Table 3

List of Arabidopsis RING domains

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.

Kosarev et al. Genome Biology 2002 3:research0016.1-research0016.12   doi:10.1186/gb-2002-3-4-research0016

Open Data