O88689 (PCDA4_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Protocadherin alpha-4
Short name=PCDH-alpha-4

Gene names

Name:	Pcdha4
Synonyms:	Cnr1

Organism

Mus musculus (Mouse) [Reference proteome]

Taxonomic identifier

10090 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Glires › Rodentia › Sciurognathi › Muroidea › Muridae › Murinae › Mus › Mus

Protein attributes

Sequence length	947 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence 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 process	Cell adhesion
Cellular component	Cell membrane Membrane
Coding sequence diversity	Alternative splicing
Domain	Repeat Signal Transmembrane Transmembrane helix
Ligand	Calcium
PTM	Glycoprotein
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	homophilic cell adhesion Inferred from electronic annotation. Source: InterPro
Cellular_component	integral to membrane Inferred from electronic annotation. Source: UniProtKB-KW plasma membrane Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	calcium 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 key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Signal peptide

1 – 29

29

Potential

Chain

30 – 947

918

Protocadherin alpha-4

PRO_0000240663

Regions

Topological domain

30 – 697

668

Extracellular Potential

Transmembrane

698 – 718

21

Helical; Potential

Topological domain

719 – 947

229

Cytoplasmic Potential

Domain

30 – 133

104

Cadherin 1

Domain

134 – 242

109

Cadherin 2

Domain

243 – 350

108

Cadherin 3

Domain

351 – 455

105

Cadherin 4

Domain

456 – 565

110

Cadherin 5

Domain

573 – 681

109

Cadherin 6

Repeat

734 – 737

4

PXXP 1

Repeat

774 – 777

4

PXXP 2

Repeat

796 – 799

4

PXXP 3

Repeat

829 – 832

4

PXXP 4

Repeat

870 – 873

4

PXXP 5

Repeat

888 – 891

4

PXXP 6

Region

734 – 891

158

6 X 4 AA repeats of P-X-X-P

Compositional bias

920 – 927

8

Poly-Lys

Amino acid modifications

Glycosylation

257

1

N-linked (GlcNAc...) Potential

Glycosylation

265

1

N-linked (GlcNAc...) Potential

Glycosylation

548

1

N-linked (GlcNAc...) Potential

Natural variations

Alternative sequence

535 – 795

261

Missing in isoform 2.

VSP_019413

Alternative sequence

796 – 947

152

PRQPN…DNSDQ → QAPPNTDWRFSQAQRPGTSG SQNGDETGTWPNNQFDTEML QAMILASASEAADGSSTLGG GAGTMGLSARYGPQFTLQHV PDYRQNVYIPGSNATLTNAA GKRDGKAPAGGNGNKKKSGK KEKK in isoform 3.

VSP_019414

Alternative sequence

879 – 947

69

GELPD…DNSDQ → EPKKQTQVSFLPRRKGEASQ PRQ in isoform 2.

VSP_019415

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

947

Helix Strand Turn

Details...

Beta strand

30 – 38

9

Helix

48 – 52

5

Helix

56 – 59

4

Turn

60 – 63

4

Beta strand

74 – 77

4

Turn

79 – 81

3

Beta strand

84 – 86

3

Helix

92 – 95

4

Beta strand

97 – 101

5

Beta strand

103 – 110

8

Turn

111 – 114

4

Beta strand

115 – 124

10

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified November 1, 1998. Version 1. Checksum: 082497DBBAEFB503	FASTA	947	103,143
	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
	Isoform 2 [UniParc]. Checksum: 7B8393620F457915	FASTA	640	70,430
	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 LRFQPRQPNP 550 560 570 580 590 600 DWRYSASLRA GMHSSVHLEE AGILRAGPGG PDQQWPTVSS ATPEPEAGEV SPPVGAGVNS 610 620 630 640 NSWTFKYGPG NPKQSGPEPK KQTQVSFLPR RKGEASQPRQ
	Isoform 3 [UniParc]. Checksum: 21D65CCE53617EB5	FASTA	919	99,666
	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 DSSGKQAPPN TDWRFSQAQR PGTSGSQNGD ETGTWPNNQF DTEMLQAMIL 850 860 870 880 890 900 ASASEAADGS STLGGGAGTM GLSARYGPQF TLQHVPDYRQ NVYIPGSNAT LTNAAGKRDG 910 KAPAGGNGNK KKSGKKEKK

References

	« Hide 'large scale' referencesShow '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. , 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.

IPI

IPI00133210.
IPI00761203.
IPI00762745.

RefSeq

NP_001167625.1. NM_001174154.1.
NP_031792.1. NM_007766.2.

UniGene

Mm.308500.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1WUZ	NMR	-	A	27-129	[»]

ProteinModelPortal

O88689.

SMR

O88689. Positions 27-667.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-41020N.

PTM databases

PhosphoSite

O88689.

Proteomic databases

PaxDb

O88689.

PRIDE

O88689.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENSMUST00000115661; ENSMUSP00000111325; ENSMUSG00000007440.

GeneID

100384868.
12936.

KEGG

mmu:100384868.
mmu:12936.

UCSC

uc008eox.2. mouse.
uc008eoy.1. mouse.

Organism-specific databases

CTD

100384868.
56144.

MGI

MGI:1298406. Pcdha4.

Phylogenomic databases

eggNOG

NOG267459.

GeneTree

ENSGT00700000104401.

HOGENOM

HOG000220892.

HOVERGEN

HBG054878.

KO

K16493.

Gene expression databases

ArrayExpress

O88689.

Bgee

O88689.

CleanEx

MM_CNR1.
MM_PCDHA4.

Genevestigator

O88689.

Family and domain databases

Gene3D

2.60.40.60. 6 hits.

InterPro

IPR002126. Cadherin.
IPR015919. Cadherin-like.
IPR020894. Cadherin_CS.
IPR013164. Cadherin_N.
[Graphical view]

Pfam

PF00028. Cadherin. 5 hits.
PF08266. Cadherin_2. 1 hit.
[Graphical view]

PRINTS

PR00205. CADHERIN.

SMART

SM00112. CA. 6 hits.
[Graphical view]

SUPFAM

SSF49313. Cadherin. 6 hits.

PROSITE

PS00232. CADHERIN_1. 5 hits.
PS50268. CADHERIN_2. 6 hits.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

O88689.

NextBio

282614.

SOURCE

Search...

Entry information

Entry name

PCDA4_MOUSE

Accession

Primary (citable) accession number: O88689
Secondary accession number(s): Q3UEX3 , Q6PAM9, Q8K487, Q8K489

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 27, 2006
Last sequence update:	November 1, 1998
Last modified:	May 1, 2013
This is version 87 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program