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O88689 (PCDA4_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 99. 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:
Protocadherin alpha-4

Short name=PCDH-alpha-4
Gene names
Name:Pcdha4
Synonyms:Cnr1
OrganismMus musculus (Mouse) [Reference proteome]
Taxonomic identifier10090 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus

Protein attributes

Sequence length947 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance of specific neuronal connections in the brain By similarity.

Subunit structure

Interacts with FYN. Ref.1

Subcellular location

Cell membrane; Single-pass type I membrane protein. Note: Detected in dendrites and synapses. Ref.1

Tissue specificity

Detected in brain throughout embryonic development. Detected in adult brain, in particular in cerebellum and forebrain. Ref.1

Sequence similarities

Contains 6 cadherin domains.

Ontologies

Keywords
   Biological processCell adhesion
   Cellular componentCell membrane
Membrane
   Coding sequence diversityAlternative splicing
   DomainRepeat
Signal
Transmembrane
Transmembrane helix
   LigandCalcium
   PTMGlycoprotein
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processhomophilic cell adhesion

Inferred from electronic annotation. Source: InterPro

   Cellular_componentintegral component of membrane

Inferred from electronic annotation. Source: UniProtKB-KW

plasma membrane

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_functioncalcium ion binding

Inferred from electronic annotation. Source: InterPro

Complete GO annotation...

Alternative products

This entry describes 3 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: O88689-1)

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 2 (identifier: O88689-2)

The sequence of this isoform differs from the canonical sequence as follows:
     535-795: Missing.
     879-947: GELPDKFIIP...GNSTTDNSDQ → EPKKQTQVSFLPRRKGEASQPRQ
Isoform 3 (identifier: O88689-3)

The sequence of this isoform differs from the canonical sequence as follows:
     796-947: PRQPNPDWRY...GNSTTDNSDQ → QAPPNTDWRF...KKKSGKKEKK

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Signal peptide1 – 2929 Potential
Chain30 – 947918Protocadherin alpha-4
PRO_0000240663

Regions

Topological domain30 – 697668Extracellular Potential
Transmembrane698 – 71821Helical; Potential
Topological domain719 – 947229Cytoplasmic Potential
Domain30 – 133104Cadherin 1
Domain134 – 242109Cadherin 2
Domain243 – 350108Cadherin 3
Domain351 – 455105Cadherin 4
Domain456 – 565110Cadherin 5
Domain573 – 681109Cadherin 6
Repeat734 – 7374PXXP 1
Repeat774 – 7774PXXP 2
Repeat796 – 7994PXXP 3
Repeat829 – 8324PXXP 4
Repeat870 – 8734PXXP 5
Repeat888 – 8914PXXP 6
Region734 – 8911586 X 4 AA repeats of P-X-X-P
Compositional bias920 – 9278Poly-Lys

Amino acid modifications

Glycosylation2571N-linked (GlcNAc...) Potential
Glycosylation2651N-linked (GlcNAc...) Potential
Glycosylation5481N-linked (GlcNAc...) Potential

Natural variations

Alternative sequence535 – 795261Missing in isoform 2.
VSP_019413
Alternative sequence796 – 947152PRQPN…DNSDQ → QAPPNTDWRFSQAQRPGTSG SQNGDETGTWPNNQFDTEML QAMILASASEAADGSSTLGG GAGTMGLSARYGPQFTLQHV PDYRQNVYIPGSNATLTNAA GKRDGKAPAGGNGNKKKSGK KEKK in isoform 3.
VSP_019414
Alternative sequence879 – 94769GELPD…DNSDQ → EPKKQTQVSFLPRRKGEASQ PRQ in isoform 2.
VSP_019415

Secondary structure

...................... 947
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified November 1, 1998. Version 1.
Checksum: 082497DBBAEFB503

FASTA947103,143
        10         20         30         40         50         60 
MEFSWGSGQE SQRLLLSFLL LAIWEAGNSQ IHYSIPEEAK HGTFVGRIAQ DLGLELTELV 

        70         80         90        100        110        120 
PRLFRVASKD RGDLLEVNLQ NGILFVNSRI DREELCGRSA ECSIHLEVIV DRPLQVFHVE 

       130        140        150        160        170        180 
VEVRDINDNP PRFPTTQKNL FIAESRPLDT WFPLEGASDA DIGINAVLTY RLSPNDYFSL 

       190        200        210        220        230        240 
EKPSNDERVK GLGLVLRKSL DREETPEIIL VLTVTDGGKP ELTGSVQLLI TVLDANDNAP 

       250        260        270        280        290        300 
VFDRSLYTVK LPENVPNGTL VVKVNASDLD EGVNGDIMYS FSTDISPNVK YKFHIDPVSG 

       310        320        330        340        350        360 
EIIVKGYIDF EECKSYEILI EGIDKGQLPL SGHCKVIVQV EDINDNVPEL EFKSLSLPIR 

       370        380        390        400        410        420 
ENSPVGTVIA LISVSDRDTG VNGQVTCSLT SHVPFKLVST FKNYYSLVLD SALDRETTAD 

       430        440        450        460        470        480 
YKVVVTARDG GSPSLWATAS VSVEVADVND NAPVFAQPEY TVFVKENNPP GAHIFTVSAM 

       490        500        510        520        530        540 
DADAQENALV SYSLVERRVG ERLLSSYVSV HAESGKVFAL QPLDHEELEL LRFQVSARDA 

       550        560        570        580        590        600 
GVPALGSNVT LQVFVLDEND NAPTLLEPEA GVSGGIVSRL VSRSVGAGHV VAKVRAVDAD 

       610        620        630        640        650        660 
SGYNAWLSYE LQSSEGNSRS LFRVGLYTGE ISTTRILDEA DSPRQRLLVL VKDHGDPAMI 

       670        680        690        700        710        720 
VTATVLVSLV ENGPVPKAPS RVSTSVTHSE ASLVDVNVYL IIAICAVSSL LVLTLLLYTA 

       730        740        750        760        770        780 
LRCSTVPSES VCGPPKPVMV CSSAVGSWSY SQQRRQRVCS GEYPPKTDLM AFSPSLSDSR 

       790        800        810        820        830        840 
DREDQLQSAE DSSGKPRQPN PDWRYSASLR AGMHSSVHLE EAGILRAGPG GPDQQWPTVS 

       850        860        870        880        890        900 
SATPEPEAGE VSPPVGAGVN SNSWTFKYGP GNPKQSGPGE LPDKFIIPGS PAIISIRQEP 

       910        920        930        940 
ANNQIDKSDF ITFGKKEETK KKKKKKKGNK TQEKKEKGNS TTDNSDQ 

« Hide

Isoform 2 [UniParc].

Checksum: 7B8393620F457915
Show »

FASTA64070,430
Isoform 3 [UniParc].

Checksum: 21D65CCE53617EB5
Show »

FASTA91999,666

References

« Hide 'large scale' references
[1]"Diversity revealed by a novel family of cadherins expressed in neurons at a synaptic complex."
Kohmura N., Senzaki K., Hamada S., Kai N., Yasuda R., Watanabe M., Ishii H., Yasuda M., Mishina M., Yagi T.
Neuron 20:1137-1151(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), INTERACTION WITH FYN, SUBCELLULAR LOCATION, TISSUE SPECIFICITY.
Strain: C57BL/6J.
Tissue: Brain.
[2]"Comparative DNA sequence analysis of mouse and human protocadherin gene clusters."
Wu Q., Zhang T., Cheng J.-F., Kim Y., Grimwood J., Schmutz J., Dickson M., Noonan J.P., Zhang M.Q., Myers R.M., Maniatis T.
Genome Res. 11:389-404(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
Tissue: Brain.
[3]"Molecular mechanisms governing Pcdh-gamma gene expression: evidence for a multiple promoter and cis-alternative splicing model."
Wang X., Su H., Bradley A.
Genes Dev. 16:1890-1905(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA] (ISOFORM 3).
Strain: C57BL/6J.
[4]"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).
Strain: C57BL/6.
Tissue: Brain.
[5]"The transcriptional landscape of the mammalian genome."
Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J. expand/collapse author list , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1-919 (ISOFORM 1).
Strain: C57BL/6J.
Tissue: Retina.
[6]"1H, 13C and 15N resonance assignments of the first cadherin domain of cadherin-related neuronal receptor (CNR)/protocadherin alpha."
Umitsu M., Morishita H., Murata Y., Udaka K., Akutsu H., Yagi T., Ikegami T.
J. Biomol. NMR 31:365-366(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: STRUCTURE BY NMR OF 27-129.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
D86916 mRNA. Translation: BAA29045.1.
AY013762 mRNA. Translation: AAK26051.1.
AF464178 Genomic DNA. Translation: AAM93577.1.
AF464180 mRNA. Translation: AAM93579.1.
BC060211 mRNA. Translation: AAH60211.1.
AK149282 mRNA. Translation: BAE28788.1.
CCDSCCDS37776.1. [O88689-1]
RefSeqNP_001167625.1. NM_001174154.1. [O88689-3]
NP_031792.1. NM_007766.2. [O88689-1]
UniGeneMm.308500.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1WUZNMR-A27-129[»]
ProteinModelPortalO88689.
SMRO88689. Positions 27-667.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-41020N.
MINTMINT-113982.

PTM databases

PhosphoSiteO88689.

Proteomic databases

PaxDbO88689.
PRIDEO88689.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENSMUST00000115661; ENSMUSP00000111325; ENSMUSG00000007440. [O88689-1]
GeneID100384868.
12936.
KEGGmmu:100384868.
mmu:12936.
UCSCuc008eox.2. mouse. [O88689-1]
uc008eoy.1. mouse. [O88689-3]

Organism-specific databases

CTD100384868.
56144.
MGIMGI:1298406. Pcdha4.

Phylogenomic databases

eggNOGNOG267459.
GeneTreeENSGT00750000117438.
HOGENOMHOG000220892.
HOVERGENHBG054878.
KOK16493.

Gene expression databases

ArrayExpressO88689.
BgeeO88689.
CleanExMM_CNR1.
MM_PCDHA4.
GenevestigatorO88689.

Family and domain databases

Gene3D2.60.40.60. 6 hits.
InterProIPR002126. Cadherin.
IPR015919. Cadherin-like.
IPR020894. Cadherin_CS.
IPR013164. Cadherin_N.
[Graphical view]
PfamPF00028. Cadherin. 5 hits.
PF08266. Cadherin_2. 1 hit.
[Graphical view]
PRINTSPR00205. CADHERIN.
SMARTSM00112. CA. 6 hits.
[Graphical view]
SUPFAMSSF49313. SSF49313. 6 hits.
PROSITEPS00232. CADHERIN_1. 5 hits.
PS50268. CADHERIN_2. 6 hits.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceO88689.
NextBio282614.
PROO88689.
SOURCESearch...

Entry information

Entry namePCDA4_MOUSE
AccessionPrimary (citable) accession number: O88689
Secondary accession number(s): Q3UEX3 expand/collapse secondary AC list , Q6PAM9, Q8K487, Q8K489
Entry history
Integrated into UniProtKB/Swiss-Prot: June 27, 2006
Last sequence update: November 1, 1998
Last modified: July 9, 2014
This is version 99 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MGD cross-references

Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot