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E3 ubiquitin-protein ligase RLIM (EC 2.3.2.27) (LIM domain-interacting RING finger protein) (RING finger LIM domain-binding protein) (R-LIM) (RING finger protein 12) (RING-type E3 ubiquitin transferase RLIM)

 RNF12_MOUSE             Reviewed;         600 AA.
Q9WTV7; Q8CE02; Q91X19; Q9CYY2;
21-FEB-2001, integrated into UniProtKB/Swiss-Prot.
22-SEP-2009, sequence version 2.
12-SEP-2018, entry version 142.
RecName: Full=E3 ubiquitin-protein ligase RLIM;
EC=2.3.2.27;
AltName: Full=LIM domain-interacting RING finger protein;
AltName: Full=RING finger LIM domain-binding protein;
Short=R-LIM;
AltName: Full=RING finger protein 12;
AltName: Full=RING-type E3 ubiquitin transferase RLIM {ECO:0000305};
Name=Rlim; Synonyms=Rnf12;
Mus musculus (Mouse).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
Muroidea; Muridae; Murinae; Mus; Mus.
NCBI_TaxID=10090;
[1]
NUCLEOTIDE SEQUENCE [MRNA], AND FUNCTION.
TISSUE=Pituitary;
PubMed=10431247; DOI=10.1038/11970;
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.;
"RLIM inhibits functional activity of LIM homeodomain transcription
factors via recruitment of the histone deacetylase complex.";
Nat. Genet. 22:394-399(1999).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
STRAIN=C57BL/6J; TISSUE=Embryo, and Head;
PubMed=16141072; DOI=10.1126/science.1112014;
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.;
"The transcriptional landscape of the mammalian genome.";
Science 309:1559-1563(2005).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=C57BL/6J;
PubMed=19468303; DOI=10.1371/journal.pbio.1000112;
Church D.M., Goodstadt L., Hillier L.W., Zody M.C., Goldstein S.,
She X., Bult C.J., Agarwala R., Cherry J.L., DiCuccio M., Hlavina W.,
Kapustin Y., Meric P., Maglott D., Birtle Z., Marques A.C., Graves T.,
Zhou S., Teague B., Potamousis K., Churas C., Place M., Herschleb J.,
Runnheim R., Forrest D., Amos-Landgraf J., Schwartz D.C., Cheng Z.,
Lindblad-Toh K., Eichler E.E., Ponting C.P.;
"Lineage-specific biology revealed by a finished genome assembly of
the mouse.";
PLoS Biol. 7:E1000112-E1000112(2009).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Mural R.J., Adams M.D., Myers E.W., Smith H.O., Venter J.C.;
Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases.
[5]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
STRAIN=FVB/N; TISSUE=Salivary gland;
PubMed=15489334; DOI=10.1101/gr.2596504;
The MGC Project Team;
"The status, quality, and expansion of the NIH full-length cDNA
project: the Mammalian Gene Collection (MGC).";
Genome Res. 14:2121-2127(2004).
[6]
FUNCTION, AND INTERACTION WITH LHX3; LDB1; LDB2 AND SIN3A.
PubMed=11882901; DOI=10.1038/416099a;
Ostendorff H.P., Peirano R.I., Peters M.A., Schluter A., Bossenz M.,
Scheffner M., Bach I.;
"Ubiquitination-dependent cofactor exchange on LIM homeodomain
transcription factors.";
Nature 416:99-103(2002).
[7]
INTERACTION WITH LIMK1.
PubMed=16204183; DOI=10.1101/gad.1340605;
Tursun B., Schlueter A., Peters M.A., Viehweger B., Ostendorff H.P.,
Soosairajah J., Drung A., Bossenz M., Johnsen S.A., Schweizer M.,
Bernard O., Bach I.;
"The ubiquitin ligase Rnf6 regulates local LIM kinase 1 levels in
axonal growth cones.";
Genes Dev. 19:2307-2319(2005).
[8]
FUNCTION, SUBCELLULAR LOCATION, INDUCTION, AND DEVELOPMENTAL STAGE.
PubMed=19945382; DOI=10.1016/j.cell.2009.10.034;
Jonkers I., Barakat T.S., Achame E.M., Monkhorst K., Kenter A.,
Rentmeester E., Grosveld F., Grootegoed J.A., Gribnau J.;
"RNF12 is an X-encoded dose-dependent activator of X chromosome
inactivation.";
Cell 139:999-1011(2009).
[9]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-163; SER-227 AND
SER-229, AND IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE
ANALYSIS].
TISSUE=Brain, Brown adipose tissue, Heart, Kidney, Liver, Lung,
Pancreas, Spleen, and Testis;
PubMed=21183079; DOI=10.1016/j.cell.2010.12.001;
Huttlin E.L., Jedrychowski M.P., Elias J.E., Goswami T., Rad R.,
Beausoleil S.A., Villen J., Haas W., Sowa M.E., Gygi S.P.;
"A tissue-specific atlas of mouse protein phosphorylation and
expression.";
Cell 143:1174-1189(2010).
[10]
FUNCTION.
PubMed=22596162; DOI=10.1038/nature11070;
Gontan C., Achame E.M., Demmers J., Barakat T.S., Rentmeester E.,
van Ijcken W., Grootegoed J.A., Gribnau J.;
"RNF12 initiates X-chromosome inactivation by targeting REX1 for
degradation.";
Nature 485:386-390(2012).
-!- FUNCTION: 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. {ECO:0000269|PubMed:10431247,
ECO:0000269|PubMed:11882901, ECO:0000269|PubMed:19945382,
ECO:0000269|PubMed:22596162}.
-!- CATALYTIC ACTIVITY: S-ubiquitinyl-[E2 ubiquitin-conjugating
enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-
conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor
protein]-L-lysine.
-!- PATHWAY: Protein modification; protein ubiquitination.
-!- SUBUNIT: 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. {ECO:0000250, ECO:0000269|PubMed:11882901,
ECO:0000269|PubMed:16204183}.
-!- INTERACTION:
O55203:Ldb2; NbExp=2; IntAct=EBI-15657872, EBI-15657830;
P22227:Zfp42; NbExp=8; IntAct=EBI-15657872, EBI-2313372;
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:19945382}.
-!- DEVELOPMENTAL STAGE: Ubiquitously expressed in early development.
Expressed in the time window of embryonic stem (ES) cell
differentiation. {ECO:0000269|PubMed:19945382}.
-!- INDUCTION: Expressed at higher level in female compared to males
cells (at protein level). {ECO:0000269|PubMed:19945382}.
-!- SIMILARITY: Belongs to the RNF12 family. {ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; AF069992; AAD34209.1; -; mRNA.
EMBL; AK013207; BAB28712.1; -; mRNA.
EMBL; AK029295; BAC26379.1; -; mRNA.
EMBL; AL805911; CAM26768.1; -; Genomic_DNA.
EMBL; CH466564; EDL14089.1; -; Genomic_DNA.
EMBL; CH466564; EDL14090.1; -; Genomic_DNA.
EMBL; BC012960; AAH12960.1; -; mRNA.
CCDS; CCDS30331.1; -.
RefSeq; NP_035406.3; NM_011276.3.
RefSeq; XP_006527981.1; XM_006527918.3.
RefSeq; XP_006527982.1; XM_006527919.3.
RefSeq; XP_006527983.1; XM_006527920.3.
RefSeq; XP_006527984.1; XM_006527921.3.
RefSeq; XP_011245853.1; XM_011247551.2.
RefSeq; XP_011245854.1; XM_011247552.2.
UniGene; Mm.427762; -.
UniGene; Mm.490660; -.
ProteinModelPortal; Q9WTV7; -.
SMR; Q9WTV7; -.
BioGrid; 202918; 4.
DIP; DIP-46445N; -.
IntAct; Q9WTV7; 10.
STRING; 10090.ENSMUSP00000070662; -.
iPTMnet; Q9WTV7; -.
PhosphoSitePlus; Q9WTV7; -.
EPD; Q9WTV7; -.
MaxQB; Q9WTV7; -.
PaxDb; Q9WTV7; -.
PeptideAtlas; Q9WTV7; -.
PRIDE; Q9WTV7; -.
Ensembl; ENSMUST00000070705; ENSMUSP00000070662; ENSMUSG00000056537.
Ensembl; ENSMUST00000121153; ENSMUSP00000112820; ENSMUSG00000056537.
GeneID; 19820; -.
KEGG; mmu:19820; -.
UCSC; uc009tzz.1; mouse.
CTD; 51132; -.
MGI; MGI:1342291; Rlim.
eggNOG; KOG0800; Eukaryota.
eggNOG; ENOG41121N2; LUCA.
GeneTree; ENSGT00730000110459; -.
HOGENOM; HOG000273881; -.
InParanoid; Q9WTV7; -.
KO; K16271; -.
OMA; MRNFGES; -.
OrthoDB; EOG091G0B6K; -.
PhylomeDB; Q9WTV7; -.
TreeFam; TF325756; -.
Reactome; R-MMU-983168; Antigen processing: Ubiquitination & Proteasome degradation.
UniPathway; UPA00143; -.
PRO; PR:Q9WTV7; -.
Proteomes; UP000000589; Chromosome X.
Bgee; ENSMUSG00000056537; Expressed in 305 organ(s), highest expression level in female gonad.
CleanEx; MM_RNF12; -.
Genevisible; Q9WTV7; MM.
GO; GO:0005829; C:cytosol; ISO:MGI.
GO; GO:0005654; C:nucleoplasm; ISO:MGI.
GO; GO:0005634; C:nucleus; IDA:UniProtKB.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0061630; F:ubiquitin protein ligase activity; IDA:MGI.
GO; GO:0004842; F:ubiquitin-protein transferase activity; IDA:UniProtKB.
GO; GO:0043433; P:negative regulation of DNA-binding transcription factor activity; IGI:MGI.
GO; GO:0000122; P:negative regulation of transcription by RNA polymerase II; IGI:MGI.
GO; GO:0043161; P:proteasome-mediated ubiquitin-dependent protein catabolic process; IBA:GO_Central.
GO; GO:0016567; P:protein ubiquitination; IDA:UniProtKB.
GO; GO:0060816; P:random inactivation of X chromosome; IDA:UniProtKB.
GO; GO:1900095; P:regulation of dosage compensation by inactivation of X chromosome; IMP:MGI.
GO; GO:0006351; P:transcription, DNA-templated; IEA:UniProtKB-KW.
GO; GO:0006511; P:ubiquitin-dependent protein catabolic process; IDA:UniProtKB.
Gene3D; 3.30.40.10; -; 1.
InterPro; IPR001841; Znf_RING.
InterPro; IPR013083; Znf_RING/FYVE/PHD.
Pfam; PF13639; zf-RING_2; 1.
SMART; SM00184; RING; 1.
PROSITE; PS50089; ZF_RING_2; 1.
1: Evidence at protein level;
Acetylation; Complete proteome; Metal-binding; Nucleus;
Phosphoprotein; Reference proteome; Transcription;
Transcription regulation; Transferase; Ubl conjugation pathway; Zinc;
Zinc-finger.
CHAIN 1 600 E3 ubiquitin-protein ligase RLIM.
/FTId=PRO_0000056053.
ZN_FING 546 587 RING-type. {ECO:0000255|PROSITE-
ProRule:PRU00175}.
MOTIF 597 600 PDZ-binding. {ECO:0000255}.
COMPBIAS 415 484 Ser-rich.
COMPBIAS 447 461 Poly-Ser.
MOD_RES 1 1 N-acetylmethionine.
{ECO:0000250|UniProtKB:Q9NVW2}.
MOD_RES 163 163 Phosphoserine.
{ECO:0000244|PubMed:21183079}.
MOD_RES 194 194 Phosphoserine.
{ECO:0000250|UniProtKB:Q9NVW2}.
MOD_RES 227 227 Phosphoserine.
{ECO:0000244|PubMed:21183079}.
MOD_RES 229 229 Phosphoserine.
{ECO:0000244|PubMed:21183079}.
MOD_RES 269 269 Phosphoserine.
{ECO:0000250|UniProtKB:Q9NVW2}.
CONFLICT 114 114 G -> R (in Ref. 1; AAD34209).
{ECO:0000305}.
CONFLICT 146 146 N -> S (in Ref. 2; BAC26379).
{ECO:0000305}.
CONFLICT 195 195 A -> T (in Ref. 1; AAD34209).
{ECO:0000305}.
CONFLICT 228 228 R -> M (in Ref. 1; AAD34209).
{ECO:0000305}.
CONFLICT 320 320 R -> G (in Ref. 2; BAC26379).
{ECO:0000305}.
CONFLICT 362 362 R -> S (in Ref. 2; BAB28712).
{ECO:0000305}.
CONFLICT 470 470 E -> K (in Ref. 1; AAD34209).
{ECO:0000305}.
CONFLICT 486 486 R -> K (in Ref. 1; AAD34209).
{ECO:0000305}.
CONFLICT 505 505 L -> F (in Ref. 1; AAD34209).
{ECO:0000305}.
CONFLICT 557 557 N -> D (in Ref. 1; AAD34209).
{ECO:0000305}.
CONFLICT 568 568 Y -> F (in Ref. 1; AAD34209).
{ECO:0000305}.
SEQUENCE 600 AA; 66377 MW; 6BFB9958502FDAED CRC64;
MENSDSNDKG SDQSAAQRRS QMDRLDREEA FYQFVNNLSE EDYRLMRDNN LLGTPGESTE
EELLRRLQQI KEGPPPQSPD ENRAGESSDD VTNSDSIIDW LNSVRQTGNT TRSGQRGNQS
WRAVSRTNPN SGDFRFSLEI NVNRNNGSQT SENESEPSTR RLSVENMESS SQRQMENSAS
ESASARPSRA ERNSAEAVTE VPTTRAQRRA RSRSPEHRRT RARAERSRSP LQPTSEIPRR
APTLEQSSEN EPEGSSRTRH HVTLRQQISG PELLGRGLFA ASGSRNPSQG TSSSDTGSNS
ESSGSGQRPP TIVLDLQVRR VRPGEYRQRD SIASRTRSRS QAPNNTVTYE SERGGFRRTF
SRSERAGVRT YVSTIRIPIR RILNTGLSET TSVAIQTMLR QIMTGFGELS YFMYSDSDSE
PSASVSSRNV ERVESRNGRG SSGGGNSSGS SSSSSPSPSS SGESSESSSE MFEGSSEGGS
SGPSRRDGRH RAPVTFDESG SLPFLSLAQF FLLNEDDEDQ PRGLTKEQID NLAMRSFGEN
DALKTCSVCI TEYTEGNKLR KLPCSHEYHV HCIDRWLSEN STCPICRRAV LSSGNRESVV


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