RUFY4_MOUSE
ID RUFY4_MOUSE Reviewed; 563 AA.
AC Q3TYX8; B2RX43; D3YY30;
DT 17-APR-2007, integrated into UniProtKB/Swiss-Prot.
DT 27-JUL-2011, sequence version 3.
DT 03-AUG-2022, entry version 104.
DE RecName: Full=RUN and FYVE domain-containing protein 4;
GN Name=Rufy4;
OS Mus musculus (Mouse).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Mus; Mus.
OX NCBI_TaxID=10090;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RC STRAIN=C57BL/6J; TISSUE=Inner ear;
RX PubMed=16141072; DOI=10.1126/science.1112014;
RA Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N.,
RA Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K.,
RA Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.,
RA Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R.,
RA Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T.,
RA Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A.,
RA Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B.,
RA Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M.,
RA Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S.,
RA Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E.,
RA Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D.,
RA Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M.,
RA Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H.,
RA Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V.,
RA Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S.,
RA Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H.,
RA Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N.,
RA Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F.,
RA Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G.,
RA Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z.,
RA Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C.,
RA Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y.,
RA Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S.,
RA Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K.,
RA Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R.,
RA van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H.,
RA Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M.,
RA Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C.,
RA Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S.,
RA Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K.,
RA Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M.,
RA Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C.,
RA Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A.,
RA Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.;
RT "The transcriptional landscape of the mammalian genome.";
RL Science 309:1559-1563(2005).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=C57BL/6J;
RX PubMed=19468303; DOI=10.1371/journal.pbio.1000112;
RA Church D.M., Goodstadt L., Hillier L.W., Zody M.C., Goldstein S., She X.,
RA Bult C.J., Agarwala R., Cherry J.L., DiCuccio M., Hlavina W., Kapustin Y.,
RA Meric P., Maglott D., Birtle Z., Marques A.C., Graves T., Zhou S.,
RA Teague B., Potamousis K., Churas C., Place M., Herschleb J., Runnheim R.,
RA Forrest D., Amos-Landgraf J., Schwartz D.C., Cheng Z., Lindblad-Toh K.,
RA Eichler E.E., Ponting C.P.;
RT "Lineage-specific biology revealed by a finished genome assembly of the
RT mouse.";
RL PLoS Biol. 7:E1000112-E1000112(2009).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC TISSUE=Brain;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [4]
RP INDUCTION.
RX PubMed=26416964; DOI=10.1083/jcb.201501059;
RA Terawaki S., Camosseto V., Prete F., Wenger T., Papadopoulos A.,
RA Rondeau C., Combes A., Rodriguez Rodrigues C., Vu Manh T.P., Fallet M.,
RA English L., Santamaria R., Soares A.R., Weil T., Hammad H., Desjardins M.,
RA Gorvel J.P., Santos M.A., Gatti E., Pierre P.;
RT "RUN and FYVE domain-containing protein 4 enhances autophagy and lysosome
RT tethering in response to Interleukin-4.";
RL J. Cell Biol. 210:1133-1152(2015).
CC -!- FUNCTION: Positively regulates macroautophagy in primary dendritic
CC cells. Increases autophagic flux, probably by stimulating both
CC autophagosome formation and facilitating tethering with lysosomes.
CC Binds to phosphatidylinositol 3-phosphate (PtdIns3P) through its FYVE-
CC type zinc finger. {ECO:0000250|UniProtKB:Q6ZNE9}.
CC -!- SUBUNIT: Interacts (via RUN domain) with RAB7A.
CC {ECO:0000250|UniProtKB:Q6ZNE9}.
CC -!- SUBCELLULAR LOCATION: Cytoplasmic vesicle, autophagosome
CC {ECO:0000250|UniProtKB:Q6ZNE9}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q3TYX8-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q3TYX8-2; Sequence=VSP_035817;
CC -!- INDUCTION: By IL4/interleukin-4 in dendritic cells.
CC {ECO:0000269|PubMed:26416964}.
CC -!- DOMAIN: The RUN domain and the FYVE-type zinc finger are essential for
CC its function in the positive regulation of macroautophagy.
CC {ECO:0000250|UniProtKB:Q6ZNE9}.
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DR EMBL; AK158260; BAE34432.1; -; mRNA.
DR EMBL; AC117757; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; BC150907; AAI50908.1; -; mRNA.
DR EMBL; BC150910; AAI50911.1; -; mRNA.
DR CCDS; CCDS15039.1; -. [Q3TYX8-2]
DR CCDS; CCDS48289.1; -. [Q3TYX8-1]
DR RefSeq; NP_001029232.2; NM_001034060.3. [Q3TYX8-2]
DR RefSeq; NP_001164112.1; NM_001170641.1. [Q3TYX8-1]
DR AlphaFoldDB; Q3TYX8; -.
DR SMR; Q3TYX8; -.
DR STRING; 10090.ENSMUSP00000115873; -.
DR iPTMnet; Q3TYX8; -.
DR PhosphoSitePlus; Q3TYX8; -.
DR EPD; Q3TYX8; -.
DR PaxDb; Q3TYX8; -.
DR PRIDE; Q3TYX8; -.
DR ProteomicsDB; 260956; -. [Q3TYX8-1]
DR ProteomicsDB; 260957; -. [Q3TYX8-2]
DR Antibodypedia; 34256; 60 antibodies from 16 providers.
DR Ensembl; ENSMUST00000080167; ENSMUSP00000079062; ENSMUSG00000061815. [Q3TYX8-2]
DR Ensembl; ENSMUST00000127134; ENSMUSP00000115873; ENSMUSG00000061815. [Q3TYX8-1]
DR GeneID; 435626; -.
DR KEGG; mmu:435626; -.
DR UCSC; uc007blk.2; mouse. [Q3TYX8-1]
DR CTD; 285180; -.
DR MGI; MGI:3588214; Rufy4.
DR VEuPathDB; HostDB:ENSMUSG00000061815; -.
DR eggNOG; KOG1729; Eukaryota.
DR GeneTree; ENSGT00940000154044; -.
DR HOGENOM; CLU_037214_0_0_1; -.
DR InParanoid; Q3TYX8; -.
DR OMA; KRERRCP; -.
DR OrthoDB; 962969at2759; -.
DR PhylomeDB; Q3TYX8; -.
DR TreeFam; TF341788; -.
DR BioGRID-ORCS; 435626; 3 hits in 73 CRISPR screens.
DR PRO; PR:Q3TYX8; -.
DR Proteomes; UP000000589; Chromosome 1.
DR RNAct; Q3TYX8; protein.
DR Bgee; ENSMUSG00000061815; Expressed in granulocyte and 29 other tissues.
DR GO; GO:0005776; C:autophagosome; ISS:UniProtKB.
DR GO; GO:0031410; C:cytoplasmic vesicle; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0032266; F:phosphatidylinositol-3-phosphate binding; ISS:UniProtKB.
DR GO; GO:0000045; P:autophagosome assembly; ISS:UniProtKB.
DR GO; GO:0071353; P:cellular response to interleukin-4; IDA:UniProtKB.
DR GO; GO:0016239; P:positive regulation of macroautophagy; ISS:UniProtKB.
DR Gene3D; 1.20.58.900; -; 1.
DR Gene3D; 3.30.40.10; -; 1.
DR InterPro; IPR042939; RUFY4.
DR InterPro; IPR004012; Run_dom.
DR InterPro; IPR037213; Run_dom_sf.
DR InterPro; IPR017455; Znf_FYVE-rel.
DR InterPro; IPR011011; Znf_FYVE_PHD.
DR InterPro; IPR013083; Znf_RING/FYVE/PHD.
DR PANTHER; PTHR47732; PTHR47732; 1.
DR Pfam; PF02759; RUN; 1.
DR SMART; SM00593; RUN; 1.
DR SUPFAM; SSF140741; SSF140741; 1.
DR SUPFAM; SSF57903; SSF57903; 1.
DR PROSITE; PS50826; RUN; 1.
DR PROSITE; PS50178; ZF_FYVE; 1.
PE 2: Evidence at transcript level;
KW Alternative splicing; Autophagy; Cytoplasmic vesicle; Metal-binding;
KW Reference proteome; Zinc; Zinc-finger.
FT CHAIN 1..563
FT /note="RUN and FYVE domain-containing protein 4"
FT /id="PRO_0000284672"
FT DOMAIN 33..166
FT /note="RUN"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00178"
FT ZN_FING 428..558
FT /note="FYVE-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00091"
FT REGION 176..327
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 375..397
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 192..207
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 267..281
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 285..300
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 513
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00091"
FT BINDING 516
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00091"
FT BINDING 529
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00091"
FT BINDING 532
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00091"
FT BINDING 537
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00091"
FT BINDING 540
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00091"
FT BINDING 551
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00091"
FT BINDING 554
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00091"
FT VAR_SEQ 1..84
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:16141072"
FT /id="VSP_035817"
FT CONFLICT 34
FT /note="E -> D (in Ref. 3; AAI50908/AAI50911)"
FT /evidence="ECO:0000305"
FT CONFLICT 141
FT /note="A -> P (in Ref. 3; AAI50908/AAI50911/BAE34432)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 563 AA; 64036 MW; 2D2F11ACE0F80F78 CRC64;
MANNGTILKI SRSLKNAVSA ILQGYGDGQE PVTETSAELH RLCGCLELLL QFDQKEQRSF
LGARKDYWDF LFTALRRHRG YTEQMSFICS QDKLKTSLGK GRAFIRLCLA RGQLAESMQL
CLLNPQLTRE WYGPRSPLLC AELQEDILDS LYALNGVAFN LDLQRPDLDE AWPMFSESRC
SSPSRTGKRR PGKPKGFPEE VRCSRGEQLQ EPDTGGTSCL QDATREDRTP DLCKPLQPSH
LPTFLEEKRE DSRSLSCPQS TWETEREGFQ LDQKDGGPKP RKFLENSTAS IQQQRSRAKD
VKMQLTGRKV EGKGSLSGTE DQRTTEGIQK RAADWDLGQG LMAPGLQGRE DAELGYRCEW
NQPDVLRQSW VLGTKKSSPT EKPQEWTGVT SGTMQEDGSE VPLQQEVIKD PGYGLQLAKE
QAQCQEQLRA QEAELQALQE QLSRCQKERA LLQVKLEQKQ QEAERRDAMY QTELEGQRDL
VQAMKRRVLE LIHEKDLQWQ RLQQLSTVAP GHCIGCNKVF RRLSRRYPCR LCGGLVCHAC
SVDYKKRERC CPTCAQQEEI QDT
