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O88689

- PCDA4_MOUSE

UniProt

O88689 - PCDA4_MOUSE

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Protein
Protocadherin alpha-4
Gene
Pcdha4, Cnr1
Organism
Mus musculus (Mouse)
Status
Reviewed - Annotation score: 4 out of 5 - Experimental evidence at protein leveli

Functioni

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

GO - Molecular functioni

  1. calcium ion binding Source: InterPro
Complete GO annotation...

GO - Biological processi

  1. homophilic cell adhesion Source: InterPro
Complete GO annotation...

Keywords - Biological processi

Cell adhesion

Keywords - Ligandi

Calcium

Names & Taxonomyi

Protein namesi
Recommended name:
Protocadherin alpha-4
Short name:
PCDH-alpha-4
Gene namesi
Name:Pcdha4
Synonyms:Cnr1
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
ProteomesiUP000000589: Chromosome 18

Organism-specific databases

MGIiMGI:1298406. Pcdha4.

Subcellular locationi

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

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini30 – 697668Extracellular Reviewed prediction
Add
BLAST
Transmembranei698 – 71821Helical; Reviewed prediction
Add
BLAST
Topological domaini719 – 947229Cytoplasmic Reviewed prediction
Add
BLAST

GO - Cellular componenti

  1. integral component of membrane Source: UniProtKB-KW
  2. plasma membrane Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Membrane

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 2929 Reviewed prediction
Add
BLAST
Chaini30 – 947918Protocadherin alpha-4
PRO_0000240663Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi257 – 2571N-linked (GlcNAc...) Reviewed prediction
Glycosylationi265 – 2651N-linked (GlcNAc...) Reviewed prediction
Glycosylationi548 – 5481N-linked (GlcNAc...) Reviewed prediction

Keywords - PTMi

Glycoprotein

Proteomic databases

PaxDbiO88689.
PRIDEiO88689.

PTM databases

PhosphoSiteiO88689.

Expressioni

Tissue specificityi

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

Gene expression databases

ArrayExpressiO88689.
BgeeiO88689.
CleanExiMM_CNR1.
MM_PCDHA4.
GenevestigatoriO88689.

Interactioni

Subunit structurei

Interacts with FYN.1 Publication

Protein-protein interaction databases

DIPiDIP-41020N.
MINTiMINT-113982.

Structurei

Secondary structure

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi30 – 389
Helixi48 – 525
Helixi56 – 594
Turni60 – 634
Beta strandi74 – 774
Turni79 – 813
Beta strandi84 – 863
Helixi92 – 954
Beta strandi97 – 1015
Beta strandi103 – 1108
Turni111 – 1144
Beta strandi115 – 12410

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1WUZNMR-A27-129[»]
ProteinModelPortaliO88689.
SMRiO88689. Positions 27-667.

Miscellaneous databases

EvolutionaryTraceiO88689.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini30 – 133104Cadherin 1
Add
BLAST
Domaini134 – 242109Cadherin 2
Add
BLAST
Domaini243 – 350108Cadherin 3
Add
BLAST
Domaini351 – 455105Cadherin 4
Add
BLAST
Domaini456 – 565110Cadherin 5
Add
BLAST
Domaini573 – 681109Cadherin 6
Add
BLAST
Repeati734 – 7374PXXP 1
Repeati774 – 7774PXXP 2
Repeati796 – 7994PXXP 3
Repeati829 – 8324PXXP 4
Repeati870 – 8734PXXP 5
Repeati888 – 8914PXXP 6

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni734 – 8911586 X 4 AA repeats of P-X-X-P
Add
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi920 – 9278Poly-Lys

Sequence similaritiesi

Contains 6 cadherin domains.

Keywords - Domaini

Repeat, Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiNOG267459.
GeneTreeiENSGT00750000117438.
HOGENOMiHOG000220892.
HOVERGENiHBG054878.
KOiK16493.

Family and domain databases

Gene3Di2.60.40.60. 6 hits.
InterProiIPR002126. Cadherin.
IPR015919. Cadherin-like.
IPR020894. Cadherin_CS.
IPR013164. Cadherin_N.
[Graphical view]
PfamiPF00028. Cadherin. 5 hits.
PF08266. Cadherin_2. 1 hit.
[Graphical view]
PRINTSiPR00205. CADHERIN.
SMARTiSM00112. CA. 6 hits.
[Graphical view]
SUPFAMiSSF49313. SSF49313. 6 hits.
PROSITEiPS00232. CADHERIN_1. 5 hits.
PS50268. CADHERIN_2. 6 hits.
[Graphical view]

Sequences (3)i

Sequence statusi: Complete.

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

This entry describes 3 isoformsi produced by alternative splicing. Align

Isoform 1 (identifier: O88689-1) [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

MEFSWGSGQE SQRLLLSFLL LAIWEAGNSQ IHYSIPEEAK HGTFVGRIAQ    50
DLGLELTELV PRLFRVASKD RGDLLEVNLQ NGILFVNSRI DREELCGRSA 100
ECSIHLEVIV DRPLQVFHVE VEVRDINDNP PRFPTTQKNL FIAESRPLDT 150
WFPLEGASDA DIGINAVLTY RLSPNDYFSL EKPSNDERVK GLGLVLRKSL 200
DREETPEIIL VLTVTDGGKP ELTGSVQLLI TVLDANDNAP VFDRSLYTVK 250
LPENVPNGTL VVKVNASDLD EGVNGDIMYS FSTDISPNVK YKFHIDPVSG 300
EIIVKGYIDF EECKSYEILI EGIDKGQLPL SGHCKVIVQV EDINDNVPEL 350
EFKSLSLPIR ENSPVGTVIA LISVSDRDTG VNGQVTCSLT SHVPFKLVST 400
FKNYYSLVLD SALDRETTAD YKVVVTARDG GSPSLWATAS VSVEVADVND 450
NAPVFAQPEY TVFVKENNPP GAHIFTVSAM DADAQENALV SYSLVERRVG 500
ERLLSSYVSV HAESGKVFAL QPLDHEELEL LRFQVSARDA GVPALGSNVT 550
LQVFVLDEND NAPTLLEPEA GVSGGIVSRL VSRSVGAGHV VAKVRAVDAD 600
SGYNAWLSYE LQSSEGNSRS LFRVGLYTGE ISTTRILDEA DSPRQRLLVL 650
VKDHGDPAMI VTATVLVSLV ENGPVPKAPS RVSTSVTHSE ASLVDVNVYL 700
IIAICAVSSL LVLTLLLYTA LRCSTVPSES VCGPPKPVMV CSSAVGSWSY 750
SQQRRQRVCS GEYPPKTDLM AFSPSLSDSR DREDQLQSAE DSSGKPRQPN 800
PDWRYSASLR AGMHSSVHLE EAGILRAGPG GPDQQWPTVS SATPEPEAGE 850
VSPPVGAGVN SNSWTFKYGP GNPKQSGPGE LPDKFIIPGS PAIISIRQEP 900
ANNQIDKSDF ITFGKKEETK KKKKKKKGNK TQEKKEKGNS TTDNSDQ 947
Length:947
Mass (Da):103,143
Last modified:November 1, 1998 - v1
Checksum:i082497DBBAEFB503
GO
Isoform 2 (identifier: O88689-2) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     535-795: Missing.
     879-947: GELPDKFIIP...GNSTTDNSDQ → EPKKQTQVSFLPRRKGEASQPRQ

Show »
Length:640
Mass (Da):70,430
Checksum:i7B8393620F457915
GO
Isoform 3 (identifier: O88689-3) [UniParc]FASTAAdd to Basket

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

Show »
Length:919
Mass (Da):99,666
Checksum:i21D65CCE53617EB5
GO

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei535 – 795261Missing in isoform 2.
VSP_019413Add
BLAST
Alternative sequencei796 – 947152PRQPN…DNSDQ → QAPPNTDWRFSQAQRPGTSG SQNGDETGTWPNNQFDTEML QAMILASASEAADGSSTLGG GAGTMGLSARYGPQFTLQHV PDYRQNVYIPGSNATLTNAA GKRDGKAPAGGNGNKKKSGK KEKK in isoform 3.
VSP_019414Add
BLAST
Alternative sequencei879 – 94769GELPD…DNSDQ → EPKKQTQVSFLPRRKGEASQ PRQ in isoform 2.
VSP_019415Add
BLAST

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
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.
CCDSiCCDS37776.1. [O88689-1]
RefSeqiNP_001167625.1. NM_001174154.1. [O88689-3]
NP_031792.1. NM_007766.2. [O88689-1]
UniGeneiMm.308500.

Genome annotation databases

EnsembliENSMUST00000115661; ENSMUSP00000111325; ENSMUSG00000007440. [O88689-1]
GeneIDi100384868.
12936.
KEGGimmu:100384868.
mmu:12936.
UCSCiuc008eox.2. mouse. [O88689-1]
uc008eoy.1. mouse. [O88689-3]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
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 .
CCDSi CCDS37776.1. [O88689-1 ]
RefSeqi NP_001167625.1. NM_001174154.1. [O88689-3 ]
NP_031792.1. NM_007766.2. [O88689-1 ]
UniGenei Mm.308500.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1WUZ NMR - A 27-129 [» ]
ProteinModelPortali O88689.
SMRi O88689. Positions 27-667.
ModBasei Search...

Protein-protein interaction databases

DIPi DIP-41020N.
MINTi MINT-113982.

PTM databases

PhosphoSitei O88689.

Proteomic databases

PaxDbi O88689.
PRIDEi O88689.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENSMUST00000115661 ; ENSMUSP00000111325 ; ENSMUSG00000007440 . [O88689-1 ]
GeneIDi 100384868.
12936.
KEGGi mmu:100384868.
mmu:12936.
UCSCi uc008eox.2. mouse. [O88689-1 ]
uc008eoy.1. mouse. [O88689-3 ]

Organism-specific databases

CTDi 100384868.
56144.
MGIi MGI:1298406. Pcdha4.

Phylogenomic databases

eggNOGi NOG267459.
GeneTreei ENSGT00750000117438.
HOGENOMi HOG000220892.
HOVERGENi HBG054878.
KOi K16493.

Miscellaneous databases

EvolutionaryTracei O88689.
NextBioi 282614.
PROi O88689.
SOURCEi Search...

Gene expression databases

ArrayExpressi O88689.
Bgeei O88689.
CleanExi MM_CNR1.
MM_PCDHA4.
Genevestigatori O88689.

Family and domain databases

Gene3Di 2.60.40.60. 6 hits.
InterProi IPR002126. Cadherin.
IPR015919. Cadherin-like.
IPR020894. Cadherin_CS.
IPR013164. Cadherin_N.
[Graphical view ]
Pfami PF00028. Cadherin. 5 hits.
PF08266. Cadherin_2. 1 hit.
[Graphical view ]
PRINTSi PR00205. CADHERIN.
SMARTi SM00112. CA. 6 hits.
[Graphical view ]
SUPFAMi SSF49313. SSF49313. 6 hits.
PROSITEi PS00232. CADHERIN_1. 5 hits.
PS50268. CADHERIN_2. 6 hits.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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.
    , 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.

Entry informationi

Entry nameiPCDA4_MOUSE
AccessioniPrimary (citable) accession number: O88689
Secondary accession number(s): Q3UEX3
, Q6PAM9, Q8K487, Q8K489
Entry historyi
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 statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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