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Protein

Leucine-rich repeat-containing protein 4B

Gene

Lrrc4b

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Synaptic adhesion protein. Regulates the formation of excitatory synapses. The trans-synaptic adhesion between LRRC4B and PTPRF regulates the formation of excitatory synapses in a bidirectional manner.1 Publication

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Names & Taxonomyi

Protein namesi
Recommended name:
Leucine-rich repeat-containing protein 4B
Alternative name(s):
Netrin-G3 ligand
Short name:
NGL-3
Gene namesi
Name:Lrrc4b
Synonyms:Lrig4
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Chromosome 1

Organism-specific databases

RGDi1307121. Lrrc4b.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transmembranei575 – 59521HelicalSequence analysisAdd
BLAST

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cell junction, Cell membrane, Membrane, Synapse

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 3838Sequence analysisAdd
BLAST
Chaini39 – 709671Leucine-rich repeat-containing protein 4BPRO_0000390416Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi376 – 3761N-linked (GlcNAc...)Sequence analysis
Disulfide bondi387 ↔ 438PROSITE-ProRule annotation
Glycosylationi402 – 4021N-linked (GlcNAc...)Sequence analysis
Glycosylationi424 – 4241N-linked (GlcNAc...)Sequence analysis
Glycosylationi427 – 4271N-linked (GlcNAc...)Sequence analysis
Glycosylationi446 – 4461N-linked (GlcNAc...)Sequence analysis
Modified residuei689 – 6891PhosphoserineBy similarity

Post-translational modificationi

N-glycosylated. O-glycosylated; contains sialic acid.2 Publications

Keywords - PTMi

Disulfide bond, Glycoprotein, Phosphoprotein

Proteomic databases

PaxDbiP0CC10.
PRIDEiP0CC10.

PTM databases

UniCarbKBiP0CC10.

Expressioni

Tissue specificityi

Mainly expressed in the brain. Widespread distribution in various brain regions (at protein level). Detected both embryonically and postnatally with stronger expression in postnatal stages.1 Publication

Gene expression databases

GenevisibleiP0CC10. RN.

Interactioni

Subunit structurei

Interacts with PTPRF. Interacts with DLG4 (By similarity).By similarity

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000026259.

Structurei

3D structure databases

ProteinModelPortaliP0CC10.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini50 – 8839LRRNTAdd
BLAST
Repeati89 – 11022LRR 1Add
BLAST
Repeati113 – 13422LRR 2Add
BLAST
Repeati137 – 15822LRR 3Add
BLAST
Repeati161 – 18222LRR 4Add
BLAST
Repeati185 – 20723LRR 5Add
BLAST
Repeati210 – 23122LRR 6Add
BLAST
Repeati232 – 25322LRR 7Add
BLAST
Repeati256 – 27722LRR 8Add
BLAST
Repeati280 – 30122LRR 9Add
BLAST
Domaini313 – 36553LRRCTAdd
BLAST
Domaini366 – 45489Ig-like C2-typeAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi39 – 424Poly-Gly
Compositional biasi464 – 48219Gly-richAdd
BLAST
Compositional biasi631 – 6377Poly-Ala

Domaini

The extreme C-terminus binds to the first 2 PDZ domains of DLG4.By similarity

Sequence similaritiesi

Contains 9 LRR (leucine-rich) repeats.Curated
Contains 1 LRRCT domain.Curated
Contains 1 LRRNT domain.Curated

Keywords - Domaini

Immunoglobulin domain, Leucine-rich repeat, Repeat, Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiKOG0619. Eukaryota.
COG4886. LUCA.
GeneTreeiENSGT00760000118831.
HOGENOMiHOG000252924.
InParanoidiP0CC10.
KOiK16360.
OMAiTEGMGPG.
OrthoDBiEOG769ZHZ.
PhylomeDBiP0CC10.
TreeFamiTF324303.

Family and domain databases

Gene3Di2.60.40.10. 1 hit.
3.80.10.10. 2 hits.
InterProiIPR000483. Cys-rich_flank_reg_C.
IPR007110. Ig-like_dom.
IPR013783. Ig-like_fold.
IPR013098. Ig_I-set.
IPR003599. Ig_sub.
IPR003598. Ig_sub2.
IPR032675. L_dom-like.
IPR001611. Leu-rich_rpt.
IPR003591. Leu-rich_rpt_typical-subtyp.
IPR026883. LRRC4B.
IPR000372. LRRNT.
[Graphical view]
PANTHERiPTHR24369:SF66. PTHR24369:SF66. 4 hits.
PfamiPF07679. I-set. 1 hit.
PF13855. LRR_8. 3 hits.
[Graphical view]
SMARTiSM00409. IG. 1 hit.
SM00408. IGc2. 1 hit.
SM00369. LRR_TYP. 8 hits.
SM00082. LRRCT. 1 hit.
SM00013. LRRNT. 1 hit.
[Graphical view]
SUPFAMiSSF48726. SSF48726. 1 hit.
SSF52058. SSF52058. 1 hit.
PROSITEiPS50835. IG_LIKE. 1 hit.
PS51450. LRR. 7 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

P0CC10-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAQAHIQGSP CPLLPPGRMS WPQGALLLLW LFSPPLRAGG GGVAVTSAAG
60 70 80 90 100
GGSPPATSCP AACSCSNQAS RVICTRRELA EVPASIPVNT RYLNLQENSI
110 120 130 140 150
QVIRTDTFKH LRHLEILQLS KNLVRKIEVG AFNGLPSLNT LELFDNRLTT
160 170 180 190 200
VPTQAFEYLS KLRELWLRNN PIESIPSYAF NRVPSLRRLD LGELKRLEYI
210 220 230 240 250
SEAAFEGLVN LRYLNLGMCN LKDIPNLTAL VRLEELELSG NRLDLIRPGS
260 270 280 290 300
FQGLTSLRKL WLMHAQVATI ERNAFDDLKS LEELNLSHNN LMSLPHDLFT
310 320 330 340 350
PLHRLERVHL NHNPWHCNCD VLWLSWWLKE TVPSNTTCCA RCHAPAGLKG
360 370 380 390 400
RYIGELDQSH FTCYAPVIVE PPTDLNVTEG MAAELKCRTG TSMTSVNWLT
410 420 430 440 450
PNGTLMTHGS YRVRISVLHD GTLNFTNVTV QDTGQYTCMV TNSAGNTTAS
460 470 480 490 500
ATLNVSAVDP VAAGGPGGGG PGGGGGAGGA GGYTYFTTVT VETLETQPGE
510 520 530 540 550
EAQQPRGTEK EPPGPTTDGA WGGGRPDAAA PASASTTAPA PRSSRPTEKA
560 570 580 590 600
FTVPITDVTE NALKDLDDVM KTTKIIIGCF VAITFMAAVM LVAFYKLRKQ
610 620 630 640 650
HQLHKHHGPT RTVEIINVED ELPAASAVSV AAAAAVAGGA GVGGDSHLAL
660 670 680 690 700
PALERDHLNH HHYVAAAFKA HYGGNPGGGC GAKGPGLNSI HEPLLFKSGS

KENVQETQI
Length:709
Mass (Da):76,119
Last modified:December 15, 2009 - v1
Checksum:iBB59CD872BD409BD
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CB608563 mRNA. No translation available.
RefSeqiNP_001258010.1. NM_001271081.1.
XP_006229117.1. XM_006229055.2.
UniGeneiRn.22207.

Genome annotation databases

EnsembliENSRNOT00000026259; ENSRNOP00000026259; ENSRNOG00000019418.
GeneIDi308571.
KEGGirno:308571.
UCSCiRGD:1307121. rat.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CB608563 mRNA. No translation available.
RefSeqiNP_001258010.1. NM_001271081.1.
XP_006229117.1. XM_006229055.2.
UniGeneiRn.22207.

3D structure databases

ProteinModelPortaliP0CC10.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000026259.

PTM databases

UniCarbKBiP0CC10.

Proteomic databases

PaxDbiP0CC10.
PRIDEiP0CC10.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSRNOT00000026259; ENSRNOP00000026259; ENSRNOG00000019418.
GeneIDi308571.
KEGGirno:308571.
UCSCiRGD:1307121. rat.

Organism-specific databases

CTDi94030.
RGDi1307121. Lrrc4b.

Phylogenomic databases

eggNOGiKOG0619. Eukaryota.
COG4886. LUCA.
GeneTreeiENSGT00760000118831.
HOGENOMiHOG000252924.
InParanoidiP0CC10.
KOiK16360.
OMAiTEGMGPG.
OrthoDBiEOG769ZHZ.
PhylomeDBiP0CC10.
TreeFamiTF324303.

Miscellaneous databases

PROiP0CC10.

Gene expression databases

GenevisibleiP0CC10. RN.

Family and domain databases

Gene3Di2.60.40.10. 1 hit.
3.80.10.10. 2 hits.
InterProiIPR000483. Cys-rich_flank_reg_C.
IPR007110. Ig-like_dom.
IPR013783. Ig-like_fold.
IPR013098. Ig_I-set.
IPR003599. Ig_sub.
IPR003598. Ig_sub2.
IPR032675. L_dom-like.
IPR001611. Leu-rich_rpt.
IPR003591. Leu-rich_rpt_typical-subtyp.
IPR026883. LRRC4B.
IPR000372. LRRNT.
[Graphical view]
PANTHERiPTHR24369:SF66. PTHR24369:SF66. 4 hits.
PfamiPF07679. I-set. 1 hit.
PF13855. LRR_8. 3 hits.
[Graphical view]
SMARTiSM00409. IG. 1 hit.
SM00408. IGc2. 1 hit.
SM00369. LRR_TYP. 8 hits.
SM00082. LRRCT. 1 hit.
SM00013. LRRNT. 1 hit.
[Graphical view]
SUPFAMiSSF48726. SSF48726. 1 hit.
SSF52058. SSF52058. 1 hit.
PROSITEiPS50835. IG_LIKE. 1 hit.
PS51450. LRR. 7 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Amgen rat EST program."
    Amgen EST program
    Submitted (APR-2003) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1-189.
  2. "NGL family PSD-95-interacting adhesion molecules regulate excitatory synapse formation."
    Kim S., Burette A., Chung H.S., Kwon S.-K., Woo J., Lee H.W., Kim K., Kim H., Weinberg R.J., Kim E.
    Nat. Neurosci. 9:1294-1301(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: TISSUE SPECIFICITY, GLYCOSYLATION.
  3. "Trans-synaptic adhesion between NGL-3 and LAR regulates the formation of excitatory synapses."
    Woo J., Kwon S.K., Choi S., Kim S., Lee J.-R., Dunah A.W., Sheng M., Kim E.
    Nat. Neurosci. 12:428-437(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH PTPRF, SUBCELLULAR LOCATION, GLYCOSYLATION.

Entry informationi

Entry nameiLRC4B_RAT
AccessioniPrimary (citable) accession number: P0CC10
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 15, 2009
Last sequence update: December 15, 2009
Last modified: July 6, 2016
This is version 55 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, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.