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Term
Gene name

Class

Subclass

Chromosome

External id

In atlas

Reliability

Reliability

Reliability

Validation

Method

Validation

Method

Validation

Method

Validation

Location

Searches

Tissue

Cell type

Expression

Tissue

Specificity

Cell line

Specificity

Tissue

Detectable

Cell line

Detectable

Category

Score

Score

Score

Antibodies

Column

 
 
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PCDHA1
  • TISSUE

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TISSUE ATLAS PRIMARY DATA

GENE/PROTEIN

Antibody validation


Dictionary


Tissue proteome

GENERAL INFORMATION

Gene name

PCDHA1

Gene description

Protocadherin alpha 1

Protein class

Predicted membrane proteins
Predicted secreted proteins

Predicted localization

Membrane,Secreted

Number of transcripts

3
SHOW MORE

HUMAN PROTEIN ATLAS INFORMATION

RNA tissue category

HPA:Tissue enhanced (cerebral cortex, testis)
GTEx:Tissue enhanced (testis, cerebellum)

Protein evidence

Evidence at transcript level

Protein expression

Cytoplasmic expression in cerebral, hippocampal and lateral ventricle neurons.

DATA RELIABILITY

Data reliability
description

Antibody staining mainly consistent with RNA expression data. Presumed off target binding observed and disregarded.

Reliability score

Approved based on 1 antibody.
HPA035969
SHOW MORE

RNA AND PROTEIN EXPRESSION SUMMARY

RNA expression (TPM) Protein expression (score)
Brain
Cerebral cortex
Hippocampus
N/A
Caudate
N/A
Cerebellum
N/A
Endocrine tissues
Thyroid gland
Parathyroid gland
Adrenal gland
Bone marrow & immune system
Appendix
Bone marrow
Lymph node
Tonsil
Spleen
Muscle tissues
Heart muscle
Skeletal muscle
Smooth muscle
Lung
Nasopharynx
N/A
Bronchus
N/A
Lung
Liver & gallbladder
Liver
Gallbladder
Pancreas
Pancreas
Gastrointestinal tract
Oral mucosa
N/A
Salivary gland
Esophagus
Stomach
Duodenum
Small intestine
Colon
Rectum
Kidney & urinary bladder
Kidney
Urinary bladder
Male tissues
Testis
Epididymis
Prostate
Seminal vesicle
Female tissues
Breast
Vagina
N/A
Cervix, uterine
Endometrium
Fallopian tube
Ovary
Placenta
Adipose & soft tissue
Adipose tissue
Soft tissue
N/A
Skin
Skin
Cerebral cortex

Hippocampus

Lymph node

Liver

Colon

Kidney

Testis

PROTEIN EXPRESSION OVERVIEW

Organ
Expression
Alphabetical
Cerebral cortexHippocampusCaudateCerebellumThyroid glandParathyroid glandAdrenal glandAppendixBone marrowLymph nodeTonsilSpleenHeart muscleSkeletal muscleSmooth muscleNasopharynxBronchusLungLiverGallbladderPancreasOral mucosaSalivary glandEsophagusStomachDuodenumSmall intestineColonRectumKidneyUrinary bladderTestisEpididymisProstateSeminal vesicleBreastVaginaCervix, uterineEndometriumFallopian tubeOvaryPlacentaAdipose tissueSoft tissueSkinNotdetectedLowMediumHighSCORE

RNA EXPRESSION OVERVIEW

HPA dataset
Organ
Expression
Alphabetical
RNA tissue category: Tissue enhanced (cerebral cortex, testis)
Cerebral cortexThyroid glandParathyroid glandAdrenal glandAppendixBone marrowLymph nodeTonsilSpleenHeart muscleSkeletal muscleSmooth muscleLungLiverGallbladderPancreasSalivary glandEsophagusStomachDuodenumSmall intestineColonRectumKidneyUrinary bladderTestisEpididymisProstateSeminal vesicleBreastCervix, uterineEndometriumFallopian tubeOvaryPlacentaAdipose tissueSkin0246810TPM
GTEx dataset
Organ
Expression
Alphabetical
RNA tissue category: Tissue enhanced (testis, cerebellum)
HypothalamusPituitary glandCerebral cortexHippocampusCaudateCerebellumThyroid glandAdrenal glandSpleenHeart muscleSkeletal muscleLungLiverPancreasSalivary glandEsophagusStomachSmall intestineColonKidneyUrinary bladderTestisProstateBreastVaginaCervix, uterineEndometriumFallopian tubeOvaryAdipose tissueSkin0246810RPKM

GENE INFORMATION

Gene name

PCDHA1

Synonyms

Description

Protocadherin alpha 1 (HGNC Symbol)

Entrez gene summary

This gene is a member of the protocadherin alpha gene cluster, one of three related gene clusters tandemly linked on chromosome five that demonstrate an unusual genomic organization similar to that of B-cell and T-cell receptor gene clusters. The alpha gene cluster is composed of 15 cadherin superfamily genes related to the mouse CNR genes and consists of 13 highly similar and 2 more distantly related coding sequences. The tandem array of 15 N-terminal exons, or variable exons, are followed by downstream C-terminal exons, or constant exons, which are shared by all genes in the cluster. The large, uninterrupted N-terminal exons each encode six cadherin ectodomains while the C-terminal exons encode the cytoplasmic domain. These neural cadherin-like cell adhesion proteins are integral plasma membrane proteins that most likely play a critical role in the establishment and function of specific cell-cell connections in the brain. Alternative splicing has been observed and additional variants have been suggested but their full-length nature has yet to be determined. [provided by RefSeq, Jul 2008]

Chromosome

5

Cytoband

q31.3

Chromosome location (bp)

140786136 - 141012347

Protein evidence

Evidence at transcript level (all genes)

Ensembl

ENSG00000204970 (version 83.38)

Entrez gene

56147

UniProt

Q9Y5I3 (UniProt - Evidence at transcript level)

neXtProt

NX_Q9Y5I3

Antibodypedia

PCDHA1 antibodies

PROTEIN BROWSER

PCDHA1-001
PCDHA1-002
PCDHA1-003

PROTEIN INFORMATION

Splice variant

UniProt

Protein class

Gene ontology

Length & mass

Signal peptide
(predicted)

Transmembrane regions
(predicted)

PCDHA1-001
ENSP00000378129
ENST00000394633
Q9Y5I3 [Direct mapping]
Protocadherin alpha-1
Show all
   MEMSAT3 predicted membrane proteins
   THUMBUP predicted membrane proteins
Predicted secreted proteins
   Secreted proteins predicted by MDSEC
   SignalP predicted secreted proteins
   Phobius predicted secreted proteins
   SPOCTOPUS predicted secreted proteins
Show all
GO:0005509 [calcium ion binding]
GO:0005576 [extracellular region]
GO:0005886 [plasma membrane]
GO:0005887 [integral component of plasma membrane]
GO:0007155 [cell adhesion]
GO:0007156 [homophilic cell adhesion via plasma membrane adhesion molecules]
GO:0007399 [nervous system development]
GO:0016020 [membrane]
Show all
686 aa
75.5 kDa
Yes 0
PCDHA1-002
ENSP00000420840
ENST00000504120
Q9Y5I3 [Direct mapping]
Protocadherin alpha-1
Show all
Predicted membrane proteins
   Prediction method-based
   Membrane proteins predicted by MDM
   MEMSAT3 predicted membrane proteins
   MEMSAT-SVM predicted membrane proteins
   Phobius predicted membrane proteins
   SCAMPI predicted membrane proteins
   SPOCTOPUS predicted membrane proteins
   THUMBUP predicted membrane proteins
   # TM segments-based
   1TM proteins predicted by MDM
Show all
GO:0005509 [calcium ion binding]
GO:0005576 [extracellular region]
GO:0005783 [endoplasmic reticulum]
GO:0005886 [plasma membrane]
GO:0005887 [integral component of plasma membrane]
GO:0007155 [cell adhesion]
GO:0007156 [homophilic cell adhesion via plasma membrane adhesion molecules]
GO:0007399 [nervous system development]
GO:0016020 [membrane]
Show all
950 aa
103 kDa
Yes 1
PCDHA1-003
ENSP00000367373
ENST00000378133
Q9Y5I3 [Direct mapping]
Protocadherin alpha-1
Show all
Predicted membrane proteins
   Prediction method-based
   Membrane proteins predicted by MDM
   MEMSAT3 predicted membrane proteins
   MEMSAT-SVM predicted membrane proteins
   Phobius predicted membrane proteins
   SCAMPI predicted membrane proteins
   SPOCTOPUS predicted membrane proteins
   THUMBUP predicted membrane proteins
   TMHMM predicted membrane proteins
   # TM segments-based
   1TM proteins predicted by MDM
Show all
GO:0005509 [calcium ion binding]
GO:0005576 [extracellular region]
GO:0005886 [plasma membrane]
GO:0005887 [integral component of plasma membrane]
GO:0007155 [cell adhesion]
GO:0007156 [homophilic cell adhesion via plasma membrane adhesion molecules]
GO:0007399 [nervous system development]
GO:0016020 [membrane]
Show all
807 aa
87.6 kDa
Yes 1

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The Human Protein Atlas project is funded
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