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Protein

Protocadherin beta-12

Gene

PCDHB12

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -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: GO_Central
  • homophilic cell adhesion via plasma membrane adhesion molecules Source: InterPro
  • nervous system development Source: ProtInc

Keywordsi

Biological processCell adhesion
LigandCalcium

Names & Taxonomyi

Protein namesi
Recommended name:
Protocadherin beta-12
Short name:
PCDH-beta-12
Gene namesi
Name:PCDHB12
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 5

Organism-specific databases

EuPathDBiHostDB:ENSG00000120328.6
HGNCiHGNC:8683 PCDHB12
MIMi604967 gene
606338 gene
neXtProtiNX_Q9Y5F1

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini27 – 690ExtracellularSequence analysisAdd BLAST664
Transmembranei691 – 711HelicalSequence analysisAdd BLAST21
Topological domaini712 – 795CytoplasmicSequence analysisAdd BLAST84

Keywords - Cellular componenti

Cell membrane, Membrane

Pathology & Biotechi

Organism-specific databases

OpenTargetsiENSG00000120328
PharmGKBiPA33028

Polymorphism and mutation databases

BioMutaiPCDHB12
DMDMi13431382

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 26Sequence analysisAdd BLAST26
ChainiPRO_000000393627 – 795Protocadherin beta-12Add BLAST769

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Glycosylationi418N-linked (GlcNAc...) asparagineSequence analysis1
Glycosylationi436N-linked (GlcNAc...) asparagineSequence analysis1
Glycosylationi487N-linked (GlcNAc...) asparagineSequence analysis1
Glycosylationi567N-linked (GlcNAc...) asparagineSequence analysis1

Keywords - PTMi

Glycoprotein

Proteomic databases

EPDiQ9Y5F1
PaxDbiQ9Y5F1
PeptideAtlasiQ9Y5F1
PRIDEiQ9Y5F1
ProteomicsDBi86350

PTM databases

iPTMnetiQ9Y5F1
PhosphoSitePlusiQ9Y5F1

Expressioni

Gene expression databases

BgeeiENSG00000120328 Expressed in 86 organ(s), highest expression level in left coronary artery
CleanExiHS_PCDHB12
ExpressionAtlasiQ9Y5F1 baseline and differential
GenevisibleiQ9Y5F1 HS

Organism-specific databases

HPAiHPA045042

Interactioni

Protein-protein interaction databases

BioGridi121064, 2 interactors
IntActiQ9Y5F1, 9 interactors
STRINGi9606.ENSP00000239450

Structurei

3D structure databases

ProteinModelPortaliQ9Y5F1
SMRiQ9Y5F1
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini35 – 133Cadherin 1PROSITE-ProRule annotationAdd BLAST99
Domaini138 – 242Cadherin 2PROSITE-ProRule annotationAdd BLAST105
Domaini247 – 347Cadherin 3PROSITE-ProRule annotationAdd BLAST101
Domaini352 – 451Cadherin 4PROSITE-ProRule annotationAdd BLAST100
Domaini456 – 561Cadherin 5PROSITE-ProRule annotationAdd BLAST106
Domaini568 – 671Cadherin 6PROSITE-ProRule annotationAdd BLAST104

Keywords - Domaini

Repeat, Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiKOG3594 Eukaryota
ENOG410XQHI LUCA
GeneTreeiENSGT00920000148964
HOGENOMiHOG000220892
HOVERGENiHBG054878
InParanoidiQ9Y5F1
KOiK16494
OMAiDFTMFHR
OrthoDBiEOG091G024L
PhylomeDBiQ9Y5F1
TreeFamiTF332299

Family and domain databases

InterProiView protein in InterPro
IPR002126 Cadherin-like_dom
IPR015919 Cadherin-like_sf
IPR032455 Cadherin_C
IPR020894 Cadherin_CS
IPR013164 Cadherin_N
PfamiView protein in Pfam
PF00028 Cadherin, 5 hits
PF08266 Cadherin_2, 1 hit
PF16492 Cadherin_C_2, 1 hit
PRINTSiPR00205 CADHERIN
SMARTiView protein in SMART
SM00112 CA, 6 hits
SUPFAMiSSF49313 SSF49313, 6 hits
PROSITEiView protein in PROSITE
PS00232 CADHERIN_1, 5 hits
PS50268 CADHERIN_2, 6 hits

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

This entry has 2 described isoforms and 1 potential isoform that is computationally mapped.Show allAlign All

Isoform 1 (identifier: Q9Y5F1-1) [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
MENGGAGTLQ IRQVLLFFVL LGMSQAGSET GNFLVMEELQ SGSFVGNLAK
60 70 80 90 100
TLGLEVSELS SRGARVVSND NKECLQLDTN TGDLLLREML DREELCGSNE
110 120 130 140 150
PCVLYFQVLM KNPTQFLQIE LQVRDINDHS PVFLEKEMLL EIPENSPVGA
160 170 180 190 200
VFLLESAKDL DVGINAVKSY TINPNSHFHV KIRVNPDNRK YPELVLDKAL
210 220 230 240 250
DYEERPELSF ILTALDGGSP PRSGTALVRV VVVDINDNSP EFEQAFYEVK
260 270 280 290 300
ILENSILGSL VVTVSAWDLD SGTNSELSYT FSHASEDIRK TFEINQKSGD
310 320 330 340 350
ITLTAPLDFE AIESYSIIIQ ATDGGGLFGK STVRIQVMDV NDNAPEITVS
360 370 380 390 400
SITSPIPENT PETVVMVFRI RDRDSGDNGK MVCSIPEDIP FVLKSSVNNY
410 420 430 440 450
YTLETERPLD RESRAEYNIT ITVTDLGTPR LKTEHNITVL VSDVNDNAPA
460 470 480 490 500
FTQTSYALFV RENNSPALHI GSISATDRDS GTNAQVNYSL LPSQDPHLPL
510 520 530 540 550
ASLVSINADN GHLFALRSLD YEALQGFQFR VGATDHGSPA LSSEALVRVL
560 570 580 590 600
VLDANDNSPF VLYPLQNGSA PCTELVPWAA EPGYLVTKVV AVDGDSGQNA
610 620 630 640 650
WLSYQLLKAT EPGLFGVWAH NGEVRTARLL SERDAAKHRL VVLVKDNGEP
660 670 680 690 700
PRSATATLHV LLVDGFSQPY LPLPEAAPAQ AQADSLTVYL VVALASVSSL
710 720 730 740 750
FLFSVLLFVA VRLCRRSRAA PVGRCSVPEG PFPGHLVDVS GTGTLSQSYH
760 770 780 790
YEVCVTGGSR SNKFKFLKPI IPNFLPQSTG SEVEENPPFQ NNLGF
Length:795
Mass (Da):86,770
Last modified:November 1, 1999 - v1
Checksum:i0A32163F81A0D37C
GO
Isoform 2 (identifier: Q9Y5F1-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-337: Missing.

Note: No experimental confirmation available.
Show »
Length:458
Mass (Da):49,631
Checksum:i38F8CDBC97FAE5AD
GO

Computationally mapped potential isoform sequencesi

There is 1 potential isoform mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
A0A096LP27A0A096LP27_HUMAN
Protocadherin beta-12
PCDHB12
67Annotation score:

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_033710420T → I. Corresponds to variant dbSNP:rs2910327Ensembl.1
Natural variantiVAR_048554763K → E. Corresponds to variant dbSNP:rs2910006Ensembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0538621 – 337Missing in isoform 2. 1 PublicationAdd BLAST337

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF152491 mRNA Translation: AAD43752.1
AF217746 mRNA Translation: AAK51614.1
AK293336 mRNA Translation: BAG56852.1
AK316160 mRNA Translation: BAH14531.1
AC005752 Genomic DNA No translation available.
BC045637 mRNA Translation: AAH45637.1
CCDSiCCDS4254.1 [Q9Y5F1-1]
RefSeqiNP_061755.1, NM_018932.3 [Q9Y5F1-1]
UniGeneiHs.429820
Hs.744755

Genome annotation databases

EnsembliENST00000239450; ENSP00000239450; ENSG00000120328 [Q9Y5F1-1]
ENST00000624949; ENSP00000485303; ENSG00000120328 [Q9Y5F1-2]
GeneIDi56124
KEGGihsa:56124
UCSCiuc003liz.4 human [Q9Y5F1-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF152491 mRNA Translation: AAD43752.1
AF217746 mRNA Translation: AAK51614.1
AK293336 mRNA Translation: BAG56852.1
AK316160 mRNA Translation: BAH14531.1
AC005752 Genomic DNA No translation available.
BC045637 mRNA Translation: AAH45637.1
CCDSiCCDS4254.1 [Q9Y5F1-1]
RefSeqiNP_061755.1, NM_018932.3 [Q9Y5F1-1]
UniGeneiHs.429820
Hs.744755

3D structure databases

ProteinModelPortaliQ9Y5F1
SMRiQ9Y5F1
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi121064, 2 interactors
IntActiQ9Y5F1, 9 interactors
STRINGi9606.ENSP00000239450

PTM databases

iPTMnetiQ9Y5F1
PhosphoSitePlusiQ9Y5F1

Polymorphism and mutation databases

BioMutaiPCDHB12
DMDMi13431382

Proteomic databases

EPDiQ9Y5F1
PaxDbiQ9Y5F1
PeptideAtlasiQ9Y5F1
PRIDEiQ9Y5F1
ProteomicsDBi86350

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000239450; ENSP00000239450; ENSG00000120328 [Q9Y5F1-1]
ENST00000624949; ENSP00000485303; ENSG00000120328 [Q9Y5F1-2]
GeneIDi56124
KEGGihsa:56124
UCSCiuc003liz.4 human [Q9Y5F1-1]

Organism-specific databases

CTDi56124
EuPathDBiHostDB:ENSG00000120328.6
GeneCardsiPCDHB12
HGNCiHGNC:8683 PCDHB12
HPAiHPA045042
MIMi604967 gene
606338 gene
neXtProtiNX_Q9Y5F1
OpenTargetsiENSG00000120328
PharmGKBiPA33028
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG3594 Eukaryota
ENOG410XQHI LUCA
GeneTreeiENSGT00920000148964
HOGENOMiHOG000220892
HOVERGENiHBG054878
InParanoidiQ9Y5F1
KOiK16494
OMAiDFTMFHR
OrthoDBiEOG091G024L
PhylomeDBiQ9Y5F1
TreeFamiTF332299

Miscellaneous databases

GeneWikiiPCDHB12
GenomeRNAii56124
PROiPR:Q9Y5F1
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000120328 Expressed in 86 organ(s), highest expression level in left coronary artery
CleanExiHS_PCDHB12
ExpressionAtlasiQ9Y5F1 baseline and differential
GenevisibleiQ9Y5F1 HS

Family and domain databases

InterProiView protein in InterPro
IPR002126 Cadherin-like_dom
IPR015919 Cadherin-like_sf
IPR032455 Cadherin_C
IPR020894 Cadherin_CS
IPR013164 Cadherin_N
PfamiView protein in Pfam
PF00028 Cadherin, 5 hits
PF08266 Cadherin_2, 1 hit
PF16492 Cadherin_C_2, 1 hit
PRINTSiPR00205 CADHERIN
SMARTiView protein in SMART
SM00112 CA, 6 hits
SUPFAMiSSF49313 SSF49313, 6 hits
PROSITEiView protein in PROSITE
PS00232 CADHERIN_1, 5 hits
PS50268 CADHERIN_2, 6 hits
ProtoNetiSearch...

Entry informationi

Entry nameiPCDBC_HUMAN
AccessioniPrimary (citable) accession number: Q9Y5F1
Secondary accession number(s): B4DDU1
Entry historyiIntegrated into UniProtKB/Swiss-Prot: April 27, 2001
Last sequence update: November 1, 1999
Last modified: November 7, 2018
This is version 153 of the entry and version 1 of the sequence. See 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 entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  2. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  3. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  4. Human chromosome 5
    Human chromosome 5: entries, gene names and cross-references to MIM
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Main funding by: National Institutes of Health

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