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Protein

Protocadherin beta-13

Gene

PCDHB13

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

  1. calcium ion binding Source: InterPro

GO - Biological processi

  1. calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules Source: UniProtKB
  2. homophilic cell adhesion via plasma membrane adhesion molecules Source: InterPro
  3. synapse assembly Source: UniProtKB
  4. synaptic transmission Source: UniProtKB
Complete GO annotation...

Keywords - Biological processi

Cell adhesion

Keywords - Ligandi

Calcium

Names & Taxonomyi

Protein namesi
Recommended name:
Protocadherin beta-13
Short name:
PCDH-beta-13
Gene namesi
Name:PCDHB13
ORF Names:UNQ332/PRO531
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640 Componenti: Chromosome 5

Organism-specific databases

HGNCiHGNC:8684. PCDHB13.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini29 – 690662ExtracellularSequence AnalysisAdd
BLAST
Transmembranei691 – 71121HelicalSequence AnalysisAdd
BLAST
Topological domaini712 – 79887CytoplasmicSequence AnalysisAdd
BLAST

GO - Cellular componenti

  1. integral component of membrane Source: UniProtKB
  2. plasma membrane Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Membrane

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA33029.

Polymorphism and mutation databases

BioMutaiPCDHB13.
DMDMi13431381.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 2828Sequence AnalysisAdd
BLAST
Chaini29 – 798770Protocadherin beta-13PRO_0000003938Add
BLAST

Amino acid modifications

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

Keywords - PTMi

Glycoprotein

Proteomic databases

PaxDbiQ9Y5F0.
PRIDEiQ9Y5F0.

PTM databases

PhosphoSiteiQ9Y5F0.

Expressioni

Gene expression databases

BgeeiQ9Y5F0.
CleanExiHS_PCDHB13.
GenevestigatoriQ9Y5F0.

Structurei

3D structure databases

ProteinModelPortaliQ9Y5F0.
SMRiQ9Y5F0. Positions 33-679.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini36 – 13499Cadherin 1PROSITE-ProRule annotationAdd
BLAST
Domaini139 – 243105Cadherin 2PROSITE-ProRule annotationAdd
BLAST
Domaini248 – 348101Cadherin 3PROSITE-ProRule annotationAdd
BLAST
Domaini353 – 45199Cadherin 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

eggNOGiNOG323456.
GeneTreeiENSGT00780000121859.
HOGENOMiHOG000220892.
HOVERGENiHBG054878.
InParanoidiQ9Y5F0.
KOiK16494.
OMAiMVCSIEG.
OrthoDBiEOG7KSX80.
PhylomeDBiQ9Y5F0.
TreeFamiTF332299.

Family and domain databases

Gene3Di2.60.40.60. 5 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. 5 hits.
PROSITEiPS00232. CADHERIN_1. 5 hits.
PS50268. CADHERIN_2. 5 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

Q9Y5F0-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEASGKLICR QRQVLFSFLL LGLSLAGAAE PRSYSVVEET EGSSFVTNLA
60 70 80 90 100
KDLGLEQREF SRRGVRVVSR GNKLHLQLNQ ETADLLLNEK LDREDLCGHT
110 120 130 140 150
EPCVLRFQVL LESPFEFFQA ELQVIDINDH SPVFLDKQML VKVSESSPPG
160 170 180 190 200
TTFPLKNAED LDVGQNNIEN YIISPNSYFR VLTRKRSDGR KYPELVLDKA
210 220 230 240 250
LDREEEAELR LTLTALDGGS PPRSGTAQVY IEVLDVNDNA PEFEQPFYRV
260 270 280 290 300
QISEDSPVGF LVVKVSATDV DTGVNGEISY SLFQASEEIG KTFKINPLTG
310 320 330 340 350
EIELKKQLDF EKLQSYEVNI EARDAGTFSG KCTVLIQVID VNDHAPEVTM
360 370 380 390 400
SAFTSPIPEN APETVVALFS VSDLDSGENG KISCSIQEDL PFLLKSAENF
410 420 430 440 450
YTLLTERPLD RESRAEYNIT ITVTDLGTPM LITQLNMTVL IADVNDNAPA
460 470 480 490 500
FTQTSYTLFV RENNSPALHI RSVSATDRDS GTNAQVTYSL LPPQDPHLPL
510 520 530 540 550
TSLVSINADN GHLFALRSLD YEALQGFQFR VGASDHGSPA LSSEALVRVV
560 570 580 590 600
VLDANDNSPF VLYPLQNGSA PCTELVPRAA EPGYLVTKVV AVDGDSGQNA
610 620 630 640 650
WLSYQLLKAT ELGLFGVWAH NGEVRTARLL SERDAAKHRL VVLVKDNGEP
660 670 680 690 700
PRSATATLHV LLVDGFSQPY LPLPEAAPTQ AQADLLTVYL VVALASVSSL
710 720 730 740 750
FLFSVLLFVA VRLCRRSRAA SVGRCLVPEG PLPGHLVDMS GTRTLSQSYQ
760 770 780 790
YEVCLAGGSG TNEFKFLKPI IPNFPPQCPG KEIQGNSTFP NNFGFNIQ
Length:798
Mass (Da):87,552
Last modified:November 1, 1999 - v1
Checksum:i2A478554498B41A3
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti705 – 7051V → E in BAF85510 (PubMed:14702039).Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti471 – 4711R → G.
Corresponds to variant rs2910329 [ dbSNP | Ensembl ].
VAR_059189

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF152492 mRNA. Translation: AAD43753.1.
AF217745 mRNA. Translation: AAK51613.1.
AY358427 mRNA. Translation: AAQ88793.1.
AK292821 mRNA. Translation: BAF85510.1.
BC033068 mRNA. Translation: AAH33068.1.
BC051348 mRNA. Translation: AAH51348.1.
BC071934 mRNA. Translation: AAH71934.1.
CCDSiCCDS4255.1.
RefSeqiNP_061756.1. NM_018933.3.
UniGeneiHs.283803.

Genome annotation databases

EnsembliENST00000341948; ENSP00000345491; ENSG00000187372.
GeneIDi56123.
KEGGihsa:56123.
UCSCiuc003lja.1. human.

Polymorphism and mutation databases

BioMutaiPCDHB13.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF152492 mRNA. Translation: AAD43753.1.
AF217745 mRNA. Translation: AAK51613.1.
AY358427 mRNA. Translation: AAQ88793.1.
AK292821 mRNA. Translation: BAF85510.1.
BC033068 mRNA. Translation: AAH33068.1.
BC051348 mRNA. Translation: AAH51348.1.
BC071934 mRNA. Translation: AAH71934.1.
CCDSiCCDS4255.1.
RefSeqiNP_061756.1. NM_018933.3.
UniGeneiHs.283803.

3D structure databases

ProteinModelPortaliQ9Y5F0.
SMRiQ9Y5F0. Positions 33-679.
ModBaseiSearch...
MobiDBiSearch...

PTM databases

PhosphoSiteiQ9Y5F0.

Polymorphism and mutation databases

BioMutaiPCDHB13.
DMDMi13431381.

Proteomic databases

PaxDbiQ9Y5F0.
PRIDEiQ9Y5F0.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000341948; ENSP00000345491; ENSG00000187372.
GeneIDi56123.
KEGGihsa:56123.
UCSCiuc003lja.1. human.

Organism-specific databases

CTDi56123.
GeneCardsiGC05P141366.
HGNCiHGNC:8684. PCDHB13.
MIMi604967. gene.
606339. gene.
neXtProtiNX_Q9Y5F0.
PharmGKBiPA33029.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiNOG323456.
GeneTreeiENSGT00780000121859.
HOGENOMiHOG000220892.
HOVERGENiHBG054878.
InParanoidiQ9Y5F0.
KOiK16494.
OMAiMVCSIEG.
OrthoDBiEOG7KSX80.
PhylomeDBiQ9Y5F0.
TreeFamiTF332299.

Miscellaneous databases

GeneWikiiPCDHB13.
GenomeRNAii56123.
NextBioi35464687.
PROiQ9Y5F0.
SOURCEiSearch...

Gene expression databases

BgeeiQ9Y5F0.
CleanExiHS_PCDHB13.
GenevestigatoriQ9Y5F0.

Family and domain databases

Gene3Di2.60.40.60. 5 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. 5 hits.
PROSITEiPS00232. CADHERIN_1. 5 hits.
PS50268. CADHERIN_2. 5 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].
  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].
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
  4. "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].
    Tissue: Trachea.
  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].
    Tissue: Lung and Prostate.

Entry informationi

Entry nameiPCDBD_HUMAN
AccessioniPrimary (citable) accession number: Q9Y5F0
Secondary accession number(s): A8K9V6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 27, 2001
Last sequence update: November 1, 1999
Last modified: April 29, 2015
This is version 127 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.