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Set Analyses:

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PKD1 Gene

protein-coding GIFtS: 66
GCID: GC16M002138

Polycystic Kidney Disease 1 (Autosomal Dominant)

Pneumococci & Pneumococcal Diseases Congress

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at

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(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc, ⁷Ensembl, ⁸DME, ⁹miRBase, ¹⁰fRNAdb, ¹²H-InvDB, ¹³NCBI, ¹⁴NONCODE, and/or ¹⁵RNAdb)
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Aliases
Polycystic Kidney Disease 1 (Autosomal Dominant)¹ ²		PBP²
Polycystin 1¹ ²		Pc-1²
Autosomal Dominant Polycystic Kidney Disease 1 Protein² ³		TRPP1²
Member 1¹		Polycystic Kidney Disease-Associated Protein²
Subfamily P¹		polycystin-1²
Transient Receptor Potential Cation Channel¹		Transient Receptor Potential Cation Channel, Subfamily P, Member 1²

External Ids:	HGNC: 9008¹	Entrez Gene: 5310²	Ensembl: ENSG00000008710⁷	OMIM: 601313⁵	UniProtKB: P98161³

Export aliases for PKD1 gene to outside databases

Previous GC identifers: GC16P016714 GC16M002165 GC16M002078 GC16M002063

(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for PKD1 Gene:

This gene encodes a member of the polycystin protein family. The encoded glycoprotein contains a large N-terminal

extracellular region, multiple transmembrane domains and a cytoplasmic C-tail. It is an integral membrane protein

that functions as a regulator of calcium permeable cation channels and intracellular calcium homoeostasis. It is

also involved in cell-cell/matrix interactions and may modulate G-protein-coupled signal-transduction pathways.

It plays a role in renal tubular development, and mutations in this gene cause autosomal dominant polycystic

kidney disease type 1 (ADPKD1). ADPKD1 is characterized by the growth of fluid-filled cysts that replace normal

renal tissue and result in end-stage renal failure. Splice variants encoding different isoforms have been noted

for this gene. Also, six pseudogenes, closely linked in a known duplicated region on chromosome 16p, have been

described. (provided by RefSeq, Oct 2008)

GeneCards Summary for PKD1 Gene:

PKD1 (polycystic kidney disease 1 (autosomal dominant)) is a protein-coding gene. Diseases associated with PKD1 include polycystic kidney disease, type 1, and polycystic kidney disease, adult type i. GO annotations related to this gene include carbohydrate binding and protein kinase binding. An important paralog of this gene is PKD2.

UniProtKB/Swiss-Prot: PKD1_HUMAN, P98161

Function: Involved in renal tubulogenesis. Involved in fluid-flow mechanosensation by the primary cilium in renal

epithelium. Acts as a regulator of cilium length, together with PKD2. The dynamic control of cilium length is

essential in the regulation of mechanotransductive signaling. The cilium length response creates a negative

feedback loop whereby fluid shear-mediated deflection of the primary cilium, which decreases intracellular cAMP,

leads to cilium shortening and thus decreases flow-induced signaling (By similarity). May be an ion-channel

regulator. Involved in adhesive protein-protein and protein-carbohydrate interactions

Gene Wiki entry for PKD1 Gene

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:

NC_000016.10 NT_010393.17 NC_018927.2

Regulatory elements:

Regulatory transcription factor binding sites in the PKD1 gene promoter:
CREB AP-1 deltaCREB
Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): PKD1 promoter sequence

Search Chromatin IP Primers for PKD1

Epigenetics:

DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat PKD1

Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 16p13.3 Ensembl cytogenetic band: 16p13.3 HGNC cytogenetic band: 16p13.3

PKD1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PKD1 gene location

GeneLoc information about chromosome 16 GeneLoc Exon Structure

GeneLoc location for GC16M002138: view genomic region (about GC identifiers)

Start:	2,138,711 bp from pter	End:	2,185,899 bp from pter
Size:	47,189 bases	Orientation:	minus strand

(According to ¹UniProtKB, HORDE, ²neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: PKD1_HUMAN, P98161 (See protein sequence)

Recommended Name: Polycystin-1 precursor

Size: 4303 amino acids; 462529 Da

Subunit: Interacts with PKD2 and PKD2L1. Interacts with PRKX; involved in differentiation and controlled

morphogenesis of the kidney. Interacts with NPHP1 (via SH3 domain)

Caution: Variant Cys-2379 has been originally described as a benign polymorphism (PubMed:10854095). However, it is

a likely pathogenic mutation (PubMed:PubMed:22508176)

1 PDB 3D structure from and Proteopedia for PKD1:

1B4R (3D)

Secondary accessions: Q15140 Q15141

Alternative splicing: 3 isoforms: P98161-1 P98161-2 P98161-3

Explore the universe of human proteins at neXtProt for PKD1: NX_P98161

Explore proteomics data for PKD1 at MOPED

Post-translational modifications:

After synthesis, undergoes cleavage between Leu-3048 and Thr-3049 in the GPS domain. Cleavage at the GPS domain

occurs through a cis-autoproteolytic mechanism involving an ester-intermediate via N-O acyl rearrangement. This

process takes place in the early secretory pathway, depends on initial N-glycosylation, and requires the REJ

domain. There is evidence that cleavage at GPS domain is incomplete. Uncleaved and cleaved products may have

different functions in vivo¹

Glycosylation² at Asn50, Asn89, Asn116, Asn121, Asn187, Asn621, Asn632, Asn746, Asn810, Asn841,
Asn854, Asn890, Asn921, Asn1004, Asn1010, Asn1034, Asn1072, Asn1113, Asn1178, Asn1194 (see all 60)

Modification sites at PhosphoSitePlus

See PKD1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins (2 alternative transcripts):

NP_000287.3 NP_001009944.2

ENSEMBL proteins:

ENSP00000262304 ENSP00000399501 ENSP00000461391 ENSP00000457132 ENSP00000455753

ENSP00000457984 ENSP00000457162 ENSP00000456670 ENSP00000456672

PKD1 Human Recombinant Protein Products:

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	Cloud-Clone Corp. Proteins for PKD1

PKD1 Antibody Products:

	EMD Millipore Mono- and Polyclonal Antibodies for the study of PKD1
	R&D Systems Antibodies for PKD1 (Polycystin-1/PKD1)
	OriGene Antibodies for PKD1 OriGene Custom Antibody Services for PKD1
	Novus Biologicals PKD1 Antibodies
	Abcam antibodies for PKD1
	Cloud-Clone Corp. Antibodies for PKD1
	ThermoFisher Antibodies for PKD1
	LSBio Antibodies in human, mouse, rat for PKD1

PKD1 Assay Products:

	Browse Kits and Assays available from EMD Millipore
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	GenScript Custom Assay Services for PKD1
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	Cloud-Clone Corp. ELISAs for PKD1 Cloud-Clone Corp. CLIAs for PKD1

(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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HGNC Gene Families:

TRP: Voltage-gated ion channels / Transient receptor potential cation channels

Selected InterPro protein domains (see all 19):

IPR002859 PKD/REJ-like

IPR000483 Cys-rich_flank_reg_C

IPR000601 PKD_dom

IPR001611 Leu-rich_rpt

IPR002889 WSC_carb-bd

Graphical View of Domain Structure for InterPro Entry P98161

ProtoNet protein and cluster: P98161

Selected Blocks protein domains (see all 8):

IPB000372 Cysteine-rich flanking region

IPB000434 Polycystic kidney disease type 1 protein (PKD1) signature

IPB000483 Cysteine-rich flanking region

IPB000601 PKD

IPB001052 Rubredoxin

UniProtKB/Swiss-Prot: PKD1_HUMAN, P98161

Domain: The LDL-receptor class A domain is atypical; the potential calcium-binding site is missing

Similarity: Belongs to the polycystin family

Similarity: Contains 1 C-type lectin domain

Similarity: Contains 1 GPS domain

Similarity: Contains 1 LDL-receptor class A domain

Similarity: Contains 2 LRR (leucine-rich) repeats

Similarity: Contains 1 LRRCT domain

Similarity: Contains 1 LRRNT domain

Similarity: Contains 17 PKD domains

Similarity: Contains 1 PLAT domain

Similarity: Contains 1 REJ domain

Similarity: Contains 1 WSC domain

PKD1 for domains About GeneDecksing

(According to ¹UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or ²DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Molecular Function:

UniProtKB/Swiss-Prot Summary: PKD1_HUMAN, P98161

Function: Involved in renal tubulogenesis. Involved in fluid-flow mechanosensation by the primary cilium in renal

epithelium. Acts as a regulator of cilium length, together with PKD2. The dynamic control of cilium length is

essential in the regulation of mechanotransductive signaling. The cilium length response creates a negative

feedback loop whereby fluid shear-mediated deflection of the primary cilium, which decreases intracellular cAMP,

leads to cilium shortening and thus decreases flow-induced signaling (By similarity). May be an ion-channel

regulator. Involved in adhesive protein-protein and protein-carbohydrate interactions

Genatlas biochemistry entry for PKD1:

polycystin 1,integral membrane protein with a duplicated portion,involved in cell/matrix interactions,expressed by

epithelial renal tubular cells in fetal,ductal epithelia of the liver,pancreas,lung,breast,reproductive

organs,modulating WNT signaling during renal development,binding and activating heteromeric G-proteins in

vitro,required for the structural integrity of blood vessels,homolog to C elegans lov-1,involved in regulating

ion transport

Gene Ontology (GO): Selected molecular function terms (see all 7): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005261	cation channel activity	ISS	--
GO:0005262	calcium channel activity	IBA	--
GO:0005515	protein binding	IPI	15563610
GO:0019901	protein kinase binding	IPI	17980165
GO:0019904	protein domain specific binding	IPI	9171830

PKD1 for ontologies About GeneDecksing

Phenotypes:
1 GenomeRNAi human phenotype for PKD1:

Decreased focal adhesion (FA)

Selected MGI mutant phenotypes (inferred from 30 alleles) (MGI details for Pkd1) (see all 23):

adipose tissue	cardiovascular system	cellular	craniofacial	digestive/alimentary
embryogenesis	endocrine/exocrine gland	growth/size/body	hematopoietic system	homeostasis/metabolism
immune system	integument	limbs/digits/tail	liver/biliary system	mortality/aging

PKD1 for phenotypes           About GeneDecksing

Animal Models:
     MGI mouse knock-outs for PKD1: Pkd1^tm2.1Ggg Pkd1^tm1Jzh Pkd1^tm1Maa Pkd1^tm1.2Djmp Pkd1^tm2.2Bol Pkd1^tm1.2Bol
                                                     Pkd1^tm1Shh Pkd1^tm2.1Som Pkd1^tm3.2Bol Pkd1^tm2Jzh Pkd1^tm3.1Jzh Pkd1^tm1Ggg Pkd1^tm1Som

inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for PKD1

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genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for PKD1

genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for PKD1

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		Block miRNA regulation of human, mouse, rat PKD1 using miScript Target Protectors
		Selected qRT-PCR Assays for microRNAs that regulate PKD1 (see all 33):
		hsa-miR-3194-5p hsa-miR-520e hsa-miR-302d hsa-miR-429 hsa-miR-106a hsa-miR-372 hsa-miR-93 hsa-miR-200b

		SwitchGear 3'UTR luciferase reporter plasmid: PKD1 3' UTR sequence

Inhib. RNA Products:		OriGene RNAi products in human, mouse, rat for PKD1
		Predesigned siRNA for gene silencing in human, mouse, rat PKD1

Gene Editing
Products:

DNA2.0 Custom Protein Engineering Service for PKD1

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		GenScript: all cDNA clones in your preferred vector (see all 2): PKD1 (NM_000296)
		Browse Sino Biological Human cDNA Clones
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Cell Line Products:		GenScript Custom overexpressing Cell Line Services for PKD1
		Browse ESI BIO Cell Lines and PureStem Progenitors for PKD1

In Situ Assay
Products:

Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PKD1

(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Subcellular locations from UniProtKB/Swiss-Prot

PKD1_HUMAN, P98161: Membrane; Multi-pass membrane protein. Cell projection, cilium (By similarity). Note=PKD1

localization to the plasma and ciliary membranes requires PKD2, is independent of PKD2 channel activity, and

involves stimulation of PKD1 autoproteolytic cleavage at the GPS domain

Subcellular locations from COMPARTMENTS:

Compartment	Confidence
plasma membrane	4
nucleus	3
cytoskeleton	2
cytosol	2
endoplasmic reticulum	2
extracellular	2
golgi apparatus	1

About this image

Gene Ontology (GO): Selected cellular component terms (see all 13): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0002133	polycystin complex	ISS	--
GO:0005634	nucleus	ISS	--
GO:0005737	cytoplasm	ISS	--
GO:0005794	Golgi apparatus	IEA	--
GO:0005886	plasma membrane	IDA	--

PKD1 for ontologies About GeneDecksing

(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to ¹UniProtKB, ²MINT, ³I2D, and/or ⁴STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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SuperPaths for PKD1 About

See pathways by source

SuperPath

Contained pathways About

Calcium channels

Calcium channels

1 Downloadable PowerPoint Slide of GeneGlobe Pathway Central Maps for PKD1

Phospholipase-C Pathway

Pathway & Disease-focused RT² Profiler PCR Arrays including PKD1:

Cell Cycle in human mouse rat

Primary Cilia in human mouse rat

Interactions:

GeneGlobe Interaction Network for PKD1

STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

Selected Interacting proteins for PKD1 (P98161^{1, 2, 3} ENSP00000262304⁴) via UniProtKB, MINT, STRING, and/or I2D (see all 38)

Interactant		Interaction Details
GeneCard	External ID(s)	Interaction Details
PKD2	Q13563¹^,²^,³, ENSP00000237596⁴	EBI-1752013,EBI-7813714 MINT-7895347 MINT-7895311 MINT-7895557 MINT-7895283 MINT-7895327 MINT-7895498 MINT-7895375 I2D: score=7 STRING: ENSP00000237596
NPHP1	O15259¹^,²^,³, ENSP00000313169⁴	EBI-1752013,EBI-953828 MINT-8109642 MINT-8109661 I2D: score=1 STRING: ENSP00000313169
ABL1	P00519²^,³, ENSP00000361423⁴	MINT-8110647 I2D: score=3 STRING: ENSP00000361423
FYN	P06241²^,³, ENSP00000357656⁴	MINT-8111439 I2D: score=3 STRING: ENSP00000357656
ATF7IP	Q6VMQ6²^,³	MINT-61896 I2D: score=3

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Gene Ontology (GO): Selected biological process terms (see all 44): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0001502	cartilage condensation	IEA	--
GO:0001568	blood vessel development	--	--
GO:0001701	in utero embryonic development	ISS	--
GO:0001822	kidney development	ISS	--
GO:0001889	liver development	IEA	--

PKD1 for ontologies About GeneDecksing

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Small Molecules at EMD Millipore

Browse drugs & compounds from Enzo Life Sciences

Browse compounds at ApexBio

Browse Tocris compounds for PKD1

1 HMDB Compound for PKD1 About this table

Compound	Synonyms	CAS #	PubMed Ids
Calcium	Ca (see all 2)	7440-70-2	--

Selected Novoseek inferred chemical compound relationships for PKD1 gene (see all 22) About this table

Compound	-log (P-Val)	Hits	PubMed IDs for Articles with Shared Sentences (# sentences)
trp-p-2	75.2	5	18273441 (1), 19879844 (1), 15971078 (1), 19556541 (1) (see all 5)
penicillin	47.5	23	12051565 (4), 12196546 (1), 12845845 (1), 8769609 (1) (see all 12)
threonine	43.2	9	17077180 (1), 19173301 (1), 19243594 (1), 19258390 (1) (see all 8)
beta-lactam	39.7	3	16303769 (1), 14691653 (1), 2230238 (1)
calcium	33.6	23	18285569 (3), 9326320 (1), 9192675 (1), 18422703 (1) (see all 13)
serine	30.8	13	17077180 (1), 19173301 (1), 15695390 (1), 19243594 (1) (see all 12)
vidarabine	24.3	1	9773786 (1)
rapamycin	22.8	1	18845692 (1)
pkcs	19.9	3	12689594 (2), 15590638 (1)
pneumococcal	13.3	1	20194703 (1)

PKD1 for compounds About GeneDecksing

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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REFSEQ mRNAs for PKD1 gene (2 alternative transcripts):

NM_000296.3 NM_001009944.2

Unigene Cluster for PKD1:

Polycystic kidney disease 1 (autosomal dominant)

Hs.75813 [show with all ESTs]

Unigene Representative Sequence: NM_001009944

Selected Ensembl transcripts including schematic representations, and UCSC links where relevant (see all 40):

ENST00000262304(uc002cos.1) ENST00000423118(uc010bse.1 uc002cot.1)

ENST00000472577 ENST00000564313 ENST00000561668 ENST00000487932 ENST00000485120

ENST00000562425 ENST00000567355 ENST00000472659 ENST00000568796 ENST00000570253

ENST00000562297 ENST00000567946 ENST00000486339 ENST00000415938 ENST00000483731

ENST00000566905

miRNA Products:		Block miRNA regulation of human, mouse, rat PKD1 using miScript Target Protectors
		Selected qRT-PCR Assays for microRNAs that regulate PKD1 (see all 33):
		hsa-miR-3194-5p hsa-miR-520e hsa-miR-302d hsa-miR-429 hsa-miR-106a hsa-miR-372 hsa-miR-93 hsa-miR-200b

		SwitchGear 3'UTR luciferase reporter plasmid: PKD1 3' UTR sequence

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		GenScript: all cDNA clones in your preferred vector (see all 2): PKD1 (NM_000296)
		DNA2.0 Custom Codon Optimized Gene Synthesis Service for PKD1
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Primer Products:		OriGene qSTAR qPCR primer pairs in human, mouse for PKD1
		Pre-validated RT² qPCR Primer Assay in human, mouse, rat PKD1
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		QuantiFast Probe-based Assays in human, mouse, rat PKD1

Additional mRNA sequence:

AB209025.1 AB209675.1 AK309422.1 L33243.1 U24497.1

21 DOTS entries:

DT.70104277 DT.87077312 DT.91644432 DT.86858932 DT.97760273 DT.100059201 DT.120674876 DT.100892089

DT.120674921 DT.120674969 DT.120674995 DT.120675018 DT.91864894 DT.95283226 DT.100892088 DT.100892094

DT.120705612 DT.120705686 DT.91718243 DT.91733091 DT.92360713

Selected AceView cDNA sequences (see all 33):

NM_000296 CR590016 L33243 CR613181 AI140269 BF847876 CD608089 AA831732

AW192878 BI825250 U24497 AI199962 CD608091 AI660209 AI192483 BF928319

CD608087 BF058936 CD608085 AI188663 AW090455 AL134818 BF081888 BF058046

GeneLoc Exon Structure

Selected Alternative Splicing Database (ASD) splice patterns (SP) for PKD1 (see all 26) About this scheme

ExUns:	1	^	2	^	3	^	4	^	5	^	6a	·	6b	^	7	^	8	^	9	^	10	^	11	^	12a	·	12b	^	13	^	14	^	15a	·	15b	^	16a	·	16b	^	17	^	18a	·	18b	^	19a	·	19b	·	19c	·
SP1:
SP2:
SP3:
SP4:
SP5:

ExUns:	19d	^	20a	·	20b	^	21a	·	21b	^	22	^	23	^	24a	·	24b	^	25	^	26	^	27	^	28a	·	28b	^	29a	·	29b	^	30a	·	30b	·	30c	·	30d	^	31a	·	31b	^	32a	·	32b	^	33a	·	33b	^
SP1:
SP2:
SP3:
SP4:																																											-				-
SP5:																																											-				-

ExUns:	34a	·	34b	·	34c	^	35a	·	35b	·	35c	·	35d	^	36a	·	36b	^	37	^	38	^	39a	·	39b	·	39c	^	40a	·	40b	^	41
SP1:
SP2:
SP3:
SP4:
SP5:

ECgene alternative splicing isoforms for PKD1

(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE ¹MOPED, ²PaxDb, and ³MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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PKD1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>^2/3
CGAP TAG: GCCGCTTCTA

About this image

PKD1 expression in embryonic tissues and stem cells About this table

Data from LifeMap, the Embryonic Development and Stem Cells Database
selected tissues (see all 7) fully expand


Bone (Muscoskeletal System) fully expand to see all 4 entries
Chondrocytes Synchondroses
Stylopod Long Bone

Cartilage (Muscoskeletal System) fully expand to see all 3 entries
Chondrocytes Synchondroses

Kidney (Urinary System)
Metanephros

Lower Urinary Tract (Urinary System)
Ureter

Neural Tube (Nervous System)
Primitive Spinal Cord

PKD1 Protein expression data from MOPED¹, PaxDb² and MaxQB³:

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PKD1 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.75813

Pathway & Disease-focused RT² Profiler PCR Arrays including PKD1:

Cell Cycle in human mouse rat

Primary Cilia in human mouse rat

Primer Products:		OriGene qSTAR qPCR primer pairs in human, mouse for PKD1
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(Orthologs according to ^1,2HomoloGene (²older version, for species not in ¹newer version), ³euGenes, ⁴SGD , ⁵MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or ⁶Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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This gene was present in the common ancestor of chordates.

Orthologs for PKD1 gene from Selected species (see all 11) About this table

Organism	Taxonomic classification	Gene	Description	Human Similarity	Orthology Type	Details
mouse (Mus musculus)	Mammalia	Pkd1^{1 , 5}	polycystic kidney disease 1 homolog^{1, 5}	78.7(n)¹ 78.6(a)¹		17 (12.40 cM)⁵ 18763¹ NM_013630.2¹ NP_038658.2¹ 24549950⁵
chicken (Gallus gallus)	Aves	PKD1¹	polycystic kidney disease 1 (autosomal dominant)	61.46(n) 56.15(a)		416553 XM_414854.4 XP_414854.4
lizard (Anolis carolinensis)	Reptilia	PKD1⁶	polycystic kidney disease 1 (autosomal dominant)	55(a)	1 ↔ 1	AAWZ02038689(715-4378)
tropical clawed frog (Xenopus tropicalis)	Amphibia	pkd1¹	polycystic kidney disease 1 (autosomal dominant)	56.13(n) 49.17(a)		100494429 XM_002932471.2 XP_002932517.2
zebrafish (Danio rerio)	Actinopterygii	LOC100149562¹	polycystin-1-like	51.93(n) 42.82(a)		100149562 XM_003197739.2 XP_003197787.2

ENSEMBL Gene Tree for PKD1 (if available)
TreeFam Gene Tree for PKD1 (if available)

(Paralogs according to ¹HomoloGene,
²Ensembl, and ³SIMAP, Pseudogenes according to ⁴Pseudogene.org Build 68)
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Paralogs for PKD1 gene

PKD2² PKDREJ² PKD2L2² PKD1L2² PKD2L1² PKD1L1²

1 SIMAP similar gene for PKD1 using alignment to 13 protein entries: PKD1_HUMAN (see all proteins):

NPIP

PKD1 for paralogs About GeneDecksing

Selected Pseudogenes.org Pseudogenes for PKD1 (see all 8)
PGOHUM00000248733 PGOHUM00000262927 PGOHUM00000259017 PGOHUM00000248747 PGOHUM00000248991

(SNPs/Variants according to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, ⁴UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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SNP ID	Valid	Clinical significance	Chr 16 pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
rs79000340^1,2,,4	C,F	Polycystic kidney disease 1 (PKD1)⁴ --	2143955(+)	`GAGCCC/TGTGGG`	4	R G	mis¹		2		EA	298
rs45478794^1,2,,4	C,F	Polycystic kidney disease 1 (PKD1)⁴ --	2144182(+)	`CCAGCG/ATCTCT`	4	/T /M	mis¹		7		NA EA EU	5267
rs77028972^1,2,,4	C,F	Polycystic kidney disease 1 (PKD1)⁴ --	2152387(+)	`AGGAAA/GCACAA`	4	L F	mis¹		1		EU	730
rs9936785^1,2,,4	C,F	Polycystic kidney disease 1 (PKD1)⁴ --	2155426(+)	`CTCGGT/CGCTGC`	4	/H /R	mis¹		3		NA EU	1109
rs140869992^1,2,,4	C	Polycystic kidney disease 1 (PKD1)⁴ --	2158570(+)	`TGGGCA/GCCCCG`	4	R C	mis¹		0	--	--	--	--
rs143690392^1,2,,4	C,F	Polycystic kidney disease 1 (PKD1)⁴ --	2161150(+)	`CCCCCG/ACACGG`	4	/R /W	mis¹		2		NA EU	4925
rs2549677^1,2,,4	C,F,H	Polycystic kidney disease 1 (PKD1)⁴ --	2162361(-)	`TGTCAT/CGCACA`	4	/T /M	mis¹		7		NA MN CSA WA EU	920
VAR_013838⁴		Polycystic kidney disease 1 (PKD1)⁴	--	see VAR_013838	2	R H	mis⁴		0	--	--	--	--
VAR_064383⁴		Polycystic kidney disease 1 (PKD1)⁴	--	see VAR_064383	2	L P	mis⁴		0	--	--	--	--
VAR_058819⁴		Polycystic kidney disease 1 (PKD1)⁴	--	see VAR_058819	2	P S	mis⁴		0	--	--	--	--

HapMap Linkage Disequilibrium report for PKD1 (2138711 - 2185899 bp)

Structural Variations
Database of Genomic Variants (DGV) Selected variations for PKD1 (see all 33): About this table

Variant ID	Type	Subtype	PubMed ID
nsv820654	CNV	Deletion	20802225
nsv471381	CNV	Duplication	19718026
esv2422427	CNV	Duplication	17116639
nsv1709	CNV	Insertion	18451855
dgv2562n71	CNV	Loss	21882294
dgv2545n71	CNV	Loss	21882294
dgv2546n71	CNV	Loss	21882294
esv26637	CNV	Loss	19812545
dgv2540n71	CNV	Loss	21882294
nsv905102	CNV	Loss	21882294

Human Gene Mutation Database (HGMD): PKD1
Locus Specific Mutation Databases (LSDB): PKD1

Site Specific Mutation Identification with PCR Assays

SeqTarget long-range PCR primers for resequencing PKD1

DNA2.0 Custom Variant and Variant Library Synthesis for PKD1

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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OMIM gene information: 601313
OMIM disorders: 173900
UniProtKB/Swiss-Prot: PKD1_HUMAN, P98161

Polycystic kidney disease 1 (PKD1) [MIM:173900]: A disorder characterized by renal cysts, liver cysts and

intracranial aneurysm. Clinical variability is due to differences in the rate of loss of glomerular filtration,

the age of reaching end-stage renal disease and the occurrence of hypertension, symptomatic extrarenal cysts, and

subarachnoid hemorrhage from intracranial 'berry' aneurysm. Note=The disease is caused by mutations affecting the

gene represented in this entry

Selected diseases for PKD1 (see all 48):
About MalaCards

polycystic kidney disease, type 1 polycystic kidney disease, adult type i end stage renal failure polycystic kidney disease, type 2

polycystic kidney disease polycystic kidney disease, autosomal dominant autosomal dominant polycystic kidney disease type 1 with tuberous sclerosis kidney disease

cystic kidney cerebral aneurysms congenital hepatic fibrosis tuberous sclerosis

polycystic liver disease autosomal dominant disease marfan syndrome von hippel-lindau disease

intracranial aneurysm renal dysplasia dysostosis liver disease

5 diseases from the University of Copenhagen DISEASES database for PKD1:

Polycystic kidney disease Cystic kidney Polycystic liver disease Kidney failure

Tuberous sclerosis

PKD1 for disorders About GeneDecksing

Congresses - knowledge worth sharing:
The International Symposium on Pneumococci and Pneumococcal Diseases (ISPPD) 9 - 13 March 2014

Selected Novoseek inferred disease relationships for PKD1 gene (see all 34) About this table

Disease	-log (P-Val)	Hits	PubMed IDs for Articles with Shared Sentences (# sentences)
adpkd	98.3	503	12007219 (5), 11773467 (4), 10729710 (4), 12220456 (4) (see all 99)
polycystic kidney diseases	95.5	112	17102641 (2), 8666666 (2), 17715262 (2), 8661056 (2) (see all 90)
renal cyst	89.5	29	19194729 (4), 2215575 (2), 1605247 (1), 1583643 (1) (see all 20)
polycystic kidney type 2 autosomal dominant disease	87.4	1	10023895 (1)
arpkd	85.3	13	11981261 (2), 10200981 (1), 15674734 (1), 12647363 (1) (see all 9)
polycystic kidney type 1 autosomal dominant disease	83.8	1	10364515 (1)
cystic kidney disease	83	10	16207829 (2), 9631851 (1), 16536277 (1), 10362797 (1) (see all 7)
cysts	79.8	89	10504485 (4), 11689485 (3), 19346236 (3), 10835625 (2) (see all 56)
polycystic liver disease	75.7	4	16294159 (1), 19766642 (1)
tuberous sclerosis	70.9	23	9382094 (2), 18598780 (1), 11812941 (1), 17373211 (1) (see all 17)

GeneTests: PKD1
GeneReviews: PKD1
Genetic Association Database (GAD): PKD1
Human Genome Epidemiology (HuGE) Navigator: PKD1 (14 documents)

Export disorders for PKD1 gene to outside databases

(in PubMed. Associations of this gene to articles via ¹Entrez Gene, ²UniProtKB/Swiss-Prot, ³HGNC, ⁴GAD, ⁵PharmGKB, ⁶HMDB, ⁷DrugBank, ⁸UniProtKB/TrEMBL, ⁹ Novoseek, and/or ¹⁰fRNAdb)
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PubMed articles for PKD1 gene, integrated from 10 sources (see all 533):
(articles sorted by number of sources associating them with PKD1)

Utopia: connect your pdf to the dynamic
world of online information

Three novel mutations of the PKD1 gene in Korean patients with autosomal dominant polycystic kidney disease. (PubMed id 12220456)^{1, 2, 4, 9} Eo H.-S....Kim U.K. (Clin. Genet. 2002)
Thirteen novel mutations of the replicated region of PKD1 in an Asian population. (PubMed id 11012875)^{1, 2, 9} Phakdeekitcharoen B....Germino G.G. (Kidney Int. 2000)
Identification of mutations in the duplicated region of the polycystic kidney disease 1 gene (PKD1) by a novel approach. (PubMed id 9199561)^{1, 2, 9} Peral B.... Harris P.C. (Am. J. Hum. Genet. 1997)
Genotype-phenotype correlation in children with autosomal dominant polycystic kidney disease. (PubMed id 19194729)^{1, 4, 9} Fencl F....Seeman T. (Pediatr. Nephrol. 2009)
Protein kinase X (PRKX) can rescue the effects of polycystic kidney disease-1 gene (PKD1) deficiency. (PubMed id 17980165)^{1, 2, 9} Li X.... Wilson P.D. (Biochim. Biophys. Acta 2008)
Novel mutations of the PKD1 gene in Korean patients with autosomal dominant polycystic kidney disease. (PubMed id 10729710)^{1, 2, 9} Kim U.K.... Lee C.C. (Mutat. Res. 2000)
Mutational analysis within the 3' region of the PKD1 gene. (PubMed id 10200984)^{1, 2, 9} Badenas C.... Darnell A. (Kidney Int. 1999)
An unusual pattern of mutation in the duplicated portion of PKD1 is revealed by use of a novel strategy for mutation detection. (PubMed id 9285784)^{1, 2, 9} Watnick T.J.... Germino G.G. (Hum. Mol. Genet. 1997)
Polycystic kidney disease: the complete structure of the PKD1 gene and its protein. (PubMed id 7736581)^{1, 2, 9} Gluecksmann-Kuis M.A.... Frischauf A.-M. (Cell 1995)
Novel PKD1 deletions and missense variants in a cohort of Hellenic polycystic kidney disease families. (PubMed id 11571556)^{1, 2, 9} Bouba I.... Deltas C.C. (Eur. J. Hum. Genet. 2001)

(in PubMed, OMIM, and NCBI Bookshelf)
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		AND	OR
Aliases
Disorders
Free Text

Query String		PubMed OMIM NCBI Bookshelf
	(Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 5310	HGNC: 9008	AceView: PKD1	Ensembl:ENSG00000008710	euGenes: HUgn5310
ECgene: PKD1	H-InvDB: PKD1

(According to HUGE)
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(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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Name	Description
PharmGKB entry for PKD1	Pharmacogenomics, SNPs, Pathways
ATLAS Chromosomes in Cancer entry for PKD1	Genetics and Cytogenetics in Oncology and Haematology
GeneReviews	http://www.ncbi.nlm.nih.gov/books/NBK1116/?term=PKD1[genesymbol]
Functional Glycomics Gateway - Glycan Binding	http://www.functionalglycomics.org/glycomics/GBPServlet?&operationType=view&cbpId=cbp_hum_Ctlect_204

Intellectual Property for PKD1 gene
(Patent information from GeneIP, Licensable technologies from WIS Yeda, Salk, Tufts, IP news from LifeMap Sciences, Inc.)

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Patent Information for PKD1 gene:
Search GeneIP for patents involving PKD1

GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search

(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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Polycystic Kidney Disease 1 (Autosomal Dominant)

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Medullary cystic kidney
NPHP1
von Hippel-Lindau Disease
ARPKD
POLYCYSTIC LIVER DISEASE
Cystic Fibrosis
Carolis Disease
Polycystic Kidney Diseases
Intracranial Aneurysm
Systemic Disease
Liver diseases
Breast Cancer
Tuberous Sclerosis
Polycystic Kidney Type 2 Autosomal Dominant Disease
Cancer
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Connective Tissue Diseases
somatic mutations
Polycystic Kidney Disease, Autosomal Dominant
RENAL DISEASE
ADPKD
Germ-Line Mutation
Hamartoma
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Cysts
Polycystic Kidney Type 1 Autosomal Dominant Disease
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prostate cancer
RENAL CYST
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PKD1 Gene

Polycystic Kidney Disease 1 (Autosomal Dominant)

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