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Protein

Leucine-rich repeat-containing protein 4C

Gene

LRRC4C

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

May promote neurite outgrowth of developing thalamic neurons.1 Publication

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Names & Taxonomyi

Protein namesi
Recommended name:
Leucine-rich repeat-containing protein 4C
Alternative name(s):
Netrin-G1 ligand
Short name:
NGL-1
Gene namesi
Name:LRRC4C
Synonyms:KIAA1580, NGL1
ORF Names:UNQ292/PRO331
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 11

Organism-specific databases

HGNCiHGNC:29317. LRRC4C.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transmembranei528 – 54821HelicalSequence analysisAdd
BLAST

GO - Cellular componenti

  • cell junction Source: UniProtKB-KW
  • cytoplasm Source: GO_Central
  • extracellular space Source: UniProtKB
  • integral component of membrane Source: UniProtKB
  • membrane Source: UniProtKB
  • postsynaptic membrane Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cell junction, Cell membrane, Membrane, Postsynaptic cell membrane, Synapse

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA142671534.

Polymorphism and mutation databases

BioMutaiLRRC4C.
DMDMi57012973.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 4444Sequence analysisAdd
BLAST
Chaini45 – 640596Leucine-rich repeat-containing protein 4CPRO_0000015108Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi375 ↔ 426PROSITE-ProRule annotation
Modified residuei631 – 6311PhosphoserineBy similarity

Keywords - PTMi

Disulfide bond, Phosphoprotein

Proteomic databases

PaxDbiQ9HCJ2.
PRIDEiQ9HCJ2.

PTM databases

iPTMnetiQ9HCJ2.
PhosphoSiteiQ9HCJ2.

Expressioni

Tissue specificityi

Highly expressed in the cerebral cortex, including frontal, parietal and occipital lobes. Putamen, amygdala, hippocampus and medulla oblongata show moderate expression. Caudate nucleus and thalamus express small amounts, whereas other brain regions show very weak or no expression.1 Publication

Gene expression databases

BgeeiQ9HCJ2.
CleanExiHS_LRRC4C.
ExpressionAtlasiQ9HCJ2. baseline and differential.
GenevisibleiQ9HCJ2. HS.

Organism-specific databases

HPAiHPA051335.

Interactioni

Subunit structurei

Interacts with NTNG1 and WHRN.2 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
NTNG1Q9Y2I24EBI-3925442,EBI-7444396
NTNG2Q96CW92EBI-3925442,EBI-750795

Protein-protein interaction databases

BioGridi121715. 25 interactions.
IntActiQ9HCJ2. 3 interactions.
MINTiMINT-3070603.
STRINGi9606.ENSP00000278198.

Structurei

Secondary structure

1
640
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi49 – 535Combined sources
Beta strandi59 – 613Combined sources
Beta strandi79 – 824Combined sources
Turni93 – 964Combined sources
Beta strandi104 – 1063Combined sources
Helixi117 – 1204Combined sources
Beta strandi128 – 1303Combined sources
Turni141 – 1433Combined sources
Beta strandi152 – 1543Combined sources
Turni165 – 1706Combined sources
Beta strandi176 – 1783Combined sources
Turni190 – 1956Combined sources
Beta strandi201 – 2033Combined sources
Beta strandi223 – 2253Combined sources
Turni236 – 2416Combined sources
Beta strandi247 – 2493Combined sources
Beta strandi271 – 2733Combined sources
Turni284 – 2874Combined sources
Beta strandi295 – 2973Combined sources
Helixi310 – 3178Combined sources
Beta strandi329 – 3335Combined sources
Turni334 – 3385Combined sources
Beta strandi356 – 3583Combined sources
Beta strandi363 – 3664Combined sources
Beta strandi376 – 3794Combined sources
Beta strandi382 – 3876Combined sources
Beta strandi393 – 3986Combined sources
Beta strandi401 – 4055Combined sources
Beta strandi411 – 4155Combined sources
Beta strandi422 – 4298Combined sources
Beta strandi434 – 44411Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3ZYJX-ray3.25A/C44-444[»]
ProteinModelPortaliQ9HCJ2.
SMRiQ9HCJ2. Positions 45-482.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini45 – 7632LRRNTAdd
BLAST
Repeati77 – 9822LRR 1Add
BLAST
Repeati101 – 12222LRR 2Add
BLAST
Repeati125 – 14622LRR 3Add
BLAST
Repeati149 – 17022LRR 4Add
BLAST
Repeati173 – 19523LRR 5Add
BLAST
Repeati198 – 21922LRR 6Add
BLAST
Repeati220 – 24122LRR 7Add
BLAST
Repeati244 – 26522LRR 8Add
BLAST
Repeati268 – 28922LRR 9Add
BLAST
Domaini301 – 35353LRRCTAdd
BLAST
Domaini354 – 44289Ig-like C2-typeAdd
BLAST

Domaini

The LRR region is both necessary and sufficient for the interaction with NTNG1.

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.
InParanoidiQ9HCJ2.
KOiK07523.
OMAiIMTHGAY.
OrthoDBiEOG769ZHZ.
PhylomeDBiQ9HCJ2.
TreeFamiTF324303.

Family and domain databases

Gene3Di2.60.40.10. 1 hit.
3.80.10.10. 2 hits.
InterProiIPR007110. Ig-like_dom.
IPR013783. Ig-like_fold.
IPR013098. Ig_I-set.
IPR003599. Ig_sub.
IPR003598. Ig_sub2.
IPR013106. Ig_V-set.
IPR032675. L_dom-like.
IPR001611. Leu-rich_rpt.
IPR003591. Leu-rich_rpt_typical-subtyp.
IPR026906. LRR_5.
IPR026878. LRRC4C.
IPR000372. LRRNT.
[Graphical view]
PANTHERiPTHR24369:SF8. PTHR24369:SF8. 2 hits.
PfamiPF07679. I-set. 1 hit.
PF00560. LRR_1. 1 hit.
PF13306. LRR_5. 1 hit.
PF13855. LRR_8. 1 hit.
[Graphical view]
SMARTiSM00409. IG. 1 hit.
SM00408. IGc2. 1 hit.
SM00406. IGv. 1 hit.
SM00369. LRR_TYP. 8 hits.
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.

Q9HCJ2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLNKMTLHPQ QIMIGPRFNR ALFDPLLVVL LALQLLVVAG LVRAQTCPSV
60 70 80 90 100
CSCSNQFSKV ICVRKNLREV PDGISTNTRL LNLHENQIQI IKVNSFKHLR
110 120 130 140 150
HLEILQLSRN HIRTIEIGAF NGLANLNTLE LFDNRLTTIP NGAFVYLSKL
160 170 180 190 200
KELWLRNNPI ESIPSYAFNR IPSLRRLDLG ELKRLSYISE GAFEGLSNLR
210 220 230 240 250
YLNLAMCNLR EIPNLTPLIK LDELDLSGNH LSAIRPGSFQ GLMHLQKLWM
260 270 280 290 300
IQSQIQVIER NAFDNLQSLV EINLAHNNLT LLPHDLFTPL HHLERIHLHH
310 320 330 340 350
NPWNCNCDIL WLSWWIKDMA PSNTACCARC NTPPNLKGRY IGELDQNYFT
360 370 380 390 400
CYAPVIVEPP ADLNVTEGMA AELKCRASTS LTSVSWITPN GTVMTHGAYK
410 420 430 440 450
VRIAVLSDGT LNFTNVTVQD TGMYTCMVSN SVGNTTASAT LNVTAATTTP
460 470 480 490 500
FSYFSTVTVE TMEPSQDEAR TTDNNVGPTP VVDWETTNVT TSLTPQSTRS
510 520 530 540 550
TEKTFTIPVT DINSGIPGID EVMKTTKIII GCFVAITLMA AVMLVIFYKM
560 570 580 590 600
RKQHHRQNHH APTRTVEIIN VDDEITGDTP MESHLPMPAI EHEHLNHYNS
610 620 630 640
YKSPFNHTTT VNTINSIHSS VHEPLLIRMN SKDNVQETQI
Length:640
Mass (Da):71,950
Last modified:March 1, 2001 - v1
Checksum:i6058974872636838
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB046800 mRNA. Translation: BAB13406.1.
AY358293 mRNA. Translation: AAQ88660.1.
AK289646 mRNA. Translation: BAF82335.1.
CH471064 Genomic DNA. Translation: EAW68107.1.
BC041374 mRNA. Translation: AAH41374.3.
CCDSiCCDS31464.1.
RefSeqiNP_001245348.1. NM_001258419.1.
NP_065980.1. NM_020929.2.
XP_011518540.1. XM_011520238.1.
XP_011518541.1. XM_011520239.1.
XP_011518542.1. XM_011520240.1.
XP_011518543.1. XM_011520241.1.
XP_011518544.1. XM_011520242.1.
XP_011518545.1. XM_011520243.1.
XP_011518546.1. XM_011520244.1.
XP_011518547.1. XM_011520245.1.
UniGeneiHs.745123.

Genome annotation databases

EnsembliENST00000278198; ENSP00000278198; ENSG00000148948.
ENST00000527150; ENSP00000436976; ENSG00000148948.
ENST00000528697; ENSP00000437132; ENSG00000148948.
ENST00000530763; ENSP00000434761; ENSG00000148948.
ENST00000619527; ENSP00000480903; ENSG00000148948.
GeneIDi57689.
KEGGihsa:57689.
UCSCiuc031pzt.2. human.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB046800 mRNA. Translation: BAB13406.1.
AY358293 mRNA. Translation: AAQ88660.1.
AK289646 mRNA. Translation: BAF82335.1.
CH471064 Genomic DNA. Translation: EAW68107.1.
BC041374 mRNA. Translation: AAH41374.3.
CCDSiCCDS31464.1.
RefSeqiNP_001245348.1. NM_001258419.1.
NP_065980.1. NM_020929.2.
XP_011518540.1. XM_011520238.1.
XP_011518541.1. XM_011520239.1.
XP_011518542.1. XM_011520240.1.
XP_011518543.1. XM_011520241.1.
XP_011518544.1. XM_011520242.1.
XP_011518545.1. XM_011520243.1.
XP_011518546.1. XM_011520244.1.
XP_011518547.1. XM_011520245.1.
UniGeneiHs.745123.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3ZYJX-ray3.25A/C44-444[»]
ProteinModelPortaliQ9HCJ2.
SMRiQ9HCJ2. Positions 45-482.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi121715. 25 interactions.
IntActiQ9HCJ2. 3 interactions.
MINTiMINT-3070603.
STRINGi9606.ENSP00000278198.

PTM databases

iPTMnetiQ9HCJ2.
PhosphoSiteiQ9HCJ2.

Polymorphism and mutation databases

BioMutaiLRRC4C.
DMDMi57012973.

Proteomic databases

PaxDbiQ9HCJ2.
PRIDEiQ9HCJ2.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000278198; ENSP00000278198; ENSG00000148948.
ENST00000527150; ENSP00000436976; ENSG00000148948.
ENST00000528697; ENSP00000437132; ENSG00000148948.
ENST00000530763; ENSP00000434761; ENSG00000148948.
ENST00000619527; ENSP00000480903; ENSG00000148948.
GeneIDi57689.
KEGGihsa:57689.
UCSCiuc031pzt.2. human.

Organism-specific databases

CTDi57689.
GeneCardsiLRRC4C.
HGNCiHGNC:29317. LRRC4C.
HPAiHPA051335.
MIMi608817. gene.
neXtProtiNX_Q9HCJ2.
PharmGKBiPA142671534.
HUGEiSearch...
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0619. Eukaryota.
COG4886. LUCA.
GeneTreeiENSGT00760000118831.
HOGENOMiHOG000252924.
HOVERGENiHBG052359.
InParanoidiQ9HCJ2.
KOiK07523.
OMAiIMTHGAY.
OrthoDBiEOG769ZHZ.
PhylomeDBiQ9HCJ2.
TreeFamiTF324303.

Miscellaneous databases

ChiTaRSiLRRC4C. human.
GenomeRNAii57689.
NextBioi64523.
PROiQ9HCJ2.
SOURCEiSearch...

Gene expression databases

BgeeiQ9HCJ2.
CleanExiHS_LRRC4C.
ExpressionAtlasiQ9HCJ2. baseline and differential.
GenevisibleiQ9HCJ2. HS.

Family and domain databases

Gene3Di2.60.40.10. 1 hit.
3.80.10.10. 2 hits.
InterProiIPR007110. Ig-like_dom.
IPR013783. Ig-like_fold.
IPR013098. Ig_I-set.
IPR003599. Ig_sub.
IPR003598. Ig_sub2.
IPR013106. Ig_V-set.
IPR032675. L_dom-like.
IPR001611. Leu-rich_rpt.
IPR003591. Leu-rich_rpt_typical-subtyp.
IPR026906. LRR_5.
IPR026878. LRRC4C.
IPR000372. LRRNT.
[Graphical view]
PANTHERiPTHR24369:SF8. PTHR24369:SF8. 2 hits.
PfamiPF07679. I-set. 1 hit.
PF00560. LRR_1. 1 hit.
PF13306. LRR_5. 1 hit.
PF13855. LRR_8. 1 hit.
[Graphical view]
SMARTiSM00409. IG. 1 hit.
SM00408. IGc2. 1 hit.
SM00406. IGv. 1 hit.
SM00369. LRR_TYP. 8 hits.
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. "Prediction of the coding sequences of unidentified human genes. XVIII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro."
    Nagase T., Kikuno R., Nakayama M., Hirosawa M., Ohara O.
    DNA Res. 7:273-281(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Brain.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
  3. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
    Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
    , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
    Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Amygdala.
  4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  5. "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].
    Tissue: Hippocampus.
  6. "The netrin-G1 ligand NGL-1 promotes the outgrowth of thalamocortical axons."
    Lin J.C., Ho W.-H., Gurney A.L., Rosenthal A.
    Nat. Neurosci. 6:1270-1276(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH NTNG1, SUBCELLULAR LOCATION, TISSUE SPECIFICITY.
  7. "Structural basis for cell surface patterning through NetrinG-NGL interactions."
    Seiradake E., Coles C.H., Perestenko P.V., Harlos K., McIlhinney R.A., Aricescu A.R., Jones E.Y.
    EMBO J. 30:4479-4488(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.25 ANGSTROMS) OF 44-444 IN COMPLEX WITH NTNG1, SUBCELLULAR LOCATION.

Entry informationi

Entry nameiLRC4C_HUMAN
AccessioniPrimary (citable) accession number: Q9HCJ2
Secondary accession number(s): A8K0T1, Q7L0N3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 4, 2005
Last sequence update: March 1, 2001
Last modified: May 11, 2016
This is version 130 of the entry and version 1 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

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 11
    Human chromosome 11: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. 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.