Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Protocadherin-9

Gene

PCDH9

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Potential calcium-dependent cell-adhesion protein.

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

Cell adhesion

Keywords - Ligandi

Calcium

Names & Taxonomyi

Protein namesi
Recommended name:
Protocadherin-9
Gene namesi
Name:PCDH9
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 13

Organism-specific databases

HGNCiHGNC:8661. PCDH9.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini24 – 814791ExtracellularSequence analysisAdd
BLAST
Transmembranei815 – 83521HelicalSequence analysisAdd
BLAST
Topological domaini836 – 1237402CytoplasmicSequence analysisAdd
BLAST

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Membrane

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA33008.

Polymorphism and mutation databases

BioMutaiPCDH9.
DMDMi206729886.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 2323Sequence analysisAdd
BLAST
Chaini24 – 12371214Protocadherin-9PRO_0000003994Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi48 – 481N-linked (GlcNAc...)Sequence analysis
Glycosylationi148 – 1481N-linked (GlcNAc...)Sequence analysis
Glycosylationi306 – 3061N-linked (GlcNAc...)Sequence analysis
Glycosylationi307 – 3071N-linked (GlcNAc...)Sequence analysis
Glycosylationi347 – 3471N-linked (GlcNAc...)Sequence analysis
Glycosylationi368 – 3681N-linked (GlcNAc...)Sequence analysis
Glycosylationi450 – 4501N-linked (GlcNAc...)Sequence analysis
Glycosylationi511 – 5111N-linked (GlcNAc...)Sequence analysis
Glycosylationi630 – 6301N-linked (GlcNAc...)Sequence analysis
Glycosylationi681 – 6811N-linked (GlcNAc...)Sequence analysis
Glycosylationi734 – 7341N-linked (GlcNAc...)Sequence analysis
Glycosylationi754 – 7541N-linked (GlcNAc...)Sequence analysis
Glycosylationi775 – 7751N-linked (GlcNAc...)Sequence analysis
Glycosylationi780 – 7801N-linked (GlcNAc...)Sequence analysis

Keywords - PTMi

Glycoprotein

Proteomic databases

EPDiQ9HC56.
PaxDbiQ9HC56.
PRIDEiQ9HC56.

PTM databases

iPTMnetiQ9HC56.
PhosphoSiteiQ9HC56.

Expressioni

Gene expression databases

BgeeiQ9HC56.
CleanExiHS_PCDH9.
ExpressionAtlasiQ9HC56. baseline and differential.
GenevisibleiQ9HC56. HS.

Organism-specific databases

HPAiHPA015581.

Interactioni

Protein-protein interaction databases

BioGridi111134. 13 interactions.
IntActiQ9HC56. 1 interaction.
STRINGi9606.ENSP00000367096.

Structurei

Secondary structure

1
1237
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi255 – 2628Combined sources
Beta strandi270 – 2734Combined sources
Beta strandi288 – 2914Combined sources
Helixi297 – 3026Combined sources
Beta strandi303 – 3053Combined sources
Turni307 – 3093Combined sources
Beta strandi311 – 3144Combined sources
Turni320 – 3223Combined sources
Beta strandi324 – 33815Combined sources
Beta strandi340 – 34910Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2EE0NMR-A246-352[»]
ProteinModelPortaliQ9HC56.
SMRiQ9HC56. Positions 243-352.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9HC56.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini26 – 142117Cadherin 1PROSITE-ProRule annotationAdd
BLAST
Domaini143 – 252110Cadherin 2PROSITE-ProRule annotationAdd
BLAST
Domaini253 – 358106Cadherin 3PROSITE-ProRule annotationAdd
BLAST
Domaini365 – 469105Cadherin 4PROSITE-ProRule annotationAdd
BLAST
Domaini470 – 572103Cadherin 5PROSITE-ProRule annotationAdd
BLAST
Domaini573 – 675103Cadherin 6PROSITE-ProRule annotationAdd
BLAST
Domaini679 – 784106Cadherin 7PROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Contains 7 cadherin domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat, Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiKOG3594. Eukaryota.
ENOG410XQHI. LUCA.
GeneTreeiENSGT00840000129706.
HOGENOMiHOG000234535.
HOVERGENiHBG053523.
InParanoidiQ9HC56.
KOiK16498.
OMAiYESQRRV.
OrthoDBiEOG7WMCHN.
PhylomeDBiQ9HC56.
TreeFamiTF320624.

Family and domain databases

Gene3Di2.60.40.60. 6 hits.
InterProiIPR002126. Cadherin.
IPR015919. Cadherin-like.
IPR020894. Cadherin_CS.
IPR013164. Cadherin_N.
IPR013585. Protocadherin.
[Graphical view]
PfamiPF00028. Cadherin. 6 hits.
PF08266. Cadherin_2. 1 hit.
PF08374. Protocadherin. 1 hit.
[Graphical view]
PRINTSiPR00205. CADHERIN.
SMARTiSM00112. CA. 7 hits.
[Graphical view]
SUPFAMiSSF49313. SSF49313. 6 hits.
PROSITEiPS00232. CADHERIN_1. 6 hits.
PS50268. CADHERIN_2. 7 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: Q9HC56-1) [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
MDLRDFYLLA ALIACLRLDS AIAQELIYTI REELPENVPI GNIPKDLNIS
60 70 80 90 100
HINAATGTSA SLVYRLVSKA GDAPLVKVSS STGEIFTTSN RIDREKLCAG
110 120 130 140 150
ASYAEENECF FELEVVILPN DFFRLIKIKI IVKDTNDNAP MFPSPVINIS
160 170 180 190 200
IPENTLINSR FPIPSATDPD TGFNGVQHYE LLNGQSVFGL DIVETPEGEK
210 220 230 240 250
WPQLIVQQNL DREQKDTYVM KIKVEDGGTP QKSSTAILQV TVSDVNDNRP
260 270 280 290 300
VFKEGQVEVH IPENAPVGTS VIQLHATDAD IGSNAEIRYI FGAQVAPATK
310 320 330 340 350
RLFALNNTTG LITVQRSLDR EETAIHKVTV LASDGSSTPA RATVTINVTD
360 370 380 390 400
VNDNPPNIDL RYIISPINGT VYLSEKDPVN TKIALITVSD KDTDVNGKVI
410 420 430 440 450
CFIEREVPFH LKAVYDNQYL LETSSLLDYE GTKEFSFKIV ASDSGKPSLN
460 470 480 490 500
QTALVRVKLE DENDNPPIFN QPVIELSVSE NNRRGLYLTT ISATDEDSGK
510 520 530 540 550
NADIVYQLGP NASFFDLDRK TGVLTASRVF DREEQERFIF TVTARDNGTP
560 570 580 590 600
PLQSQAAVIV TVLDENDNSP KFTHNHFQFF VSENLPKYST VGVITVTDAD
610 620 630 640 650
AGENKAVTLS ILNDNDNFVL DPYSGVIKSN VSFDREQQSS YTFDVKATDG
660 670 680 690 700
GQPPRSSTAK VTINVMDVND NSPVVISPPS NTSFKLVPLS AIPGSVVAEV
710 720 730 740 750
FAVDVDTGMN AELKYTIVSG NNKGLFRIDP VTGNITLEEK PAPTDVGLHR
760 770 780 790 800
LVVNISDLGY PKSLHTLVLV FLYVNDTAGN ASYIYDLIRR TMETPLDRNI
810 820 830 840 850
GDSSQPYQNE DYLTIMIAII AGAMVVIVVI FVTVLVRCRH ASRFKAAQRS
860 870 880 890 900
KQGAEWMSPN QENKQNKKKK RKKRKSPKSS LLNFVTIEES KPDDAVHEPI
910 920 930 940 950
NGTISLPAEL EEQSIGRFDW GPAPPTTFKP NSPDLAKHYK SASPQPAFHL
960 970 980 990 1000
KPDTPVSVKK HHVIQELPLD NTFVGGCDTL SKRSSTSSDH FSASECSSQG
1010 1020 1030 1040 1050
GFKTKGPLHT RQCNSHSKSD NIPVTPQKCP SSTGFHIQEN EESHYESQRR
1060 1070 1080 1090 1100
VTFHLPDGSQ ESCSDSGLGD HEPVGSGTLI SHPLPLVQPQ DEFYDQASPD
1110 1120 1130 1140 1150
KRTEADGNSD PNSDGPLGPR GLAEATEMCT QECLVLGHSD NCWMPPGLGP
1160 1170 1180 1190 1200
YQHPKSPLST FAPQKEWVKK DKLVNGHTLT RAWKEDSNRN QFNDRKQYGS
1210 1220 1230
NEGHFNNGSH MTDIPLANLK SYKQAGGATE SPKEHQL
Length:1,237
Mass (Da):136,064
Last modified:September 23, 2008 - v2
Checksum:iE2EA8FCC24735C7D
GO
Isoform 2 (identifier: Q9HC56-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1013-1046: Missing.

Show »
Length:1,203
Mass (Da):132,251
Checksum:iCEEDD24FC1CF8BE2
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti907 – 9071P → A in CAD97664 (PubMed:17974005).Curated
Sequence conflicti922 – 9221P → S in CAD97664 (PubMed:17974005).Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1013 – 104634Missing in isoform 2. 2 PublicationsVSP_035430Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF169692 mRNA. Translation: AAF89689.2.
AL834258 mRNA. Translation: CAD38933.1.
BX537422 mRNA. Translation: CAD97664.1.
AL603863, AL136999, AL355173 Genomic DNA. Translation: CAH72759.1.
AL136999, AL355173, AL603863 Genomic DNA. Translation: CAI12502.1.
AL355173, AL603863, AL136999 Genomic DNA. Translation: CAH72612.1.
AL138814
, AL136999, AL355173, AL603863 Genomic DNA. Translation: CAM13066.1.
AL136999
, AL138814, AL355173, AL603863 Genomic DNA. Translation: CAM13771.1.
AL355173
, AL136999, AL138814, AL603863 Genomic DNA. Translation: CAM17290.1.
AL603863
, AL136999, AL138814, AL355173 Genomic DNA. Translation: CAM17491.1.
BC136626 mRNA. Translation: AAI36627.1.
BC136627 mRNA. Translation: AAI36628.1.
CCDSiCCDS9443.1. [Q9HC56-2]
CCDS9444.1. [Q9HC56-1]
RefSeqiNP_001305301.1. NM_001318372.1.
NP_001305302.1. NM_001318373.1.
NP_065136.1. NM_020403.4. [Q9HC56-2]
NP_982354.1. NM_203487.2. [Q9HC56-1]
UniGeneiHs.654709.

Genome annotation databases

EnsembliENST00000377865; ENSP00000367096; ENSG00000184226. [Q9HC56-1]
ENST00000544246; ENSP00000442186; ENSG00000184226. [Q9HC56-2]
GeneIDi5101.
KEGGihsa:5101.
UCSCiuc001vil.4. human. [Q9HC56-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF169692 mRNA. Translation: AAF89689.2.
AL834258 mRNA. Translation: CAD38933.1.
BX537422 mRNA. Translation: CAD97664.1.
AL603863, AL136999, AL355173 Genomic DNA. Translation: CAH72759.1.
AL136999, AL355173, AL603863 Genomic DNA. Translation: CAI12502.1.
AL355173, AL603863, AL136999 Genomic DNA. Translation: CAH72612.1.
AL138814
, AL136999, AL355173, AL603863 Genomic DNA. Translation: CAM13066.1.
AL136999
, AL138814, AL355173, AL603863 Genomic DNA. Translation: CAM13771.1.
AL355173
, AL136999, AL138814, AL603863 Genomic DNA. Translation: CAM17290.1.
AL603863
, AL136999, AL138814, AL355173 Genomic DNA. Translation: CAM17491.1.
BC136626 mRNA. Translation: AAI36627.1.
BC136627 mRNA. Translation: AAI36628.1.
CCDSiCCDS9443.1. [Q9HC56-2]
CCDS9444.1. [Q9HC56-1]
RefSeqiNP_001305301.1. NM_001318372.1.
NP_001305302.1. NM_001318373.1.
NP_065136.1. NM_020403.4. [Q9HC56-2]
NP_982354.1. NM_203487.2. [Q9HC56-1]
UniGeneiHs.654709.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2EE0NMR-A246-352[»]
ProteinModelPortaliQ9HC56.
SMRiQ9HC56. Positions 243-352.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi111134. 13 interactions.
IntActiQ9HC56. 1 interaction.
STRINGi9606.ENSP00000367096.

PTM databases

iPTMnetiQ9HC56.
PhosphoSiteiQ9HC56.

Polymorphism and mutation databases

BioMutaiPCDH9.
DMDMi206729886.

Proteomic databases

EPDiQ9HC56.
PaxDbiQ9HC56.
PRIDEiQ9HC56.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000377865; ENSP00000367096; ENSG00000184226. [Q9HC56-1]
ENST00000544246; ENSP00000442186; ENSG00000184226. [Q9HC56-2]
GeneIDi5101.
KEGGihsa:5101.
UCSCiuc001vil.4. human. [Q9HC56-1]

Organism-specific databases

CTDi5101.
GeneCardsiPCDH9.
H-InvDBHIX0011357.
HGNCiHGNC:8661. PCDH9.
HPAiHPA015581.
MIMi603581. gene.
neXtProtiNX_Q9HC56.
PharmGKBiPA33008.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG3594. Eukaryota.
ENOG410XQHI. LUCA.
GeneTreeiENSGT00840000129706.
HOGENOMiHOG000234535.
HOVERGENiHBG053523.
InParanoidiQ9HC56.
KOiK16498.
OMAiYESQRRV.
OrthoDBiEOG7WMCHN.
PhylomeDBiQ9HC56.
TreeFamiTF320624.

Miscellaneous databases

ChiTaRSiPCDH9. human.
EvolutionaryTraceiQ9HC56.
GenomeRNAii5101.
PROiQ9HC56.
SOURCEiSearch...

Gene expression databases

BgeeiQ9HC56.
CleanExiHS_PCDH9.
ExpressionAtlasiQ9HC56. baseline and differential.
GenevisibleiQ9HC56. HS.

Family and domain databases

Gene3Di2.60.40.60. 6 hits.
InterProiIPR002126. Cadherin.
IPR015919. Cadherin-like.
IPR020894. Cadherin_CS.
IPR013164. Cadherin_N.
IPR013585. Protocadherin.
[Graphical view]
PfamiPF00028. Cadherin. 6 hits.
PF08266. Cadherin_2. 1 hit.
PF08374. Protocadherin. 1 hit.
[Graphical view]
PRINTSiPR00205. CADHERIN.
SMARTiSM00112. CA. 7 hits.
[Graphical view]
SUPFAMiSSF49313. SSF49313. 6 hits.
PROSITEiPS00232. CADHERIN_1. 6 hits.
PS50268. CADHERIN_2. 7 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Identification and characterization of a novel human protocadherin gene with high homology to a chromosome X-linked protocadherin."
    Kools P.F.J., van Roy F.
    Submitted (AUG-2000) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2).
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2), NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 154-1237 (ISOFORM 1).
    Tissue: Amygdala.
  3. "The DNA sequence and analysis of human chromosome 13."
    Dunham A., Matthews L.H., Burton J., Ashurst J.L., Howe K.L., Ashcroft K.J., Beare D.M., Burford D.C., Hunt S.E., Griffiths-Jones S., Jones M.C., Keenan S.J., Oliver K., Scott C.E., Ainscough R., Almeida J.P., Ambrose K.D., Andrews D.T.
    , Ashwell R.I.S., Babbage A.K., Bagguley C.L., Bailey J., Bannerjee R., Barlow K.F., Bates K., Beasley H., Bird C.P., Bray-Allen S., Brown A.J., Brown J.Y., Burrill W., Carder C., Carter N.P., Chapman J.C., Clamp M.E., Clark S.Y., Clarke G., Clee C.M., Clegg S.C., Cobley V., Collins J.E., Corby N., Coville G.J., Deloukas P., Dhami P., Dunham I., Dunn M., Earthrowl M.E., Ellington A.G., Faulkner L., Frankish A.G., Frankland J., French L., Garner P., Garnett J., Gilbert J.G.R., Gilson C.J., Ghori J., Grafham D.V., Gribble S.M., Griffiths C., Hall R.E., Hammond S., Harley J.L., Hart E.A., Heath P.D., Howden P.J., Huckle E.J., Hunt P.J., Hunt A.R., Johnson C., Johnson D., Kay M., Kimberley A.M., King A., Laird G.K., Langford C.J., Lawlor S., Leongamornlert D.A., Lloyd D.M., Lloyd C., Loveland J.E., Lovell J., Martin S., Mashreghi-Mohammadi M., McLaren S.J., McMurray A., Milne S., Moore M.J.F., Nickerson T., Palmer S.A., Pearce A.V., Peck A.I., Pelan S., Phillimore B., Porter K.M., Rice C.M., Searle S., Sehra H.K., Shownkeen R., Skuce C.D., Smith M., Steward C.A., Sycamore N., Tester J., Thomas D.W., Tracey A., Tromans A., Tubby B., Wall M., Wallis J.M., West A.P., Whitehead S.L., Willey D.L., Wilming L., Wray P.W., Wright M.W., Young L., Coulson A., Durbin R.M., Hubbard T., Sulston J.E., Beck S., Bentley D.R., Rogers J., Ross M.T.
    Nature 428:522-528(2004) [PubMed] [Europe PMC] [Abstract]
    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] (ISOFORM 1).
  5. "Solution structures of the CA domain of human protocadherin 9."
    RIKEN structural genomics initiative (RSGI)
    Submitted (AUG-2007) to the PDB data bank
    Cited for: STRUCTURE BY NMR OF 243-352.

Entry informationi

Entry nameiPCDH9_HUMAN
AccessioniPrimary (citable) accession number: Q9HC56
Secondary accession number(s): A2A6U1
, Q5VT83, Q7Z3U0, Q8N3K7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 16, 2004
Last sequence update: September 23, 2008
Last modified: June 8, 2016
This is version 122 of the entry and version 2 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

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 13
    Human chromosome 13: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. 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.