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Protein

Leucine-rich repeat transmembrane neuronal protein 4

Gene

LRRTM4

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at transcript leveli

Functioni

May play a role in the development and maintenance of the vertebrate nervous system. Exhibits strong synaptogenic activity, restricted to excitatory presynaptic differentiation (By similarity).By similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Names & Taxonomyi

Protein namesi
Recommended name:
Leucine-rich repeat transmembrane neuronal protein 4
Gene namesi
Name:LRRTM4
ORF Names:UNQ3075/PRO9907
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 2

Organism-specific databases

HGNCiHGNC:19411. LRRTM4.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini31 – 424394ExtracellularSequence analysisAdd
BLAST
Transmembranei425 – 44521HelicalSequence analysisAdd
BLAST
Topological domaini446 – 590145CytoplasmicSequence analysisAdd
BLAST

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

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

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA134972631.

Polymorphism and mutation databases

BioMutaiLRRTM4.
DMDMi166897996.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 3030Sequence analysisAdd
BLAST
Chaini31 – 590560Leucine-rich repeat transmembrane neuronal protein 4PRO_0000018358Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi58 – 581N-linked (GlcNAc...)Sequence analysis
Glycosylationi126 – 1261N-linked (GlcNAc...)Sequence analysis
Glycosylationi291 – 2911N-linked (GlcNAc...)Sequence analysis

Keywords - PTMi

Glycoprotein

Proteomic databases

MaxQBiQ86VH4.
PaxDbiQ86VH4.
PRIDEiQ86VH4.

PTM databases

iPTMnetiQ86VH4.
PhosphoSiteiQ86VH4.

Expressioni

Tissue specificityi

Expressed in neuronal tissues.1 Publication

Gene expression databases

BgeeiQ86VH4.
CleanExiHS_LRRTM4.
ExpressionAtlasiQ86VH4. baseline and differential.
GenevisibleiQ86VH4. HS.

Interactioni

Subunit structurei

Peripherally associated with AMPAR complex. AMPAR complex consists of an inner core made of 4 pore-forming GluA/GRIA proteins (GRIA1, GRIA2, GRIA3 and GRIA4) and 4 major auxiliary subunits arranged in a twofold symmetry. One of the two pairs of distinct binding sites is occupied either by CNIH2, CNIH3 or CACNG2, CACNG3. The other harbors CACNG2, CACNG3, CACNG4, CACNG8 or GSG1L. This inner core of AMPAR complex is complemented by outer core constituents binding directly to the GluA/GRIA proteins at sites distinct from the interaction sites of the inner core constituents. Outer core constituents include at least PRRT1, PRRT2, CKAMP44/SHISA9, FRRS1L and NRN1. The proteins of the inner and outer core serve as a platform for other, more peripherally associated AMPAR constituents, including LRRTM4. Alone or in combination, these auxiliary subunits control the gating and pharmacology of the AMPAR complex and profoundly impact their biogenesis and protein processing (By similarity).By similarity

Protein-protein interaction databases

BioGridi123095. 2 interactions.
IntActiQ86VH4. 1 interaction.
MINTiMINT-7970553.
STRINGi9606.ENSP00000386357.

Structurei

3D structure databases

ProteinModelPortaliQ86VH4.
SMRiQ86VH4. Positions 34-368.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini31 – 6131LRRNTAdd
BLAST
Repeati62 – 8322LRR 1Add
BLAST
Repeati86 – 10722LRR 2Add
BLAST
Repeati110 – 13122LRR 3Add
BLAST
Repeati134 – 15522LRR 4Add
BLAST
Repeati158 – 17922LRR 5Add
BLAST
Repeati182 – 20322LRR 6Add
BLAST
Repeati206 – 22621LRR 7Add
BLAST
Repeati230 – 25122LRR 8Add
BLAST
Repeati254 – 27522LRR 9Add
BLAST
Repeati278 – 29922LRR 10Add
BLAST
Domaini311 – 36252LRRCTAdd
BLAST

Sequence similaritiesi

Belongs to the LRRTM family.Curated
Contains 10 LRR (leucine-rich) repeats.Curated
Contains 1 LRRCT domain.Curated
Contains 1 LRRNT domain.Curated

Keywords - Domaini

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

Phylogenomic databases

eggNOGiKOG0619. Eukaryota.
COG4886. LUCA.
GeneTreeiENSGT00760000118777.
HOGENOMiHOG000290681.
HOVERGENiHBG052362.
InParanoidiQ86VH4.
PhylomeDBiQ86VH4.
TreeFamiTF332659.

Family and domain databases

Gene3Di3.80.10.10. 2 hits.
InterProiIPR032675. L_dom-like.
IPR001611. Leu-rich_rpt.
IPR003591. Leu-rich_rpt_typical-subtyp.
[Graphical view]
PfamiPF00560. LRR_1. 1 hit.
PF13855. LRR_8. 3 hits.
[Graphical view]
SMARTiSM00369. LRR_TYP. 9 hits.
[Graphical view]
SUPFAMiSSF52058. SSF52058. 1 hit.
PROSITEiPS51450. LRR. 9 hits.
[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. AlignAdd to basket

Isoform 1 (identifier: Q86VH4-1) [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

        10         20         30         40         50
MGFHLITQLK GMSVVLVLLP TLLLVMLTGA QRACPKNCRC DGKIVYCESH
60 70 80 90 100
AFADIPENIS GGSQGLSLRF NSIQKLKSNQ FAGLNQLIWL YLDHNYISSV
110 120 130 140 150
DEDAFQGIRR LKELILSSNK ITYLHNKTFH PVPNLRNLDL SYNKLQTLQS
160 170 180 190 200
EQFKGLRKLI ILHLRSNSLK TVPIRVFQDC RNLDFLDLGY NRLRSLSRNA
210 220 230 240 250
FAGLLKLKEL HLEHNQFSKI NFAHFPRLFN LRSIYLQWNR IRSISQGLTW
260 270 280 290 300
TWSSLHNLDL SGNDIQGIEP GTFKCLPNLQ KLNLDSNKLT NISQETVNAW
310 320 330 340 350
ISLISITLSG NMWECSRSIC PLFYWLKNFK GNKESTMICA GPKHIQGEKV
360 370 380 390 400
SDAVETYNIC SEVQVVNTER SHLVPQTPQK PLIIPRPTIF KPDVTQSTFE
410 420 430 440 450
TPSPSPGFQI PGAEQEYEHV SFHKIIAGSV ALFLSVAMIL LVIYVSWKRY
460 470 480 490 500
PASMKQLQQH SLMKRRRKKA RESERQMNSP LQEYYVDYKP TNSETMDISV
510 520 530 540 550
NGSGPCTYTI SGSRECEMPH HMKPLPYYSY DQPVIGYCQA HQPLHVTKGY
560 570 580 590
ETVSPEQDES PGLELGRDHS FIATIARSAA PAIYLERIAN
Length:590
Mass (Da):67,217
Last modified:February 5, 2008 - v2
Checksum:iB7CD270E816CD72F
GO
Isoform 2 (identifier: Q86VH4-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     518-518: M → V
     519-590: Missing.

Show »
Length:518
Mass (Da):59,126
Checksum:iF271C0477C170BC6
GO

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei518 – 5181M → V in isoform 2. 2 PublicationsVSP_030989
Alternative sequencei519 – 59072Missing in isoform 2. 2 PublicationsVSP_030990Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY182030 mRNA. Translation: AAO67551.1.
AY358324 mRNA. Translation: AAQ88690.1.
BC099738 mRNA. Translation: AAH99738.1.
BC110058 mRNA. Translation: AAI10059.1.
CCDSiCCDS46346.1. [Q86VH4-1]
CCDS46347.1. [Q86VH4-2]
RefSeqiNP_001128217.1. NM_001134745.1. [Q86VH4-1]
NP_001269853.1. NM_001282924.1. [Q86VH4-1]
NP_079269.4. NM_024993.4. [Q86VH4-2]
UniGeneiHs.285782.

Genome annotation databases

EnsembliENST00000409088; ENSP00000386236; ENSG00000176204. [Q86VH4-2]
ENST00000409093; ENSP00000386357; ENSG00000176204. [Q86VH4-1]
ENST00000409884; ENSP00000387297; ENSG00000176204. [Q86VH4-1]
GeneIDi80059.
KEGGihsa:80059.
UCSCiuc002snq.4. human. [Q86VH4-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY182030 mRNA. Translation: AAO67551.1.
AY358324 mRNA. Translation: AAQ88690.1.
BC099738 mRNA. Translation: AAH99738.1.
BC110058 mRNA. Translation: AAI10059.1.
CCDSiCCDS46346.1. [Q86VH4-1]
CCDS46347.1. [Q86VH4-2]
RefSeqiNP_001128217.1. NM_001134745.1. [Q86VH4-1]
NP_001269853.1. NM_001282924.1. [Q86VH4-1]
NP_079269.4. NM_024993.4. [Q86VH4-2]
UniGeneiHs.285782.

3D structure databases

ProteinModelPortaliQ86VH4.
SMRiQ86VH4. Positions 34-368.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi123095. 2 interactions.
IntActiQ86VH4. 1 interaction.
MINTiMINT-7970553.
STRINGi9606.ENSP00000386357.

PTM databases

iPTMnetiQ86VH4.
PhosphoSiteiQ86VH4.

Polymorphism and mutation databases

BioMutaiLRRTM4.
DMDMi166897996.

Proteomic databases

MaxQBiQ86VH4.
PaxDbiQ86VH4.
PRIDEiQ86VH4.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000409088; ENSP00000386236; ENSG00000176204. [Q86VH4-2]
ENST00000409093; ENSP00000386357; ENSG00000176204. [Q86VH4-1]
ENST00000409884; ENSP00000387297; ENSG00000176204. [Q86VH4-1]
GeneIDi80059.
KEGGihsa:80059.
UCSCiuc002snq.4. human. [Q86VH4-1]

Organism-specific databases

CTDi80059.
GeneCardsiLRRTM4.
HGNCiHGNC:19411. LRRTM4.
MIMi610870. gene.
neXtProtiNX_Q86VH4.
PharmGKBiPA134972631.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0619. Eukaryota.
COG4886. LUCA.
GeneTreeiENSGT00760000118777.
HOGENOMiHOG000290681.
HOVERGENiHBG052362.
InParanoidiQ86VH4.
PhylomeDBiQ86VH4.
TreeFamiTF332659.

Miscellaneous databases

ChiTaRSiLRRTM4. human.
GenomeRNAii80059.
PROiQ86VH4.
SOURCEiSearch...

Gene expression databases

BgeeiQ86VH4.
CleanExiHS_LRRTM4.
ExpressionAtlasiQ86VH4. baseline and differential.
GenevisibleiQ86VH4. HS.

Family and domain databases

Gene3Di3.80.10.10. 2 hits.
InterProiIPR032675. L_dom-like.
IPR001611. Leu-rich_rpt.
IPR003591. Leu-rich_rpt_typical-subtyp.
[Graphical view]
PfamiPF00560. LRR_1. 1 hit.
PF13855. LRR_8. 3 hits.
[Graphical view]
SMARTiSM00369. LRR_TYP. 9 hits.
[Graphical view]
SUPFAMiSSF52058. SSF52058. 1 hit.
PROSITEiPS51450. LRR. 9 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "A novel gene family encoding leucine-rich repeat transmembrane proteins differentially expressed in the nervous system."
    Lauren J., Airaksinen M.S., Saarma M., Timmusk T.T.
    Genomics 81:411-421(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2), TISSUE SPECIFICITY.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
  3. "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] (ISOFORM 2).

Entry informationi

Entry nameiLRRT4_HUMAN
AccessioniPrimary (citable) accession number: Q86VH4
Secondary accession number(s): Q4FZ98, Q6UXJ7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 21, 2005
Last sequence update: February 5, 2008
Last modified: June 8, 2016
This is version 108 of the entry and version 2 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 2
    Human chromosome 2: 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. 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.