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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)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri546 – 58742RING-typePROSITE-ProRule annotationAdd
BLAST

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
  • 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

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
  • nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 600600E3 ubiquitin-protein ligase RLIMPRO_0000056053Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei1 – 11N-acetylmethionineBy similarity
Modified residuei163 – 1631PhosphoserineCombined sources
Modified residuei227 – 2271PhosphoserineCombined sources
Modified residuei229 – 2291PhosphoserineCombined sources

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

EPDiQ9WTV7.
MaxQBiQ9WTV7.
PaxDbiQ9WTV7.
PRIDEiQ9WTV7.

PTM databases

iPTMnetiQ9WTV7.
PhosphoSiteiQ9WTV7.

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

BgeeiQ9WTV7.
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 interactions.
DIPiDIP-46445N.
STRINGi10090.ENSMUSP00000070662.

Structurei

3D structure databases

ProteinModelPortaliQ9WTV7.
SMRiQ9WTV7. Positions 546-587.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi597 – 6004PDZ-bindingSequence analysis

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi415 – 48470Ser-richAdd
BLAST
Compositional biasi447 – 46115Poly-SerAdd
BLAST

Sequence similaritiesi

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

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri546 – 58742RING-typePROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiKOG0800. Eukaryota.
ENOG41121N2. LUCA.
GeneTreeiENSGT00730000110459.
HOGENOMiHOG000273881.
InParanoidiQ9WTV7.
KOiK16271.
OMAiDNLAMRN.
OrthoDBiEOG7Z69CK.
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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti114 – 1141G → R in AAD34209 (PubMed:10431247).Curated
Sequence conflicti146 – 1461N → S in BAC26379 (PubMed:16141072).Curated
Sequence conflicti195 – 1951A → T in AAD34209 (PubMed:10431247).Curated
Sequence conflicti228 – 2281R → M in AAD34209 (PubMed:10431247).Curated
Sequence conflicti320 – 3201R → G in BAC26379 (PubMed:16141072).Curated
Sequence conflicti362 – 3621R → S in BAB28712 (PubMed:16141072).Curated
Sequence conflicti470 – 4701E → K in AAD34209 (PubMed:10431247).Curated
Sequence conflicti486 – 4861R → K in AAD34209 (PubMed:10431247).Curated
Sequence conflicti505 – 5051L → F in AAD34209 (PubMed:10431247).Curated
Sequence conflicti557 – 5571N → D in AAD34209 (PubMed:10431247).Curated
Sequence conflicti568 – 5681Y → F in AAD34209 (PubMed:10431247).Curated

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_006527918.2.
XP_006527982.1. XM_006527919.2.
XP_006527983.1. XM_006527920.2.
XP_006527984.1. XM_006527921.2.
XP_011245853.1. XM_011247551.1.
XP_011245854.1. XM_011247552.1.
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_006527918.2.
XP_006527982.1. XM_006527919.2.
XP_006527983.1. XM_006527920.2.
XP_006527984.1. XM_006527921.2.
XP_011245853.1. XM_011247551.1.
XP_011245854.1. XM_011247552.1.
UniGeneiMm.427762.
Mm.490660.

3D structure databases

ProteinModelPortaliQ9WTV7.
SMRiQ9WTV7. Positions 546-587.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

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

PTM databases

iPTMnetiQ9WTV7.
PhosphoSiteiQ9WTV7.

Proteomic databases

EPDiQ9WTV7.
MaxQBiQ9WTV7.
PaxDbiQ9WTV7.
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.
OrthoDBiEOG7Z69CK.
PhylomeDBiQ9WTV7.
TreeFamiTF325756.

Enzyme and pathway databases

UniPathwayiUPA00143.

Miscellaneous databases

NextBioi297281.
PROiQ9WTV7.
SOURCEiSearch...

Gene expression databases

BgeeiQ9WTV7.
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...

Publicationsi

« Hide 'large scale' publications
  1. "RLIM inhibits functional activity of LIM homeodomain transcription factors via recruitment of the histone deacetylase complex."
    Bach I., Rodriguez-Esteban C., Carriere C., Bhushan A., Krones A., Rose D.W., Glass C.K., Andersen B., Izpisua-Belmonte J.-C., Rosenfeld M.G.
    Nat. Genet. 22:394-399(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION.
    Tissue: Pituitary.
  2. "The transcriptional landscape of the mammalian genome."
    Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
    , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
    Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: C57BL/6J.
    Tissue: Embryo and Head.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: C57BL/6J.
  4. Mural R.J., Adams M.D., Myers E.W., Smith H.O., Venter J.C.
    Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  5. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: FVB/N.
    Tissue: Salivary gland.
  6. "Ubiquitination-dependent cofactor exchange on LIM homeodomain transcription factors."
    Ostendorff H.P., Peirano R.I., Peters M.A., Schluter A., Bossenz M., Scheffner M., Bach I.
    Nature 416:99-103(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH LHX3; LDB1; LDB2 AND SIN3A.
  7. Cited for: INTERACTION WITH LIMK1.
  8. "RNF12 is an X-encoded dose-dependent activator of X chromosome inactivation."
    Jonkers I., Barakat T.S., Achame E.M., Monkhorst K., Kenter A., Rentmeester E., Grosveld F., Grootegoed J.A., Gribnau J.
    Cell 139:999-1011(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION, INDUCTION, DEVELOPMENTAL STAGE.
  9. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-163; SER-227 AND SER-229, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Brain, Brown adipose tissue, Heart, Kidney, Liver, Lung, Pancreas, Spleen and Testis.
  10. "RNF12 initiates X-chromosome inactivation by targeting REX1 for degradation."
    Gontan C., Achame E.M., Demmers J., Barakat T.S., Rentmeester E., van Ijcken W., Grootegoed J.A., Gribnau J.
    Nature 485:386-390(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.

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: May 11, 2016
This is version 125 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.