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O54965

- RNF13_MOUSE

UniProt

O54965 - RNF13_MOUSE

Protein

E3 ubiquitin-protein ligase RNF13

Gene

Rnf13

Organism
Mus musculus (Mouse)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 101 (01 Oct 2014)
      Sequence version 2 (27 Jul 2011)
      Previous versions | rss
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    Functioni

    E3 ubiquitin-protein ligase that may play a role in controlling cell proliferation.1 Publication

    Pathwayi

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri240 – 28243RING-type; atypicalPROSITE-ProRule annotationAdd
    BLAST

    GO - Molecular functioni

    1. ligase activity Source: UniProtKB-KW
    2. ubiquitin-protein transferase activity Source: UniProtKB
    3. zinc ion binding Source: InterPro

    GO - Biological processi

    1. protein autoubiquitination Source: UniProtKB

    Keywords - Molecular functioni

    Ligase

    Keywords - Biological processi

    Ubl conjugation pathway

    Keywords - Ligandi

    Metal-binding, Zinc

    Enzyme and pathway databases

    UniPathwayiUPA00143.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    E3 ubiquitin-protein ligase RNF13 (EC:6.3.2.-)
    Alternative name(s):
    RING finger protein 13
    Gene namesi
    Name:Rnf13
    Synonyms:Rzf
    OrganismiMus musculus (Mouse)
    Taxonomic identifieri10090 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
    ProteomesiUP000000589: Chromosome 3

    Organism-specific databases

    MGIiMGI:1346341. Rnf13.

    Subcellular locationi

    Late endosome membrane; Single-pass membrane protein. Lysosome membrane. Cytoplasmcytosol. Nucleus inner membrane
    Note: The mature protein is subjected to extensive proteolysis that leads to the shedding of the ectodomain into the lumen of vesicles and the release of the C-terminal fragment into the cytosol. Not detected in early endosomes. Treatment of the cells with either PMA or ionomycin stabilizes the full-length protein which relocalizes to recycling endosomes and to the inner nuclear membrane.

    GO - Cellular componenti

    1. cytosol Source: UniProtKB-SubCell
    2. integral component of membrane Source: UniProtKB-KW
    3. late endosome membrane Source: UniProtKB
    4. lysosomal membrane Source: UniProtKB
    5. nuclear inner membrane Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Cytoplasm, Endosome, Lysosome, Membrane, Nucleus

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi266 – 2661C → A: Loss of E3 ligase activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Signal peptidei1 – 3434Sequence AnalysisAdd
    BLAST
    Chaini35 – 381347E3 ubiquitin-protein ligase RNF13PRO_0000056055Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Glycosylationi88 – 881N-linked (GlcNAc...)Sequence Analysis

    Post-translational modificationi

    Auto-ubiquitinated.1 Publication
    N-glycosylated and also modified with chondroitin sulfate.1 Publication

    Keywords - PTMi

    Glycoprotein, Ubl conjugation

    Proteomic databases

    PRIDEiO54965.

    PTM databases

    PhosphoSiteiO54965.

    Expressioni

    Tissue specificityi

    Expressed in the brain, heart, kidney, liver and spleen. Higher expression in adult tissues compared to the embryonic counterparts.1 Publication

    Gene expression databases

    BgeeiO54965.
    CleanExiMM_RNF13.
    GenevestigatoriO54965.

    Structurei

    3D structure databases

    ProteinModelPortaliO54965.
    SMRiO54965. Positions 240-286.
    ModBaseiSearch...
    MobiDBiSearch...

    Topological domain

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Topological domaini35 – 182148LumenalSequence AnalysisAdd
    BLAST
    Topological domaini204 – 381178CytoplasmicSequence AnalysisAdd
    BLAST

    Transmembrane

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Transmembranei183 – 20321HelicalSequence AnalysisAdd
    BLAST

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini64 – 16097PAAdd
    BLAST

    Domaini

    The RING-type zinc finger domain is required for E3 ligase activity.

    Sequence similaritiesi

    Contains 1 RING-type zinc finger.PROSITE-ProRule annotation

    Zinc finger

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri240 – 28243RING-type; atypicalPROSITE-ProRule annotationAdd
    BLAST

    Keywords - Domaini

    Signal, Transmembrane, Transmembrane helix, Zinc-finger

    Phylogenomic databases

    eggNOGiNOG260066.
    GeneTreeiENSGT00730000110795.
    HOGENOMiHOG000234362.
    HOVERGENiHBG063762.
    InParanoidiQ6PEA8.
    KOiK15692.
    OMAiMGSNDID.
    OrthoDBiEOG7NW68S.
    TreeFamiTF317486.

    Family and domain databases

    Gene3Di3.30.40.10. 1 hit.
    InterProiIPR003137. Protease-assoc_domain.
    IPR001841. Znf_RING.
    IPR013083. Znf_RING/FYVE/PHD.
    [Graphical view]
    PfamiPF02225. PA. 1 hit.
    PF13639. 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.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    This entry describes 2 isoformsi produced by alternative splicing. Align

    Isoform 1 (identifier: O54965-1) [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

    MLLSIGMLML SATQVYTILT VQLFAFLNLL PVEADILAYN FENASQTFED    50
    LPARFGYRLP AEGLKGFLIN SKPENACEPI VPPPLKDNSS GTFIVLIRRL 100
    DCNFDIKVLN AQRAGYKAAI VHNVDSDDLI SMGSNDIDTL KKIDIPSVFI 150
    GESSANSLKD EFTYEKGGHI ILVPELSLPL EYYLIPFLII VGICLILIVI 200
    FMITKFVQDR HRNRRNRLRK DQLKKLPVHK FKKGDEYDVC AICLEEYEDG 250
    DKLRILPCSH AYHCKCVDPW LTKTKKTCPV CKQKVVPSQG DSDSDTDSSQ 300
    EENQVSEHTP LLPPSASART QSFGSLSESH SHHNMTESSD YEDDDNEETD 350
    SSDADNEITD HSVVVQLQPN GEQDYNIANT V 381
    Length:381
    Mass (Da):42,732
    Last modified:July 27, 2011 - v2
    Checksum:i1E0EF4801A2C6FE8
    GO
    Isoform 2 (identifier: O54965-2) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         261-268: AYHCKCVD → GMSTHTVL
         269-381: Missing.

    Show »
    Length:268
    Mass (Da):30,249
    Checksum:iEB09D3ECF7660546
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti362 – 3621S → I in AAC03770. 1 PublicationCurated

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei261 – 2688AYHCKCVD → GMSTHTVL in isoform 2. 1 PublicationVSP_005749
    Alternative sequencei269 – 381113Missing in isoform 2. 1 PublicationVSP_005750Add
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF037205 mRNA. Translation: AAC03770.1.
    AF037206 mRNA. Translation: AAC03771.1.
    AK158046 mRNA. Translation: BAE34334.1.
    CH466530 Genomic DNA. Translation: EDL35322.1.
    CH466530 Genomic DNA. Translation: EDL35326.1.
    BC058182 mRNA. Translation: AAH58182.1.
    CCDSiCCDS50913.1. [O54965-1]
    RefSeqiNP_001106884.1. NM_001113413.1. [O54965-1]
    NP_036013.1. NM_011883.3. [O54965-2]
    XP_006501520.1. XM_006501457.1. [O54965-1]
    UniGeneiMm.274360.

    Genome annotation databases

    EnsembliENSMUST00000041826; ENSMUSP00000049331; ENSMUSG00000036503. [O54965-1]
    GeneIDi24017.
    KEGGimmu:24017.
    UCSCiuc008phj.2. mouse. [O54965-1]

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF037205 mRNA. Translation: AAC03770.1 .
    AF037206 mRNA. Translation: AAC03771.1 .
    AK158046 mRNA. Translation: BAE34334.1 .
    CH466530 Genomic DNA. Translation: EDL35322.1 .
    CH466530 Genomic DNA. Translation: EDL35326.1 .
    BC058182 mRNA. Translation: AAH58182.1 .
    CCDSi CCDS50913.1. [O54965-1 ]
    RefSeqi NP_001106884.1. NM_001113413.1. [O54965-1 ]
    NP_036013.1. NM_011883.3. [O54965-2 ]
    XP_006501520.1. XM_006501457.1. [O54965-1 ]
    UniGenei Mm.274360.

    3D structure databases

    ProteinModelPortali O54965.
    SMRi O54965. Positions 240-286.
    ModBasei Search...
    MobiDBi Search...

    PTM databases

    PhosphoSitei O54965.

    Proteomic databases

    PRIDEi O54965.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENSMUST00000041826 ; ENSMUSP00000049331 ; ENSMUSG00000036503 . [O54965-1 ]
    GeneIDi 24017.
    KEGGi mmu:24017.
    UCSCi uc008phj.2. mouse. [O54965-1 ]

    Organism-specific databases

    CTDi 11342.
    MGIi MGI:1346341. Rnf13.

    Phylogenomic databases

    eggNOGi NOG260066.
    GeneTreei ENSGT00730000110795.
    HOGENOMi HOG000234362.
    HOVERGENi HBG063762.
    InParanoidi Q6PEA8.
    KOi K15692.
    OMAi MGSNDID.
    OrthoDBi EOG7NW68S.
    TreeFami TF317486.

    Enzyme and pathway databases

    UniPathwayi UPA00143 .

    Miscellaneous databases

    NextBioi 303955.
    PROi O54965.
    SOURCEi Search...

    Gene expression databases

    Bgeei O54965.
    CleanExi MM_RNF13.
    Genevestigatori O54965.

    Family and domain databases

    Gene3Di 3.30.40.10. 1 hit.
    InterProi IPR003137. Protease-assoc_domain.
    IPR001841. Znf_RING.
    IPR013083. Znf_RING/FYVE/PHD.
    [Graphical view ]
    Pfami PF02225. PA. 1 hit.
    PF13639. zf-RING_2. 1 hit.
    [Graphical view ]
    SMARTi SM00184. RING. 1 hit.
    [Graphical view ]
    PROSITEi PS50089. ZF_RING_2. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "The gene for a RING zinc finger protein is expressed in the inner chick ear after noise exposure."
      Lomax M.I., Warner S.J., Bersirli C.G., Gong T.-W.L.
      Prim. Sens. Neuron 2:305-316(1998)
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 2).
    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: Inner ear.
    3. Mural R.J., Adams M.D., Myers E.W., Smith H.O., Venter J.C.
      Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    4. "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: Mammary tumor.
    5. "The PA-TM-RING protein RING finger protein 13 is an endosomal integral membrane E3 ubiquitin ligase whose RING finger domain is released to the cytoplasm by proteolysis."
      Bocock J.P., Carmicle S., Chhotani S., Ruffolo M.R., Chu H., Erickson A.H.
      FEBS J. 276:1860-1877(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, SUBCELLULAR LOCATION, TOPOGRAPHY, TISSUE SPECIFICITY, AUTOUBIQUITINATION, GLYCOSYLATION, MUTAGENESIS OF CYS-266.
    6. "Nuclear targeting of an endosomal E3 ubiquitin ligase."
      Bocock J.P., Carmicle S., Madamba E., Erickson A.H.
      Traffic 11:756-766(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBCELLULAR LOCATION.

    Entry informationi

    Entry nameiRNF13_MOUSE
    AccessioniPrimary (citable) accession number: O54965
    Secondary accession number(s): O54966, Q6PEA8
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: June 6, 2002
    Last sequence update: July 27, 2011
    Last modified: October 1, 2014
    This is version 101 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

    External Data

    Dasty 3