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Protein

Leucine-rich repeat-containing protein 4B

Gene

LRRC4B

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at transcript 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 (By similarity).By similarity

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
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 19

Organism-specific databases

HGNCiHGNC:25042. LRRC4B.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini36 – 576541ExtracellularSequence analysisAdd
BLAST
Transmembranei577 – 59721HelicalSequence analysisAdd
BLAST
Topological domaini598 – 713116CytoplasmicSequence analysisAdd
BLAST

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cell junction, Cell membrane, Membrane, Synapse

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA134890612.

Polymorphism and mutation databases

BioMutaiLRRC4B.
DMDMi91207142.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 3535Sequence analysisAdd
BLAST
Chaini36 – 713678Leucine-rich repeat-containing protein 4BPRO_0000231654Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi224 – 2241N-linked (GlcNAc...)Sequence analysis
Glycosylationi283 – 2831N-linked (GlcNAc...)Sequence analysis
Glycosylationi333 – 3331N-linked (GlcNAc...)Sequence analysis
Glycosylationi374 – 3741N-linked (GlcNAc...)Sequence analysis
Disulfide bondi385 ↔ 436PROSITE-ProRule annotation
Glycosylationi400 – 4001N-linked (GlcNAc...)Sequence analysis
Glycosylationi422 – 4221N-linked (GlcNAc...)Sequence analysis
Glycosylationi425 – 4251N-linked (GlcNAc...)Sequence analysis
Glycosylationi444 – 4441N-linked (GlcNAc...)Sequence analysis
Glycosylationi452 – 4521N-linked (GlcNAc...)Sequence analysis
Modified residuei693 – 6931PhosphoserineBy similarity

Post-translational modificationi

N-glycosylated. O-glycosylated; contains sialic acid.By similarity

Keywords - PTMi

Disulfide bond, Glycoprotein, Phosphoprotein

Proteomic databases

EPDiQ9NT99.
MaxQBiQ9NT99.
PaxDbiQ9NT99.
PRIDEiQ9NT99.

PTM databases

iPTMnetiQ9NT99.
PhosphoSiteiQ9NT99.

Expressioni

Gene expression databases

BgeeiQ9NT99.
CleanExiHS_LRRC4B.
ExpressionAtlasiQ9NT99. baseline and differential.
GenevisibleiQ9NT99. HS.

Organism-specific databases

HPAiHPA058986.

Interactioni

Subunit structurei

Interacts with PTPRF. Interacts with DLG4.By similarity

Protein-protein interaction databases

BioGridi125098. 5 interactions.
STRINGi9606.ENSP00000373853.

Structurei

3D structure databases

ProteinModelPortaliQ9NT99.
SMRiQ9NT99. Positions 55-452.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini48 – 8639LRRNTAdd
BLAST
Repeati87 – 10822LRR 1Add
BLAST
Repeati111 – 13222LRR 2Add
BLAST
Repeati135 – 15622LRR 3Add
BLAST
Repeati159 – 18022LRR 4Add
BLAST
Repeati183 – 20523LRR 5Add
BLAST
Repeati208 – 22922LRR 6Add
BLAST
Repeati230 – 25122LRR 7Add
BLAST
Repeati254 – 27522LRR 8Add
BLAST
Repeati278 – 29922LRR 9Add
BLAST
Domaini311 – 36353LRRCTAdd
BLAST
Domaini364 – 45289Ig-like C2-typeAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi462 – 53271Gly-richAdd
BLAST
Compositional biasi633 – 6397Poly-Ala

Domaini

The last 4 C-terminal residues bind 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.
HOVERGENiHBG052359.
InParanoidiQ9NT99.
KOiK16360.
OMAiTEGMGPG.
OrthoDBiEOG769ZHZ.
PhylomeDBiQ9NT99.
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.

Q9NT99-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MARARGSPCP PLPPGRMSWP HGALLFLWLF SPPLGAGGGG VAVTSAAGGG
60 70 80 90 100
SPPATSCPVA CSCSNQASRV ICTRRDLAEV PASIPVNTRY LNLQENGIQV
110 120 130 140 150
IRTDTFKHLR HLEILQLSKN LVRKIEVGAF NGLPSLNTLE LFDNRLTTVP
160 170 180 190 200
TQAFEYLSKL RELWLRNNPI ESIPSYAFNR VPSLRRLDLG ELKRLEYISE
210 220 230 240 250
AAFEGLVNLR YLNLGMCNLK DIPNLTALVR LEELELSGNR LDLIRPGSFQ
260 270 280 290 300
GLTSLRKLWL MHAQVATIER NAFDDLKSLE ELNLSHNNLM SLPHDLFTPL
310 320 330 340 350
HRLERVHLNH NPWHCNCDVL WLSWWLKETV PSNTTCCARC HAPAGLKGRY
360 370 380 390 400
IGELDQSHFT CYAPVIVEPP TDLNVTEGMA AELKCRTGTS MTSVNWLTPN
410 420 430 440 450
GTLMTHGSYR VRISVLHDGT LNFTNVTVQD TGQYTCMVTN SAGNTTASAT
460 470 480 490 500
LNVSAVDPVA AGGTGSGGGG PGGSGGVGGG SGGYTYFTTV TVETLETQPG
510 520 530 540 550
EEALQPRGTE KEPPGPTTDG VWGGGRPGDA AGPASSSTTA PAPRSSRPTE
560 570 580 590 600
KAFTVPITDV TENALKDLDD VMKTTKIIIG CFVAITFMAA VMLVAFYKLR
610 620 630 640 650
KQHQLHKHHG PTRTVEIINV EDELPAASAV SVAAAAAVAS GGGVGGDSHL
660 670 680 690 700
ALPALERDHL NHHHYVAAAF KAHYSSNPSG GGCGGKGPPG LNSIHEPLLF
710
KSGSKENVQE TQI
Length:713
Mass (Da):76,434
Last modified:April 4, 2006 - v3
Checksum:i085B5CACE28038D9
GO

Sequence cautioni

The sequence AAH19687.1 differs from that shown. Reason: Erroneous initiation. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti637 – 6382AV → TA in AAH56207 (PubMed:15489334).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AC008743 Genomic DNA. No translation available.
BC019687 mRNA. Translation: AAH19687.1. Different initiation.
BC056207 mRNA. Translation: AAH56207.1.
AL137451 mRNA. Translation: CAB70743.2.
CCDSiCCDS42595.1.
PIRiT46266.
RefSeqiNP_001073926.1. NM_001080457.1.
XP_005259486.1. XM_005259429.3.
XP_006723569.1. XM_006723506.2.
XP_011525822.1. XM_011527520.1.
UniGeneiHs.120873.

Genome annotation databases

EnsembliENST00000389201; ENSP00000373853; ENSG00000131409.
ENST00000599957; ENSP00000471502; ENSG00000131409.
GeneIDi94030.
KEGGihsa:94030.
UCSCiuc002pss.4. human.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AC008743 Genomic DNA. No translation available.
BC019687 mRNA. Translation: AAH19687.1. Different initiation.
BC056207 mRNA. Translation: AAH56207.1.
AL137451 mRNA. Translation: CAB70743.2.
CCDSiCCDS42595.1.
PIRiT46266.
RefSeqiNP_001073926.1. NM_001080457.1.
XP_005259486.1. XM_005259429.3.
XP_006723569.1. XM_006723506.2.
XP_011525822.1. XM_011527520.1.
UniGeneiHs.120873.

3D structure databases

ProteinModelPortaliQ9NT99.
SMRiQ9NT99. Positions 55-452.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi125098. 5 interactions.
STRINGi9606.ENSP00000373853.

PTM databases

iPTMnetiQ9NT99.
PhosphoSiteiQ9NT99.

Polymorphism and mutation databases

BioMutaiLRRC4B.
DMDMi91207142.

Proteomic databases

EPDiQ9NT99.
MaxQBiQ9NT99.
PaxDbiQ9NT99.
PRIDEiQ9NT99.

Protocols and materials databases

DNASUi94030.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000389201; ENSP00000373853; ENSG00000131409.
ENST00000599957; ENSP00000471502; ENSG00000131409.
GeneIDi94030.
KEGGihsa:94030.
UCSCiuc002pss.4. human.

Organism-specific databases

CTDi94030.
GeneCardsiLRRC4B.
H-InvDBHIX0015363.
HGNCiHGNC:25042. LRRC4B.
HPAiHPA058986.
neXtProtiNX_Q9NT99.
PharmGKBiPA134890612.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0619. Eukaryota.
COG4886. LUCA.
GeneTreeiENSGT00760000118831.
HOGENOMiHOG000252924.
HOVERGENiHBG052359.
InParanoidiQ9NT99.
KOiK16360.
OMAiTEGMGPG.
OrthoDBiEOG769ZHZ.
PhylomeDBiQ9NT99.
TreeFamiTF324303.

Miscellaneous databases

ChiTaRSiLRRC4B. human.
GenomeRNAii94030.
PROiQ9NT99.

Gene expression databases

BgeeiQ9NT99.
CleanExiHS_LRRC4B.
ExpressionAtlasiQ9NT99. baseline and differential.
GenevisibleiQ9NT99. HS.

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

  1. "The DNA sequence and biology of human chromosome 19."
    Grimwood J., Gordon L.A., Olsen A.S., Terry A., Schmutz J., Lamerdin J.E., Hellsten U., Goodstein D., Couronne O., Tran-Gyamfi M., Aerts A., Altherr M., Ashworth L., Bajorek E., Black S., Branscomb E., Caenepeel S., Carrano A.V.
    , Caoile C., Chan Y.M., Christensen M., Cleland C.A., Copeland A., Dalin E., Dehal P., Denys M., Detter J.C., Escobar J., Flowers D., Fotopulos D., Garcia C., Georgescu A.M., Glavina T., Gomez M., Gonzales E., Groza M., Hammon N., Hawkins T., Haydu L., Ho I., Huang W., Israni S., Jett J., Kadner K., Kimball H., Kobayashi A., Larionov V., Leem S.-H., Lopez F., Lou Y., Lowry S., Malfatti S., Martinez D., McCready P.M., Medina C., Morgan J., Nelson K., Nolan M., Ovcharenko I., Pitluck S., Pollard M., Popkie A.P., Predki P., Quan G., Ramirez L., Rash S., Retterer J., Rodriguez A., Rogers S., Salamov A., Salazar A., She X., Smith D., Slezak T., Solovyev V., Thayer N., Tice H., Tsai M., Ustaszewska A., Vo N., Wagner M., Wheeler J., Wu K., Xie G., Yang J., Dubchak I., Furey T.S., DeJong P., Dickson M., Gordon D., Eichler E.E., Pennacchio L.A., Richardson P., Stubbs L., Rokhsar D.S., Myers R.M., Rubin E.M., Lucas S.M.
    Nature 428:529-535(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  2. "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] OF 208-713.
    Tissue: Brain.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 216-636.
    Tissue: Amygdala.

Entry informationi

Entry nameiLRC4B_HUMAN
AccessioniPrimary (citable) accession number: Q9NT99
Secondary accession number(s): Q3ZCQ4, Q58F20
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 4, 2006
Last sequence update: April 4, 2006
Last modified: June 8, 2016
This is version 117 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 19
    Human chromosome 19: entries, gene names and cross-references to MIM
  2. 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.