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O54965

- RNF13_MOUSE

UniProt

O54965 - RNF13_MOUSE

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Protein
E3 ubiquitin-protein ligase RNF13
Gene
Rnf13, Rzf
Organism
Mus musculus (Mouse)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

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; atypical
Add
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
Complete GO annotation...

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.2 Publications

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini35 – 182148Lumenal Reviewed prediction
Add
BLAST
Transmembranei183 – 20321Helical; Reviewed prediction
Add
BLAST
Topological domaini204 – 381178Cytoplasmic Reviewed prediction
Add
BLAST

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
Complete GO annotation...

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 – 3434 Reviewed prediction
Add
BLAST
Chaini35 – 381347E3 ubiquitin-protein ligase RNF13
PRO_0000056055Add
BLAST

Amino acid modifications

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

Post-translational modificationi

Auto-ubiquitinated.
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.

Family & Domainsi

Domains and Repeats

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

Domaini

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

Sequence similaritiesi

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

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei261 – 2688AYHCKCVD → GMSTHTVL in isoform 2.
VSP_005749
Alternative sequencei269 – 381113Missing in isoform 2.
VSP_005750Add
BLAST

Sequence conflict

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

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

« Hide 'large scale' publications
  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: September 3, 2014
This is version 100 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

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