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Protein

Leucine-rich repeat and fibronectin type-III domain-containing protein 2

Gene

LRFN2

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

Functioni

Promotes neurite outgrowth in hippocampal neurons. Enhances the cell surface expression of 2 NMDA receptor subunits GRIN1 and GRIN2A. May play a role in redistributing DLG4 to the cell periphery (By similarity).By similarity

GO - Biological processi

Complete GO annotation...

Enzyme and pathway databases

ReactomeiR-HSA-8849932. SALM protein interactions at the synapse.

Names & Taxonomyi

Protein namesi
Recommended name:
Leucine-rich repeat and fibronectin type-III domain-containing protein 2
Alternative name(s):
Synaptic adhesion-like molecule 1
Gene namesi
Name:LRFN2
Synonyms:KIAA1246, SALM1
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 6

Organism-specific databases

HGNCiHGNC:21226. LRFN2.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini21 – 534514ExtracellularSequence analysisAdd
BLAST
Transmembranei535 – 55521HelicalSequence analysisAdd
BLAST
Topological domaini556 – 789234CytoplasmicSequence analysisAdd
BLAST

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

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

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi787 – 7893Missing : Loss of DLG1-, DLG3- and DLG4-binding. 1 Publication

Organism-specific databases

PharmGKBiPA134913285.

Polymorphism and mutation databases

BioMutaiLRFN2.
DMDMi62286951.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 2020Sequence analysisAdd
BLAST
Chaini21 – 789769Leucine-rich repeat and fibronectin type-III domain-containing protein 2PRO_0000014838Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi29 – 291N-linked (GlcNAc...)Sequence analysis
Disulfide bondi310 ↔ 359PROSITE-ProRule annotation
Glycosylationi332 – 3321N-linked (GlcNAc...)Sequence analysis
Glycosylationi341 – 3411N-linked (GlcNAc...)Sequence analysis
Glycosylationi384 – 3841N-linked (GlcNAc...)Sequence analysis

Post-translational modificationi

Glycosylated.By similarity

Keywords - PTMi

Disulfide bond, Glycoprotein

Proteomic databases

PaxDbiQ9ULH4.
PeptideAtlasiQ9ULH4.
PRIDEiQ9ULH4.

PTM databases

iPTMnetiQ9ULH4.
PhosphoSiteiQ9ULH4.

Expressioni

Gene expression databases

BgeeiQ9ULH4.
CleanExiHS_LRFN2.
GenevisibleiQ9ULH4. HS.

Organism-specific databases

HPAiHPA013653.

Interactioni

Subunit structurei

Forms heteromeric complexes with LRFN1, LRFN3, LRFN4 and LRFN5. Can form homomeric complexes, but not across cell junctions. Directly interacts with 2 NMDA receptor subunits GRIN1 and GRIN2A (By similarity). Interacts with DLG1, DLG2, DLG3 and DLG4.By similarity1 Publication

Protein-protein interaction databases

BioGridi121564. 1 interaction.
STRINGi9606.ENSP00000345985.

Structurei

3D structure databases

ProteinModelPortaliQ9ULH4.
SMRiQ9ULH4. Positions 20-499.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini21 – 5232LRRNTAdd
BLAST
Repeati53 – 7422LRR 1Add
BLAST
Repeati77 – 9822LRR 2Add
BLAST
Repeati101 – 12222LRR 3Add
BLAST
Repeati125 – 14622LRR 4Add
BLAST
Repeati150 – 17122LRR 5Add
BLAST
Repeati174 – 19522LRR 6Add
BLAST
Repeati198 – 21922LRR 7Add
BLAST
Domaini242 – 28847LRRCTAdd
BLAST
Domaini289 – 37587Ig-likeAdd
BLAST
Domaini421 – 51898Fibronectin type-IIIPROSITE-ProRule annotationAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi786 – 7894PDZ-binding

Domaini

The PDZ-binding motif is required for cell surface expression, neurite outgrowth promotion (By similarity). This motif is also involved in DLG1-, DLG3- and DLG4-binding.By similarity

Sequence similaritiesi

Belongs to the LRFN family.Curated
Contains 1 fibronectin type-III domain.PROSITE-ProRule annotation
Contains 7 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.
HOGENOMiHOG000237343.
HOVERGENiHBG052352.
InParanoidiQ9ULH4.
KOiK16355.
OMAiRMIPASN.
OrthoDBiEOG75B84P.
PhylomeDBiQ9ULH4.
TreeFamiTF350185.

Family and domain databases

Gene3Di2.60.40.10. 2 hits.
3.80.10.10. 1 hit.
InterProiIPR000483. Cys-rich_flank_reg_C.
IPR003961. FN3_dom.
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.
[Graphical view]
PfamiPF00041. fn3. 1 hit.
PF07679. I-set. 1 hit.
PF13855. LRR_8. 2 hits.
[Graphical view]
SMARTiSM00409. IG. 1 hit.
SM00408. IGc2. 1 hit.
SM00369. LRR_TYP. 6 hits.
SM00082. LRRCT. 1 hit.
[Graphical view]
SUPFAMiSSF48726. SSF48726. 1 hit.
SSF49265. SSF49265. 1 hit.
SSF52058. SSF52058. 1 hit.
PROSITEiPS50853. FN3. 1 hit.
PS50835. IG_LIKE. 1 hit.
PS51450. LRR. 6 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

Q9ULH4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
METLLGGLLA FGMAFAVVDA CPKYCVCQNL SESLGTLCPS KGLLFVPPDI
60 70 80 90 100
DRRTVELRLG GNFIIHISRQ DFANMTGLVD LTLSRNTISH IQPFSFLDLE
110 120 130 140 150
SLRSLHLDSN RLPSLGEDTL RGLVNLQHLI VNNNQLGGIA DEAFEDFLLT
160 170 180 190 200
LEDLDLSYNN LHGLPWDSVR RMVNLHQLSL DHNLLDHIAE GTFADLQKLA
210 220 230 240 250
RLDLTSNRLQ KLPPDPIFAR SQASALTATP FAPPLSFSFG GNPLHCNCEL
260 270 280 290 300
LWLRRLERDD DLETCGSPGG LKGRYFWHVR EEEFVCEPPL ITQHTHKLLV
310 320 330 340 350
LEGQAATLKC KAIGDPSPLI HWVAPDDRLV GNSSRTAVYD NGTLDIFITT
360 370 380 390 400
SQDSGAFTCI AANAAGEATA MVEVSIVQLP HLSNSTSRTA PPKSRLSDIT
410 420 430 440 450
GSSKTSRGGG GSGGGEPPKS PPERAVLVSE VTTTSALVKW SVSKSAPRVK
460 470 480 490 500
MYQLQYNCSD DEVLIYRMIP ASNKAFVVNN LVSGTGYDLC VLAMWDDTAT
510 520 530 540 550
TLTATNIVGC AQFFTKADYP QCQSMHSQIL GGTMILVIGG IIVATLLVFI
560 570 580 590 600
VILMVRYKVC NHEAPSKMAA AVSNVYSQTN GAQPPPPSSA PAGAPPQGPP
610 620 630 640 650
KVVVRNELLD FTASLARASD SSSSSSLGSG EAAGLGRAPW RIPPSAPRPK
660 670 680 690 700
PSLDRLMGAF ASLDLKSQRK EELLDSRTPA GRGAGTSARG HHSDREPLLG
710 720 730 740 750
PPAARARSLL PLPLEGKAKR SHSFDMGDFA AAAAGGVVPG GYSPPRKVSN
760 770 780
IWTKRSLSVN GMLLPFEESD LVGARGTFGS SEWVMESTV
Length:789
Mass (Da):84,731
Last modified:March 29, 2005 - v2
Checksum:i3D1D298909267F38
GO

Sequence cautioni

The sequence BAA86560.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti770 – 7701D → N.
Corresponds to variant rs3734559 [ dbSNP | Ensembl ].
VAR_049894

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB033072 mRNA. Translation: BAA86560.1. Different initiation.
AK291474 mRNA. Translation: BAF84163.1.
AL591063 Genomic DNA. Translation: CAI15264.1.
CH471081 Genomic DNA. Translation: EAX04006.1.
BC142616 mRNA. Translation: AAI42617.1.
CCDSiCCDS34443.1.
RefSeqiNP_065788.1. NM_020737.2.
XP_011513063.1. XM_011514761.1.
XP_011513064.1. XM_011514762.1.
UniGeneiHs.250015.

Genome annotation databases

EnsembliENST00000338305; ENSP00000345985; ENSG00000156564.
GeneIDi57497.
KEGGihsa:57497.
UCSCiuc003oph.2. human.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB033072 mRNA. Translation: BAA86560.1. Different initiation.
AK291474 mRNA. Translation: BAF84163.1.
AL591063 Genomic DNA. Translation: CAI15264.1.
CH471081 Genomic DNA. Translation: EAX04006.1.
BC142616 mRNA. Translation: AAI42617.1.
CCDSiCCDS34443.1.
RefSeqiNP_065788.1. NM_020737.2.
XP_011513063.1. XM_011514761.1.
XP_011513064.1. XM_011514762.1.
UniGeneiHs.250015.

3D structure databases

ProteinModelPortaliQ9ULH4.
SMRiQ9ULH4. Positions 20-499.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi121564. 1 interaction.
STRINGi9606.ENSP00000345985.

PTM databases

iPTMnetiQ9ULH4.
PhosphoSiteiQ9ULH4.

Polymorphism and mutation databases

BioMutaiLRFN2.
DMDMi62286951.

Proteomic databases

PaxDbiQ9ULH4.
PeptideAtlasiQ9ULH4.
PRIDEiQ9ULH4.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000338305; ENSP00000345985; ENSG00000156564.
GeneIDi57497.
KEGGihsa:57497.
UCSCiuc003oph.2. human.

Organism-specific databases

CTDi57497.
GeneCardsiLRFN2.
HGNCiHGNC:21226. LRFN2.
HPAiHPA013653.
MIMi612808. gene.
neXtProtiNX_Q9ULH4.
PharmGKBiPA134913285.
HUGEiSearch...
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0619. Eukaryota.
COG4886. LUCA.
GeneTreeiENSGT00760000118831.
HOGENOMiHOG000237343.
HOVERGENiHBG052352.
InParanoidiQ9ULH4.
KOiK16355.
OMAiRMIPASN.
OrthoDBiEOG75B84P.
PhylomeDBiQ9ULH4.
TreeFamiTF350185.

Enzyme and pathway databases

ReactomeiR-HSA-8849932. SALM protein interactions at the synapse.

Miscellaneous databases

ChiTaRSiLRFN2. human.
GenomeRNAii57497.
PROiQ9ULH4.
SOURCEiSearch...

Gene expression databases

BgeeiQ9ULH4.
CleanExiHS_LRFN2.
GenevisibleiQ9ULH4. HS.

Family and domain databases

Gene3Di2.60.40.10. 2 hits.
3.80.10.10. 1 hit.
InterProiIPR000483. Cys-rich_flank_reg_C.
IPR003961. FN3_dom.
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.
[Graphical view]
PfamiPF00041. fn3. 1 hit.
PF07679. I-set. 1 hit.
PF13855. LRR_8. 2 hits.
[Graphical view]
SMARTiSM00409. IG. 1 hit.
SM00408. IGc2. 1 hit.
SM00369. LRR_TYP. 6 hits.
SM00082. LRRCT. 1 hit.
[Graphical view]
SUPFAMiSSF48726. SSF48726. 1 hit.
SSF49265. SSF49265. 1 hit.
SSF52058. SSF52058. 1 hit.
PROSITEiPS50853. FN3. 1 hit.
PS50835. IG_LIKE. 1 hit.
PS51450. LRR. 6 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Prediction of the coding sequences of unidentified human genes. XV. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro."
    Nagase T., Ishikawa K., Kikuno R., Hirosawa M., Nomura N., Ohara O.
    DNA Res. 6:337-345(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Brain.
  2. "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: Fetal brain.
  3. "The DNA sequence and analysis of human chromosome 6."
    Mungall A.J., Palmer S.A., Sims S.K., Edwards C.A., Ashurst J.L., Wilming L., Jones M.C., Horton R., Hunt S.E., Scott C.E., Gilbert J.G.R., Clamp M.E., Bethel G., Milne S., Ainscough R., Almeida J.P., Ambrose K.D., Andrews T.D.
    , Ashwell R.I.S., Babbage A.K., Bagguley C.L., Bailey J., Banerjee R., Barker D.J., Barlow K.F., Bates K., Beare D.M., Beasley H., Beasley O., Bird C.P., Blakey S.E., Bray-Allen S., Brook J., Brown A.J., Brown J.Y., Burford D.C., Burrill W., Burton J., Carder C., Carter N.P., Chapman J.C., Clark S.Y., Clark G., Clee C.M., Clegg S., Cobley V., Collier R.E., Collins J.E., Colman L.K., Corby N.R., Coville G.J., Culley K.M., Dhami P., Davies J., Dunn M., Earthrowl M.E., Ellington A.E., Evans K.A., Faulkner L., Francis M.D., Frankish A., Frankland J., French L., Garner P., Garnett J., Ghori M.J., Gilby L.M., Gillson C.J., Glithero R.J., Grafham D.V., Grant M., Gribble S., Griffiths C., Griffiths M.N.D., Hall R., Halls K.S., Hammond S., Harley J.L., Hart E.A., Heath P.D., Heathcott R., Holmes S.J., Howden P.J., Howe K.L., Howell G.R., Huckle E., Humphray S.J., Humphries M.D., Hunt A.R., Johnson C.M., Joy A.A., Kay M., Keenan S.J., Kimberley A.M., King A., Laird G.K., Langford C., Lawlor S., Leongamornlert D.A., Leversha M., Lloyd C.R., Lloyd D.M., Loveland J.E., Lovell J., Martin S., Mashreghi-Mohammadi M., Maslen G.L., Matthews L., McCann O.T., McLaren S.J., McLay K., McMurray A., Moore M.J.F., Mullikin J.C., Niblett D., Nickerson T., Novik K.L., Oliver K., Overton-Larty E.K., Parker A., Patel R., Pearce A.V., Peck A.I., Phillimore B.J.C.T., Phillips S., Plumb R.W., Porter K.M., Ramsey Y., Ranby S.A., Rice C.M., Ross M.T., Searle S.M., Sehra H.K., Sheridan E., Skuce C.D., Smith S., Smith M., Spraggon L., Squares S.L., Steward C.A., Sycamore N., Tamlyn-Hall G., Tester J., Theaker A.J., Thomas D.W., Thorpe A., Tracey A., Tromans A., Tubby B., Wall M., Wallis J.M., West A.P., White S.S., Whitehead S.L., Whittaker H., Wild A., Willey D.J., Wilmer T.E., Wood J.M., Wray P.W., Wyatt J.C., Young L., Younger R.M., Bentley D.R., Coulson A., Durbin R.M., Hubbard T., Sulston J.E., Dunham I., Rogers J., Beck S.
    Nature 425:805-811(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  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].
  6. "SALM synaptic cell adhesion-like molecules regulate the differentiation of excitatory synapses."
    Ko J., Kim S., Chung H.S., Kim K., Han K., Kim H., Jun H., Kaang B.-K., Kim E.
    Neuron 50:233-245(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH DLG1; DLG2; DLG3 AND DLG4, MUTAGENESIS OF 787-SER--VAL-789.

Entry informationi

Entry nameiLRFN2_HUMAN
AccessioniPrimary (citable) accession number: Q9ULH4
Secondary accession number(s): A5PKU3, Q5SYP9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 29, 2005
Last sequence update: March 29, 2005
Last modified: July 6, 2016
This is version 132 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 6
    Human chromosome 6: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. 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.