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Protein

E3 ubiquitin-protein ligase RLIM

Gene

RLIM

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

E3 ubiquitin-protein ligase. Acts as a negative coregulator for LIM homeodomain transcription factors by mediating the ubiquitination and subsequent degradation of LIM cofactors LDB1 and LDB2 and by mediating the recruitment the SIN3a/histone deacetylase corepressor complex. Ubiquitination and degradation of LIM cofactors LDB1 and LDB2 allows DNA-bound LIM homeodomain transcription factors to interact with other protein partners such as RLIM. Plays a role in telomere length-mediated growth suppression by mediating the ubiquitination and degradation of TERF1. By targeting ZFP42 for degradation, acts as an activator of random inactivation of X chromosome in the embryo, a stochastic process in which one X chromosome is inactivated to minimize sex-related dosage differences of X-encoded genes in somatic cells of female placental mammals.2 Publications

Pathwayi: protein ubiquitination

This protein is involved in the pathway protein ubiquitination, which is part of Protein modification.
View all proteins of this organism that are known to be involved in the pathway protein ubiquitination and in Protein modification.

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri570 – 611RING-typePROSITE-ProRule annotationAdd BLAST42

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Ligase

Keywords - Biological processi

Transcription, Transcription regulation, Ubl conjugation pathway

Keywords - Ligandi

Metal-binding, Zinc

Enzyme and pathway databases

BioCyciZFISH:ENSG00000131263-MONOMER.
ReactomeiR-HSA-983168. Antigen processing: Ubiquitination & Proteasome degradation.
UniPathwayiUPA00143.

Names & Taxonomyi

Protein namesi
Recommended name:
E3 ubiquitin-protein ligase RLIM (EC:6.3.2.-)
Alternative name(s):
LIM domain-interacting RING finger protein
RING finger LIM domain-binding protein
Short name:
R-LIM
RING finger protein 12
Renal carcinoma antigen NY-REN-43
Gene namesi
Name:RLIM
Synonyms:RNF12
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome X

Organism-specific databases

HGNCiHGNC:13429. RLIM.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: HPA
  • cytosol Source: Reactome
  • nucleoplasm Source: GO_Central
  • nucleus Source: UniProtKB
  • transcriptional repressor complex Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Organism-specific databases

DisGeNETi51132.
OpenTargetsiENSG00000131263.
PharmGKBiPA164725373.

Polymorphism and mutation databases

BioMutaiRLIM.
DMDMi143811451.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000560521 – 624E3 ubiquitin-protein ligase RLIMAdd BLAST624

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei1N-acetylmethionineCombined sources1
Modified residuei164PhosphoserineBy similarity1
Modified residuei195PhosphoserineCombined sources1
Modified residuei228PhosphoserineCombined sources1
Modified residuei230PhosphoserineCombined sources1
Modified residuei276PhosphoserineCombined sources1

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

EPDiQ9NVW2.
MaxQBiQ9NVW2.
PaxDbiQ9NVW2.
PeptideAtlasiQ9NVW2.
PRIDEiQ9NVW2.

PTM databases

iPTMnetiQ9NVW2.
PhosphoSitePlusiQ9NVW2.

Expressioni

Tissue specificityi

Expressed in many tissues.

Gene expression databases

BgeeiENSG00000131263.
CleanExiHS_RNF12.
GenevisibleiQ9NVW2. HS.

Organism-specific databases

HPAiHPA018895.

Interactioni

Subunit structurei

Interacts with LIM/homeobox factors such as LHX3. Interacts with LDB1, LDB2 and SIN3A (By similarity). Interacts with LIMK1 (By similarity). Interacts (via N-terminus) with TERF1. Interacts (via C-terminus) with ESR1.By similarity2 Publications

Protein-protein interaction databases

BioGridi119319. 34 interactors.
IntActiQ9NVW2. 13 interactors.
MINTiMINT-233446.
STRINGi9606.ENSP00000253571.

Structurei

3D structure databases

ProteinModelPortaliQ9NVW2.
SMRiQ9NVW2.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi621 – 624PDZ-bindingSequence analysis4

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi422 – 506Ser-richAdd BLAST85
Compositional biasi453 – 481Poly-SerAdd BLAST29
Compositional biasi500 – 506Poly-Ser7

Sequence similaritiesi

Belongs to the RNF12 family.Curated
Contains 1 RING-type zinc finger.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri570 – 611RING-typePROSITE-ProRule annotationAdd BLAST42

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiKOG0800. Eukaryota.
ENOG41121N2. LUCA.
GeneTreeiENSGT00730000110459.
HOGENOMiHOG000273881.
InParanoidiQ9NVW2.
KOiK16271.
OMAiDNLAMRN.
OrthoDBiEOG091G0B6K.
PhylomeDBiQ9NVW2.
TreeFamiTF325756.

Family and domain databases

Gene3Di3.30.40.10. 1 hit.
InterProiIPR001841. Znf_RING.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]
PfamiPF13639. zf-RING_2. 1 hit.
[Graphical view]
SMARTiSM00184. RING. 1 hit.
[Graphical view]
PROSITEiPS50089. ZF_RING_2. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9NVW2-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MENSDSNDKG SGDQSAAQRR SQMDRLDREE AFYQFVNNLS EEDYRLMRDN
60 70 80 90 100
NLLGTPGEST EEELLRRLQQ IKEGPPPQNS DENRGGDSSD DVSNGDSIID
110 120 130 140 150
WLNSVRQTGN TTRSGQRGNQ SWRAVSRTNP NSGDFRFSLE INVNRNNGSQ
160 170 180 190 200
NSENENEPSA RRSSGENVEN NSQRQVENPR SESTSARPSR SERNSTEALT
210 220 230 240 250
EVPPTRGQRR ARSRSPDHRR TRARAERSRS PLHPMSEIPR RSHHSISSQT
260 270 280 290 300
FEHPLVNETE GSSRTRHHVT LRQQISGPEL LSRGLFAASG TRNASQGAGS
310 320 330 340 350
SDTAASGEST GSGQRPPTIV LDLQVRRVRP GEYRQRDSIA SRTRSRSQTP
360 370 380 390 400
NNTVTYESER GGFRRTFSRS ERAGVRTYVS TIRIPIRRIL NTGLSETTSV
410 420 430 440 450
AIQTMLRQIM TGFGELSYFM YSDSDSEPTG SVSNRNMERA ESRSGRGGSG
460 470 480 490 500
GGSSSGSSSS SSSSSSSSSS SSSSSSPSSS SGGESSETSS DLFEGSNEGS
510 520 530 540 550
SSSGSSGARR EGRHRAPVTF DESGSLPFLS LAQFFLLNED DDDQPRGLTK
560 570 580 590 600
EQIDNLAMRS FGENDALKTC SVCITEYTEG NKLRKLPCSH EYHVHCIDRW
610 620
LSENSTCPIC RRAVLASGNR ESVV
Length:624
Mass (Da):68,549
Last modified:April 3, 2007 - v3
Checksum:i4D583FA6872B51D3
GO
Isoform 2 (identifier: Q9NVW2-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-3: MEN → MLT
     4-144: Missing.

Note: No experimental confirmation available.
Show »
Length:483
Mass (Da):52,638
Checksum:i1167FBEDA180A3A9
GO

Sequence cautioni

The sequence AAD42875 differs from that shown. Reason: Frameshift at positions 134 and 142.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti126S → C in CAC14228 (PubMed:11013082).Curated1
Sequence conflicti134D → N in CAC14228 (PubMed:11013082).Curated1
Sequence conflicti144 – 145NR → YS in CAC14228 (PubMed:11013082).Curated2
Sequence conflicti418Y → H in BAA91632 (PubMed:14702039).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_074175590H → P.1 Publication1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0554281 – 3MEN → MLT in isoform 2. 1 Publication3
Alternative sequenceiVSP_0554294 – 144Missing in isoform 2. 1 PublicationAdd BLAST141

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF155109 mRNA. Translation: AAD42875.1. Frameshift.
AJ271670 Genomic DNA. Translation: CAC14228.1.
AK001334 mRNA. Translation: BAA91632.1.
AK314760 mRNA. Translation: BAG37298.1.
AL513007 Genomic DNA. Translation: CAI41712.1.
CH471104 Genomic DNA. Translation: EAW98639.1.
CH471104 Genomic DNA. Translation: EAW98640.1.
BC013357 mRNA. Translation: AAH13357.1.
CCDSiCCDS14427.1. [Q9NVW2-1]
RefSeqiNP_057204.2. NM_016120.3. [Q9NVW2-1]
NP_899196.1. NM_183353.2. [Q9NVW2-1]
UniGeneiHs.653288.

Genome annotation databases

EnsembliENST00000332687; ENSP00000328059; ENSG00000131263. [Q9NVW2-1]
ENST00000349225; ENSP00000253571; ENSG00000131263. [Q9NVW2-1]
GeneIDi51132.
KEGGihsa:51132.
UCSCiuc004ebu.4. human. [Q9NVW2-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF155109 mRNA. Translation: AAD42875.1. Frameshift.
AJ271670 Genomic DNA. Translation: CAC14228.1.
AK001334 mRNA. Translation: BAA91632.1.
AK314760 mRNA. Translation: BAG37298.1.
AL513007 Genomic DNA. Translation: CAI41712.1.
CH471104 Genomic DNA. Translation: EAW98639.1.
CH471104 Genomic DNA. Translation: EAW98640.1.
BC013357 mRNA. Translation: AAH13357.1.
CCDSiCCDS14427.1. [Q9NVW2-1]
RefSeqiNP_057204.2. NM_016120.3. [Q9NVW2-1]
NP_899196.1. NM_183353.2. [Q9NVW2-1]
UniGeneiHs.653288.

3D structure databases

ProteinModelPortaliQ9NVW2.
SMRiQ9NVW2.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi119319. 34 interactors.
IntActiQ9NVW2. 13 interactors.
MINTiMINT-233446.
STRINGi9606.ENSP00000253571.

PTM databases

iPTMnetiQ9NVW2.
PhosphoSitePlusiQ9NVW2.

Polymorphism and mutation databases

BioMutaiRLIM.
DMDMi143811451.

Proteomic databases

EPDiQ9NVW2.
MaxQBiQ9NVW2.
PaxDbiQ9NVW2.
PeptideAtlasiQ9NVW2.
PRIDEiQ9NVW2.

Protocols and materials databases

DNASUi51132.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000332687; ENSP00000328059; ENSG00000131263. [Q9NVW2-1]
ENST00000349225; ENSP00000253571; ENSG00000131263. [Q9NVW2-1]
GeneIDi51132.
KEGGihsa:51132.
UCSCiuc004ebu.4. human. [Q9NVW2-1]

Organism-specific databases

CTDi51132.
DisGeNETi51132.
GeneCardsiRLIM.
HGNCiHGNC:13429. RLIM.
HPAiHPA018895.
MIMi300379. gene.
neXtProtiNX_Q9NVW2.
OpenTargetsiENSG00000131263.
PharmGKBiPA164725373.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0800. Eukaryota.
ENOG41121N2. LUCA.
GeneTreeiENSGT00730000110459.
HOGENOMiHOG000273881.
InParanoidiQ9NVW2.
KOiK16271.
OMAiDNLAMRN.
OrthoDBiEOG091G0B6K.
PhylomeDBiQ9NVW2.
TreeFamiTF325756.

Enzyme and pathway databases

UniPathwayiUPA00143.
BioCyciZFISH:ENSG00000131263-MONOMER.
ReactomeiR-HSA-983168. Antigen processing: Ubiquitination & Proteasome degradation.

Miscellaneous databases

ChiTaRSiRLIM. human.
GeneWikiiRNF12.
GenomeRNAii51132.
PROiQ9NVW2.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000131263.
CleanExiHS_RNF12.
GenevisibleiQ9NVW2. HS.

Family and domain databases

Gene3Di3.30.40.10. 1 hit.
InterProiIPR001841. Znf_RING.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]
PfamiPF13639. zf-RING_2. 1 hit.
[Graphical view]
SMARTiSM00184. RING. 1 hit.
[Graphical view]
PROSITEiPS50089. ZF_RING_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRNF12_HUMAN
AccessioniPrimary (citable) accession number: Q9NVW2
Secondary accession number(s): B2RBQ1
, D3DTE0, Q96D38, Q9Y598
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 21, 2001
Last sequence update: April 3, 2007
Last modified: November 2, 2016
This is version 147 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Miscellaneous

Acts as a positive coregulator of ESR1-mediated transcription in breast cancer cells.

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome X
    Human chromosome X: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  6. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.