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Protein

Protocadherin gamma-B3

Gene

PCDHGB3

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 3 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

Complete GO annotation...

Keywords - Biological processi

Cell adhesion

Keywords - Ligandi

Calcium

Names & Taxonomyi

Protein namesi
Recommended name:
Protocadherin gamma-B3
Short name:
PCDH-gamma-B3
Gene namesi
Name:PCDHGB3
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 5

Organism-specific databases

HGNCiHGNC:8710. PCDHGB3.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini31 – 691661ExtracellularSequence analysisAdd
BLAST
Transmembranei692 – 71221HelicalSequence analysisAdd
BLAST
Topological domaini713 – 929217CytoplasmicSequence analysisAdd
BLAST

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Membrane

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA33058.

Polymorphism and mutation databases

BioMutaiPCDHGB3.
DMDMi442570291.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 3030Sequence analysisAdd
BLAST
Chaini31 – 929899Protocadherin gamma-B3PRO_0000003976Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi136 – 1361N-linked (GlcNAc...)Sequence analysis
Glycosylationi419 – 4191N-linked (GlcNAc...)Sequence analysis
Glycosylationi545 – 5451N-linked (GlcNAc...)Sequence analysis

Keywords - PTMi

Glycoprotein

Proteomic databases

EPDiQ9Y5G1.
PaxDbiQ9Y5G1.
PeptideAtlasiQ9Y5G1.
PRIDEiQ9Y5G1.

PTM databases

iPTMnetiQ9Y5G1.
PhosphoSiteiQ9Y5G1.

Expressioni

Gene expression databases

ExpressionAtlasiQ9Y5G1. baseline and differential.
GenevisibleiQ9Y5G1. HS.

Organism-specific databases

HPAiHPA008755.
HPA035823.

Interactioni

Protein-protein interaction databases

BioGridi121042. 3 interactions.
STRINGi9606.ENSP00000461862.

Structurei

3D structure databases

ProteinModelPortaliQ9Y5G1.
SMRiQ9Y5G1. Positions 33-666.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini31 – 133103Cadherin 1PROSITE-ProRule annotationAdd
BLAST
Domaini134 – 242109Cadherin 2PROSITE-ProRule annotationAdd
BLAST
Domaini243 – 347105Cadherin 3PROSITE-ProRule annotationAdd
BLAST
Domaini348 – 452105Cadherin 4PROSITE-ProRule annotationAdd
BLAST
Domaini453 – 562110Cadherin 5PROSITE-ProRule annotationAdd
BLAST
Domaini570 – 675106Cadherin 6PROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Contains 6 cadherin domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat, Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiKOG3594. Eukaryota.
ENOG410XQHI. LUCA.
HOVERGENiHBG054878.
InParanoidiQ9Y5G1.
KOiK16496.
OrthoDBiEOG7J70DX.
TreeFamiTF332299.

Family and domain databases

Gene3Di2.60.40.60. 6 hits.
InterProiIPR002126. Cadherin.
IPR015919. Cadherin-like.
IPR032455. Cadherin_C.
IPR031904. Cadherin_CBD.
IPR020894. Cadherin_CS.
IPR013164. Cadherin_N.
[Graphical view]
PfamiPF00028. Cadherin. 5 hits.
PF08266. Cadherin_2. 1 hit.
PF16492. Cadherin_C_2. 1 hit.
PF15974. Cadherin_tail. 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 (2)i

Sequence statusi: Complete.

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

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9Y5G1-1) [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
MGNSSGWRGP AGQRRMLFLF LLSLLDQVLS EPIRYAIPEE LDRGSLVGNL
60 70 80 90 100
AKDLGFGVGD LPTRNLRVIA EKKFFTVSPE NGNLLVSDRI DREEICGKKS
110 120 130 140 150
TCVLEFEMVA EKPLNFFHVT VLIQDINDNP PTFSQNITEL EISELALTGA
160 170 180 190 200
TFALESAQDP DVGVNSLQQY YLSPDPHFSL IQKENLDGSR YPELVLKAPL
210 220 230 240 250
DREEQPHHHL VLTAVDGGEP SRSCTTQIRV IVADANDNPP VFTQDMYRVN
260 270 280 290 300
VAENLPAGSS VLKVMAIDMD EGINAEIIYA FINIGKEVRQ LFKLDSKTGE
310 320 330 340 350
LTTIGELDFE ERDSYTIGVE AKDGGHHTAY CKVQIDISDE NDNAPEITLA
360 370 380 390 400
SESQHIQEDA ELGTAVALIK THDLDSGFNG EILCQLKGNF PFKIVQDTKN
410 420 430 440 450
TYRLVTDGAL DREQIPEYNV TITATDKGNP PLSSSKTITL HILDVNDNVP
460 470 480 490 500
VFHQASYTVH VAENNPPGAS IAHVRASDPD LGPNGLVSYY IVASDLEPRE
510 520 530 540 550
LSSYVSVSAR SGVVFAQRAF DHEQLRAFEL TLQARDQGSP TLSANVSLRV
560 570 580 590 600
LVDDRNDNAP LVLYPALGPE GSALFDMVPR SAEPGYLVTK VVAVDADSGY
610 620 630 640 650
NAWLSYHIVQ ASEPGLFSLG LRTGEVRTAR TLGDREAARQ RLLVTVRDGG
660 670 680 690 700
QQPLSATVML HLIFADSLQE IQPDLSDRPT PSDPQAELQF HLVVALALIS
710 720 730 740 750
VLFLLAVILA ISLRLRCSSR PATEGYFQPG VCFKTVPGVL PTYSERTLPY
760 770 780 790 800
SYNPCAASHS SNTEFKFLNI KAENAAPQDL LCDEASWFES NDNPEMPSNS
810 820 830 840 850
GNLQKQAPPN TDWRFSQAQR PGTSGSQNGD DTGTWPNNQF DTEMLQAMIL
860 870 880 890 900
ASASEAADGS STLGGGAGTM GLSARYGPQF TLQHVPDYRQ NVYIPGSNAT
910 920
LTNAAGKRDG KAPAGGNGNK KKSGKKEKK
Length:929
Mass (Da):101,232
Last modified:January 9, 2013 - v3
Checksum:i47052AF74FF01809
GO
Isoform 2 (identifier: Q9Y5G1-2) [UniParc]FASTAAdd to basket

Also known as: Short

The sequence of this isoform differs from the canonical sequence as follows:
     806-814: QAPPNTDWR → VSFFKPFLP
     815-929: Missing.

Show »
Length:814
Mass (Da):89,370
Checksum:iB3033646C8F71265
GO

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti20 – 201F → Y.
Corresponds to variant rs6860590 [ dbSNP | Ensembl ].
VAR_048569
Natural varianti28 – 281V → A.1 Publication
Corresponds to variant rs6860609 [ dbSNP | Ensembl ].
VAR_061073
Natural varianti389 – 3891N → K.
Corresponds to variant rs2240697 [ dbSNP | Ensembl ].
VAR_048570

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei806 – 8149QAPPNTDWR → VSFFKPFLP in isoform 2. 1 PublicationVSP_008688
Alternative sequencei815 – 929115Missing in isoform 2. 1 PublicationVSP_008689Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF152332 mRNA. Translation: AAD43726.1.
AF152519 mRNA. Translation: AAD43779.1.
AC005366 Genomic DNA. No translation available.
AC005618 Genomic DNA. No translation available.
AC008781 Genomic DNA. No translation available.
CH471062 Genomic DNA. Translation: EAW61951.1.
BC150172 mRNA. Translation: AAI50173.1.
CCDSiCCDS58980.1. [Q9Y5G1-1]
CCDS75334.1. [Q9Y5G1-2]
RefSeqiNP_061747.2. NM_018924.4.
NP_115268.2. NM_032097.2.
UniGeneiHs.368160.

Genome annotation databases

EnsembliENST00000576222; ENSP00000461862; ENSG00000262209.
GeneIDi56102.
KEGGihsa:56102.
UCSCiuc003ljw.3. human. [Q9Y5G1-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF152332 mRNA. Translation: AAD43726.1.
AF152519 mRNA. Translation: AAD43779.1.
AC005366 Genomic DNA. No translation available.
AC005618 Genomic DNA. No translation available.
AC008781 Genomic DNA. No translation available.
CH471062 Genomic DNA. Translation: EAW61951.1.
BC150172 mRNA. Translation: AAI50173.1.
CCDSiCCDS58980.1. [Q9Y5G1-1]
CCDS75334.1. [Q9Y5G1-2]
RefSeqiNP_061747.2. NM_018924.4.
NP_115268.2. NM_032097.2.
UniGeneiHs.368160.

3D structure databases

ProteinModelPortaliQ9Y5G1.
SMRiQ9Y5G1. Positions 33-666.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi121042. 3 interactions.
STRINGi9606.ENSP00000461862.

PTM databases

iPTMnetiQ9Y5G1.
PhosphoSiteiQ9Y5G1.

Polymorphism and mutation databases

BioMutaiPCDHGB3.
DMDMi442570291.

Proteomic databases

EPDiQ9Y5G1.
PaxDbiQ9Y5G1.
PeptideAtlasiQ9Y5G1.
PRIDEiQ9Y5G1.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000576222; ENSP00000461862; ENSG00000262209.
GeneIDi56102.
KEGGihsa:56102.
UCSCiuc003ljw.3. human. [Q9Y5G1-1]

Organism-specific databases

CTDi56102.
GeneCardsiPCDHGB3.
HGNCiHGNC:8710. PCDHGB3.
HPAiHPA008755.
HPA035823.
MIMi604968. gene.
606301. gene.
neXtProtiNX_Q9Y5G1.
PharmGKBiPA33058.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG3594. Eukaryota.
ENOG410XQHI. LUCA.
HOVERGENiHBG054878.
InParanoidiQ9Y5G1.
KOiK16496.
OrthoDBiEOG7J70DX.
TreeFamiTF332299.

Miscellaneous databases

GenomeRNAii56102.
PROiQ9Y5G1.
SOURCEiSearch...

Gene expression databases

ExpressionAtlasiQ9Y5G1. baseline and differential.
GenevisibleiQ9Y5G1. HS.

Family and domain databases

Gene3Di2.60.40.60. 6 hits.
InterProiIPR002126. Cadherin.
IPR015919. Cadherin-like.
IPR032455. Cadherin_C.
IPR031904. Cadherin_CBD.
IPR020894. Cadherin_CS.
IPR013164. Cadherin_N.
[Graphical view]
PfamiPF00028. Cadherin. 5 hits.
PF08266. Cadherin_2. 1 hit.
PF16492. Cadherin_C_2. 1 hit.
PF15974. Cadherin_tail. 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 2).
    Tissue: Brain.
  2. "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].
  3. 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], VARIANT ALA-28.

Entry informationi

Entry nameiPCDGF_HUMAN
AccessioniPrimary (citable) accession number: Q9Y5G1
Secondary accession number(s): A7E229, Q9Y5C7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 24, 2003
Last sequence update: January 9, 2013
Last modified: July 6, 2016
This is version 122 of the entry and version 3 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

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 one 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.