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NOMO3 Gene

protein-coding GIFtS: 42
GCID: GC16P016326

NODAL Modulator 3

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MalaCards

disease database

(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc, ⁷Ensembl, ⁸DME, ⁹miRBase, ¹⁰fRNAdb, ¹²H-InvDB, ¹³NCBI, ¹⁴NONCODE, and/or ¹⁵RNAdb)
About This Section

Aliases
NODAL Modulator 3¹ ²
PM5 Protein 3² ³
Nomo²
PM5 Protein, Middle Copy²

External Ids:	HGNC: 25242¹	Entrez Gene: 408050²	Ensembl: ENSG00000103226⁷	OMIM: 609159⁵	UniProtKB: P69849³

Export aliases for NOMO3 gene to outside databases

Previous GC identifers: GC16P014835 GC16P016233 GC16U900522

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

Entrez Gene summary for NOMO3 Gene:

This gene encodes a protein originally thought to be related to the collagenase gene family. This gene is one of

three highly similar genes in a duplicated region on the short arm of chromosome 16. These three genes encode

closely related proteins that may have the same function. The protein encoded by one of these genes has been

identified as part of a protein complex that participates in the Nodal signaling pathway during vertebrate

development. Mutations in ABCC6, which is located nearby, rather than mutations in this gene are associated with

pseudoxanthoma elasticum. (provided by RefSeq, Jul 2008)

GeneCards Summary for NOMO3 Gene:

NOMO3 (NODAL modulator 3) is a protein-coding gene. GO annotations related to this gene include carbohydrate binding. An important paralog of this gene is NOMO2.

UniProtKB/Swiss-Prot: NOMO3_HUMAN, P69849

Function: May antagonize Nodal signaling (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)
About This Section

Regulatory elements:

Regulatory transcription factor binding sites in the NOMO3 gene promoter:
GR Elk-1 AML1a Sp1 Lmo2 GATA-1 c-Ets-1 GR-alpha
Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids

Search Chromatin IP Primers for NOMO3

Epigenetics:

DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat NOMO3

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

Entrez Gene cytogenetic band: 16p13 Ensembl cytogenetic band: 16p13.11 HGNC cytogenetic band: 16p13

NOMO3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
NOMO3 gene location

GeneLoc information about chromosome 16 GeneLoc Exon Structure

GeneLoc location for GC16P016326: view genomic region (about GC identifiers)

Start:	16,326,352 bp from pter	End:	16,388,668 bp from pter
Size:	62,317 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., eBioscience, antibodies-online, and/or GeneTex,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
About This Section

UniProtKB/Swiss-Prot: NOMO3_HUMAN, P69849 (See protein sequence)

Recommended Name: Nodal modulator 3 precursor

Size: 1222 amino acids; 134134 Da

Caution: There are 3 copies of the NOMO gene on chromosome 16p12-p13: NOMO1 (AC Q5JPE7), NOMO2 (AC Q5JPE7) and

NOMO3. All 3 are extremely similar, which makes their individual characterization difficult. Thus, most

experiments probably do not discriminate between the different members. The results reported in other entries may

therefore apply for this protein

Explore the universe of human proteins at neXtProt for NOMO3: NX_P69849

Explore proteomics data for NOMO3 at MOPED

Post-translational modifications:

Ubiquitination² at Lys134, Lys138, Lys159, Lys170, Lys175, Lys193, Lys356, Lys630, Lys770, Lys927,
Lys1019, Lys1079

Glycosylation² at Asn50, Asn218, Asn369, Asn618

Modification sites at PhosphoSitePlus

See NOMO3 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_001004067.1

ENSEMBL proteins:

ENSP00000382274 ENSP00000461721 ENSP00000263012 ENSP00000458267 ENSP00000458821

ENSP00000461870 ENSP00000459996 ENSP00000443768

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

4 InterPro protein domains:

IPR008969 CarboxyPept-like_regulatory

IPR013783 Ig-like_fold

IPR013784 Carb-bd-like_fold

IPR014766 CarboxyPept_regulatory_dom

Graphical View of Domain Structure for InterPro Entry P69849

ProtoNet protein and cluster: P69849

1 Blocks protein domain: IPB008454 Cna B-type

Find genes that share domains with NOMO3 About GenesLikeMe

(According to ¹UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or ²DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, 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, Sets of similar genes according to GenesLikeMe)
About This Section

Molecular Function:

UniProtKB/Swiss-Prot Summary: NOMO3_HUMAN, P69849

Function: May antagonize Nodal signaling (By similarity)

Gene Ontology (GO): 2 molecular function terms: About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0003674	molecular_function	ND	--
GO:0030246	carbohydrate binding	IEA	--

Find genes that share ontologies with NOMO3 About GenesLikeMe

Animal Models:

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In Situ Assay
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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene, Sets of similar genes according to GenesLikeMe)
About This Section

Subcellular locations from UniProtKB/Swiss-Prot

NOMO3_HUMAN, P69849: Membrane; Single-pass type I membrane protein (Potential)

Subcellular locations from COMPARTMENTS:

Compartment	Confidence
extracellular	2
plasma membrane	2
endoplasmic reticulum	1
golgi apparatus	1
peroxisome	1

About this image

Gene Ontology (GO): 2 cellular component terms: About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005575	cellular_component	ND	--
GO:0016021	integral component of membrane	IEA	--

Find genes that share ontologies with NOMO3 About GenesLikeMe

(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 GenesLikeMe, 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, Sets of similar genes according to GenesLikeMe)
About This Section

Custom Pathway & Disease-focused RT² Profiler PCR Arrays for NOMO3
Interactions:

Search GeneGlobe Interaction Network for NOMO3

STRING Interaction Network Preview (showing 5 interactants - click image to see 23)

Selected Interacting proteins for NOMO3 (P69849^{2, 3} ENSP00000382274⁴) via UniProtKB, MINT, STRING, and/or I2D (see all 23)

Interactant		Interaction Details
GeneCard	External ID(s)	Interaction Details
UBQLN4	Q9NRR5²^,³, ENSP00000357292⁴	MINT-2879707 I2D: score=3 STRING: ENSP00000357292
NCLN	Q969V3³, ENSP00000246117⁴	I2D: score=1 STRING: ENSP00000246117
RYK	P34925³, ENSP00000296084⁴	I2D: score=1 STRING: ENSP00000296084
CAD	ENSP00000264705⁴	STRING: ENSP00000264705
UBC	ENSP00000344818⁴	STRING: ENSP00000344818

About this table

Gene Ontology (GO): 1 biological process term: About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0008150	biological_process	ND	--

Find genes that share ontologies with NOMO3 About GenesLikeMe

(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, Sets of similar genes according to GenesLikeMe)
About This Section

Browse Small Molecules at EMD Millipore

Browse drugs & compounds from Enzo Life Sciences

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(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 )
About This Section

REFSEQ mRNAs for NOMO3 gene (3 alternative transcripts):

NM_001004067.3 XM_005255318.1 XM_006725195.1

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

ENST00000399336(uc002dep.3 uc010bvp.2 uc002deq.3) ENST00000576589

ENST00000263012 ENST00000575225 ENST00000572830 ENST00000570519 ENST00000576427

ENST00000576269 ENST00000576460 ENST00000572033 ENST00000574894 ENST00000574157

ENST00000572932 ENST00000573635 ENST00000571167 ENST00000570732 ENST00000570346

ENST00000538468

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		8 qRT-PCR Assays for microRNAs that regulate NOMO3:
		hsa-miR-4291 hsa-miR-922 hsa-miR-342-3p hsa-miR-33a hsa-miR-214 hsa-miR-542-3p hsa-miR-33b hsa-miR-761

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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 GenesLikeMe, 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)
About This Section

NOMO3 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>^2/3
CGAP TAG: GCGGGGTACC

About this image

NOMO3 Protein expression data from MOPED¹, PaxDb² and MaxQB³:

About this image

NOMO3 Protein Expression

Custom PCR Arrays for NOMO3

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In Situ
Assay Products:

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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)
About This Section

This gene was present in the common ancestor of eukaryotes.

Orthologs for NOMO3 gene from Selected species (see all 16) About this table

Organism	Taxonomic classification	Gene	Description	Human Similarity	Orthology Type	Details
mouse (Mus musculus)	Mammalia	Nomo1¹	nodal modulator 1	86.37(n) 93.28(a)		211548 NM_153057.4 NP_694697.3
chicken (Gallus gallus)	Aves	PM5¹	pM5 protein	77.23(n) 87.14(a)		416602 XM_004945285.1 XP_004945342.1
lizard (Anolis carolinensis)	Reptilia	--	Uncharacterized protein	86(a)	1 → many	GL343580.1(301242-312387)
tropical clawed frog (Xenopus tropicalis)	Amphibia	nomo3¹	NODAL modulator 3	72.13(n) 79.9(a)		100158535 NM_001127971.1 NP_001121443.1
zebrafish (Danio rerio)	Actinopterygii	nomo¹	nodal modulator	66.69(n) 70.85(a)		446115 XM_002662315.2 XP_002662361.1
fruit fly (Drosophila melanogaster)	Insecta	CG1371¹	CG1371	46.05(n) 34.28(a)		36053 NM_136707.2 NP_610551.1
worm (Caenorhabditis elegans)	Secernentea	nra-4¹	nra-4	43.06(n) 27.77(a)		3565008 NM_070966.3 NP_503367.1
thale cress (Arabidopsis thaliana)	eudicotyledons	AT3G62360¹	AT3G62360	45.03(n) 34.26(a)		825409 NM_116101.3 NP_191795.1
rice (Oryza sativa)	Liliopsida	Os01g0300600¹	Os01g0300600	45.37(n) 39.65(a)		4325779 NM_001049353.1 NP_001042818.2

ENSEMBL Gene Tree for NOMO3 (if available)
TreeFam Gene Tree for NOMO3 (if available)

(Paralogs according to ¹HomoloGene,
²Ensembl, and ³SIMAP, Pseudogenes according to ⁴Pseudogene.org Build 68,Sets of similar genes according to GenesLikeMe)
About This Section

Paralogs for NOMO3 gene

NOMO2¹ ² NOMO1¹ ²

3 SIMAP similar genes for NOMO3 using alignment to 9 protein entries: NOMO3_HUMAN (see all proteins):

DKFZp547A1913 NOMO1 NOMO2

Find genes that share paralogs with NOMO3 About GenesLikeMe

(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)
About This Section

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
				--	--	--		--	--
rs149603479^1,2		--	16325013(+)	`CTCATA/GATTAT`	1	--	us2k¹		0	--	--	--	--
rs201012712^1,2	C	--	16325930(+)	`GTGTG-/GT/TG CGTGT`	1	--	us2k¹		0	--	--	--	--
rs140994940^1,2		--	16326030(+)	`TCCACC/TCACCT`	1	--	us2k¹		0	--	--	--	--
rs144648477^1,2	C	--	16326171(+)	`CCAACA/GAAATC`	1	--	us2k¹		0	--	--	--	--
rs147873265^1,2	C	--	16326364(+)	`TGTGAA/CCGTGG`	1	--	us2k¹		0	--	--	--	--
rs201681904^1,2	C	--	16327885(+)	`CTTTAA/GCAAGC`	1	--	int¹		0	--	--	--	--
rs9935495^1,2	C	--	16328533(+)	`GttcaT/Ctgagt`	1	--	int¹		1		NA	2
rs9922914^1,2	C	--	16328557(+)	`CTGAGC/TCCCGG`	1	--	int¹		0	--	--	--	--
rs9935584^1,2	C	--	16328634(+)	`tactcT/Ccatga`	1	--	int¹		1		NA	2
rs140835370^1,2		--	16328720(+)	`CAATCA/CGCAGG`	1	--	int¹		0	--	--	--	--

HapMap Linkage Disequilibrium report for NOMO3 (16326352 - 16388668 bp)

Structural Variations
Database of Genomic Variants (DGV) Selected variations for NOMO3 (see all 17): About this table

Variant ID	Type	Subtype	PubMed ID
nsv435664	CNV	Deletion	17901297
esv2714015	CNV	Deletion	23290073
nsv509599	CNV	Insertion	20534489
nsv9362	CNV	Loss	18304495
nsv428319	CNV	Loss	18775914
nsv9363	CNV	Loss	18304495
dgv2616n71	CNV	Gain	21882294
nsv905424	CNV	Gain	21882294
nsv457428	CNV	Gain	19166990
nsv905415	CNV	Gain	21882294

Site Specific Mutation Identification with PCR Assays

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DNA2.0 Custom Variant and Variant Library Synthesis for NOMO3

(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, Sets of similar genes according to GenesLikeMe)
About This Section

OMIM gene information: 609159 OMIM disorders: --

Find genes that share disorders with NOMO3 About GenesLikeMe

Export disorders for NOMO3 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)
About This Section

PubMed articles for NOMO3 gene, integrated from 10 sources (see all 23):
(articles sorted by number of sources associating them with NOMO3)

The sequence and analysis of duplication-rich human chromosome 16. (PubMed id 15616553)^{1, 2} Martin J.... Pennacchio L.A. (Nature 2004)
Nicalin and its binding partner Nomo are novel Nodal signaling antagonists. (PubMed id 15257293)^{1, 3} Haffner C.... Haass C. (EMBO J. 2004)
Genome duplications and other features in 12 Mb of DNA sequence from human chromosome 16p and 16q. (PubMed id 10493829)^{1, 2} Loftus B.J.... Adams M.D. (Genomics 1999)
Charting the landscape of tandem BRCT domain-mediated protein interactions. (PubMed id 22990118)¹ Woods N.T....Monteiro A.N. (Sci Signal 2012)
Systems-wide analysis of ubiquitylation dynamics reveals a key role for PAF15 ubiquitylation in DNA-damage bypass. (PubMed id 23000965)¹ Povlsen L.K....Choudhary C. (Nat. Cell Biol. 2012)
Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition. (PubMed id 22505724)¹ Udeshi N.D....Carr S.A. (amp 2012)
Proteomic identification of common SCF ubiquitin ligase FBXO6-interacting glycoproteins in three kinds of cells. (PubMed id 22268729)¹ Liu B....Wang L.S. (J. Proteome Res. 2012)
A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. (PubMed id 21890473)¹ Wagner S.A....Choudhary C. (amp 2011)
Systematic and quantitative assessment of the ubiquitin-modified proteome. (PubMed id 21906983)¹ Kim W....Gygi S.P. (Mol. Cell 2011)
Mindbomb 1, an E3 ubiquitin ligase, forms a complex with RYK to activate Wnt/I^-catenin signaling. (PubMed id 21875946)¹ Berndt J.D....Moon R.T. (J. Cell Biol. 2011)

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section

		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)
About This Section

Entrez Gene: 408050	HGNC: 25242	Ensembl:ENSG00000103226	euGenes: HUgn408050	ECgene: NOMO3
H-InvDB: NOMO3

(According to HUGE)
About This Section

(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 NOMO3	Pharmacogenomics, SNPs, Pathways

Intellectual Property for NOMO3 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 NOMO3 gene:
Search GeneIP for patents involving NOMO3

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, eBioscience, antibodies-online, GeneTex, 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
Advanced Cell Diagnostics, Animal models from genOway)
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