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Protein

Protocadherin alpha-6

Gene

PCDHA6

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

Functioni

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

GO - Molecular functioni

GO - Biological processi

  • cell adhesion Source: ProtInc
  • homophilic cell adhesion via plasma membrane adhesion molecules Source: InterPro
  • nervous system development Source: ProtInc
Complete GO annotation...

Keywords - Biological processi

Cell adhesion

Keywords - Ligandi

Calcium

Names & Taxonomyi

Protein namesi
Recommended name:
Protocadherin alpha-6
Short name:
PCDH-alpha-6
Gene namesi
Name:PCDHA6
Synonyms:CNRS2
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640 Componenti: Chromosome 5

Organism-specific databases

HGNCiHGNC:8672. PCDHA6.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini30 – 697668ExtracellularSequence AnalysisAdd
BLAST
Transmembranei698 – 71821HelicalSequence AnalysisAdd
BLAST
Topological domaini719 – 950232CytoplasmicSequence AnalysisAdd
BLAST

GO - Cellular componenti

  • extracellular region Source: UniProtKB-SubCell
  • integral component of plasma membrane Source: ProtInc
Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Membrane, Secreted

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA33018.

Polymorphism and mutation databases

BioMutaiPCDHA6.
DMDMi13878423.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 2929Sequence AnalysisAdd
BLAST
Chaini30 – 950921Protocadherin alpha-6PRO_0000003894Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi257 – 2571N-linked (GlcNAc...)Sequence Analysis
Glycosylationi265 – 2651N-linked (GlcNAc...)Sequence Analysis
Glycosylationi386 – 3861N-linked (GlcNAc...)Sequence Analysis
Glycosylationi548 – 5481N-linked (GlcNAc...)Sequence Analysis

Keywords - PTMi

Glycoprotein

Proteomic databases

PaxDbiQ9UN73.
PRIDEiQ9UN73.

PTM databases

PhosphoSiteiQ9UN73.

Expressioni

Gene expression databases

BgeeiQ9UN73.
CleanExiHS_PCDHA6.
GenevisibleiQ9UN73. HS.

Interactioni

Protein-protein interaction databases

BioGridi121082. 2 interactions.
IntActiQ9UN73. 2 interactions.
STRINGi9606.ENSP00000433378.

Structurei

3D structure databases

ProteinModelPortaliQ9UN73.
SMRiQ9UN73. Positions 27-681.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini34 – 133100Cadherin 1PROSITE-ProRule annotationAdd
BLAST
Domaini157 – 24286Cadherin 2PROSITE-ProRule annotationAdd
BLAST
Domaini243 – 350108Cadherin 3PROSITE-ProRule annotationAdd
BLAST
Domaini351 – 455105Cadherin 4PROSITE-ProRule annotationAdd
BLAST
Domaini456 – 565110Cadherin 5PROSITE-ProRule annotationAdd
BLAST
Domaini581 – 67898Cadherin 6PROSITE-ProRule annotationAdd
BLAST
Repeati799 – 8024PXXP 1
Repeati832 – 8354PXXP 2
Repeati873 – 8764PXXP 3
Repeati891 – 8944PXXP 4

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni799 – 894964 X 4 AA repeats of P-X-X-PAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi923 – 9308Poly-Lys

Sequence similaritiesi

Contains 6 cadherin domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat, Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiNOG267459.
GeneTreeiENSGT00760000118847.
HOGENOMiHOG000220892.
HOVERGENiHBG054878.
InParanoidiQ9UN73.
KOiK16493.
OMAiSNEYFAL.
OrthoDBiEOG7KSX80.
PhylomeDBiQ9UN73.
TreeFamiTF332299.

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. AlignAdd to basket

Note: Additional isoforms seem to exist.

Isoform 1 (identifier: Q9UN73-1) [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

        10         20         30         40         50
MVFTPEDRLG KQCLLLPLLL LAAWKVGSGQ LHYSVPEEAK HGTFVGRIAQ
60 70 80 90 100
DLGLELAELV PRLFRMASKD REDLLEVNLQ NGILFVNSRI DREELCGRSA
110 120 130 140 150
ECSIHLEVIV DRPLQVFHVD VEVRDINDNP PLFPVEEQRV LIYESRLPDS
160 170 180 190 200
VFPLEGASDA DVGSNSILTY KLSSSEYFGL DVKINSDDNK QIGLLLKKSL
210 220 230 240 250
DREEAPAHNL FLTATDGGKP ELTGTVQLLV TVLDVNDNAP TFEQSEYEVR
260 270 280 290 300
IFENADNGTT VIRLNASDRD EGANGAISYS FNSLVAAMVI DHFSIDRNTG
310 320 330 340 350
EIVIRGNLDF EQENLYKILI DATDKGHPPM AGHCTVLVRI LDKNDNVPEI
360 370 380 390 400
ALTSLSLPVR EDAQFGTVIA LISVNDLDSG ANGQVNCSLT PHVPFKLVST
410 420 430 440 450
FKNYYSLVLD SALDRESVSA YELVVTARDG GSPSLWATAS LSVEVADMND
460 470 480 490 500
NAPAFAQPEY TVFVKENNPP GCHIFTVSAR DADAQENALV SYSLVERRVG
510 520 530 540 550
ERALSSYISV HAESGKVYAL QPLDHEELEL LQFQVSARDA GVPPLGSNVT
560 570 580 590 600
LQVFVLDEND NAPALLAPRV GGTGGAVSEL VPRSLGAGQV VAKVRAVDAD
610 620 630 640 650
SGYNAWLSYE LQPPASSARF PFRVGLYTGE ISTTRVLDEA DSPRHRLLVL
660 670 680 690 700
VKDHGEPALT ATATVLVSLV ESGQAPKASS RASVGAAGPE AALVDVNVYL
710 720 730 740 750
IIAICAVSSL LVLTLLLYTA LRCSAPPTEG ACTADKPTLV CSSAVGSWSY
760 770 780 790 800
SQQRRQRVCS GEGPPKMDLM AFSPSLSPCP IMMGKAENQD LNEDHDAKPR
810 820 830 840 850
QPNPDWRYSA SLRAGMHSSV HLEEAGILRA GPGGPDQQWP TVSSATPEPE
860 870 880 890 900
AGEVSPPVGA GVNSNSWTFK YGPGNPKQSG PGELPDKFII PGSPAIISIR
910 920 930 940 950
QEPTNSQIDK SDFITFGKKE ETKKKKKKKK GNKTQEKKEK GNSTTDNSDQ
Length:950
Mass (Da):102,716
Last modified:May 1, 2000 - v1
Checksum:i894B97B9737C52B9
GO
Isoform 2 (identifier: Q9UN73-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     535-798: Missing.

Show »
Length:686
Mass (Da):75,250
Checksum:i683E33D08C967700
GO
Isoform 3 (identifier: Q9UN73-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     799-803: PRQPN → VSEFS
     804-950: Missing.

Show »
Length:803
Mass (Da):86,845
Checksum:iD95B0E37DD1B0F17
GO

Sequence cautioni

The sequence AAF89691.1 differs from that shown. Reason: Erroneous initiation. Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti585 – 5851L → V.
Corresponds to variant rs60309716 [ dbSNP | Ensembl ].
VAR_061061

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei535 – 798264Missing in isoform 2. 1 PublicationVSP_000681Add
BLAST
Alternative sequencei799 – 8035PRQPN → VSEFS in isoform 3. 1 PublicationVSP_000682
Alternative sequencei804 – 950147Missing in isoform 3. 1 PublicationVSP_000683Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF152314 mRNA. Translation: AAD43708.1.
AF152484 mRNA. Translation: AAD43745.1.
AF169694 mRNA. Translation: AAF89691.1. Different initiation.
AC005609 Genomic DNA. Translation: AAC34320.1.
BC036674 mRNA. Translation: AAH36674.1.
CCDSiCCDS47281.1. [Q9UN73-1]
CCDS47282.1. [Q9UN73-2]
RefSeqiNP_061732.1. NM_018909.3. [Q9UN73-1]
NP_114036.1. NM_031848.2. [Q9UN73-3]
NP_114037.1. NM_031849.2. [Q9UN73-2]
UniGeneiHs.199343.
Hs.570901.
Hs.599714.
Hs.621225.

Genome annotation databases

EnsembliENST00000378126; ENSP00000367366; ENSG00000081842. [Q9UN73-3]
ENST00000527624; ENSP00000434113; ENSG00000081842. [Q9UN73-2]
ENST00000529310; ENSP00000433378; ENSG00000081842.
GeneIDi56142.
KEGGihsa:56142.
UCSCiuc003lhn.2. human. [Q9UN73-2]
uc003lho.2. human. [Q9UN73-1]
uc011dab.2. human. [Q9UN73-3]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF152314 mRNA. Translation: AAD43708.1.
AF152484 mRNA. Translation: AAD43745.1.
AF169694 mRNA. Translation: AAF89691.1. Different initiation.
AC005609 Genomic DNA. Translation: AAC34320.1.
BC036674 mRNA. Translation: AAH36674.1.
CCDSiCCDS47281.1. [Q9UN73-1]
CCDS47282.1. [Q9UN73-2]
RefSeqiNP_061732.1. NM_018909.3. [Q9UN73-1]
NP_114036.1. NM_031848.2. [Q9UN73-3]
NP_114037.1. NM_031849.2. [Q9UN73-2]
UniGeneiHs.199343.
Hs.570901.
Hs.599714.
Hs.621225.

3D structure databases

ProteinModelPortaliQ9UN73.
SMRiQ9UN73. Positions 27-681.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi121082. 2 interactions.
IntActiQ9UN73. 2 interactions.
STRINGi9606.ENSP00000433378.

PTM databases

PhosphoSiteiQ9UN73.

Polymorphism and mutation databases

BioMutaiPCDHA6.
DMDMi13878423.

Proteomic databases

PaxDbiQ9UN73.
PRIDEiQ9UN73.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000378126; ENSP00000367366; ENSG00000081842. [Q9UN73-3]
ENST00000527624; ENSP00000434113; ENSG00000081842. [Q9UN73-2]
ENST00000529310; ENSP00000433378; ENSG00000081842.
GeneIDi56142.
KEGGihsa:56142.
UCSCiuc003lhn.2. human. [Q9UN73-2]
uc003lho.2. human. [Q9UN73-1]
uc011dab.2. human. [Q9UN73-3]

Organism-specific databases

CTDi56142.
GeneCardsiGC05P140456.
HGNCiHGNC:8672. PCDHA6.
MIMi604966. gene.
606312. gene.
neXtProtiNX_Q9UN73.
PharmGKBiPA33018.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiNOG267459.
GeneTreeiENSGT00760000118847.
HOGENOMiHOG000220892.
HOVERGENiHBG054878.
InParanoidiQ9UN73.
KOiK16493.
OMAiSNEYFAL.
OrthoDBiEOG7KSX80.
PhylomeDBiQ9UN73.
TreeFamiTF332299.

Miscellaneous databases

GeneWikiiPCDHA6.
GenomeRNAii56142.
NextBioi61718.
PROiQ9UN73.
SOURCEiSearch...

Gene expression databases

BgeeiQ9UN73.
CleanExiHS_PCDHA6.
GenevisibleiQ9UN73. HS.

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]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "A striking organization of a large family of human neural cadherin-like cell adhesion genes."
    Wu Q., Maniatis T.
    Cell 97:779-790(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 3).
    Tissue: Brain.
  2. "Alternative splicing within the human CNR family of protocadherins (PCDH-alpha) produces transcripts encoding secreted proteins."
    Kools P.F.J., van Roy F.
    Submitted (JUL-1999) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2).
    Tissue: Brain.
  3. "The DNA sequence and comparative analysis of human chromosome 5."
    Schmutz J., Martin J., Terry A., Couronne O., Grimwood J., Lowry S., Gordon L.A., Scott D., Xie G., Huang W., Hellsten U., Tran-Gyamfi M., She X., Prabhakar S., Aerts A., Altherr M., Bajorek E., Black S.
    , Branscomb E., Caoile C., Challacombe J.F., Chan Y.M., Denys M., Detter J.C., Escobar J., Flowers D., Fotopulos D., Glavina T., Gomez M., Gonzales E., Goodstein D., Grigoriev I., Groza M., Hammon N., Hawkins T., Haydu L., Israni S., Jett J., Kadner K., Kimball H., Kobayashi A., Lopez F., Lou Y., Martinez D., Medina C., Morgan J., Nandkeshwar R., Noonan J.P., Pitluck S., Pollard M., Predki P., Priest J., Ramirez L., Retterer J., Rodriguez A., Rogers S., Salamov A., Salazar A., Thayer N., Tice H., Tsai M., Ustaszewska A., Vo N., Wheeler J., Wu K., Yang J., Dickson M., Cheng J.-F., Eichler E.E., Olsen A., Pennacchio L.A., Rokhsar D.S., Richardson P., Lucas S.M., Myers R.M., Rubin E.M.
    Nature 431:268-274(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  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 1).
    Tissue: Brain.

Entry informationi

Entry nameiPCDA6_HUMAN
AccessioniPrimary (citable) accession number: Q9UN73
Secondary accession number(s): O75283, Q9NRT8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 27, 2001
Last sequence update: May 1, 2000
Last modified: July 22, 2015
This is version 136 of the entry and version 1 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 5
    Human chromosome 5: 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

External Data

Dasty 3

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 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.