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Q9Y639 (NPTN_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 111. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Neuroplastin
Alternative name(s):
Stromal cell-derived receptor 1
Short name=SDR-1
Gene names
Name:NPTN
Synonyms:SDFR1, SDR1
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length398 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Probable homophilic and heterophilic cell adhesion molecule involved in long term potentiation at hippocampal excitatory synapses through activation of p38MAPK. May also regulate neurite outgrowth by activating the FGFR1 signaling pathway. May play a role in synaptic plasticity By similarity.

Subcellular location

Cell membrane; Single-pass type I membrane protein Potential. Note: Enriched at postsynaptic density By similarity.

Tissue specificity

Isoform 1 is ubiquitously expressed. Isoform 2 is expressed in brain cortex and cerebellum (at protein level). Ref.1 Ref.7

Domain

Some isoforms lack the first Ig-like domain which may confer homophilic adhesion activity. However, they can bind and activate FGFR1 By similarity.

Sequence similarities

Contains 3 Ig-like (immunoglobulin-like) domains.

Sequence caution

The sequence BAD93049.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.

Ontologies

Keywords
   Biological processCell adhesion
Neurogenesis
   Cellular componentCell membrane
Membrane
   Coding sequence diversityAlternative splicing
   DomainImmunoglobulin domain
Repeat
Signal
Transmembrane
Transmembrane helix
   PTMDisulfide bond
Glycoprotein
   Technical termComplete proteome
Direct protein sequencing
Reference proteome
Gene Ontology (GO)
   Biological_processhomophilic cell adhesion

Inferred from sequence or structural similarity. Source: HGNC

long-term synaptic potentiation

Inferred from sequence or structural similarity. Source: UniProtKB

positive regulation of cytosolic calcium ion concentration

Inferred from sequence or structural similarity. Source: UniProtKB

positive regulation of fibroblast growth factor receptor signaling pathway

Inferred from sequence or structural similarity. Source: UniProtKB

positive regulation of long-term neuronal synaptic plasticity

Inferred from sequence or structural similarity. Source: HGNC

positive regulation of neuron projection development

Inferred from sequence or structural similarity. Source: UniProtKB

positive regulation of protein phosphorylation

Inferred from sequence or structural similarity. Source: UniProtKB

   Cellular_componentintegral component of membrane

Inferred from electronic annotation. Source: UniProtKB-KW

presynaptic membrane

Inferred from sequence or structural similarity. Source: HGNC

   Molecular_functioncell adhesion molecule binding

Inferred from sequence or structural similarity. Source: HGNC

type 1 fibroblast growth factor receptor binding

Inferred from sequence or structural similarity. Source: UniProtKB

Complete GO annotation...

Alternative products

This entry describes 5 isoforms produced by alternative splicing. [Align] [Select]
Isoform 2 (identifier: Q9Y639-2)

Also known as: SDR-1-beta;

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.
Isoform 1 (identifier: Q9Y639-1)

Also known as: SDR-1-alpha;

The sequence of this isoform differs from the canonical sequence as follows:
     31-147: AGFVKSPMSE...AQATISVLQK → E
Isoform 3 (identifier: Q9Y639-3)

The sequence of this isoform differs from the canonical sequence as follows:
     31-147: AGFVKSPMSE...AQATISVLQK → E
     372-375: Missing.
Isoform 4 (identifier: Q9Y639-4)

The sequence of this isoform differs from the canonical sequence as follows:
     320-398: NAIGSASVVT...DKNLRQRNTN → WPHSGLSWEFWLKLSSLW
Note: No experimental confirmation available.
Isoform 5 (identifier: Q9Y639-5)

The sequence of this isoform differs from the canonical sequence as follows:
     372-375: Missing.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Signal peptide1 – 2828 Ref.6
Chain29 – 398370Neuroplastin
PRO_0000394470

Regions

Topological domain29 – 339311Extracellular Potential
Transmembrane340 – 36021Helical; Potential
Topological domain361 – 39838Cytoplasmic Potential
Domain29 – 134106Ig-like 1
Domain148 – 23588Ig-like 2
Domain238 – 32992Ig-like 3
Region149 – 16113Narpin; mediates binding with FGFR1 and has antidepressant-like activity By similarity

Amino acid modifications

Glycosylation1711N-linked (GlcNAc...) Potential
Glycosylation1971N-linked (GlcNAc...) Potential
Glycosylation2291N-linked (GlcNAc...) Ref.9
Glycosylation2841N-linked (GlcNAc...) Ref.8
Glycosylation2961N-linked (GlcNAc...) Ref.8
Glycosylation3171N-linked (GlcNAc...) Potential
Disulfide bond52 ↔ 116 By similarity
Disulfide bond170 ↔ 218 By similarity
Disulfide bond259 ↔ 316 By similarity

Natural variations

Alternative sequence31 – 147117AGFVK…SVLQK → E in isoform 1 and isoform 3.
VSP_039251
Alternative sequence320 – 39879NAIGS…QRNTN → WPHSGLSWEFWLKLSSLW in isoform 4.
VSP_039252
Alternative sequence372 – 3754Missing in isoform 3 and isoform 5.
VSP_039253

Experimental info

Sequence conflict2991E → K in BAH12519. Ref.2

Sequences

Sequence LengthMass (Da)Tools
Isoform 2 (SDR-1-beta) [UniParc].

Last modified June 15, 2010. Version 2.
Checksum: 5109E3C03B4967EA

FASTA39844,387
        10         20         30         40         50         60 
MSGSSLPSAL ALSLLLVSGS LLPGPGAAQN AGFVKSPMSE TKLTGDAFEL YCDVVGSPTP 

        70         80         90        100        110        120 
EIQWWYAEVN RAESFRQLWD GARKRRVTVN TAYGSNGVSV LRITRLTLED SGTYECRASN 

       130        140        150        160        170        180 
DPKRNDLRQN PSITWIRAQA TISVLQKPRI VTSEEVIIRD SPVLPVTLQC NLTSSSHTLT 

       190        200        210        220        230        240 
YSYWTKNGVE LSATRKNASN MEYRINKPRA EDSGEYHCVY HFVSAPKANA TIEVKAAPDI 

       250        260        270        280        290        300 
TGHKRSENKN EGQDATMYCK SVGYPHPDWI WRKKENGMPM DIVNTSGRFF IINKENYTEL 

       310        320        330        340        350        360 
NIVNLQITED PGEYECNATN AIGSASVVTV LRVRSHLAPL WPFLGILAEI IILVVIIVVY 

       370        380        390 
EKRKRPDEVP DDDEPAGPMK TNSTNNHKDK NLRQRNTN 

« Hide

Isoform 1 (SDR-1-alpha) [UniParc].

Checksum: B3E48A23984A6C4A
Show »

FASTA28231,291
Isoform 3 [UniParc].

Checksum: 458E026CC87DD657
Show »

FASTA27830,835
Isoform 4 [UniParc].

Checksum: 8C043513B3BCD50C
Show »

FASTA33737,792
Isoform 5 [UniParc].

Checksum: C68D09CC61FB4B49
Show »

FASTA39443,931

References

« Hide 'large scale' references
[1]"Isoform specific expression of the SDR-1 protein, alpha and beta in subregions of adult rodent brain."
Lopez N.D., Kinoshita A., Taniwaki M., Tada H., Shirozu M., Nakano T., Tashiro K., Honjo T.
Biomed. Res. 20:43-49(1999)
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1; 2 AND 3), TISSUE SPECIFICITY.
[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. expand/collapse author list , 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] (ISOFORMS 1 AND 5).
Tissue: Brain and Stomach.
[3]Totoki Y., Toyoda A., Takeda T., Sakaki Y., Tanaka A., Yokoyama S., Ohara O., Nagase T., Kikuno R.F.
Submitted (MAR-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 4).
Tissue: Brain.
[4]Mural R.J., Istrail S., Sutton G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases
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] (ISOFORMS 1 AND 3).
Tissue: Brain and Skin.
[6]"Signal peptide prediction based on analysis of experimentally verified cleavage sites."
Zhang Z., Henzel W.J.
Protein Sci. 13:2819-2824(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 29-43 (ISOFORM 1).
[7]"The immunolocalization of the synaptic glycoprotein neuroplastin differs substantially between the human and the rodent brain."
Bernstein H.G., Smalla K.H., Bogerts B., Gordon-Weeks P.R., Beesley P.W., Gundelfinger E.D., Kreutz M.R.
Brain Res. 1134:107-112(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: TISSUE SPECIFICITY.
[8]"Glycoproteomics analysis of human liver tissue by combination of multiple enzyme digestion and hydrazide chemistry."
Chen R., Jiang X., Sun D., Han G., Wang F., Ye M., Wang L., Zou H.
J. Proteome Res. 8:651-661(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: GLYCOSYLATION [LARGE SCALE ANALYSIS] AT ASN-284 AND ASN-296.
Tissue: Liver.
[9]"Mass-spectrometric identification and relative quantification of N-linked cell surface glycoproteins."
Wollscheid B., Bausch-Fluck D., Henderson C., O'Brien R., Bibel M., Schiess R., Aebersold R., Watts J.D.
Nat. Biotechnol. 27:378-386(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: GLYCOSYLATION [LARGE SCALE ANALYSIS] AT ASN-229.
Tissue: Leukemic T-cell.
[10]"Initial characterization of the human central proteome."
Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.
BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AF109126 mRNA. Translation: AAD43217.1.
AF109127 mRNA. Translation: AAD43218.1.
AK297184 mRNA. Translation: BAH12519.1.
AK314248 mRNA. Translation: BAG36914.1.
AB209812 mRNA. Translation: BAD93049.1. Different initiation.
CH471082 Genomic DNA. Translation: EAW77931.1.
BC105979 mRNA. Translation: AAI05980.1.
BC117462 mRNA. Translation: AAI17463.1.
BC143880 mRNA. Translation: AAI43881.1.
BC143881 mRNA. Translation: AAI43882.1.
PIRT17219.
RefSeqNP_001154835.1. NM_001161363.1.
NP_001154836.1. NM_001161364.1.
NP_036560.1. NM_012428.3.
NP_059429.1. NM_017455.3.
UniGeneHs.744867.

3D structure databases

ProteinModelPortalQ9Y639.
SMRQ9Y639. Positions 31-334.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid117958. 9 interactions.
IntActQ9Y639. 3 interactions.
MINTMINT-4542281.
STRING9606.ENSP00000290401.

PTM databases

PhosphoSiteQ9Y639.

Polymorphism databases

DMDM298286871.

Proteomic databases

PaxDbQ9Y639.
PRIDEQ9Y639.

Protocols and materials databases

DNASU27020.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000345330; ENSP00000290401; ENSG00000156642. [Q9Y639-2]
ENST00000351217; ENSP00000342958; ENSG00000156642. [Q9Y639-1]
ENST00000562924; ENSP00000456349; ENSG00000156642. [Q9Y639-3]
ENST00000563691; ENSP00000457028; ENSG00000156642. [Q9Y639-5]
GeneID27020.
KEGGhsa:27020.
UCSCuc002avr.3. human. [Q9Y639-3]
uc002avs.3. human. [Q9Y639-2]
uc002avt.3. human. [Q9Y639-1]
uc010bjc.3. human. [Q9Y639-5]

Organism-specific databases

CTD27020.
GeneCardsGC15M073852.
HGNCHGNC:17867. NPTN.
HPAHPA051497.
MIM612820. gene.
neXtProtNX_Q9Y639.
PharmGKBPA134927704.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG149118.
HOVERGENHBG008120.
OMAAITWIRA.
OrthoDBEOG7V1FQN.
PhylomeDBQ9Y639.
TreeFamTF326759.

Gene expression databases

ArrayExpressQ9Y639.
BgeeQ9Y639.
CleanExHS_NPTN.
GenevestigatorQ9Y639.

Family and domain databases

Gene3D2.60.40.10. 3 hits.
InterProIPR007110. Ig-like_dom.
IPR013783. Ig-like_fold.
IPR013098. Ig_I-set.
IPR003599. Ig_sub.
IPR003598. Ig_sub2.
IPR027112. Neuroplastin.
[Graphical view]
PANTHERPTHR10075:SF5. PTHR10075:SF5. 1 hit.
PfamPF07679. I-set. 2 hits.
[Graphical view]
SMARTSM00409. IG. 1 hit.
SM00408. IGc2. 2 hits.
[Graphical view]
PROSITEPS50835. IG_LIKE. 3 hits.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSNPTN. human.
GeneWikiNPTN.
GenomeRNAi27020.
NextBio49544.
PROQ9Y639.
SOURCESearch...

Entry information

Entry nameNPTN_HUMAN
AccessionPrimary (citable) accession number: Q9Y639
Secondary accession number(s): B2RAL7 expand/collapse secondary AC list , B7Z4D3, B7ZLL2, Q17R52, Q59EJ9, Q6NVX7, Q9Y640
Entry history
Integrated into UniProtKB/Swiss-Prot: January 10, 2006
Last sequence update: June 15, 2010
Last modified: April 16, 2014
This is version 111 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human chromosome 15

Human chromosome 15: entries, gene names and cross-references to MIM