Mayer, Klaus FX; Hardtke, Christian S

doi:10.1186/gb-2002-3-4-research0016

Table 3 List of Arabidopsis RING domains

From: Evaluation and classification of RING-finger domains encoded by the Arabidopsis genome

	Protein-ID	S1	S2	S3	S4	Alternative names and remarks
(1) RING-HC: 118 domains in 111 proteins
Cluster 1.1	At1g19310	+	+	+	+
	At1g74990	+	+	+	+
	At2g23780	+	+	+	+
	At2g42030	+	+	+	+
	AT3g58030	+	+	+	+
	AT4g03510	+	+	+	+	RMA1, ubiquitin ligase activity [29]
	AT4g27470	+	+	+	+
	AT4g28270	+	+	+	+
Cluster 1.2	At1g62370	+	+	-	-
	AT3g07120	+	+	-	-
	AT3g25030	+	+	-	-
	AT4g03960	+	+	-	-
	AT4g13100	+	+	-	-
	AT4g22250	+	+	-	-
Cluster 1.3	At1g57800	+	+	+	+	Second motif in protein
	At1g57820	+	+	+	+	Second motif in protein
	At1g66040	+	+	+	+	Second motif in protein
	At1g66050	+	+	+	+	Second motif in protein
	AT4g08590	+	+	+	+
	AT5g39550	+	+	+	+	Second motif in protein
Cluster 1.4	At1g57800	+	+	+	-	Second motif in protein
	At1g57820	+	+	+	-	Second motif in protein
	At1g66040	+	+	+	-	Second motif in protein
	At1g66050	+	+	+	-	Second motif in protein
	AT5g39550	+	+	+	-	Second motif in protein
Cluster 1.5	AT3g06140	+	+	+	+
	AT3g09770	+	+	+	+
	AT3g53410	+	+	+	+
	AT5g03200	+	+	+	+
	AT5g19080	+	+	+	+
Cluster 1.6	At1g24440	+	+	+	+
	AT3g47160	+	+	+	+	Potential RNA-binding protein
	AT5g01520	+	+	+	+
	AT5g58790	+	+	+	+
Cluster 1.7	At1g66620	+	-	-	-
	At1g66630	-	-	-	-	Likely not to be a RING
	AT5g37870	+	-	-	-
	AT5g37910	+	-	-	-
Cluster 1.8	At2g41980	+	-	-	-
	AT3g58040	+	-	-	-
	AT3g61790	+	-	-	-	Seven in absentia-like
	AT4g27880	+	-	-	-
Cluster 1.9	At1g69330	+	+	+	-
	At1g74370	+	+	+	-
	AT3g29270	+	+	+	-
Cluster 1.10	At1g01350	+	+	+	+
	AT4g01020	+	+	+	+	Second motif in protein
	AT5g06420	+	+	+	+
Cluster 1.11	At1g30860	+	+	+	+
	At2g34920	+	+	+	+
	AT5g44690	+	+	+	-
Cluster 1.12	AT5g07270	+	+	+	-
	AT5g57740	+	+	+	-
Cluster 1.13	At1g59560	+	-	-	-
	At1g63900	+	-	-	-
Cluster 1.14	At1g79110	+	-	-	-
	AT3g12920	+	-	-	-
Cluster 1.15	AT5g22750	+	+	+	+
	AT5g43530	+	+	+	+	Putative DNA-repair protein
Cluster 1.16	At1g03370	+	-	-	-
	AT4g03000	+	-	-	-
Cluster 1.17	AT3g01650	+	-	-	-
	AT5g14420	+	-	-	-
Cluster 1.18	At1g03770	+	+	+	+
	AT5g44280	+	+	+	+
Cluster 1.19	At1g32530	+	+	-	-
	At2g35330	+	+	-	-
Cluster 1.20	At1g10650	+	-	-	-	Apoptosis inhibitor-like
	At1g60610	+	-	-	-
Cluster 1.21	At2g38190	+	-	-	-
	AT5g01450	+	-	-	-
Cluster 1.22	At2g47090	+	+	+	+
	AT3g62240	+	+	+	+
Cluster 1.23	AT4g19700	+	-	-	-
	AT5g45100	+	-	-	-
Cluster 1.24	AT3g23280	-	-	-	-	Likely not to be a RING
	AT4g14360	+	-	-	-	Ankyrin-like protein
Unique	At1g05050	+	-	-	-	Putative transcription factor
	At1g05120	+	+	+	-
	At1g18660	+	+	+	+
	At1g21650	+	+	+	-	Putative SecA-type plastid protein transport factor
	At1g32740	+	-	-	-
	At1g55250	+	+	+	+
	At1g61620	+	+	+	+
	At1g67180	+	+	+	+
	At1g67800	+	-	-	-
	At1g68820	+	-	-	-
	At1g79380	+	-	-	-
	At1g79810	-	-	-	-	Likely not to be a RING
	At2g22010	+	+	+	+
	At2g25380	+	+	+	+
	At2g26350	+	+	+	+	Putative peroxisome membrane protein
	At2g28840	+	+	-	-	Ankyrin repeat protein
	At2g30580	+	+	+	+
	At2g32950	+	+	+	+	COP1, putative ubiquitin ligase [39]
	At2g39100	+	+	+	+
	At2g40770	+	+	+	-	SNF2/SWI2-like protein
	At2g44410	+	+	+	+
	At2g44950	+	+	+	+
	AT3g05250	+	+	+	-
	AT3g05670	+	+	+	+
	AT3g07200	+	+	+	-
	AT3g24800	+	+	+	+	PRT1, N-end rule ubiquitin ligase [35]
						Second motif in protein
	AT3g24800	+	+	+	-	PRT1, N-end rule ubiquitin ligase [35]
						Second motif in protein
	AT3g26730	+	+	+	+
	AT3g27330	+	+	+	+
	AT3g54360	+	+	+	+
	AT4g01740	+	+	+	+
	AT4g17680	+	+	+	+
	AT4g21070	+	+	+	-
	AT4g33940	+	+	+	+
	AT5g01160	+	+	+	+
	AT5g05130	+	+	+	+	Helicase-like protein
	AT5g13530	+	+	+	-	Ankyrin repeat protein
	AT5g19430	+	+	+	+
	AT5g23110	+	+	-	-
	AT5g47050	+	-	-	-
	AT5g63700	+	+	+	+
(2) RING-H2: 215 domains in 214 proteins
Cluster 2.1	At1g04360	+	+	+	-
	At1g20810	+	+	+	+
	At1g22500	+	+	+	+
	At1g23980	+	+	+	+
	At1g28040	+	+	+	+
	At1g32360	+	+	+	+
	At1g33480	+	+	+	+
	At1g35330	+	+	+	+
	At1g49200	+	+	+	+
	At1g49210	+	+	+	+
	At1g49220	+	+	+	+
	At1g49230	+	+	+	+
	At1g53820	+	+	+	+
	At1g72200	+	+	+	+
	At1g72220	+	+	+	+
	At1g72310	+	+	+	+	ATL3
	At1g74410	+	+	+	+
	At1g76410	+	+	+	+
	At2g17460	+	+	+	+	Pseudogene
	At2g17730	+	+	+	-
	At2g18650	+	+	+	+
	At2g20030	+	+	+	-
	At2g27940	+	+	+	-
	At2g34990	+	+	+	+
	At2g35000	+	+	+	+
	At2g35420	+	+	+	+
	At2g35910	+	+	+	+
	At2g37580	+	+	+	+
	At2g42350	+	+	+	+
	At2g42360	+	+	+	+
	At2g46160	+	+	+	+
	At2g47560	+	+	+	+
	AT3g03550	+	+	+	+
	AT3g05200	+	+	+	-	ATL6
	AT3g10910	+	+	+	+
	AT3g11110	+	+	+	+
	AT3g14320	+	+	+	+
	AT3g16720	+	+	+	+
	AT3g18930	+	+	+	+
	AT3g19140	-	-	-	-	Likely not to be a RING
	AT3g48030	+	+	+	+
	AT3g60220	+	+	+	+	ATL4
	AT3g61550	+	+	+	+
	AT3g62690	+	+	+	+	ATL5
	AT4g09100	+	+	+	+
	AT4g09110	+	+	+	+
	AT4g09120	+	+	+	+
	AT4g09130	+	+	+	+
	AT4g10150	+	+	+	+
	AT4g10160	+	+	+	+
	AT4g15970	+	+	+	+
	AT4g17910	+	+	+	+
	AT4g17920	+	+	+	+
	AT4g28890	+	+	+	-
	AT4g30400	+	+	+	+
	AT4g35480	+	+	+	+	RHA3b
	AT4g35840	+	+	+	-
	AT4g38140	+	+	+	-
	AT4g40070	+	+	+	-
	AT5g01880	+	+	+	+
	AT5g05280	+	+	+	+
	AT5g05810	+	+	+	+
	AT5g06490	+	+	+	+
	AT5g07040	+	+	+	-
	AT5g10380	+	+	+	+
	AT5g17600	+	+	+	+
	AT5g27420	+	+	+	-
	AT5g40250	+	+	+	+
	AT5g42200	+	+	+	+
	AT5g43420	+	+	+	-
	AT5g46650	+	+	+	+
	AT5g47610	+	+	+	+
	AT5g57750	+	+	+	+
	AT5g58580	+	+	+	+
	AT5g66070	+	+	+	-
Cluster 2.2	At1g14200	+	+	+	-
	At1g26800	+	+	+	+
	At1g55530	+	+	+	+
	At1g60360	+	+	+	+
	At1g68180	+	+	+	+
	At2g03000	+	+	+	+
	At2g39720	+	+	+	+
	At2g40830	+	+	+	+
	At2g44330	+	+	+	+
	AT3g02340	+	+	+	+
	AT3g10810	+	+	+	+
	AT3g13430	+	+	+	+
	AT3g19950	+	+	+	+
	AT3g30460	+	+	+	+
	AT3g46620	+	+	+	+
	AT3g60080	+	+	+	+
	AT4g26400	+	+	+	+
	AT5g01980	+	+	+	+
	AT5g02750	+	+	+	+
	AT5g08140	+	+	+	+
	AT5g15820	+	+	+	+
	AT5g20910	+	+	+	+	AIP2
	AT5g56340	+	+	+	+
	AT5g59550	+	+	+	+
	AT5g60820	+	+	+	+
	AT5g64920	+	+	+	+	CIP8, ubiquitin ligase activity [32]
Cluster 2.3	At1g17970	+	+	+	+
	At1g45180	+	+	+	+
	At1g53190	+	+	+	+
	At1g73760	+	+	+	+
	At2g15530	+	+	+	+
	AT3g15070	+	+	+	+
	AT4g31450	+	+	+	+
	AT4g34040	+	+	+	+
	AT5g10650	+	+	+	+
	AT5g24870	+	+	+	+
	AT5g42940	+	+	+	+
Cluster 2.4	At1g12760	+	+	+	-
	At1g63170	+	+	+	-
	At1g68070	+	+	+	-
	At1g80400	+	+	+	-
	AT3g61180	+	+	+	-
	AT4g11680	+	+	+	+
	AT4g26580	+	+	+	+
	AT4g32600	+	+	+	-
Cluster 2.5	At1g63840	+	+	+	-
	AT3g43430	+	+	+	+
	AT3g61460	+	+	+	+
	AT4g11360	+	+	+	-	RHA1b
	AT4g11370	+	+	+	-
	AT5g20880	+	+	+	+
	AT5g41400	+	+	+	-
Cluster 2.6	AT5g37200	+	+	+	+
	AT5g37230	+	+	+	+
	AT5g37250	+	+	+	+
	AT5g37270	+	+	+	+
	AT5g37280	+	+	+	+
Cluster 2.7	AT3g02290	+	+	+	+
	AT4g23450	+	+	+	+
	AT5g15790	+	+	+	+
	AT5g38890	+	+	+	+
	AT5g41350	+	+	+	+
Cluster 2.8	AT4g05350	+	+	+	+
	AT4g12140	+	+	+	+
	AT4g12150	-	-	-	-	Variant, ligand missing!
	AT4g12190	+	+	+	+
	AT4g12210	+	+	+	+
Cluster 2.9	At1g19680	+	+	+	+
	At1g75400	+	+	+	+
	At2g21500	+	+	+	+
	AT4g39140	+	+	+	+
	AT5g18260	+	+	+	+
Cluster 2.10	At1g22670	+	+	+	+
	At1g35630	+	+	+	+
	At1g71980	+	+	+	+	RMRJR702
	AT4g09560	+	+	+	+
	AT5g66160	+	+	+	+	RMRJR700
Cluster 2.11	At1g51930	+	+	+	+
	AT5g41430	+	+	+	+
	AT5g41440	+	+	+	+
	AT5g41450	+	+	+	-
Cluster 2.12	AT3g62970	-	-	-	-
	AT5g18650	-	-	-	-
	AT5g22920	-	-	-	-	PGPD14-like protein
	AT5g25560	-	-	-	-
Cluster 2.13	At1g08050	+	+	+	+
	At2g38970	+	+	+	+	Putative pol polyprotein
	AT3g54780	+	+	+	+
	AT5g60710	+	+	+	+
Cluster 2.14	At1g18910	-	-	-	-	Likely not to be a RING
	At1g74760	-	-	-	-	Likely not to be a RING
	AT3g18290	-	-	-	-	Likely not to be a RING
Cluster 2.15	At2g24480	+	+	+	+
	AT3g28620	+	+	+	+
	AT5g43200	+	+	+	+
Cluster 2.16	At1g15100	-	-	-	-	Likely not to be a RING
	At2g01150	-	-	-	-	RHA2b, likely not to be a RING
Cluster 2.17	At1g65040	+	+	+	+
	AT3g16090	+	+	+	+
Cluster 2.18	AT3g14970	+	-	-	-
	AT3g15740	+	-	-	-
Cluster 2.19	At2g44580	+	+	+	+	Second nearly identical motif in protein
	At2g44580	+	+	+	+	Second nearly identical motif in protein
Cluster 2.20	At2g22680	+	+	+	-	Putative pol polyprotein
	AT4g37890	+	+	+	+
Cluster 2.21	At2g18670	+	+	+	+
	AT4g30370	+	+	+	+
Cluster 2.22	AT4g25230	-	-	-	-	Likely not to be a RING
	AT5g51450	-	-	-	-	Likely not to be a RING
Unique	At1g04790	+	+	+	+
	At1g24580	+	+	+	+
	At1g27010	+	+	+	+
	At1g49850	+	+	+	+	RHY1a
	At1g53010	+	+	+	-
	At1g55410	-	-	-	-	Likely not to be a RING
	At1g57730	+	+	+	+
	At1g70910	+	+	+	+
	At1g74620	+	+	+	+
	At2g04240	+	+	+	-
	At2g05170	+	+	+	+
	At2g15260	+	+	+	-
	At2g15580	+	+	+	-
	At2g20650	+	+	+	-
	At2g26000	+	+	+	+
	At2g28920	+	+	+	-
	At2g47700	+	+	+	-
	AT3g05870	+	+	+	-
	AT3g47180	+	+	+	+
	AT3g47990	+	+	+	-
	AT3g55530	+	+	+	+
	AT3g58720	+	+	+	+
	AT4g01270	+	+	+	+
	AT4g13490	+	+	+	-
	AT4g14220	+	+	+	+	RHF1a
	AT4g18110	+	+	+	+
	AT5g05530	+	+	+	+
	AT5g05910	+	+	+	+
	AT5g54990	+	+	+	+
	AT5g57820	+	+	+	+
	AT5g67120	+	+	+	+
RING variants
(3) RING-HC, C6 or C7 position substituted or missing: 41 domains in 39 proteins
Cluster 3.1	At2g26130	-	-	-	-	Second motif in protein
	At2g26130	-	-	-	-	Second motif in protein
	AT3g43180	+	+	+	+
	AT3g43750	-	-	-	-
	AT3g45510	-	-	-	-
	AT3g45540	-	-	-	-
	AT3g45560	-	-	-	-
	AT3g45570	-	-	-	-
	AT3g45580	-	-	-	-
	AT5g60250	+	+	+	+	Second motif in protein
Cluster 3.2	At1g05890	-	-	-	-
	At1g65430	-	-	-	-
	At2g31510	-	-	-	-	Dm Ariadne-like
	At2g31760	-	-	-	-	Dm Ariadne-like
	At2g31770	-	-	-	-	Dm Ariadne-like
	At2g31780	-	-	-	-	Dm Ariadne-like
Cluster 3.3	At1g50410	+	+	+	+	Putative DNA-binding protein
	AT3g16600	+	+	+	+	Putative DNA-binding protein
	AT3g20010	+	+	+	+	RUSH1-alpha-like protein
Cluster 3.4	At2g16090	-	-	-	-
	AT3g27710	-	-	-	-
	AT4g34370	-	-	-	-
Cluster 3.5	AT5g63750	-	-	-	-	Dm Ariadne-like
	AT5g63760	-	-	-	-
Cluster 3.6	AT4g01020	-	-	-	-	Second motif in protein
	AT5g10370	-	-	-	-
Cluster 3.7	At2g25360	-	-	-	-
	AT3g45470	-	-	-	-
Unique	At1g11100	-	-	-	-	RUSH1 alpha-like protein
	At1g32340	-	-	-	-
	At1g61140	-	-	-	-
	At2g19610	-	-	-	-
	AT3g14250	-	-	-	-
	AT3g45480	+	+	+	+
	AT3g45580	-	-	-	-	Second motif in protein
	AT3g53690	-	-	-	-
	AT3g54460	-	-	-	-
	AT4g19670	-	-	-	-	Second motif in protein
	AT4g19670	-	-	-	-	Second motif in protein
	AT5g07640	-	-	-	-
	At5g60250	-	-	-	-	Second motif in protein
	At5g60250	-	-	-	-	Second motif in protein
(4) RING-H2, C7 position substituted or missing: two domains in two proteins
	AT3g42830	+	+	+	+	Rbx1-like
	AT5g37220	-	-	-	-
(5) C4 or C5 position substituted or missing: nine domains in nine proteins
Cluster 5.1	At1g18760	-	-	-	-
	At1g18770	-	-	-	-
	At1g18780	-	-	-	-
	At1g21960	-	-	-	-
	At2g29840	-	-	-	-
	AT5g53910	-	-	-	-	Likely not to be a RING
	At1g77830	-	-	-	-	RHA1b-like
Unique	At1g36950	-	-	-	-
	At2g34000	-	-	-	-
(6) C2 position substituted or missing: two domains in two proteins
	At2g37150	-	-	-	-
	AT5g63760	-	-	-	-	Second motif in protein

List of Arabidopsis proteins (Protein-ID) that contain a manually curated RING domain according to the criteria described in the text. The table is divided into three principal sections: RING domains of the RING-HC type; RING domains of the RING-H2 type; and RING-variant domains. In addition, the domains are ordered in numbered clusters according to a single-linkage-clustering method with a 10^-15 threshold as described in the text. If an individual domain meets the requirements of one of the stringent patterns 1 to 4 (S1-S4) (see Table 2), it is indicated by a plus sign, if not, it is indicated by a minus sign. Additional remarks such as previously assigned gene names and significant similarities are given in the last column, The remark 'likely not to be a RING' refers to the presence of an aromatic residue two positions in front of metal-ligand position 7 as outlined in the text.

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