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Q9JK11

- RTN4_RAT

UniProt

Q9JK11 - RTN4_RAT

Protein

Reticulon-4

Gene

Rtn4

Organism
Rattus norvegicus (Rat)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 104 (01 Oct 2014)
      Sequence version 1 (01 Oct 2000)
      Previous versions | rss
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    Functioni

    Developmental neurite growth regulatory factor with a role as a negative regulator of axon-axon adhesion and growth, and as a facilitator of neurite branching. Regulates neurite fasciculation, branching and extension in the developing nervous system. Involved in down-regulation of growth, stabilization of wiring and restriction of plasticity in the adult CNS. Regulates the radial migration of cortical neurons via an RTN4R-LINGO1 containing receptor complex. Isoform 2 and isoform 3 inhibit BACE1 activity and amyloid precursor protein processing.3 Publications

    GO - Molecular functioni

    1. protein binding Source: IntAct
    2. protein complex binding Source: RGD

    GO - Biological processi

    1. aging Source: RGD
    2. axonal fasciculation Source: UniProtKB
    3. cerebral cortex radial glia guided migration Source: UniProtKB
    4. negative regulation of axon extension Source: UniProtKB
    5. negative regulation of axonogenesis Source: RGD
    6. negative regulation of neuron differentiation Source: RGD
    7. negative regulation of neuron projection development Source: RGD
    8. negative regulation of neuron projection regeneration Source: RGD
    9. olfactory nerve development Source: RGD
    10. oligodendrocyte differentiation Source: RGD
    11. positive regulation of dopamine secretion Source: RGD
    12. positive regulation of glial cell differentiation Source: RGD
    13. regulation of axon regeneration Source: RGD
    14. regulation of branching morphogenesis of a nerve Source: UniProtKB
    15. regulation of sensory perception of pain Source: RGD
    16. response to activity Source: RGD

    Keywords - Biological processi

    Neurogenesis

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Reticulon-4
    Alternative name(s):
    Foocen
    Glut4 vesicle 20 kDa protein
    Neurite outgrowth inhibitor
    Short name:
    Nogo protein
    Gene namesi
    Name:Rtn4
    Synonyms:Nogo
    OrganismiRattus norvegicus (Rat)
    Taxonomic identifieri10116 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
    ProteomesiUP000002494: Chromosome 14

    Organism-specific databases

    RGDi620989. Rtn4.

    Subcellular locationi

    Endoplasmic reticulum membrane By similarity; Multi-pass membrane protein By similarity
    Note: Anchored to the membrane of the endoplasmic reticulum through 2 putative transmembrane domains.By similarity

    GO - Cellular componenti

    1. cytoplasm Source: RGD
    2. endoplasmic reticulum Source: RGD
    3. integral component of endoplasmic reticulum membrane Source: UniProtKB
    4. integral component of membrane Source: RGD
    5. intracellular Source: UniProtKB
    6. myelin sheath Source: RGD
    7. neuronal cell body Source: RGD
    8. neuron projection Source: RGD
    9. nuclear envelope Source: UniProtKB
    10. plasma membrane Source: RGD
    11. protein complex Source: RGD

    Keywords - Cellular componenti

    Endoplasmic reticulum, Membrane

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 11631163Reticulon-4PRO_0000168167Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei1 – 11N-acetylmethionineBy similarity
    Modified residuei7 – 71PhosphoserineBy similarity
    Modified residuei16 – 161PhosphoserineBy similarity
    Modified residuei107 – 1071Phosphoserine1 Publication
    Modified residuei149 – 1491PhosphoserineBy similarity
    Modified residuei169 – 1691PhosphoserineBy similarity
    Modified residuei343 – 3431PhosphoserineBy similarity
    Modified residuei488 – 4881PhosphoserineBy similarity
    Modified residuei689 – 6891PhosphoserineBy similarity
    Modified residuei1075 – 10751N6-acetyllysineBy similarity

    Keywords - PTMi

    Acetylation, Phosphoprotein

    Proteomic databases

    PaxDbiQ9JK11.
    PRIDEiQ9JK11.

    PTM databases

    PhosphoSiteiQ9JK11.

    Expressioni

    Tissue specificityi

    Isoforms 1, 2 and 3 are present in optic nerve, spinal cord and cerebral cortex. Isoforms 1 and 2 are present in dorsal root ganglion, sciatic nerve and PC12 cells after longer exposure. Isoforms 2 and 3 are detected in kidney, cartilage, skin, lung and spleen. Isoform 3 is expressed at high level in skeletal muscle. In adult animals isoform 1 is expressed mainly in the nervous system.

    Gene expression databases

    GenevestigatoriQ9JK11.

    Interactioni

    Subunit structurei

    Binds to RTN4R. Interacts with Bcl-xl and Bcl-2. Isoform 2 binds to NGBR and RTN3. Isoform 2 and isoform 3 interact ith BACE1 and BACE2 By similarity. Interacts with RTN4IP1 By similarity. Interacts in trans with CNTNAP1. Interacts with ATL1.By similarity2 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    ATL1Q8WXF72EBI-920002,EBI-2410266From a different organism.
    Atl1Q6PST46EBI-919989,EBI-2410213

    Protein-protein interaction databases

    BioGridi249825. 2 interactions.
    DIPiDIP-37179N.
    IntActiQ9JK11. 3 interactions.
    MINTiMINT-4998315.
    STRINGi10116.ENSRNOP00000006443.

    Structurei

    3D structure databases

    ProteinModelPortaliQ9JK11.
    SMRiQ9JK11. Positions 1026-1085.
    ModBaseiSearch...
    MobiDBiSearch...

    Topological domain

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Topological domaini1 – 989989CytoplasmicSequence AnalysisAdd
    BLAST
    Topological domaini1011 – 110494LumenalSequence AnalysisAdd
    BLAST
    Topological domaini1126 – 116338CytoplasmicSequence AnalysisAdd
    BLAST

    Transmembrane

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Transmembranei990 – 101021HelicalSequence AnalysisAdd
    BLAST
    Transmembranei1105 – 112521HelicalSequence AnalysisAdd
    BLAST

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini976 – 1163188ReticulonPROSITE-ProRule annotationAdd
    BLAST

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi33 – 4614Poly-GluAdd
    BLAST
    Compositional biasi73 – 764Poly-Ala
    Compositional biasi140 – 1456Poly-Pro

    Domaini

    Three regions, residues 59-172, 544-725 and the loop 66 amino acids, known as Nogo-66 loop, appear to be responsible for the inhibitory effect on neurite outgrowth and the spreading of neurons. This Nogo-66 loop, mediates also the binding of RTN4 to its receptor.

    Sequence similaritiesi

    Contains 1 reticulon domain.PROSITE-ProRule annotation

    Keywords - Domaini

    Transmembrane, Transmembrane helix

    Phylogenomic databases

    eggNOGiNOG306139.
    GeneTreeiENSGT00390000009934.
    HOGENOMiHOG000148576.
    HOVERGENiHBG023134.
    InParanoidiQ9JK11.
    PhylomeDBiQ9JK11.

    Family and domain databases

    InterProiIPR003388. Reticulon.
    [Graphical view]
    PANTHERiPTHR10994. PTHR10994. 1 hit.
    PfamiPF02453. Reticulon. 1 hit.
    [Graphical view]
    PROSITEiPS50845. RETICULON. 1 hit.
    [Graphical view]

    Sequences (4)i

    Sequence statusi: Complete.

    This entry describes 4 isoformsi produced by alternative splicing. Align

    Isoform 1 (identifier: Q9JK11-1) [UniParc]FASTAAdd to Basket

    Also known as: Nogo-A, NI-220-250

    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

    MEDIDQSSLV SSSTDSPPRP PPAFKYQFVT EPEDEEDEEE EEDEEEDDED     50
    LEELEVLERK PAAGLSAAAV PPAAAAPLLD FSSDSVPPAP RGPLPAAPPA 100
    APERQPSWER SPAAPAPSLP PAAAVLPSKL PEDDEPPARP PPPPPAGASP 150
    LAEPAAPPST PAAPKRRGSG SVDETLFALP AASEPVIPSS AEKIMDLMEQ 200
    PGNTVSSGQE DFPSVLLETA ASLPSLSPLS TVSFKEHGYL GNLSAVSSSE 250
    GTIEETLNEA SKELPERATN PFVNRDLAEF SELEYSEMGS SFKGSPKGES 300
    AILVENTKEE VIVRSKDKED LVCSAALHSP QESPVGKEDR VVSPEKTMDI 350
    FNEMQMSVVA PVREEYADFK PFEQAWEVKD TYEGSRDVLA ARANVESKVD 400
    RKCLEDSLEQ KSLGKDSEGR NEDASFPSTP EPVKDSSRAY ITCASFTSAT 450
    ESTTANTFPL LEDHTSENKT DEKKIEERKA QIITEKTSPK TSNPFLVAVQ 500
    DSEADYVTTD TLSKVTEAAV SNMPEGLTPD LVQEACESEL NEATGTKIAY 550
    ETKVDLVQTS EAIQESLYPT AQLCPSFEEA EATPSPVLPD IVMEAPLNSL 600
    LPSAGASVVQ PSVSPLEAPP PVSYDSIKLE PENPPPYEEA MNVALKALGT 650
    KEGIKEPESF NAAVQETEAP YISIACDLIK ETKLSTEPSP DFSNYSEIAK 700
    FEKSVPEHAE LVEDSSPESE PVDLFSDDSI PEVPQTQEEA VMLMKESLTE 750
    VSETVAQHKE ERLSASPQEL GKPYLESFQP NLHSTKDAAS NDIPTLTKKE 800
    KISLQMEEFN TAIYSNDDLL SSKEDKIKES ETFSDSSPIE IIDEFPTFVS 850
    AKDDSPKLAK EYTDLEVSDK SEIANIQSGA DSLPCLELPC DLSFKNIYPK 900
    DEVHVSDEFS ENRSSVSKAS ISPSNVSALE PQTEMGSIVK SKSLTKEAEK 950
    KLPSDTEKED RSLSAVLSAE LSKTSVVDLL YWRDIKKTGV VFGASLFLLL 1000
    SLTVFSIVSV TAYIALALLS VTISFRIYKG VIQAIQKSDE GHPFRAYLES 1050
    EVAISEELVQ KYSNSALGHV NSTIKELRRL FLVDDLVDSL KFAVLMWVFT 1100
    YVGALFNGLT LLILALISLF SIPVIYERHQ VQIDHYLGLA NKSVKDAMAK 1150
    IQAKIPGLKR KAD 1163
    Length:1,163
    Mass (Da):126,388
    Last modified:October 1, 2000 - v1
    Checksum:i8CB894B09E94F0B6
    GO
    Isoform 2 (identifier: Q9JK11-2) [UniParc]FASTAAdd to Basket

    Also known as: Nogo-B, Foocen-M1

    The sequence of this isoform differs from the canonical sequence as follows:
         173-975: Missing.

    Show »
    Length:360
    Mass (Da):38,822
    Checksum:i149714AD6C3D65A7
    GO
    Isoform 3 (identifier: Q9JK11-3) [UniParc]FASTAAdd to Basket

    Also known as: Nogo-C, VP20

    The sequence of this isoform differs from the canonical sequence as follows:
         1-964: Missing.
         965-975: AVLSAELSKTS → MDGQKKHWKDK

    Show »
    Length:199
    Mass (Da):22,403
    Checksum:i2FD805453543DC95
    GO
    Isoform 4 (identifier: Q9JK11-4) [UniParc]FASTAAdd to Basket

    Also known as: Foocen-M2

    The sequence of this isoform differs from the canonical sequence as follows:
         192-975: Missing.

    Show »
    Length:379
    Mass (Da):40,719
    Checksum:i9F15AB942D36ED0F
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti1130 – 11312Missing in AAD31020. 1 PublicationCurated

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei1 – 964964Missing in isoform 3. 2 PublicationsVSP_005656Add
    BLAST
    Alternative sequencei173 – 975803Missing in isoform 2. 2 PublicationsVSP_005658Add
    BLAST
    Alternative sequencei192 – 975784Missing in isoform 4. 1 PublicationVSP_005659Add
    BLAST
    Alternative sequencei965 – 97511AVLSAELSKTS → MDGQKKHWKDK in isoform 3. 2 PublicationsVSP_005657Add
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF051335 mRNA. Translation: AAF01564.1.
    AJ242961 mRNA. Translation: CAB71027.1.
    AJ242962 mRNA. Translation: CAB71028.1.
    AJ242963 mRNA. Translation: CAB71029.1.
    AF132045 mRNA. Translation: AAD31019.1.
    AF132046 mRNA. Translation: AAD31020.1.
    RefSeqiNP_114019.1. NM_031831.1. [Q9JK11-1]
    XP_006251671.1. XM_006251609.1. [Q9JK11-3]
    UniGeneiRn.1348.
    Rn.163269.

    Genome annotation databases

    EnsembliENSRNOT00000006957; ENSRNOP00000006957; ENSRNOG00000004621. [Q9JK11-2]
    ENSRNOT00000041638; ENSRNOP00000042870; ENSRNOG00000004621. [Q9JK11-4]
    ENSRNOT00000042965; ENSRNOP00000040760; ENSRNOG00000004621. [Q9JK11-3]
    GeneIDi83765.
    KEGGirno:83765.
    UCSCiRGD:620989. rat. [Q9JK11-1]

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    Web resourcesi

    Protein Spotlight

    Nerve regrowth: nipped by a no-go - Issue 69 of April 2006

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF051335 mRNA. Translation: AAF01564.1 .
    AJ242961 mRNA. Translation: CAB71027.1 .
    AJ242962 mRNA. Translation: CAB71028.1 .
    AJ242963 mRNA. Translation: CAB71029.1 .
    AF132045 mRNA. Translation: AAD31019.1 .
    AF132046 mRNA. Translation: AAD31020.1 .
    RefSeqi NP_114019.1. NM_031831.1. [Q9JK11-1 ]
    XP_006251671.1. XM_006251609.1. [Q9JK11-3 ]
    UniGenei Rn.1348.
    Rn.163269.

    3D structure databases

    ProteinModelPortali Q9JK11.
    SMRi Q9JK11. Positions 1026-1085.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 249825. 2 interactions.
    DIPi DIP-37179N.
    IntActi Q9JK11. 3 interactions.
    MINTi MINT-4998315.
    STRINGi 10116.ENSRNOP00000006443.

    PTM databases

    PhosphoSitei Q9JK11.

    Proteomic databases

    PaxDbi Q9JK11.
    PRIDEi Q9JK11.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENSRNOT00000006957 ; ENSRNOP00000006957 ; ENSRNOG00000004621 . [Q9JK11-2 ]
    ENSRNOT00000041638 ; ENSRNOP00000042870 ; ENSRNOG00000004621 . [Q9JK11-4 ]
    ENSRNOT00000042965 ; ENSRNOP00000040760 ; ENSRNOG00000004621 . [Q9JK11-3 ]
    GeneIDi 83765.
    KEGGi rno:83765.
    UCSCi RGD:620989. rat. [Q9JK11-1 ]

    Organism-specific databases

    CTDi 57142.
    RGDi 620989. Rtn4.

    Phylogenomic databases

    eggNOGi NOG306139.
    GeneTreei ENSGT00390000009934.
    HOGENOMi HOG000148576.
    HOVERGENi HBG023134.
    InParanoidi Q9JK11.
    PhylomeDBi Q9JK11.

    Miscellaneous databases

    NextBioi 616333.
    PROi Q9JK11.

    Gene expression databases

    Genevestigatori Q9JK11.

    Family and domain databases

    InterProi IPR003388. Reticulon.
    [Graphical view ]
    PANTHERi PTHR10994. PTHR10994. 1 hit.
    Pfami PF02453. Reticulon. 1 hit.
    [Graphical view ]
    PROSITEi PS50845. RETICULON. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Cloning and characterization of a 22 kDa protein from rat adipocytes: a new member of the reticulon family."
      Morris N.J., Ross S.A., Neveu J.M., Lane W.S., Lienhard G.E.
      Biochim. Biophys. Acta 1450:68-76(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 3), PARTIAL PROTEIN SEQUENCE.
      Strain: Sprague-Dawley.
      Tissue: Adipocyte.
    2. "Nogo-A is a myelin-associated neurite outgrowth inhibitor and an antigen for monoclonal antibody IN-1."
      Chen M.S., Huber A.B., Van der Haar M.E., Frank M., Schnell L., Spillmann A.A., Christ F., Schwab M.E.
      Nature 403:434-439(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1; 2 AND 3).
    3. "Cloning of a member of the reticulon gene family in rat: one of two minor splice variants."
      Ito T., Schwartz S.M.
      Submitted (FEB-1999) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 2 AND 4).
      Strain: Wistar Kyoto.
      Tissue: Vascular smooth muscle.
    4. "Nogo-66 receptor antagonist peptide promotes axonal regeneration."
      GrandPre T., Li S., Strittmatter S.M.
      Nature 417:547-551(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    5. Cited for: INTERACTION WITH CNTNAP1.
    6. "Nogo-A inhibits neurite outgrowth and cell spreading with three discrete regions."
      Oertle T., van der Haar M.E., Bandtlow C.E., Robeva A., Burfeind P., Buss A., Huber A.B., Simonen M., Schnell L., Brosamle C., Kaupmann K., Vallon R., Schwab M.E.
      J. Neurosci. 23:5393-5406(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    7. "Quantitative phosphoproteomics of vasopressin-sensitive renal cells: regulation of aquaporin-2 phosphorylation at two sites."
      Hoffert J.D., Pisitkun T., Wang G., Shen R.-F., Knepper M.A.
      Proc. Natl. Acad. Sci. U.S.A. 103:7159-7164(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-107, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    8. "A class of dynamin-like GTPases involved in the generation of the tubular ER network."
      Hu J., Shibata Y., Zhu P.-P., Voss C., Rismanchi N., Prinz W.A., Rapoport T.A., Blackstone C.
      Cell 138:549-561(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH ATL1.
    9. "Neuronal Nogo-A regulates neurite fasciculation, branching and extension in the developing nervous system."
      Petrinovic M.M., Duncan C.S., Bourikas D., Weinman O., Montani L., Schroeter A., Maerki D., Sommer L., Stoeckli E.T., Schwab M.E.
      Development 137:2539-2550(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.

    Entry informationi

    Entry nameiRTN4_RAT
    AccessioniPrimary (citable) accession number: Q9JK11
    Secondary accession number(s): Q9JK10
    , Q9R0D9, Q9WUE9, Q9WUF0
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 16, 2001
    Last sequence update: October 1, 2000
    Last modified: October 1, 2014
    This is version 104 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. Protein Spotlight
      Protein Spotlight articles and cited UniProtKB/Swiss-Prot entries
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3