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SSX4 Gene

protein-coding GIFtS: 53

GC0XP048127

synovial sarcoma, X breakpoint 4
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database

(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc , and/or ⁷Ensembl, ⁸miRBase)
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Aliases
CT5.4 ^³
MGC119056 ^²
MGC12411 ^²
OTTHUMP00000024292 ^²
SSX4A ^³

Descriptions
Cancer/testis antigen 5.4 ^³
synovial sarcoma, X breakpoint 4 ^²

External Ids
HGNC: 11338¹
Entrez Gene: 6759²
UniProtKB: O60224³
Ensembl: ENSG00000204645⁷

Search outside databases for aliases for SSX4 gene

Previous GC identifers: GC0XM047064 GC0XM046522 GC0XP047069 GC0XP047288 GC0XM048017

(According to Entrez Gene, Wikipedia's Gene Wiki,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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EntrezGene summary for SSX4:

The product of this gene belongs to the family of highly homologous synovial sarcoma X (SSX)

breakpoint proteins. These proteins may function as transcriptional repressors. They are also

capable of eliciting spontaneously humoral and cellular immune responses in cancer patients, and

are potentially useful targets in cancer vaccine-based immunotherapy. SSX1, SSX2 and SSX4 genes

have been involved in the t(X;18) translocation characteristically found in all synovial sarcomas.

This translocation results in the fusion of the synovial sarcoma translocation gene on chromosome

18 to one of the SSX genes on chromosome X. Chromosome Xp11 contains a segmental duplication

resulting in two identical copies of synovial sarcoma, X breakpoint 4, SSX4 and SSX4B, in

tail-to-tail orientation. This gene, SSX4, represents the more telomeric copy. Two transcript

variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq]

UniProtKB/Swiss-Prot: SSX4_HUMAN, O60224

Function: Could act as a modulator of transcription

Gene Wiki entry for SSX4

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 36),
and/or miRBase,
Genomic Views according to UCSC and Ensembl, Transcription factor binding sites according to SABiosciences)
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Genomic View:

UCSC Golden Path with GeneCards custom track

Transcription factor binding sites upstream to the SSX4 gene

Entrez Gene cytogenetic band: Xp11.23 Ensembl cytogenetic band: Xp11.23 HGNC cytogenetic band: Xp11.23

SSX4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)

GeneLoc gene densities for chromosome X GeneLoc Exon Structure

GeneLoc location for GC0XP048127: (about GC identifiers)

Start:	48,127,912 bp from pter
End:	48,137,729 bp from pter
Size:	9,818 bases
Orientation:	plus strand

RefSeq DNA sequence:

NC_000023.9 NT_079573.3

(According to ¹UniProtKB, and/or Ensembl, Phosphorylation sites according to ²Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Enzo Life Sciences, Abnova, OriGene and/or, Abcam,
Biochemical Assays by Invitrogen, Millipore, R&D Systems, Cell Signaling Technology, and/or Enzo Life Sciences, Ontologies according to Gene Ontology Consortium 01 Apr 2009 and Entrez Gene, Antibodies by Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Cell Signaling Technology, Abcam, Abnova, and/or Novus Biologicals)
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UniProtKB/Swiss-Prot: SSX4_HUMAN, O60224 (See protein sequence)

Recommended Name: Protein SSX4

Size: 188 amino acids; 21858 Da

Secondary accessions: B2RPE3 Q5JQZ0 Q9UJU9

REFSEQ proteins (2 alternative transcripts):

NP_005627.1 NP_783856.1

ENSEMBL proteins:

ENSP00000366083 ENSP00000364667

Human Recombinant Proteins

	Browse Drug Discovery Central at Invitrogen for human recombinant proteins
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	Browse R&D Systems for human recombinant proteins
	Browse recombinant and purified proteins available from Enzo Life Sciences
	Recombinant Proteins from Abcam (SSX4)
	Human Recombinant Proteins from Abnova (SSX4)

OriGene Purified Recombinant Human Proteins (see all 2): SSX4

Antibodies for SSX4:

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	Sigma-Aldrich Antibodies for SSX4
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	Antibodies from Abcam (SSX4), each with their Abpromise^SM
	Monoclonal and Polyclonal Antibodies from Abnova (SSX4)
	Novus Biologicals Antibodies for SSX4

Assays for SSX4:

	Browse Invitrogen for biochemical assays
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(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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Graphical View of Domain Structure for InterPro Entry O60224

ProtoNet protein and cluster: O60224

1 Blocks protein family: IPB001909 KRAB box

UniProtKB/Swiss-Prot: SSX4_HUMAN, O60224

Similarity: Belongs to the SSX family

Similarity: Contains 1 KRAB-related domain

(According to MGI Jun 06 2009, UniProtKB, IUBMB,and/or Genatlas,
shRNA from OriGene, Sigma-Aldrich, RNAi from Sigma-Aldrich,
RNAi Products, Clones, and Q-PCR Products from Invitrogen, Millipore, OriGene, and/or Abnova, siRNAs from Applied Biosystems, SYBR primers from OriGene, Cell-based Assays from Millipore, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
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Inhib. RNA:		Invitrogen RNAi Products for gene knock-down (SSX4)
		Browse for Gene Knock-down Tools from Millipore
		Abnova Chimera RNAi Products for Gene knock-down (SSX4)

OriGene 29mer shRNA kit in GFP-retroviral vectors (see all 2): NM_005636

Applied Biosystems Silencer® siRNAs for SSX4

Sigma-Aldrich siRNA for SSX4

Sigma-Aldrich shRNA for SSX4

Explore Sigma-Aldrich super-pooled esiRNAs

Clones:		Invitrogen Clones for SSX4
		Browse Clones for the Expression of Recombinant Proteins Available from Millipore

OriGene GFP tagged cDNA clones in CMV expression vector (see all 2): NM_005636
Myc/DDK tagged cDNA clones in CMV expression vector (see all 2): NM_005636
untagged cDNA clones in CMV expression vector (see all 2): NM_005636

Primers:

Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers

OriGene genome-wide validated SYBR primer pairs: NM_005636

UniProtKB/Swiss-Prot: SSX4_HUMAN, O60224

Function: Could act as a modulator of transcription

Genatlas biochemistry entry for SSX4:

protein SSX4 with homology to Kruppel associated box,KRAB,not implicated in t(X;18) synovial

sarcoma

(Pathways according to Invitrogen (maps by GeneGo), Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB,
Sets of similar genes according to GeneDecks, Proteins Network according to SABiosciences, Interactions according to ¹UniProtKB, ²MINT, and/or ³STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
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5/6 Interacting proteins for SSX4 (O60224² ENSP00000366083³) via UniProtKB, MINT, and/or STRING (see all 6 )

Interactant		Interaction Details
GeneCard	External ID(s)	Interaction Details
HIF1A	Q16665²	MINT-66671
LLGL2	ENSP00000364375³	STRING (score=.899)
SNRNP70	ENSP00000221448³	STRING (score=.899)
SNRPA	ENSP00000243563³	STRING (score=.899)
SNRPA1	ENSP00000254193³	STRING (score=.899)

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(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)
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Browse drugs & compounds from Enzo Life Sciences

Browse Small Molecules at Sigma-Aldrich

Browse Tocris compounds for SSX4

(GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 219 Homo sapiens; Jun 2 2009) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView,
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 Invitrogen, Millipore, and/or Abnova,
siRNAs from Applied Biosystems, Sigma-Aldrich,
shRNA from Sigma-Aldrich, OriGene,
Tagged/untagged cDNA clones from OriGene,
Expression Assays from Applied Biosystems)
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Inhib. RNA:		Invitrogen RNAi Products for gene knock-down (SSX4)
		Browse for Gene Knock-down Tools from Millipore
		Abnova Chimera RNAi Products for Gene knock-down (SSX4)

OriGene 29mer shRNA kit in GFP-retroviral vectors (see all 2): NM_005636

Sigma-Aldrich siRNA for SSX4

Sigma-Aldrich shRNA for SSX4

Explore Sigma-Aldrich super-pooled esiRNAs

Applied Biosystems Silencer® siRNAs:

NM_005636 NM_175729

REFSEQ mRNAs for SSX4 gene (2 alternative transcripts):

NM_005636.3 NM_175729.1

Applied Biosystems TaqMan ® Gene Expression Assays:

NM_005636 NM_175729

               OriGene GFP tagged cDNA clones in CMV expression vector (see all 2): NM_005636
                                 Myc/DDK tagged cDNA clones in CMV expression vector (see all 2): NM_005636
                                 untagged cDNA clones in CMV expression vector (see all 2): NM_005636

Additional cDNA sequence:

BC005325.1 BC103864.1 BC137394.1 BC137395.1 U90841.1

2 DOTS entries:

DT.40305548 DT.40127997

16 AceView cDNA sequences:

BX102714 U90841 BU632654 NM_005636 NM_175729 BX279816 CD671169 CD671168

AA312651 BE866727 AI699644 BC005325 H99655 N24445 W00507 N72228

highest scoring ESTs for SSX4:

AA730715 BU632654 BX279816 H99655 N24445 N72228 BC005325 AI699644 BX102714 CD671168

Unigene Cluster for SSX4:

Synovial sarcoma, X breakpoint 4

Hs.558402 [show with all ESTs]

Unigene Representative Sequence: NM_005636

GeneLoc Exon Structure

2 Ensembl transcripts including schematic representations:

ENST00000376886 ENST00000375517

(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 219 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
Expression Assays from Applied Biosystems )
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SSX4 expression in normal and diseased human tissues

Applied Biosystems TaqMan ® Gene Expression Assays for SSX4

¹ / ² / ³

7 probe-sets matching SSX4 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
35950_at²^{, 3}	U95-A	11	1.00	0.13	1.00	1.00	U90841	0.80	0.79	0.80	1
208586_s_at²^{, 3}	U133-A	4	1.00	0.47	--	--	NM_005636	0.60	1.00	0.82	1
211425_x_at²^{, 3}	U133-A	11	1.00	0.23	--	--	AF257500	0.20	0.06	0.15	2
210394_x_at²^{, 3}	U133-A	11	1.00	0.19	--	--	BC005325	0.80	0.88	0.84	1
208586_s_at²	U133Plus2	4	1.00	0.47	--	--	--	--	--	--	--
211425_x_at²	U133Plus2	11	1.00	0.23	--	--	--	--	--	--	--
210394_x_at²	U133Plus2	11	1.00	0.19	--	--	--	--	--	--	--

About this table

Data from

(Publications) and GNF BioGPS
About these images
About these images

CGAP SAGE TAG: --

SOURCE GeneReport for Unigene cluster: Hs.558402
Expression variation in blood from EXPOLDB for SSX4

(Orthologs according to ^1,2HomoloGene (²older version, for species not in ¹newer version), ³euGenes, ⁴SGD and/or ⁵MGI Jun 06 2009, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
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ENSEMBL Gene Tree for SSX4

(Paralogs according to ¹HomoloGene
and ²Ensembl, Pseudogenes according to ³Pseudogene.org)
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Paralogs for SSX4 gene

SSX4B¹ ² SSX2² SSX2B² SSX6² SSX7² SSX1² SSX5² SSX10²

SSX9² SSX3²

(According to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Genotyping Reagents from Applied Biosystems)
About This Section

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

OMIM: 300326

4 Novoseek disease relationships for SSX4 gene

Disease	Score	Articles	PubMed IDs for Articles with Shared Sentences (# sentences)
sarcoma synovial	88.73	3	18519690 (1), 12007189 (1), 11308259 (1)
melanoma	32.73	3	12007189 (1), 10749136 (1), 9378559 (1)
tumors	19.94	1	16299236 (1)
cancer	8.46	5	15603546 (2), 10749136 (1)

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(Possibly Related Articles in Doctor's Guide)
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(in PubMed. Associations of this gene to articles via ¹Novoseek, ²HGNC, ³Entrez Gene, ⁴UniProtKB/Swiss-Prot, ⁵UniProtKB/TrEMBL, ⁶GAD, and/or ⁷PharmGKB)
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10/21 PubMed articles for SSX4 gene (see all 21 ):

SSX: a multigene family with several members transcribed in normal testis and human cancer. (PubMed id 9378559)^{1, 3, 4} Gure A.O....Chen Y.T. (1997)
The DNA sequence of the human X chromosome. (PubMed id 15772651)^{3, 4} 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)^{3, 4} Gerhard D.S....Malek J. (2004)
The cancer-related protein SSX2 interacts with the human homologue of a Ras-like GTPase interactor, RAB3IP, and a novel nuclear protein, SSX2IP. (PubMed id 12007189)^{1, 3} de Bruijn D.R.H....van Kessel A.G. (2002)
Cloning and characterization of spliced fusion transcript variants of synovial sarcoma: SYT/SSX4, SYT/SSX4v, and SYT/SSX2v. Possible regulatory role of the fusion gene product in wild type SYT expression. (PubMed id 11368913)^{1, 3} Brodin B.... Larsson O. (2001)
Clinical impact of molecular and cytogenetic findings in synovial sarcoma. (PubMed id 11433527)^{1, 3} Panagopoulos I....Mandahl N. (2001)
Towards a proteome-scale map of the human protein-protein interaction network. (PubMed id 16189514)³ Rual J.F....Vidal M. (2005)
CD4+ T cell responses to SSX-4 in melanoma patients. (PubMed id 15814740)³ Ayyoub M....Valmori D. (2005)
Co-existence of SYT-SSX1 and SYT-SSX2 fusions in synovial sarcomas. (PubMed id 12037676)³ Yang K....Larsson O. (2002)
The SSX gene family: characterization of 9 complete genes. (PubMed id 12216073)³ Gure A.O.... Chen Y.-T. (2002)

(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, and/or H-InvDB)
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Entrez Gene: 6759	HGNC: 11338	AceView: SSX4.1	Ensembl:ENSG00000204645	euGenes: HUgn6759
ECgene: SSX4	H-InvDB: SSX4

(According to HUGE)
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(According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
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Name	Description
ATLAS Chromosomes in Cancer entry for SSX4	Genetics and Cytogenetics in Oncology and Haematology

Licensable Technologies for SSX4
(Available from WIS Yeda, Salk, Tufts)

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(Reagents available from Applied Biosystems, Antibodies and assays by Cell Signaling Technology, Abcam, Novus Biologicals,
Sigma-Aldrich, R&D Systems, Millipore, Abnova, and/or Invitrogen, Clones available from OriGene,and/or Invitrogen, Drugs and/or compounds by Sigma-Aldrich,
Enzo Life Sciences, and/or Tocris Bioscience)
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Products for SSX4:

TaqMan ® Gene Expression Assays

TaqMan ® Genotyping Assays

Free SNP selection tool

Invitrogen iPath Pathways	Invitrogen BLOCK-iT™ RNAi
Invitrogen Antibodies	Invitrogen Assays
Invitrogen Clones	Invitrogen Q-PCR Products
Invitrogen Human Recombinant Kinases	Invitrogen Custom Antibody and Peptide Service
Invitrogen Proteins / Assays / Screening Services	Search Invitrogen catalog for SSX4-related products

	Millipore Custom Antibody & Bulk Services
	Millipore Preclinical / Clinical Development Services
	Millipore Immunoassay Services
	Millipore Target Screening & Profiling Services

	Predesigned and custom siRNAs for SSX4		Antibodies for SSX4
	Explore super-pooled esiRNAs		Browse proteins at Sigma-Aldrich
	Lentivirus-delivered shRNAs for SSX4		Browse small molecules at Sigma-Aldrich
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Search Tocris compounds for SSX4

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SSX4 Gene

protein-coding GIFtS: 53

Aliases &
Descriptions
for SSX4

Summaries
for SSX4

Genomic Location
for SSX4

Proteins
for SSX4

Protein Domains/
Families
for SSX4

Gene Function
for SSX4

Pathways & Interactions
for SSX4

Drugs & Compounds
for SSX4

Transcripts
for SSX4

Expression
for SSX4

Orthologs
for SSX4

Paralogs
for SSX4

SNPs/Variants
for SSX4

Disorders & Mutations
for SSX4

Medical News
for SSX4

Publications
for SSX4

Search for SSX4

Genome Databases showing SSX4

Other Databases showing SSX4

Specialized Databases showing SSX4

Licensable Technologies
for SSX4

Services
for SSX4

Gene Index: 3 5 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

SSX4 Gene

protein-coding GIFtS: 53

Aliases & Descriptionsfor SSX4

Summariesfor SSX4

Genomic Locationfor SSX4

Proteinsfor SSX4

Protein Domains/Familiesfor SSX4

Gene Functionfor SSX4

Pathways & Interactionsfor SSX4

Drugs & Compoundsfor SSX4

Transcriptsfor SSX4

Expression for SSX4

Orthologsfor SSX4

Paralogsfor SSX4

SNPs/Variantsfor SSX4

Disorders & Mutationsfor SSX4

Medical Newsfor SSX4

Publicationsfor SSX4

Search for SSX4

Genome Databases showing SSX4

Other Databases showing SSX4

Specialized Databases showing SSX4

Licensable Technologiesfor SSX4

Servicesfor SSX4

Gene Index: 3 5 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

Aliases &
Descriptions
for SSX4

Summaries
for SSX4

Genomic Location
for SSX4

Proteins
for SSX4

Protein Domains/
Families
for SSX4

Gene Function
for SSX4

Pathways & Interactions
for SSX4

Drugs & Compounds
for SSX4

Transcripts
for SSX4

Expression
for SSX4

Orthologs
for SSX4

Paralogs
for SSX4

SNPs/Variants
for SSX4

Disorders & Mutations
for SSX4

Medical News
for SSX4

Publications
for SSX4

Licensable Technologies
for SSX4

Services
for SSX4