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PDZD11 Gene

protein-coding GIFtS: 49

GC0XM063327

PDZ domain containing 11
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
(Previous symbol: PDZK11)

		Products

(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc , and/or ⁷Ensembl, ⁸miRBase)
About This Section

Aliases & Descriptions
PDZ domain containing 11¹ ²		ATPase-interacting PDZ protein²
PDZK11² ³		PDZ domain-containing protein 11²
AIPP1² ⁵		OTTHUMP00000023470²
PISP² ⁵

External Ids:	HGNC: 28034¹	Entrez Gene: 51248²	Ensembl: ENSG00000120509⁷	UniProtKB: Q5EBL8³

Export aliases for PDZD11 gene to outside databases

Previous GC identifers: GC0XM069289 GC0XM068822 GC0XM069422 GC0XM069506

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Gene Wiki entry for PDZD11

(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 60), Regulatory elements and Epigenetics data according to Qiagen and/or SABiosciences)
About This Section

Regulatory elements:

SABiosciences Regulatory transcription factor binding sites in the PDZD11 gene promoter:
         MEF-2A   GR-alpha   GR-beta   NF-kappaB   NF-kappaB1   RelA   STAT1beta   NF-kappaB2   STAT1alpha   STAT1
         Other transcription factors

Search SABiosciences Chromatin IP Primers for PDZD11

Epigenetics:

QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays

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

Entrez Gene cytogenetic band: Xq13.1 Ensembl cytogenetic band: Xq13.1 HGNC cytogenetic band: Xq13.1

PDZD11 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PDZD11 gene location

GeneLoc gene densities for chromosome X GeneLoc Exon Structure

GeneLoc location for GC0XM063327: view genomic region (about GC identifiers)

Start:	63,327,124 bp from pter
End:	63,330,712 bp from pter
Size:	3,589 bases
Orientation:	minus strand

1 alternative location:

ChrX- 69,506,445-69,510,364

RefSeq DNA sequence:

NC_000023.10 NT_011669.17

(According to ¹UniProtKB, neXtProt, and/or Ensembl, Phosphorylation sites according to ²Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Millipore, Sigma-Aldrich, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, and/or ProSpec,
Biochemical Assays by Millipore, Sigma-Aldrich, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Dec 2010 and Entrez Gene, Antibodies by Millipore, Sigma-Aldrich, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, and/or Epitomics)
About This Section

UniProtKB/Swiss-Prot: PDZ11_HUMAN, Q5EBL8 (See protein sequence)

Recommended Name: PDZ domain-containing protein 11

Size: 140 amino acids; 16131 Da

Subcellular location: Isoform 2: Secreted (Potential)

Secondary accessions: Q6UWE1 Q9P0Q1

Alternative splicing: 2 isoforms: Q5EBL8-1 Q5EBL8-2

Explore the universe of human proteins at neXtProt for PDZD11: NX_Q5EBL8

Post-translational modifications:

View phosphorylation sites using PhosphoSite²

REFSEQ proteins: NP_057568.1

ENSEMBL proteins:

ENSP00000363578 ENSP00000239666

Human Recombinant Proteins

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3 Gene Ontology (GO) cellular component terms (GO ID links to tree view):

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005576	extracellular region	IEA	--
GO:0005829	cytosol	IDA	12763866
GO:0016323	basolateral plasma membrane	IDA	12763866

About this table

PDZD11 for ontologies About GeneDecksing

Antibodies for PDZD11:

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Assays for PDZD11:

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	Browse R&D Systems for biochemical assays
	GenScript Custom Assay Services for PDZD11
	Browse Enzo Life Sciences for kits & assays
	Uscn ELISAs and CLIAs for PDZD11

(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section

PDZD11 for domains About GeneDecksing

1 InterPro domain/family:

IPR001478 PDZ/DHR/GLGF

Graphical View of Domain Structure for InterPro Entry Q5EBL8

ProtoNet protein and cluster: Q5EBL8

UniProtKB/Swiss-Prot: PDZ11_HUMAN, Q5EBL8

Similarity: Contains 1 PDZ (DHR) domain

(According to UniProtKB, IUBMB,and/or Genatlas, Animal models from MGI Dec 24 2010,
shRNA from OriGene, Sigma-Aldrich, RNAi from Millipore, siRNAs from Sigma-Aldrich, OriGene, Qiagen, Super-pooled esiRNAs from Sigma-Aldrich, microRNA from Sigma-Aldrich, Qiagen, SABiosciences, Clones from Millipore, Sigma-Aldrich, OriGene, GenScript, Sino Biological, Cell Lines from GenScript, Ontologies according to Gene Ontology Consortium 01 Dec 2010 via Entrez Gene.)
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Inhib. RNA:		Browse for Gene Knock-down Tools from Millipore
		Browse Nano Scale siRNA at Sigma-Aldrich Sigma-Aldrich esiRNA and siRNA for PDZD11 Sigma-Aldrich shRNA for PDZD11
		OriGene 29mer shRNA kits in GFP-retroviral vector (see all 2): PDZD11 OriGene shRNA RFP (see all 2): PDZD11 OriGene basic RS shRNA (see all 2): PDZD11 OriGene siRNA (see all 2): PDZD11
		QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing of PDZD11

miRNA:		Sigma-Aldrich microRNA Mimics for PDZD11 Browse microRNA target validation systems at Sigma-Aldrich
		QIAGEN Custom miScript Target Protector blocks miRNA-binding site of PDZD11
		1 SABiosciences Assays for microRNA that regulate PDZD11:
		hsa-miR-223

Gene
Editing:

Browse CompoZr Knockout ZFN at Sigma-Aldrich

Clones:		Browse Clones for the Expression of Recombinant Proteins Available from Millipore
		Browse iPSC Reprogramming Factors at Sigma-Aldrich
		OriGene GFP tagged cDNA clones in CMV expression vector: PDZD11 OriGene Myc/DDK tagged cDNA clones in CMV expression vector: PDZD11 OriGene untagged cDNA clones in CMV expression vector (see all 2): PDZD11 OriGene 3'-UTR clone: PDZD11 Browse MicroRNA Expression Plasmids
		GenScript Custom cDNA clone Services for PDZD11
		Browse Sino Biological Human cDNA Clones

Cell
Lines:

GenScript Custom overexpressing Cell Line Services for PDZD11

2 Gene Ontology (GO) molecular function terms (GO ID links to tree view):

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005515	protein binding	IPI	12763866
GO:0008022	protein C-terminus binding	IPI	12763866

About this table

PDZD11 for ontologies About GeneDecksing

(Pathways according to Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB, Sets of similar genes according to GeneDecks, PCR Arrays from SABiosciences, Proteins Network according to SABiosciences, Sigma-Aldrich, Interactions according to ¹UniProtKB, ²MINT, and/or ³STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Dec 2010 via Entrez Gene).
About This Section

SABiosciences Custom Pathway-Focused PCR Arrays for PDZD11

Search SABiosciences Gene Network Central^TM Interacting Genes and Proteins Networks for PDZD11

2 Interacting proteins for PDZD11 (Q5EBL8²) via UniProtKB, MINT, and/or STRING

Interactant		Interaction Details
GeneCard	External ID(s)	Interaction Details
ATP7A	Q04656²	MINT-65999 MINT-1889644 MINT-1889694 MINT-1889721 MINT-66001 MINT-66000
SFN	P31947²	MINT-3976640

About this table

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, Sigma-Aldrich, Tocris Bioscience, and/or Novoseek and Drugs according to Enzo Life Sciences and/or PharmGKB)
About This Section

Browse Small Molecules at Sigma-Aldrich

Browse drugs & compounds from Enzo Life Sciences

Browse Tocris compounds for PDZD11

(GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 228 Homo sapiens; Dec 8 2010) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
non coding RNAs according to RNAdb,
ESTs according to GeneTide,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from Millipore,
siRNAs from Sigma-Aldrich, OriGene, Qiagen, Super-pooled esiRNAs from Sigma-Aldrich,
shRNA from Sigma-Aldrich, OriGene, microRNA from Sigma-Aldrich, Qiagen, SABiosciences,
Tagged/untagged cDNA clones from OriGene, Sigma-Aldrich, GenScript, Primers from OriGene and/or SABiosciences)
About This Section

Inhib. RNA:		Browse for Gene Knock-down Tools from Millipore
		Browse Nano Scale siRNA at Sigma-Aldrich Sigma-Aldrich esiRNA and siRNA for PDZD11 Sigma-Aldrich shRNA for PDZD11
		OriGene 29mer shRNA kits in GFP-retroviral vector (see all 2): PDZD11 OriGene shRNA RFP (see all 2): PDZD11 OriGene basic RS shRNA (see all 2): PDZD11 OriGene siRNA (see all 2): PDZD11
		QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing of PDZD11

miRNA:		Sigma-Aldrich microRNA Mimics for PDZD11 Browse microRNA target validation systems at Sigma-Aldrich
		QIAGEN Custom miScript Target Protector blocks miRNA-binding site of PDZD11
		1 SABiosciences Assays for microRNA that regulate PDZD11:
		hsa-miR-223

Clones:		Browse FLAG tag genes at Sigma-Aldrich
		OriGene GFP tagged cDNA clones in CMV expression vector: PDZD11 OriGene Myc/DDK tagged cDNA clones in CMV expression vector: PDZD11 OriGene untagged cDNA clones in CMV expression vector (see all 2): PDZD11 OriGene 3'-UTR Clone: PDZD11 Browse OriGene MicroRNA Expression Plasmids
		GenScript Custom cDNA clone Services for PDZD11

Primers:		OriGene genome-wide validated SYBR primer pairs: PDZD11 Browse OriGene validated miRNA SYBR primer pairs
		SABiosciences RT² qPCR Primer Assay for PDZD11: PPH07768A

REFSEQ mRNAs for PDZD11 gene:

NM_016484.4

Additional cDNA sequence:

AF151061.1 AK024746.1 AK311539.1 AY358829.1 BC012996.2 BC089433.1 BX537725.1 CR457149.1

CR593661.1

7 DOTS entries:

DT.446978 DT.100793691 DT.100793693 DT.101984511 DT.97845948 DT.99951907 DT.121288377

24/290 AceView cDNA sequences (see all 290):

AA782712 AI359352 BQ230833 AI569646 BQ071207 BM699651 BQ441765 BM991561

BU077617 AI372995 BU903000 BU737473 AI948658 AA173940 BQ267388 BM723005

BG696577 BM974274 AA913350 AI126572 AA884566 AA809856 AI266019 AI983608

highest scoring ESTs for PDZD11:

AA292271 AA411589 AA464787 AA477247 AF151061 AI871023 AK024746 AL531025 AV734150 AV763589

Unigene Cluster for PDZD11:

PDZ domain containing 11

Hs.11042 [show with all ESTs]

Unigene Representative Sequence: BX537725

GeneLoc Exon Structure

5/6 Alternative Splicing Database (ASD) splice patterns (SP) for PDZD11 (see all 6)

ExUns:	1a	·	1b	·	1c	^	2	^	3a	·	3b	^	4	^	5	^	6	^	7	^	8	^	9a	·	9b	·	9c	·	9d	·	9e	·	9f
SP1:							-		-
SP2:
SP3:							-		-		-
SP4:							-		-
SP5:							-		-		-

About this scheme

ECgene alternative splicing isoforms for PDZD11
4 Ensembl transcripts including schematic representations, and UCSC links where relevant:

ENST00000486461 ENST00000473667 ENST00000374454 ENST00000239666(uc004dyd.1 uc004dye.1)

(Experimental results according to ¹GeneNote and GNF BioGPS,
probe sets-to-genes annotations according to ²GeneAnnot , ³GeneTide , Sets of similar genes according to GeneDecks, Electronic Northern calculations according to data from UniGene (Build 228 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
Primers from OriGene and/or SABiosciences )
About This Section

PDZD11 expression in normal and diseased human tissues

¹ / ² / ³

3 probe-sets matching PDZD11 gene

Affymetrix probe-set	Array	# genes	Sensitivity	Specificity	Correlation	Length	Gb_Accession	Consensus	Uniqueness	Score	Rank
Affymetrix probe-set	Array	GeneAnnot data			GeneNote data		GeneTide data
56450_at²^{, 3}	U95-B	1	1.00	1.00	1.00	1.00	AI871023	0.80	1.00	0.91	1
223037_at²^{, 3}	U133-B	1	1.00	1.00	--	--	AF151061	0.80	1.00	0.91	1
223037_at²	U133Plus2	1	1.00	1.00	--	--	--	--	--	--	--

About this table

PDZD11 for expression About GeneDecksing

Data from Genenote (Publications) and GNF BioGPS
About these images

PDZD11 gene electronic northern expression

About these images

CGAP SAGE TAG: CACTAGTCCC

SOURCE GeneReport for Unigene cluster: Hs.11042

Primers:		OriGene genome-wide validated SYBR primer pairs: PDZD11 Browse OriGene validated miRNA SYBR primer pairs
		SABiosciences RT² qPCR Primer Assay for PDZD11: PPH07768A

SABiosciences Custom PCR Arrays for PDZD11

(Orthologs according to ^1,2HomoloGene (²older version, for species not in ¹newer version), ³euGenes, ⁴SGD and/or ⁵MGI Dec 24 2010, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
About This Section

Orthologs for PDZD11 gene from 5/9 species (see all 9)

Organism	Gene	Locus	Description	Human Similarity	NCBI accessions
dog (Canis familiaris)	PDZD11¹	--	PDZ domain containing 11	94.05(n) 97.86(a)	491940 XM_549060.2 XP_549060.2
chimpanzee (Pan troglodytes)	PDZD11¹	--	PDZ domain containing 11	99.52(n) 100(a)	465685 XM_001152648.1 XP_001152648.1
cow (Bos taurus)	PDZD11¹	--	PDZ domain containing 11	94.76(n) 97.86(a)	515371 NM_001037603.1 NP_001032692.1
rat (Rattus norvegicus)	Pdzd11¹	--	PDZ domain containing 11	93.33(n) 97.14(a)	302422 XM_217572.4 XP_217572.1
mouse (Mus musculus)	Pdzd11^{1 , 5}	X (43.72 cM)⁵	PDZ domain containing 11^{1, 5}	92.62(n)¹ 97.14(a)¹	72621¹ NM_028303.2¹ NP_082579.1¹ AI429425⁵ AI853370⁵ (see all 15)

About this table Species with no ortholog for PDZD11

ENSEMBL Gene Tree for PDZD11 (if available)

(Paralogs according to ¹HomoloGene
and ²Ensembl, Pseudogenes according to ³Pseudogene.org)
About This Section

Paralogs for PDZD11 gene

LIN7B² LIN7A² GOPC² LIN7C²

PDZD11 for paralogs About GeneDecksing

(SNPs according to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Resequencing Primers from Qiagen)
About This Section

SNP ID	Valid	Chr X pos	Sequence	Recs	AA Chg	Type	More	Recs	Allele freq	Pop	Total sample	More
Genomic Data				Transcription Related Data				Allele Frequencies
			--	--	--		--	--
rs14492^1,2	--	69506644(+)	`ATGTAA/TGGGAC`	1	--	ut3¹ ese³		1		MN	184
rs11546429^1,2	--	69506763(-)	`CCTAGC/TTTTCT`	1	--	ut3¹ ese³		0	--	--	--	--
rs11546430^1,2	--	69507181(-)	`GCTGTC/TGAGAT`	2	V	syn¹ ref¹		0	--	--	--	--
rs112772097^1,2	--	69507843(+)	`GGGTGC/TCTCCA`	1	--	int¹		0	--	--	--	--
rs113177976^1,2	--	69506302(+)	`CTAATA/GTTCTG`	1	--	ut3¹		0	--	--	--	--

About this table

HapMap Linkage Disequilibrium images for PDZD11 (up to first 250kb)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV) variations for PDZD11: --

QIAGEN SeqTarget long-range PCR primers for resequencing PDZD11

(in which this Gene is Involved, According to OMIM, UniProtKB, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, LSDB, HGMD, GAD, HuGE Navigator, and/or TGDB.)
About This Section

PDZD11 for disorders About GeneDecksing

OMIM: 300632

Export disorders and mutations for PDZD11 gene to outside databases

(Possibly Related Articles in Doctor's Guide)
About This Section

(in PubMed. Associations of this gene to articles via ¹Entrez Gene, ²UniProtKB/Swiss-Prot, ³HGNC, ⁴GAD, ⁵PharmGKB, ⁶UniProtKB/TrEMBL, and/or ⁷Novoseek)
About This Section

10/15 PubMed articles for PDZD11 gene, integrated from 7 sources (see all 15):
(articles sorted by number of sources associating them with PDZD11)

The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PubMed id 12975309)^{1, 2, 3} Clark H.F.... Gray A.M. (2003)
Cloning and functional analysis of cDNAs with open reading frames for 300 previously undefined genes expressed in CD34+ hematopoietic stem/progenitor cells. (PubMed id 11042152)^{1, 2, 3} Zhang Q.-H.... Chen Z. (2000)
The DNA sequence of the human X chromosome. (PubMed id 15772651)^{1, 2} Ross M.T.... Bentley D.R. (2005)
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)^{1, 2} Gerhard D.S....Malek J. (2004)
A single PDZ domain protein interacts with the Menkes copper ATPase, ATP7A. A new protein implicated in copper homeostasis. (PubMed id 16051599)^{1, 7} Stephenson S.E....La Fontaine S. (2005)
An extensive survey of tyrosine phosphorylation revealing new sites in human mammary epithelial cells. (PubMed id 19534553)² Heibeck T.H.... Qian W.-J. (2009)
Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks. (PubMed id 17389395)² Wolf-Yadlin A.... White F.M. (2007)
The full-ORF clone resource of the German cDNA consortium. (PubMed id 17974005)² Bechtel S.... Schupp I. (2007)
The LIFEdb database in 2006. (PubMed id 16381901)¹ Mehrle A....Wiemann S. (2006)
Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)¹ Kimura K.... Sugano S. (2006)

(in PubMed, OMIM, and NCBI Bookshelf)
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		AND	OR
Aliases
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: 51248	HGNC: 28034	AceView: PDZK11	Ensembl:ENSG00000120509	euGenes: HUgn51248
ECgene: PDZD11	H-InvDB: PDZD11

(According to HUGE)
About This Section

(According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section

Intellectual Property for PDZD11 gene
(Patent information from GeneIP, Licensable technologies from WIS Yeda, Salk, Tufts, IP news from XenneX, Inc.)

About This Section

Patent Information for PDZD11 gene:
Search GeneIP for patents involving PDZD11

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

(Antibodies, recombinant proteins, and assays by Millipore, Sigma-Aldrich, R&D Systems, Qiagen, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Epitomics, ProSpec, Uscn,
Clones available from Millipore, Sigma-Aldrich, OriGene, GenScript, Sino Biological, PCR Arrays from SABiosciences, Drugs and/or compounds by Sigma-Aldrich, Tocris Bioscience, and/or Enzo Life Sciences)
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	QIAGEN Custom miScript Target Protector blocks miRNA-binding site of PDZD11
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PDZD11 Gene

protein-coding GIFtS: 49

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PDZD11 Gene

protein-coding GIFtS: 49

Aliases & Descriptionsfor PDZD11 gene

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Proteinsfor PDZD11 gene

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Gene Functionfor PDZD11 gene

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Expression for PDZD11 gene

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External Searches for PDZD11 gene

Genome Databases showing PDZD11 gene

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Specialized Databases showing PDZD11 gene

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Aliases &
Descriptions
for PDZD11 gene

Summaries
for PDZD11 gene

Genomic Views
for PDZD11 gene

Proteins
for PDZD11 gene

Protein Domains/
Families
for PDZD11 gene

Gene Function
for PDZD11 gene

Pathways & Interactions
for PDZD11 gene

Drugs & Compounds
for PDZD11 gene

Transcripts
for PDZD11 gene

Expression
for PDZD11 gene

Orthologs
for PDZD11 gene

Paralogs
for PDZD11 gene

Genomic Variants
for PDZD11 gene

Disorders & Mutations
for PDZD11 gene

Medical News
for PDZD11 gene

Publications
for PDZD11 gene

Intellectual Property
for PDZD11 gene

Products
for PDZD11 gene