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SNTG2 Gene

protein-coding   GIFtS: 51
GCID: GC02P000942

Syntrophin, Gamma 2

  See SNTG2-related disease
at  

(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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This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
Syntrophin, Gamma 21 2
G2SYN2 3
SYN52 3
gamma-2-syntrophin2
syntrophin-52
Syntrophin-53

External Ids:    HGNC: 137411   Entrez Gene: 542212   Ensembl: ENSG000001725547   OMIM: 6087155   UniProtKB: Q9NY993   
ORGUL members:         

Export aliases for SNTG2 gene to outside databases

Previous GC identifers: GC02P001386 GC02P9B0036


(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 SNTG2 Gene:
This gene encodes a protein belonging to the syntrophin family. Syntrophins are cytoplasmic peripheral membrane
proteins that bind to components of mechanosenstive sodium channels and the extreme carboxy-terminal domain of
dystrophin and dystrophin-related proteins. The PDZ domain of this protein product interacts with a protein
component of a mechanosensitive sodium channel that affects channel gating. Absence or reduction of this protein
product has been associated with Duchenne muscular dystrophy. There is evidence of alternative splicing yet the
full-length nature of these variants has not been described. (provided by RefSeq, Jul 2008)

GeneCards Summary for SNTG2 Gene:
SNTG2 (syntrophin, gamma 2) is a protein-coding gene. Diseases associated with SNTG2 include duchenne muscular dystrophy. GO annotations related to this gene include PDZ domain binding and phospholipid binding. An important paralog of this gene is SNTA1.

UniProtKB/Swiss-Prot: SNTG2_HUMAN, Q9NY99
Function: Adapter protein that binds to and probably organizes the subcellular localization of a variety of
proteins. May link various receptors to the actin cytoskeleton and the dystrophin glycoprotein complex (By
similarity)




(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 at NCBI GenBank:
NC_000002.11  NT_005334.17  NC_018913.2  NT_187526.1  NT_187529.1  
Regulatory elements:
   Regulatory transcription factor binding sites in the SNTG2 gene promoter:
         Pbx1a   HOXA3   NCX/Ncx   CUTL1   STAT5A   AP-2beta   AP-2alpha   En-1   RSRFC4   AP-2alphaA   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSNTG2 promoter sequence
   Search Chromatin IP Primers for SNTG2

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SNTG2


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

Entrez Gene cytogenetic band: 2p25.3   Ensembl cytogenetic band:  2p25.3   HGNC cytogenetic band: 2p25

SNTG2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SNTG2 gene location

GeneLoc information about chromosome 2         GeneLoc Exon Structure

GeneLoc location for GC02P000942:  view genomic region     (about GC identifiers)

Start:
946,554 bp from pter      End:
1,371,385 bp from pter
Size:
424,832 bases      Orientation:
plus 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, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: SNTG2_HUMAN, Q9NY99 (See protein sequence)
Recommended Name: Gamma-2-syntrophin  
Size: 539 amino acids; 60217 Da
Subunit: Interacts with the dystrophin protein DMD and related proteins DTNA and DTNB
Secondary accessions: Q05AH5
Alternative splicing: 2 isoforms:  Q9NY99-1   Q9NY99-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for SNTG2: NX_Q9NY99

Explore proteomics data for SNTG2 at MOPED


See SNTG2 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_061841.2  
ENSEMBL proteins: 
 ENSP00000412249   ENSP00000401997   ENSP00000311837   ENSP00000385020  

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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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3 InterPro protein domains:
 IPR015482 Syntrophin
 IPR001478 PDZ
 IPR001849 Pleckstrin_homology

Graphical View of Domain Structure for InterPro Entry Q9NY99

ProtoNet protein and cluster: Q9NY99

2 Blocks protein domains:
IPB001478 PDZ/DHR/GLGF domain
IPB001849 Pleckstrin-like


UniProtKB/Swiss-Prot: SNTG2_HUMAN, Q9NY99
Domain: The association with dystrophin or related proteins probably leaves the PDZ domain available to recruit
proteins to the membrane (By similarity)
Similarity: Belongs to the syntrophin family
Similarity: Contains 1 PDZ (DHR) domain
Similarity: Contains 1 PH domain


Find genes that share domains with SNTG2           About GenesLikeMe


(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, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Molecular Function:

     UniProtKB/Swiss-Prot Summary: SNTG2_HUMAN, Q9NY99
Function: Adapter protein that binds to and probably organizes the subcellular localization of a variety of
proteins. May link various receptors to the actin cytoskeleton and the dystrophin glycoprotein complex (By
similarity)

     Gene Ontology (GO): 3 molecular function terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0003779actin binding IEA--
GO:0005515protein binding ----
GO:0030165PDZ domain binding IPI17292328
     
Find genes that share ontologies with SNTG2           About GenesLikeMe


Animal Models:
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miRNA
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miRTarBase miRNAs that target SNTG2:
hsa-mir-146a-5p (MIRT021221)

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1 qRT-PCR Assays for microRNA that regulate SNTG2:
hsa-miR-625*
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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 UniProtKB/Swiss-Prot
SNTG2_HUMAN, Q9NY99: Cell membrane, sarcolemma; Peripheral membrane protein; Cytoplasmic side. Cytoplasm,
cytoskeleton. Note=In skeletal muscle, it localizes at the cytoplasmic side of the sarcolemmal membrane
Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
cytoskeleton5
plasma membrane5
cytosol2

Gene Ontology (GO): 4 cellular component terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005737cytoplasm IEA--
GO:0005856cytoskeleton IEA--
GO:0016013syntrophin complex TAS10747910
GO:0042383sarcolemma IEA--

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(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 SNTG2
Interactions:

    GeneGlobe Interaction Network for SNTG2

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

Selected Interacting proteins for SNTG2 (Q9NY992, 3 ENSP000003118374) via UniProtKB, MINT, STRING, and/or I2D (see all 33)
InteractantInteraction Details
GeneCardExternal ID(s)
SCN5AQ145242, 3, ENSP000003289684MINT-58717 MINT-58718 I2D: score=2 STRING: ENSP00000328968
DTNBO609413, ENSP000003840844I2D: score=1 STRING: ENSP00000384084
LRP1BQ9NZR23, ENSP000003741354I2D: score=1 STRING: ENSP00000374135
DMDP115323, ENSP000003549234I2D: score=1 STRING: ENSP00000354923
DTNAQ9Y4J83, ENSP000003820644I2D: score=1 STRING: ENSP00000382064
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Gene Ontology (GO): 1 biological process term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0007417central nervous system development TAS10747910

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(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 SNTG2



(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,
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, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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REFSEQ mRNAs for SNTG2 gene: 
NM_018968.3  

Unigene Cluster for SNTG2:

Syntrophin, gamma 2
Hs.595069  [show with all ESTs]
Unigene Representative Sequence: AJ003029
12 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000452177(uc002qwp.3) ENST00000450962 ENST00000308624(uc002qwq.3 uc010ewi.3)
ENST00000407292 ENST00000463442 ENST00000475201 ENST00000467759 ENST00000494178
ENST00000498321 ENST00000489646 ENST00000471239 ENST00000472606
miRNA
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hsa-miR-625*
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Additional mRNA sequence: 

AJ003029.1 BC035783.1 BC125251.1 

7 DOTS entries:

DT.304379  DT.91757858  DT.120969319  DT.92068091  DT.97782001  DT.75143463  DT.86845886 

18 AceView cDNA sequences:

BM543795 AI393344 AA405993 BC035783 BE044431 BP368994 AA405742 BV200947 
AW592765 BG216682 Z43606 BG204508 BG184880 AJ003029 BG209790 NM_018968 
BG216683 AA448072 

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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SNTG2 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: TCACTAGTTT
SNTG2 Expression
About this image

SNTG2 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

SNTG2 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.595069

UniProtKB/Swiss-Prot: SNTG2_HUMAN, Q9NY99
Tissue specificity: Widely expressed. Strong expression in brain and testis. In CNS, it is expressed in the
perikaryon and proximal portion of the neuronal processes. Strong expression in the hippocampus, neuron-rich
dendate granule cells, and pyramidal cell layers. Highly expressed in neurons of the cerebral cortex. Also
expressed in the cerebellar cortex, deep cerebellar nuclei, thalamus, and basal ganglia

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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 animals.

Orthologs for SNTG2 gene from Selected species (see all 12)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Sntg21 , 5 syntrophin, gamma 21, 5 82.68(n)1
83.12(a)1
  12 (13.00 cM)5
2685341  NM_172951.31  NP_766539.21 
 301744825 
chicken
(Gallus gallus)
Aves SNTG21 syntrophin, gamma 2 78.48(n)
83.12(a)
  421913  XM_419930.4  XP_419930.4 
lizard
(Anolis carolinensis)
Reptilia SNTG26
syntrophin, gamma 2
80(a)
1 ↔ 1
1(160760133-161150322)
tropical clawed frog
(Xenopus tropicalis)
Amphibia sntg21 syntrophin, gamma 2 70.56(n)
73.45(a)
  100495165  XM_002936301.2  XP_002936347.2 
zebrafish
(Danio rerio)
Actinopterygii LOC5693201 novel protein similar to vertebrate syntrophin, gamma more 66.41(n)
65.84(a)
  569320  NM_001126427.1  NP_001119899.1 
fruit fly
(Drosophila melanogaster)
Insecta Syn23 cytoskeletal protein binding 35(a)   53C7   --
worm
(Caenorhabditis elegans)
Secernentea F27D9.83 synapse-associated protein 31(a)   X(7711659-7713932)   --


ENSEMBL Gene Tree for SNTG2 (if available)
TreeFam Gene Tree for SNTG2 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for SNTG2 gene
SNTA12  SNTB12  SNTG12  SNTB22  GOPC2  
2 SIMAP similar genes for SNTG2 using alignment to 2 protein entries:     SNTG2_HUMAN (see all proteins):
SNTG1    DLG4

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(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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Selected SNPs for SNTG2 (see all 11291)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 2 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1159306661,2
F--944603(+) CTTACG/ATGCAG 1 -- us2k11Minor allele frequency- A:0.03WA 118
rs1818082781,2
--944634(+) AGCAGA/CTAGGC 1 -- us2k10--------
rs1868880821,2
--944639(+) ATAGGA/CAGTTA 1 -- us2k10--------
rs67092651,2
C,F,A,H--944751(+) AAAACT/CACATT 1 -- us2k111Minor allele frequency- C:0.27NA WA CSA EA 372
rs1913316201,2
--944781(+) AATTAA/CCTTTG 1 -- us2k10--------
rs739086091,2
C,F--948389(+) AGATGG/AAGCAT 1 -- int13Minor allele frequency- A:0.15WA CSA 121
rs101763531,2
C,F--948437(+) ATTAGG/ATATGT 1 -- int16Minor allele frequency- A:0.16NA WA 246
rs739086101,2
C,F--948454(+) CCTACC/GTTAGA 1 -- int13Minor allele frequency- G:0.17WA CSA 121
rs1505119331,2
C--948464(+) ACACCA/GGTGCA 1 -- int10--------
rs743445391,2
F--948495(+) CTTATG/ATATTT 1 -- int11Minor allele frequency- A:0.04WA 118

HapMap Linkage Disequilibrium report for SNTG2 (946554 - 1196554 bp, first 250kb of SNTG2)

Structural Variations
     Database of Genomic Variants (DGV) Selected variations for SNTG2 (see all 137):    About this table    
Variant IDTypeSubtypePubMed ID
dgv598e201CNV Deletion23290073
esv2719196CNV Deletion23290073
dgv597e201CNV Deletion23290073
esv2719201CNV Deletion23290073
esv1684264CNV Deletion17803354
esv2719181CNV Deletion23290073
esv2024635CNV Deletion18987734
esv2719232CNV Deletion23290073
dgv596e201CNV Deletion23290073
esv2719216CNV Deletion23290073

Human Gene Mutation Database (HGMD): SNTG2
Site Specific Mutation Identification with PCR Assays
SeqTarget long-range PCR primers for resequencing SNTG2
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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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OMIM gene information: 608715    OMIM disorders: --

1 disease for SNTG2:    
About MalaCards
duchenne muscular dystrophy


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Genetic Association Database (GAD): SNTG2

Export disorders for SNTG2 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 SNTG2 gene integrated from 10 sources:
(articles sorted by number of sources associating them with SNTG2)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Gamma1- and gamma2-syntrophins, two novel dystrophin-binding proteins localized in neuronal cells. (PubMed id 10747910)1, 2, 3, 9 Piluso G.... Nigro V. (J. Biol. Chem. 2000)
  2. Syntrophin gamma 2 regulates SCN5A gating by a PDZ domain-mediated interaction. (PubMed id 12429735)1, 9 Ou Y....Farrugia G. (J. Biol. Chem. 2003)
  3. Neuroligins 3 and 4X interact with syntrophin-gamma2, and the interactions are affected by autism-related mutations. (PubMed id 17292328)1, 9 Yamakawa H....Ishiura S. (Biochem. Biophys. Res. Commun. 2007)
  4. Brain-specific angiogenesis inhibitor-1 signaling, regulation, and enrichment in the postsynaptic density. (PubMed id 23782696)1 Stephenson J.R....Hall R.A. (J. Biol. Chem. 2013)
  5. Monozygotic twins discordant for submicroscopic chromosomal anomalies in 2p25.3 region detected by array CGH. (PubMed id 23061379)1 Rio M....Malan V. (Clin. Genet. 2013)
  6. Genome-wide association with bone mass and geometry in the Framingham Heart Study. (PubMed id 17903296)4 Kiel D.P....Karasik D. (BMC Med. Genet. 2007)
  7. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. (PubMed id 15815621)2 Hillier L.W.... Wilson R.K. (Nature 2005)
  8. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S.... Malek J. (Genome Res. 2004)
  9. 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)
  10. Creation of genome-wide protein expression libraries using random activation of gene expression. (PubMed id 11329013)1 Harrington J.J.... Ducar M. (Nat. Biotechnol. 2001)

(in PubMed, OMIM, and NCBI Bookshelf)
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(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 54221 HGNC: 13741 AceView: SNTG2 Ensembl:ENSG00000172554 euGenes: HUgn54221
ECgene: SNTG2 H-InvDB: SNTG2

(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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NameDescription
PharmGKB entry for SNTG2 Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for SNTG2 gene:
Search GeneIP for patents involving SNTG2

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, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, 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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