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Protein

Protocadherin beta-16

Gene

PCDHB16

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein 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-16
Short name:
PCDH-beta-16
Alternative name(s):
Protocadherin-3X
Gene namesi
Name:PCDHB16
Synonyms:KIAA1621, PCDH3X
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640 Componenti: Chromosome 5

Organism-specific databases

HGNCiHGNC:14546. PCDHB16.

Subcellular locationi

Membrane By similarity; Single-pass type I membrane protein By similarity

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini29 – 690662ExtracellularSequence AnalysisAdd
BLAST
Transmembranei691 – 71121HelicalSequence AnalysisAdd
BLAST
Topological domaini712 – 77665CytoplasmicSequence AnalysisAdd
BLAST

GO - Cellular componenti

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

Keywords - Cellular componenti

Membrane

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA33032.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 2828Sequence AnalysisAdd
BLAST
Chaini29 – 776748Protocadherin beta-16PRO_0000003944Add
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

PaxDbiQ9NRJ7.
PRIDEiQ9NRJ7.

PTM databases

PhosphoSiteiQ9NRJ7.

Expressioni

Gene expression databases

BgeeiQ9NRJ7.
CleanExiHS_PCDHB16.
GenevestigatoriQ9NRJ7.

Organism-specific databases

HPAiHPA014668.
HPA016475.

Structurei

3D structure databases

ProteinModelPortaliQ9NRJ7.
SMRiQ9NRJ7. Positions 32-677.
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

eggNOGiNOG251260.
HOGENOMiHOG000220892.
HOVERGENiHBG054878.
InParanoidiQ9NRJ7.
KOiK16494.
OMAiEIAVISI.
OrthoDBiEOG7KSX80.
PhylomeDBiQ9NRJ7.
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. 5 hits.
[Graphical view]
SUPFAMiSSF49313. SSF49313. 6 hits.
PROSITEiPS00232. CADHERIN_1. 5 hits.
PS50268. CADHERIN_2. 6 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

Q9NRJ7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEIGWMHNRR QRQVLVFFVL LSLSGAGAEL GSYSVVEETE RGSFVANLGK
60 70 80 90 100
DLGLGLTEMS TRKARIISQG NKQHLQLKAQ TGDLLINEKL DREELCGPTE
110 120 130 140 150
PCILHFQVLM ENPLEIFQAE LRVIDINDHS PMFTEKEMIL KIPENSPLGT
160 170 180 190 200
EFPLNHALDL DVGSNNVQNY KISPSSHFRV LIHEFRDGRK YPELVLDKEL
210 220 230 240 250
DREEEPQLRL TLTALDGGSP PRSGTAQVRI EVVDINDNAP EFEQPIYKVQ
260 270 280 290 300
IPENSPLGSL VATVSARDLD GGANGKISYT LFQPSEDISK TLEVNPMTGE
310 320 330 340 350
VRLRKQVDFE MVTSYEVRIK ATDGGGLSGK CTLLLQVVDV NDNPPQVTMS
360 370 380 390 400
ALTSPIPENS PEIVVAVFSV SDPDSGNNGK TISSIQEDLP FLLKPSVKNF
410 420 430 440 450
YTLVTERALD REARAEYNIT LTVTDMGTPR LKTEHNITVQ ISDVNDNAPT
460 470 480 490 500
FTQTSYTLFV RENNSPALHI GSVSATDRDS GTNAQVTYSL LPPQDPHLPL
510 520 530 540 550
ASLVSINADN GHLFALRSLD YEALREFEFR VSATDRGSPA LSSEALVRVL
560 570 580 590 600
VLDANDNSPF VLYPLQNGSA PCTELVPRAA EPGYLVTKVV AVDGDSGQNA
610 620 630 640 650
WLSYQLLKAT EPGLFGVWAH NGEVRTARLL SERDAAKQRL VVLVKDNGEP
660 670 680 690 700
PRSATATLHV LLVDGFSQPF LPLPEAAPGQ TQANSLTVYL VVALASVSSL
710 720 730 740 750
FLFSVLLFVA VRLCRRSRAA SVGRCSMPEG PFPGRLVDVS GTGTLSQSYQ
760 770
YEVCLTGGSE TSEFKFLKPI IPNFSP
Length:776
Mass (Da):84,983
Last modified:October 4, 2010 - v3
Checksum:i03F420D3098D6032
GO

Sequence cautioni

The sequence BAB13447.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti357 – 3571P → A in AAH36062 (PubMed:15489334).Curated
Sequence conflicti482 – 4821T → I in BAB13447 (PubMed:10997877).Curated
Sequence conflicti526 – 5261E → A in AAF81914 (PubMed:11322959).Curated
Sequence conflicti526 – 5261E → A in AAG10030 (PubMed:11322959).Curated
Sequence conflicti526 – 5261E → A in AAH36062 (PubMed:15489334).Curated
Sequence conflicti543 – 5431S → R in AAF81914 (PubMed:11322959).Curated
Sequence conflicti543 – 5431S → R in AAG10030 (PubMed:11322959).Curated
Sequence conflicti543 – 5431S → R in AAH36062 (PubMed:15489334).Curated
Sequence conflicti560 – 5601F → L in AAH36062 (PubMed:15489334).Curated
Sequence conflicti638 – 6381Q → H in BAB13447 (PubMed:10997877).Curated
Sequence conflicti652 – 6521R → C in BAB13447 (PubMed:10997877).Curated
Sequence conflicti710 – 7101A → V in BAB13447 (PubMed:10997877).Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti91 – 911D → E.
Corresponds to variant rs17096969 [ dbSNP | Ensembl ].
VAR_055587
Natural varianti347 – 3471V → L.
Corresponds to variant rs28664170 [ dbSNP | Ensembl ].
VAR_061068
Natural varianti508 – 5081A → T.
Corresponds to variant rs56327450 [ dbSNP | Ensembl ].
VAR_061069
Natural varianti525 – 5251R → Q.2 Publications
Corresponds to variant rs17844651 [ dbSNP | Ensembl ].
VAR_026478
Natural varianti532 – 5321S → G.2 Publications
Corresponds to variant rs2697532 [ dbSNP | Ensembl ].
VAR_026479

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF217757 mRNA. Translation: AAF81914.1.
AF282973 Genomic DNA. Translation: AAG10030.1.
AY013878 mRNA. Translation: AAK21988.1.
AB046841 mRNA. Translation: BAB13447.1. Different initiation.
AK056460 mRNA. Translation: BAG51717.1.
AC074130 Genomic DNA. No translation available.
CH471062 Genomic DNA. Translation: EAW61975.1.
BC036062 mRNA. Translation: AAH36062.1.
CCDSiCCDS4251.1.
RefSeqiNP_066008.2. NM_020957.3.
UniGeneiHs.147674.
Hs.582172.

Genome annotation databases

EnsembliENST00000609684; ENSP00000477314; ENSG00000272674.
GeneIDi57717.
KEGGihsa:57717.
UCSCiuc003liv.3. human.

Polymorphism databases

DMDMi308153560.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF217757 mRNA. Translation: AAF81914.1.
AF282973 Genomic DNA. Translation: AAG10030.1.
AY013878 mRNA. Translation: AAK21988.1.
AB046841 mRNA. Translation: BAB13447.1. Different initiation.
AK056460 mRNA. Translation: BAG51717.1.
AC074130 Genomic DNA. No translation available.
CH471062 Genomic DNA. Translation: EAW61975.1.
BC036062 mRNA. Translation: AAH36062.1.
CCDSiCCDS4251.1.
RefSeqiNP_066008.2. NM_020957.3.
UniGeneiHs.147674.
Hs.582172.

3D structure databases

ProteinModelPortaliQ9NRJ7.
SMRiQ9NRJ7. Positions 32-677.
ModBaseiSearch...
MobiDBiSearch...

PTM databases

PhosphoSiteiQ9NRJ7.

Polymorphism databases

DMDMi308153560.

Proteomic databases

PaxDbiQ9NRJ7.
PRIDEiQ9NRJ7.

Protocols and materials databases

DNASUi57717.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000609684; ENSP00000477314; ENSG00000272674.
GeneIDi57717.
KEGGihsa:57717.
UCSCiuc003liv.3. human.

Organism-specific databases

CTDi57717.
GeneCardsiGC05P140563.
HGNCiHGNC:14546. PCDHB16.
HPAiHPA014668.
HPA016475.
MIMi604967. gene.
606345. gene.
neXtProtiNX_Q9NRJ7.
PharmGKBiPA33032.
HUGEiSearch...
GenAtlasiSearch...

Phylogenomic databases

eggNOGiNOG251260.
HOGENOMiHOG000220892.
HOVERGENiHBG054878.
InParanoidiQ9NRJ7.
KOiK16494.
OMAiEIAVISI.
OrthoDBiEOG7KSX80.
PhylomeDBiQ9NRJ7.
TreeFamiTF332299.

Miscellaneous databases

GeneWikiiPCDHB16.
GenomeRNAii57717.
NextBioi64644.
PROiQ9NRJ7.
SOURCEiSearch...

Gene expression databases

BgeeiQ9NRJ7.
CleanExiHS_PCDHB16.
GenevestigatoriQ9NRJ7.

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. 5 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. "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(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA], VARIANTS GLN-525 AND GLY-532.
  2. "Comparative DNA sequence analysis of mouse and human protocadherin gene clusters."
    Wu Q., Zhang T., Cheng J.-F., Kim Y., Grimwood J., Schmutz J., Dickson M., Noonan J.P., Zhang M.Q., Myers R.M., Maniatis T.
    Genome Res. 11:389-404(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
  3. "Prediction of the coding sequences of unidentified human genes. XVIII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro."
    Nagase T., Kikuno R., Nakayama M., Hirosawa M., Ohara O.
    DNA Res. 7:273-281(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Brain.
  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(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
  5. "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(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  6. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  7. "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(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], VARIANTS GLN-525 AND GLY-532.
    Tissue: Brain.
  8. "Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides."
    Gevaert K., Goethals M., Martens L., Van Damme J., Staes A., Thomas G.R., Vandekerckhove J.
    Nat. Biotechnol. 21:566-569(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 518-525.
    Tissue: Platelet.

Entry informationi

Entry nameiPCDBG_HUMAN
AccessioniPrimary (citable) accession number: Q9NRJ7
Secondary accession number(s): B3KPK5
, Q8IYD5, Q96SE9, Q9HCF1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 26, 2001
Last sequence update: October 4, 2010
Last modified: March 3, 2015
This is version 125 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, Direct protein sequencing, 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.