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Protein

Protocadherin beta-12

Gene

PCDHB12

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 4 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 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

HGNCiHGNC:8683. PCDHB12.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini27 – 690664ExtracellularSequence analysisAdd
BLAST
Transmembranei691 – 71121HelicalSequence analysisAdd
BLAST
Topological domaini712 – 79584CytoplasmicSequence analysisAdd
BLAST

GO - Cellular componenti

  • integral component of plasma membrane Source: ProtInc
Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Membrane

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA33028.

Polymorphism and mutation databases

BioMutaiPCDHB12.
DMDMi13431382.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 2626Sequence analysisAdd
BLAST
Chaini27 – 795769Protocadherin beta-12PRO_0000003936Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi418 – 4181N-linked (GlcNAc...)Sequence analysis
Glycosylationi436 – 4361N-linked (GlcNAc...)Sequence analysis
Glycosylationi487 – 4871N-linked (GlcNAc...)Sequence analysis
Glycosylationi567 – 5671N-linked (GlcNAc...)Sequence analysis

Keywords - PTMi

Glycoprotein

Proteomic databases

EPDiQ9Y5F1.
PaxDbiQ9Y5F1.
PeptideAtlasiQ9Y5F1.
PRIDEiQ9Y5F1.

PTM databases

iPTMnetiQ9Y5F1.
PhosphoSiteiQ9Y5F1.

Expressioni

Gene expression databases

BgeeiQ9Y5F1.
CleanExiHS_PCDHB12.
ExpressionAtlasiQ9Y5F1. baseline and differential.
GenevisibleiQ9Y5F1. HS.

Organism-specific databases

HPAiHPA045042.

Interactioni

Protein-protein interaction databases

BioGridi121064. 2 interactions.
STRINGi9606.ENSP00000239450.

Structurei

3D structure databases

ProteinModelPortaliQ9Y5F1.
SMRiQ9Y5F1. Positions 30-677.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini35 – 13399Cadherin 1PROSITE-ProRule annotationAdd
BLAST
Domaini138 – 242105Cadherin 2PROSITE-ProRule annotationAdd
BLAST
Domaini247 – 347101Cadherin 3PROSITE-ProRule annotationAdd
BLAST
Domaini352 – 451100Cadherin 4PROSITE-ProRule annotationAdd
BLAST
Domaini456 – 561106Cadherin 5PROSITE-ProRule annotationAdd
BLAST
Domaini568 – 671104Cadherin 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.
GeneTreeiENSGT00840000129690.
HOGENOMiHOG000220892.
HOVERGENiHBG054878.
InParanoidiQ9Y5F1.
KOiK16494.
OMAiPLQFLRI.
OrthoDBiEOG7KSX80.
PhylomeDBiQ9Y5F1.
TreeFamiTF332299.

Family and domain databases

Gene3Di2.60.40.60. 6 hits.
InterProiIPR002126. Cadherin.
IPR015919. Cadherin-like.
IPR032455. Cadherin_C.
IPR020894. Cadherin_CS.
IPR013164. Cadherin_N.
[Graphical view]
PfamiPF00028. Cadherin. 5 hits.
PF08266. Cadherin_2. 1 hit.
PF16492. Cadherin_C_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 (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: 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

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti420 – 4201T → I.
Corresponds to variant rs2910327 [ dbSNP | Ensembl ].
VAR_033710
Natural varianti763 – 7631K → E.
Corresponds to variant rs2910006 [ dbSNP | Ensembl ].
VAR_048554

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 337337Missing in isoform 2. 1 PublicationVSP_053862Add
BLAST

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

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. Positions 30-677.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi121064. 2 interactions.
STRINGi9606.ENSP00000239450.

PTM databases

iPTMnetiQ9Y5F1.
PhosphoSiteiQ9Y5F1.

Polymorphism and mutation databases

BioMutaiPCDHB12.
DMDMi13431382.

Proteomic databases

EPDiQ9Y5F1.
PaxDbiQ9Y5F1.
PeptideAtlasiQ9Y5F1.
PRIDEiQ9Y5F1.

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.
GeneCardsiPCDHB12.
HGNCiHGNC:8683. PCDHB12.
HPAiHPA045042.
MIMi604967. gene.
606338. gene.
neXtProtiNX_Q9Y5F1.
PharmGKBiPA33028.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG3594. Eukaryota.
ENOG410XQHI. LUCA.
GeneTreeiENSGT00840000129690.
HOGENOMiHOG000220892.
HOVERGENiHBG054878.
InParanoidiQ9Y5F1.
KOiK16494.
OMAiPLQFLRI.
OrthoDBiEOG7KSX80.
PhylomeDBiQ9Y5F1.
TreeFamiTF332299.

Miscellaneous databases

GeneWikiiPCDHB12.
GenomeRNAii56124.
PROiQ9Y5F1.
SOURCEiSearch...

Gene expression databases

BgeeiQ9Y5F1.
CleanExiHS_PCDHB12.
ExpressionAtlasiQ9Y5F1. baseline and differential.
GenevisibleiQ9Y5F1. HS.

Family and domain databases

Gene3Di2.60.40.60. 6 hits.
InterProiIPR002126. Cadherin.
IPR015919. Cadherin-like.
IPR032455. Cadherin_C.
IPR020894. Cadherin_CS.
IPR013164. Cadherin_N.
[Graphical view]
PfamiPF00028. Cadherin. 5 hits.
PF08266. Cadherin_2. 1 hit.
PF16492. Cadherin_C_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] (ISOFORM 1).
  2. "The human and murine protocadherin-beta one-exon gene families show high evolutionary conservation, despite the difference in gene number."
    Vanhalst K., Kools P., Vanden Eynde E., van Roy F.
    FEBS Lett. 495:120-125(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
  3. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
    Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
    , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
    Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
    Tissue: Brain.
  4. "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].
  5. "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 nameiPCDBC_HUMAN
AccessioniPrimary (citable) accession number: Q9Y5F1
Secondary accession number(s): B4DDU1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 27, 2001
Last sequence update: November 1, 1999
Last modified: July 6, 2016
This is version 138 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

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.