Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

E3 ubiquitin-protein ligase RLIM

Gene

Rlim

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

E3 ubiquitin-protein ligase that 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.4 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 fingeri546 – 587RING-typePROSITE-ProRule annotationAdd BLAST42

GO - Molecular functioni

  • ligase activity Source: UniProtKB-KW
  • ubiquitin protein ligase activity Source: MGI
  • ubiquitin-protein transferase activity Source: UniProtKB
  • zinc ion binding Source: InterPro

GO - Biological processi

  • negative regulation of sequence-specific DNA binding transcription factor activity Source: MGI
  • negative regulation of transcription from RNA polymerase II promoter Source: MGI
  • proteasome-mediated ubiquitin-dependent protein catabolic process Source: GO_Central
  • protein ubiquitination Source: UniProtKB
  • random inactivation of X chromosome Source: UniProtKB
  • regulation of dosage compensation by inactivation of X chromosome Source: MGI
  • transcription, DNA-templated Source: UniProtKB-KW
  • ubiquitin-dependent protein catabolic process Source: UniProtKB
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

ReactomeiR-MMU-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
Gene namesi
Name:Rlim
Synonyms:Rnf12
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome X

Organism-specific databases

MGIiMGI:1342291. Rlim.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: MGI
  • nucleoplasm Source: GO_Central
  • nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000560531 – 600E3 ubiquitin-protein ligase RLIMAdd BLAST600

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei1N-acetylmethionineBy similarity1
Modified residuei163PhosphoserineCombined sources1
Modified residuei194PhosphoserineBy similarity1
Modified residuei227PhosphoserineCombined sources1
Modified residuei229PhosphoserineCombined sources1
Modified residuei269PhosphoserineBy similarity1

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

EPDiQ9WTV7.
MaxQBiQ9WTV7.
PaxDbiQ9WTV7.
PeptideAtlasiQ9WTV7.
PRIDEiQ9WTV7.

PTM databases

iPTMnetiQ9WTV7.
PhosphoSitePlusiQ9WTV7.

Expressioni

Developmental stagei

Ubiquitously expressed in early development. Expressed in the time window of embryonic stem (ES) cell differentiation.1 Publication

Inductioni

Expressed at higher level in female compared to males cells (at protein level).1 Publication

Gene expression databases

BgeeiENSMUSG00000056537.
CleanExiMM_RNF12.
GenevisibleiQ9WTV7. MM.

Interactioni

Subunit structurei

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

Protein-protein interaction databases

BioGridi202918. 3 interactors.
DIPiDIP-46445N.
STRINGi10090.ENSMUSP00000070662.

Structurei

3D structure databases

ProteinModelPortaliQ9WTV7.
SMRiQ9WTV7.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi597 – 600PDZ-bindingSequence analysis4

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi415 – 484Ser-richAdd BLAST70
Compositional biasi447 – 461Poly-SerAdd BLAST15

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 fingeri546 – 587RING-typePROSITE-ProRule annotationAdd BLAST42

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiKOG0800. Eukaryota.
ENOG41121N2. LUCA.
GeneTreeiENSGT00730000110459.
HOGENOMiHOG000273881.
InParanoidiQ9WTV7.
KOiK16271.
OMAiDNLAMRN.
OrthoDBiEOG091G0B6K.
PhylomeDBiQ9WTV7.
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]

Sequencei

Sequence statusi: Complete.

Q9WTV7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MENSDSNDKG SDQSAAQRRS QMDRLDREEA FYQFVNNLSE EDYRLMRDNN
60 70 80 90 100
LLGTPGESTE EELLRRLQQI KEGPPPQSPD ENRAGESSDD VTNSDSIIDW
110 120 130 140 150
LNSVRQTGNT TRSGQRGNQS WRAVSRTNPN SGDFRFSLEI NVNRNNGSQT
160 170 180 190 200
SENESEPSTR RLSVENMESS SQRQMENSAS ESASARPSRA ERNSAEAVTE
210 220 230 240 250
VPTTRAQRRA RSRSPEHRRT RARAERSRSP LQPTSEIPRR APTLEQSSEN
260 270 280 290 300
EPEGSSRTRH HVTLRQQISG PELLGRGLFA ASGSRNPSQG TSSSDTGSNS
310 320 330 340 350
ESSGSGQRPP TIVLDLQVRR VRPGEYRQRD SIASRTRSRS QAPNNTVTYE
360 370 380 390 400
SERGGFRRTF SRSERAGVRT YVSTIRIPIR RILNTGLSET TSVAIQTMLR
410 420 430 440 450
QIMTGFGELS YFMYSDSDSE PSASVSSRNV ERVESRNGRG SSGGGNSSGS
460 470 480 490 500
SSSSSPSPSS SGESSESSSE MFEGSSEGGS SGPSRRDGRH RAPVTFDESG
510 520 530 540 550
SLPFLSLAQF FLLNEDDEDQ PRGLTKEQID NLAMRSFGEN DALKTCSVCI
560 570 580 590 600
TEYTEGNKLR KLPCSHEYHV HCIDRWLSEN STCPICRRAV LSSGNRESVV
Length:600
Mass (Da):66,377
Last modified:September 22, 2009 - v2
Checksum:i6BFB9958502FDAED
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti114G → R in AAD34209 (PubMed:10431247).Curated1
Sequence conflicti146N → S in BAC26379 (PubMed:16141072).Curated1
Sequence conflicti195A → T in AAD34209 (PubMed:10431247).Curated1
Sequence conflicti228R → M in AAD34209 (PubMed:10431247).Curated1
Sequence conflicti320R → G in BAC26379 (PubMed:16141072).Curated1
Sequence conflicti362R → S in BAB28712 (PubMed:16141072).Curated1
Sequence conflicti470E → K in AAD34209 (PubMed:10431247).Curated1
Sequence conflicti486R → K in AAD34209 (PubMed:10431247).Curated1
Sequence conflicti505L → F in AAD34209 (PubMed:10431247).Curated1
Sequence conflicti557N → D in AAD34209 (PubMed:10431247).Curated1
Sequence conflicti568Y → F in AAD34209 (PubMed:10431247).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF069992 mRNA. Translation: AAD34209.1.
AK013207 mRNA. Translation: BAB28712.1.
AK029295 mRNA. Translation: BAC26379.1.
AL805911 Genomic DNA. Translation: CAM26768.1.
CH466564 Genomic DNA. Translation: EDL14089.1.
CH466564 Genomic DNA. Translation: EDL14090.1.
BC012960 mRNA. Translation: AAH12960.1.
CCDSiCCDS30331.1.
RefSeqiNP_035406.3. NM_011276.3.
XP_006527981.1. XM_006527918.3.
XP_006527982.1. XM_006527919.3.
XP_006527983.1. XM_006527920.3.
XP_006527984.1. XM_006527921.3.
XP_011245853.1. XM_011247551.2.
XP_011245854.1. XM_011247552.2.
UniGeneiMm.427762.
Mm.490660.

Genome annotation databases

EnsembliENSMUST00000070705; ENSMUSP00000070662; ENSMUSG00000056537.
ENSMUST00000121153; ENSMUSP00000112820; ENSMUSG00000056537.
GeneIDi19820.
KEGGimmu:19820.
UCSCiuc009tzz.1. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF069992 mRNA. Translation: AAD34209.1.
AK013207 mRNA. Translation: BAB28712.1.
AK029295 mRNA. Translation: BAC26379.1.
AL805911 Genomic DNA. Translation: CAM26768.1.
CH466564 Genomic DNA. Translation: EDL14089.1.
CH466564 Genomic DNA. Translation: EDL14090.1.
BC012960 mRNA. Translation: AAH12960.1.
CCDSiCCDS30331.1.
RefSeqiNP_035406.3. NM_011276.3.
XP_006527981.1. XM_006527918.3.
XP_006527982.1. XM_006527919.3.
XP_006527983.1. XM_006527920.3.
XP_006527984.1. XM_006527921.3.
XP_011245853.1. XM_011247551.2.
XP_011245854.1. XM_011247552.2.
UniGeneiMm.427762.
Mm.490660.

3D structure databases

ProteinModelPortaliQ9WTV7.
SMRiQ9WTV7.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi202918. 3 interactors.
DIPiDIP-46445N.
STRINGi10090.ENSMUSP00000070662.

PTM databases

iPTMnetiQ9WTV7.
PhosphoSitePlusiQ9WTV7.

Proteomic databases

EPDiQ9WTV7.
MaxQBiQ9WTV7.
PaxDbiQ9WTV7.
PeptideAtlasiQ9WTV7.
PRIDEiQ9WTV7.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000070705; ENSMUSP00000070662; ENSMUSG00000056537.
ENSMUST00000121153; ENSMUSP00000112820; ENSMUSG00000056537.
GeneIDi19820.
KEGGimmu:19820.
UCSCiuc009tzz.1. mouse.

Organism-specific databases

CTDi51132.
MGIiMGI:1342291. Rlim.

Phylogenomic databases

eggNOGiKOG0800. Eukaryota.
ENOG41121N2. LUCA.
GeneTreeiENSGT00730000110459.
HOGENOMiHOG000273881.
InParanoidiQ9WTV7.
KOiK16271.
OMAiDNLAMRN.
OrthoDBiEOG091G0B6K.
PhylomeDBiQ9WTV7.
TreeFamiTF325756.

Enzyme and pathway databases

UniPathwayiUPA00143.
ReactomeiR-MMU-983168. Antigen processing: Ubiquitination & Proteasome degradation.

Miscellaneous databases

PROiQ9WTV7.
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000056537.
CleanExiMM_RNF12.
GenevisibleiQ9WTV7. MM.

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_MOUSE
AccessioniPrimary (citable) accession number: Q9WTV7
Secondary accession number(s): Q8CE02, Q91X19, Q9CYY2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 21, 2001
Last sequence update: September 22, 2009
Last modified: November 2, 2016
This is version 130 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. 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.