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Set Analyses:

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XAGE3 Gene

protein-coding GIFtS: 40
GCID: GC0XM052908

X Antigen Family, Member 3

(Previous names: placenta-specific 6; G antigen, family D, 4)
(Previous symbols: PLAC6, GAGED4)

See related diseases
at

MalaCards

(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
X Antigen Family, Member 3¹ ²		Placenta-Specific 6; G Antigen, Family D, 4¹
PLAC6¹ ² ³ ⁵		CT12.3a²
GAGED4¹ ² ³		CT12.3b²
Cancer/Testis Antigen 12.3² ³		Cancer/Testis Antigen Family 12, Member 3a²
G Antigen Family D Member 4² ³		Cancer/Testis Antigen Family 12, Member 3b²
Placenta-Specific Gene 6 Protein² ³		G Antigen, Family D, 4²
CT12.3² ³		Placenta-Specific 6²
XAGE-3² ³		pp9012²
Cancer/Testis Antigen Family 12¹		Protein XAGE-3²
Member 3a¹		X Antigen Family Member 3²
Member 3b¹

External Ids:	HGNC: 14618¹	Entrez Gene: 170626²	Ensembl: ENSG00000171402⁷	OMIM: 300740⁵	UniProtKB: Q8WTP9³

Export aliases for XAGE3 gene to outside databases

Previous GC identifer: GC0XM052775

(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 XAGE3 Gene:

This gene is a member of the XAGE subfamily, which belongs to the GAGE family. The GAGE genes are expressed in a

variety of tumors and in some fetal and reproductive tissues. This gene is expressed in placenta and fetal

liver/spleen, and may function in inhibiting cancer cell growth. The protein encoded by this gene shares a

sequence similarity with other GAGE/PAGE proteins. Because of the expression pattern and the sequence similarity,

this protein also belongs to a family of CT (cancer-testis) antigens. Alternative splicing of this gene generates

2 transcript variants differing in the 5' UTR. (provided by RefSeq, Jul 2008)

GeneCards Summary for XAGE3 Gene:

XAGE3 (X antigen family, member 3) is a protein-coding gene. Diseases associated with XAGE3 include sarcoma, and melanoma. An important paralog of this gene is GAGE2D.

(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_000023.11 NC_018934.2 NT_011630.15

Regulatory elements:

Search for regulatory transcription factor binding sites for XAGE3
Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: XAGE3 promoter sequence

Search Chromatin IP Primers for XAGE3

Epigenetics:

DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat XAGE3

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

Entrez Gene cytogenetic band: Xp11.22 Ensembl cytogenetic band: Xp11.22 HGNC cytogenetic band: Xp11.22

XAGE3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
XAGE3 gene location

GeneLoc information about chromosome X GeneLoc Exon Structure

GeneLoc location for GC0XM052908: view genomic region (about GC identifiers)

Start:	52,891,557 bp from pter	End:	52,897,119 bp from pter
Size:	5,563 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: XAGE3_HUMAN, Q8WTP9 (See protein sequence)

Recommended Name: X antigen family member 3

Size: 111 amino acids; 12302 Da

Secondary accessions: Q5JS82 Q8WYS9

Explore the universe of human proteins at neXtProt for XAGE3: NX_Q8WTP9

Explore proteomics data for XAGE3 at MOPED

See XAGE3 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins (2 alternative transcripts):

NP_570132.1 NP_573440.1

ENSEMBL proteins:

ENSP00000364640 ENSP00000303061

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

IPR008625 GAGE

Graphical View of Domain Structure for InterPro Entry Q8WTP9

ProtoNet protein and cluster: Q8WTP9

1 Blocks protein domain: IPB008625 GAGE

UniProtKB/Swiss-Prot: XAGE3_HUMAN, Q8WTP9

Similarity: Belongs to the GAGE family

XAGE3 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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Gene Ontology (GO): 1 molecular function term: About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005515	protein binding	IPI	--

XAGE3 for ontologies About GeneDecksing

Phenotypes:
2 GenomeRNAi human phenotypes for XAGE3:

Increased gamma-H2AX phosphory

Synthetic lethal with Ras

Animal Models:

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(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 COMPARTMENTS:

Compartment	Confidence
mitochondrion	3
nucleus	2

About this image

(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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Custom Pathway & Disease-focused RT² Profiler PCR Arrays for XAGE3
Interactions:

Search GeneGlobe Interaction Network for XAGE3

1 Interacting protein for XAGE3 (Q8WTP9¹) via UniProtKB, MINT, STRING, and/or I2D

Interactant		Interaction Details
GeneCard	External ID(s)	Interaction Details
HTT	P42858¹	EBI-6448284,EBI-466029

About this table

(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 drugs & compounds from Enzo Life Sciences

Browse compounds at ApexBio

Browse Tocris compounds for XAGE3

(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 XAGE3 gene (2 alternative transcripts):

NM_130776.1 NM_133179.2

Unigene Cluster for XAGE3:

X antigen family, member 3

Hs.43879 [show with all ESTs]

Unigene Representative Sequence: CF993800

2 Ensembl transcripts including schematic representations, and UCSC links where relevant:

ENST00000375491(uc004dre.3) ENST00000346279(uc004drf.3)

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Additional mRNA sequence:

AF318372.1 AJ318881.1 BC062680.1

3 DOTS entries:

DT.101970658 DT.97825141 DT.410605

24 AceView cDNA sequences:

AJ318881 NM_130776 N32547 N41436 BC062680 N41892 AI189067 NM_133179

C18417 CF993800 BG354572 D59091 AF318372 BX283272 AI742551 N40147

T84951 BG436468 N41723 CB994958 CB992682 CB961487 BG436305 BG435916

GeneLoc Exon Structure

(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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XAGE3 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>^2/3
CGAP TAG: --

About this image

XAGE3 Protein expression data from MOPED¹, PaxDb² and MaxQB³:

About this image

XAGE3 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.43879

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In Situ
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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 human and chimp.

Orthologs for XAGE3 gene from 1 species (see representative species ) About this table

Organism	Taxonomic classification	Gene	Description	Human Similarity	Orthology Type	Details
chimpanzee (Pan troglodytes)	Mammalia	XAGE3¹	X antigen family, member 3	99.1(n) 99.1(a)		741714 XM_001144042.1 XP_001144042.1

ENSEMBL Gene Tree for XAGE3 (if available)
TreeFam Gene Tree for XAGE3 (if available)

(Paralogs according to ¹HomoloGene,
²Ensembl, and ³SIMAP, Pseudogenes according to ⁴Pseudogene.org Build 68)
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Paralogs for XAGE3 gene

GAGE2D² GAGE12H² GAGE10² GAGE12I² XAGE5² XAGE2B² GAGE12C² GAGE12E²

GAGE12D² GAGE2E² GAGE1² GAGE2C² GAGE12F² GAGE13² PAGE1² XAGE2²

GAGE12G² GAGE2B² GAGE2A² GAGE12J²

Selected SIMAP similar genes for XAGE3 using alignment to 2 protein entries: XAGE3_HUMAN (see all proteins) (see all similar genes):

XAGE2 XAGE2B XAGE1A XAGE1B XAGE1C XAGE1D

XAGE1E XAGE5 XAGE-4 PAGE3 GAGE2D GAGE8

GAGE2A GAGE2B GAGE2C GAGE2E GAGE1 GAGE10

XAGE3 for paralogs About GeneDecksing

2 Pseudogenes.org Pseudogenes for XAGE3
PGOHUM00000245809 PGOHUM00000241340

(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 X pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
rs112309777^1,2	C	--	52891142(+)	`TGTGTG/ATACCA`	2	--	ds500¹		1		WA	2
rs145496669^1,2		--	52891144(+)	`TGTGTA/GCCAGT`	2	--	ds500¹		0	--	--	--	--
rs189096607^1,2		--	52891154(+)	`TGTAAC/TCAGAA`	2	--	ds500¹		0	--	--	--	--
rs113929255^1,2	C	--	52891162(+)	`GAATAC/GAAAAT`	2	--	ds500¹		0	--	--	--	--
rs36178708^1,2	C	--	52891170(+)	`AATTTC/TAAAAA`	2	--	ds500¹		0	--	--	--	--
rs370449451^1,2	C	--	52891192(+)	`CCTTT-/CTTTTT`	2	--	ds500¹		0	--	--	--	--
rs144497294^1,2	C	--	52891213(+)	`TCTCA-/CTCTGTC`	2	--	ds500¹		0	--	--	--	--
rs112002658^1,2	C	--	52891259(+)	`TACCTG/ACATCC`	2	--	ds500¹		1		WA	2
rs181557873^1,2		--	52891304(+)	`AGCCTC/TAGGAG`	2	--	ds500¹		0	--	--	--	--
rs73206485^1,2	C	--	52891331(+)	`TACATA/GTATAC`	2	--	ds500¹		0	--	--	--	--

HapMap Linkage Disequilibrium report for XAGE3 (52891557 - 52897119 bp)

Structural Variations
Database of Genomic Variants (DGV) 3 variations for XAGE3: About this table

Variant ID	Type	Subtype	PubMed ID
esv2740175	CNV	Deletion	23290073
nsv435891	CNV	Deletion	17901297
esv2740170	CNV	Deletion	23290073

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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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OMIM gene information: 300740 OMIM disorders: --

2 diseases for XAGE3:
About MalaCards

sarcoma melanoma

XAGE3 for disorders About GeneDecksing

Export disorders for XAGE3 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 XAGE3 gene integrated from 10 sources:
(articles sorted by number of sources associating them with XAGE3)

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

The DNA sequence of the human X chromosome. (PubMed id 15772651)^{1, 2} Ross M.T.... Bentley D.R. (Nature 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. (Genome Res. 2004)
Large-scale cDNA transfection screening for genes related to cancer development and progression. (PubMed id 15498874)^{1, 2} Wan D....Gu J. (Proc. Natl. Acad. Sci. U.S.A. 2004)
The XAGE family of cancer/testis-associated genes: alignment and expression profile in normal tissues, melanoma lesions and Ewing's sarcoma. (PubMed id 11992404)^{1, 2} Zendman A.J.W....van Muijen G.N.P. (Int. J. Cancer 2002)
Development and application of a DNA microarray-based yeast two-hybrid system. (PubMed id 23275563)¹ Suter B....Wanker E.E. (Nucleic Acids Res. 2013)
hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. (PubMed id 17207965)¹ Lamesch P.... Vidal M. (Genomics 2007)
Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)¹ Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
Novel genes in the PAGE and GAGE family of tumor antigens found by homology walking in the dbEST database. (PubMed id 10197611)¹ Brinkmann U.... Pastan I. (Cancer Res. 1999)

(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: 170626	HGNC: 14618	AceView: GAGED4	Ensembl:ENSG00000171402	euGenes: HUgn170626
ECgene: XAGE3	H-InvDB: XAGE3

(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 XAGE3	Pharmacogenomics, SNPs, Pathways
ATLAS Chromosomes in Cancer entry for XAGE3	Genetics and Cytogenetics in Oncology and Haematology

Intellectual Property for XAGE3 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 XAGE3 gene:
Search GeneIP for patents involving XAGE3

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
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014

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Hot genes Disease genes XAGE3 gene at Home site.

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XAGE3 Gene

X Antigen Family, Member 3

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XAGE3 (Gene Symbol)
X Antigen Family, Member 3
PLAC6
GAGED4
Cancer/Testis Antigen 12.3
G Antigen Family D Member 4
Placenta-Specific Gene 6 Protein
CT12.3
XAGE-3
Cancer/Testis Antigen Family 12
Member 3a
Member 3b
Placenta-Specific 6; G Antigen, Family D, 4
CT12.3a
CT12.3b
Cancer/Testis Antigen Family 12, Member 3a
Cancer/Testis Antigen Family 12, Member 3b
G Antigen, Family D, 4
Placenta-Specific 6
pp9012
Protein XAGE-3
X Antigen Family Member 3

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XAGE3 Gene

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