ID   PCDA1_HUMAN             Reviewed;         950 AA.
AC   Q9Y5I3; O75288; Q9NRT7;
DT   27-APR-2001, integrated into UniProtKB/Swiss-Prot.
DT   01-NOV-1999, sequence version 1.
DT   24-JAN-2024, entry version 190.
DE   RecName: Full=Protocadherin alpha-1;
DE            Short=PCDH-alpha-1;
DE   Flags: Precursor;
GN   Name=PCDHA1;
OS   Homo sapiens (Human).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC   Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC   Homo.
OX   NCBI_TaxID=9606;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 3).
RC   TISSUE=Brain;
RX   PubMed=10380929; DOI=10.1016/s0092-8674(00)80789-8;
RA   Wu Q., Maniatis T.;
RT   "A striking organization of a large family of human neural cadherin-like
RT   cell adhesion genes.";
RL   Cell 97:779-790(1999).
RN   [2]
RP   NUCLEOTIDE SEQUENCE (ISOFORM 2).
RC   TISSUE=Brain;
RA   Kools P.F.J., van Roy F.;
RT   "Alternative splicing within the human CNR family of protocadherins (PCDH-
RT   alpha) produces transcripts encoding secreted proteins.";
RL   Submitted (JUL-1999) to the EMBL/GenBank/DDBJ databases.
RN   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX   PubMed=15372022; DOI=10.1038/nature02919;
RA   Schmutz J., Martin J., Terry A., Couronne O., Grimwood J., Lowry S.,
RA   Gordon L.A., Scott D., Xie G., Huang W., Hellsten U., Tran-Gyamfi M.,
RA   She X., Prabhakar S., Aerts A., Altherr M., Bajorek E., Black S.,
RA   Branscomb E., Caoile C., Challacombe J.F., Chan Y.M., Denys M.,
RA   Detter J.C., Escobar J., Flowers D., Fotopulos D., Glavina T., Gomez M.,
RA   Gonzales E., Goodstein D., Grigoriev I., Groza M., Hammon N., Hawkins T.,
RA   Haydu L., Israni S., Jett J., Kadner K., Kimball H., Kobayashi A.,
RA   Lopez F., Lou Y., Martinez D., Medina C., Morgan J., Nandkeshwar R.,
RA   Noonan J.P., Pitluck S., Pollard M., Predki P., Priest J., Ramirez L.,
RA   Retterer J., Rodriguez A., Rogers S., Salamov A., Salazar A., Thayer N.,
RA   Tice H., Tsai M., Ustaszewska A., Vo N., Wheeler J., Wu K., Yang J.,
RA   Dickson M., Cheng J.-F., Eichler E.E., Olsen A., Pennacchio L.A.,
RA   Rokhsar D.S., Richardson P., Lucas S.M., Myers R.M., Rubin E.M.;
RT   "The DNA sequence and comparative analysis of human chromosome 5.";
RL   Nature 431:268-274(2004).
CC   -!- FUNCTION: Potential calcium-dependent cell-adhesion protein. May be
CC       involved in the establishment and maintenance of specific neuronal
CC       connections in the brain.
CC   -!- SUBCELLULAR LOCATION: [Isoform 1]: Cell membrane {ECO:0000250}; Single-
CC       pass type I membrane protein {ECO:0000250}.
CC   -!- SUBCELLULAR LOCATION: [Isoform 2]: Secreted {ECO:0000305}.
CC   -!- ALTERNATIVE PRODUCTS:
CC       Event=Alternative splicing; Named isoforms=3;
CC         Comment=Additional isoforms seem to exist.;
CC       Name=1;
CC         IsoId=Q9Y5I3-1; Sequence=Displayed;
CC       Name=2;
CC         IsoId=Q9Y5I3-2; Sequence=VSP_000670;
CC       Name=3;
CC         IsoId=Q9Y5I3-3; Sequence=VSP_000671, VSP_000672;
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DR   EMBL; AF152305; AAD43699.1; -; mRNA.
DR   EMBL; AF152479; AAD43740.1; -; mRNA.
DR   EMBL; AF169695; AAF89692.1; -; mRNA.
DR   EMBL; AC005609; AAC34325.1; -; Genomic_DNA.
DR   CCDS; CCDS54912.1; -. [Q9Y5I3-2]
DR   CCDS; CCDS54913.1; -. [Q9Y5I3-1]
DR   RefSeq; NP_061723.1; NM_018900.3. [Q9Y5I3-1]
DR   RefSeq; NP_113598.1; NM_031410.2. [Q9Y5I3-3]
DR   RefSeq; NP_113599.1; NM_031411.2. [Q9Y5I3-2]
DR   AlphaFoldDB; Q9Y5I3; -.
DR   SMR; Q9Y5I3; -.
DR   BioGRID; 121087; 6.
DR   IntAct; Q9Y5I3; 3.
DR   STRING; 9606.ENSP00000420840; -.
DR   GlyCosmos; Q9Y5I3; 3 sites, No reported glycans.
DR   GlyGen; Q9Y5I3; 3 sites.
DR   iPTMnet; Q9Y5I3; -.
DR   PhosphoSitePlus; Q9Y5I3; -.
DR   BioMuta; PCDHA1; -.
DR   DMDM; 13878434; -.
DR   jPOST; Q9Y5I3; -.
DR   MassIVE; Q9Y5I3; -.
DR   PaxDb; 9606-ENSP00000420840; -.
DR   PeptideAtlas; Q9Y5I3; -.
DR   ProteomicsDB; 86411; -. [Q9Y5I3-1]
DR   ProteomicsDB; 86412; -. [Q9Y5I3-2]
DR   ProteomicsDB; 86413; -. [Q9Y5I3-3]
DR   Antibodypedia; 27106; 133 antibodies from 17 providers.
DR   DNASU; 56147; -.
DR   Ensembl; ENST00000378133.4; ENSP00000367373.3; ENSG00000204970.10. [Q9Y5I3-3]
DR   Ensembl; ENST00000394633.7; ENSP00000378129.3; ENSG00000204970.10. [Q9Y5I3-2]
DR   Ensembl; ENST00000504120.4; ENSP00000420840.3; ENSG00000204970.10. [Q9Y5I3-1]
DR   Ensembl; ENST00000708285.1; ENSP00000517136.1; ENSG00000291649.1. [Q9Y5I3-3]
DR   Ensembl; ENST00000708286.1; ENSP00000517137.1; ENSG00000291649.1. [Q9Y5I3-1]
DR   Ensembl; ENST00000708287.1; ENSP00000517138.1; ENSG00000291649.1. [Q9Y5I3-2]
DR   GeneID; 56147; -.
DR   KEGG; hsa:56147; -.
DR   MANE-Select; ENST00000504120.4; ENSP00000420840.3; NM_018900.4; NP_061723.1.
DR   UCSC; uc003lgz.5; human. [Q9Y5I3-1]
DR   AGR; HGNC:8663; -.
DR   CTD; 56147; -.
DR   DisGeNET; 56147; -.
DR   GeneCards; PCDHA1; -.
DR   HGNC; HGNC:8663; PCDHA1.
DR   HPA; ENSG00000204970; Group enriched (brain, pituitary gland, testis).
DR   MIM; 604966; gene.
DR   MIM; 606307; gene.
DR   neXtProt; NX_Q9Y5I3; -.
DR   OpenTargets; ENSG00000204970; -.
DR   PharmGKB; PA33009; -.
DR   VEuPathDB; HostDB:ENSG00000204970; -.
DR   eggNOG; KOG3594; Eukaryota.
DR   GeneTree; ENSGT00940000165185; -.
DR   HOGENOM; CLU_006480_3_0_1; -.
DR   InParanoid; Q9Y5I3; -.
DR   OMA; FGQVTCS; -.
DR   OrthoDB; 4259465at2759; -.
DR   PhylomeDB; Q9Y5I3; -.
DR   TreeFam; TF332299; -.
DR   PathwayCommons; Q9Y5I3; -.
DR   SignaLink; Q9Y5I3; -.
DR   SIGNOR; Q9Y5I3; -.
DR   BioGRID-ORCS; 56147; 45 hits in 1095 CRISPR screens.
DR   GeneWiki; Protocadherin_alpha_1; -.
DR   GenomeRNAi; 56147; -.
DR   Pharos; Q9Y5I3; Tbio.
DR   PRO; PR:Q9Y5I3; -.
DR   Proteomes; UP000005640; Chromosome 5.
DR   RNAct; Q9Y5I3; Protein.
DR   Bgee; ENSG00000204970; Expressed in cortical plate and 39 other cell types or tissues.
DR   GO; GO:0005783; C:endoplasmic reticulum; IEA:Ensembl.
DR   GO; GO:0005576; C:extracellular region; IEA:UniProtKB-SubCell.
DR   GO; GO:0005886; C:plasma membrane; TAS:ProtInc.
DR   GO; GO:0005509; F:calcium ion binding; IEA:InterPro.
DR   GO; GO:0007155; P:cell adhesion; IBA:GO_Central.
DR   GO; GO:0007156; P:homophilic cell adhesion via plasma membrane adhesion molecules; IEA:InterPro.
DR   GO; GO:0007399; P:nervous system development; TAS:ProtInc.
DR   CDD; cd11304; Cadherin_repeat; 6.
DR   Gene3D; 2.60.40.60; Cadherins; 6.
DR   InterPro; IPR002126; Cadherin-like_dom.
DR   InterPro; IPR015919; Cadherin-like_sf.
DR   InterPro; IPR031904; Cadherin_CBD.
DR   InterPro; IPR020894; Cadherin_CS.
DR   InterPro; IPR013164; Cadherin_N.
DR   PANTHER; PTHR24028; CADHERIN-87A; 1.
DR   PANTHER; PTHR24028:SF92; PROTOCADHERIN ALPHA-1; 1.
DR   Pfam; PF00028; Cadherin; 5.
DR   Pfam; PF08266; Cadherin_2; 1.
DR   Pfam; PF15974; Cadherin_tail; 1.
DR   PRINTS; PR00205; CADHERIN.
DR   SMART; SM00112; CA; 6.
DR   SUPFAM; SSF49313; Cadherin-like; 6.
DR   PROSITE; PS00232; CADHERIN_1; 5.
DR   PROSITE; PS50268; CADHERIN_2; 6.
DR   Genevisible; Q9Y5I3; HS.
PE   2: Evidence at transcript level;
KW   Alternative splicing; Calcium; Cell adhesion; Cell membrane; Glycoprotein;
KW   Membrane; Reference proteome; Repeat; Secreted; Signal; Transmembrane;
KW   Transmembrane helix.
FT   SIGNAL          1..29
FT                   /evidence="ECO:0000255"
FT   CHAIN           30..950
FT                   /note="Protocadherin alpha-1"
FT                   /id="PRO_0000003884"
FT   TOPO_DOM        30..697
FT                   /note="Extracellular"
FT                   /evidence="ECO:0000255"
FT   TRANSMEM        698..718
FT                   /note="Helical"
FT                   /evidence="ECO:0000255"
FT   TOPO_DOM        719..950
FT                   /note="Cytoplasmic"
FT                   /evidence="ECO:0000255"
FT   DOMAIN          30..133
FT                   /note="Cadherin 1"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00043"
FT   DOMAIN          157..242
FT                   /note="Cadherin 2"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00043"
FT   DOMAIN          243..350
FT                   /note="Cadherin 3"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00043"
FT   DOMAIN          351..455
FT                   /note="Cadherin 4"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00043"
FT   DOMAIN          456..565
FT                   /note="Cadherin 5"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00043"
FT   DOMAIN          588..678
FT                   /note="Cadherin 6"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00043"
FT   REPEAT          734..737
FT                   /note="PXXP 1"
FT   REPEAT          799..802
FT                   /note="PXXP 2"
FT   REPEAT          832..835
FT                   /note="PXXP 3"
FT   REPEAT          873..876
FT                   /note="PXXP 4"
FT   REPEAT          891..894
FT                   /note="PXXP 5"
FT   REGION          734..894
FT                   /note="5 X 4 AA repeats of P-X-X-P"
FT   REGION          752..808
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          828..856
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          871..890
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          900..950
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        774..805
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        935..950
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   CARBOHYD        257
FT                   /note="N-linked (GlcNAc...) asparagine"
FT                   /evidence="ECO:0000255"
FT   CARBOHYD        265
FT                   /note="N-linked (GlcNAc...) asparagine"
FT                   /evidence="ECO:0000255"
FT   CARBOHYD        548
FT                   /note="N-linked (GlcNAc...) asparagine"
FT                   /evidence="ECO:0000255"
FT   VAR_SEQ         535..798
FT                   /note="Missing (in isoform 2)"
FT                   /evidence="ECO:0000305"
FT                   /id="VSP_000670"
FT   VAR_SEQ         799..807
FT                   /note="PRQPNPDWR -> VSPTFEFWL (in isoform 3)"
FT                   /evidence="ECO:0000303|PubMed:10380929"
FT                   /id="VSP_000671"
FT   VAR_SEQ         808..950
FT                   /note="Missing (in isoform 3)"
FT                   /evidence="ECO:0000303|PubMed:10380929"
FT                   /id="VSP_000672"
FT   VARIANT         360
FT                   /note="R -> G (in dbSNP:rs34575154)"
FT                   /id="VAR_048521"
FT   VARIANT         449
FT                   /note="N -> H (in dbSNP:rs3733712)"
FT                   /id="VAR_021872"
FT   VARIANT         732
FT                   /note="Y -> C (in dbSNP:rs2240696)"
FT                   /id="VAR_021873"
FT   VARIANT         759
FT                   /note="C -> F (in dbSNP:rs2240695)"
FT                   /id="VAR_048522"
SQ   SEQUENCE   950 AA;  102952 MW;  9FC170365565908A CRC64;
     MVFSRRGGLG ARDLLLWLLL LAAWEVGSGQ LHYSIPEEAK HGTFVGRVAQ DLGLELAELV
     PRLFRVASKT HRDLLEVNLQ NGILFVNSRI DREELCQWSA ECSIHLELIA DRPLQVFHVE
     VKVKDINDNP PVFRGREQII FIPESRLLNS RFPIEGAADA DIGANALLTY TLSPSDYFSL
     DVEASDELSK SLWLELRKYL DREETPELHL LLTATDGGKP ELQGTVELLI TVLDVNDNAP
     LFDQAVYRVH LLETTANGTL VTTLNASDAD EGVNGEVVFS FDSGISRDIQ EKFKVDSSSG
     EIRLIDKLDY EETKSYEIQV KAVDKGSPPM SNHCKVLVKV LDVNDNAPEL AVTSLYLPIR
     EDAPLSTVIA LITVSDRDSG ANGQVTCSLM PHVPFKLVST FKNYYSLVLD SALDRESLSV
     YELVVTARDG GSPSLWATAR VSVEVADVND NAPAFAQPEY TVFVKENNPP GCHIFTVSAR
     DADAQENALV SYSLVERRVG ERALSNYVSV HAESGKVYAL QPLDHEELEL LQFQVSARDA
     GVPPLGSNVT LQVFVLDEND NAPALLAPRV GGTIGAVSEL VPRLVGAGHV VAKVRAVDAD
     SGYNAWLSYE LQPAAGGARI PFRVGLYTGE ISTTRVLDEA DLSRYRLLVL VKDHGEPALT
     ATATVLVSLV ESGQAPKASS RASVGVAGPE AALVDVNVYL IIAICAVSSL LVLTLLLYTA
     LRCSVPPTEG AYVPGKPTLV CSSALGSWSN SQQRRQRVCS SEGPPKTDLM AFSPGLSPSL
     NTSERNEQPE ANLDLSGNPR QPNPDWRYSA SLRAGMHSSV HLEEAGILRA GPGGPDQQWP
     TVSSATPEPE AGEVSPPVGA GVNSNSWTFK YGPGNPKQSG PGELPDKFII PGSPAIISIR
     QEPTNSQIDK SDFITFGKKE ETKKKKKKKK GNKTQEKKEK GNSTTDNSDQ
//