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KHDC3L Gene

protein-coding   GIFtS: 39
GCID: GC06P074073

KH Domain Containing 3-Like, Subcortical Maternal Complex...

(Previous name: chromosome 6 open reading frame 221)
(Previous symbol: C6orf221)
  See KHDC3L-related diseases
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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Aliases
KH Domain Containing 3-Like, Subcortical Maternal Complex Member1 2     HYDM22 5
C6orf2211 2 3 5     Chromosome 6 Open Reading Frame 2211
ECAT12 3 5     ES Cell Associated Transcript 11
ES Cell-Associated Transcript 1 Protein2 3     KHDC3-Like Protein2

External Ids:    HGNC: 336991   Entrez Gene: 1542882   Ensembl: ENSG000002039087   OMIM: 6116875   UniProtKB: Q587J83   

Export aliases for KHDC3L gene to outside databases


(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 KHDC3L Gene:
The protein encoded by this gene belongs to the KHDC1 family, members of which contain an atypical KH domain that
may not bind RNA like canonical KH domains. This gene is specifically expressed in the oocytes, and recent
studies suggest that it may function as a regulator of genomic imprinting in the oocyte. Mutations in this gene
are associated with recurrent biparental complete hydatidiform mole. (provided by RefSeq, Dec 2011)

GeneCards Summary for KHDC3L Gene:
KHDC3L (KH domain containing 3-like, subcortical maternal complex member) is a protein-coding gene. Diseases associated with KHDC3L include hydatidiform mole, recurrent, 2, and gestational trophoblastic neoplasm. An important paralog of this gene is OOEP.




(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_000006.11  NT_025741.16  NC_018917.2  
Regulatory elements:
   Search for regulatory transcription factor binding sites for KHDC3L
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidKHDC3L promoter sequence
   Search Chromatin IP Primers for KHDC3L

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat KHDC3L


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

Entrez Gene cytogenetic band: 6q13   Ensembl cytogenetic band:  6q13   HGNC cytogenetic band: 6q13

KHDC3L Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
KHDC3L gene location

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06P074073:  view genomic region     (about GC identifiers)

Start:
74,072,400 bp from pter      End:
74,073,898 bp from pter
Size:
1,499 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: KHD3L_HUMAN, Q587J8 (See protein sequence)
Recommended Name: KHDC3-like protein  
Size: 217 amino acids; 24306 Da
Caution: Considered by a number of resources to be the ortholog of rodent Khdc3/Filia. However, sequence
similarity is low and synteny is not conserved. According to PubMed:17913455, KHDC3L/ECAT1 has been lost in
rodents
Secondary accessions: B2RNW7

Explore the universe of human proteins at neXtProt for KHDC3L: NX_Q587J8

Explore proteomics data for KHDC3L at MOPED


See KHDC3L Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_001017361.1  
ENSEMBL proteins: 
 ENSP00000359392  

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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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ProtoNet protein and cluster: Q587J8

UniProtKB/Swiss-Prot: KHD3L_HUMAN, Q587J8
Domain: Contains an atypical KH domain with amino acid changes at critical sites, suggesting that it may not bind
RNA
Similarity: Belongs to the KHDC1 family
Similarity: Contains 1 KH domain


(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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Phenotypes:
     1 GenomeRNAi human phenotype for KHDC3L:
 Elongated cells with protrusio 

     2 MGI mutant phenotypes (inferred from 1 allele(MGI details for Khdc3):
 other  reproductive system 

Find genes that share phenotypes with KHDC3L           About GenesLikeMe

Animal Models:
     MGI mouse knock-out Khdc3tm1Dean for KHDC3L

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miRNA
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miRTarBase miRNAs that target KHDC3L:
hsa-mir-335-5p (MIRT018684)

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

GO IDQualified GO termEvidencePubMed IDs
GO:0043234protein complex ----
GO:0045179apical cortex ----

Find genes that share ontologies with KHDC3L           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 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 KHDC3L
Interactions:

    Search GeneGlobe Interaction Network for KHDC3L

STRING Interaction Network Preview (showing 3 interactants - click image to see more details)

3 Interacting proteins for KHDC3L (Q587J83 ENSP000003593924) via UniProtKB, MINT, STRING, and/or I2D
InteractantInteraction Details
GeneCardExternal ID(s)
OOEPA6NGQ23, ENSP000003593844STRING: ENSP00000359384 I2D: score=1 
TLE6Q9H8083, ENSP000002461124I2D: score=1 STRING: ENSP00000246112
NLRP5P590473, ENSP000003750634I2D: score=2 STRING: ENSP00000375063
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Gene Ontology (GO): 3 biological process terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0006468protein phosphorylation ----
GO:0007094mitotic spindle assembly checkpoint ----
GO:0090307spindle assembly involved in mitosis ----

Find genes that share ontologies with KHDC3L           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)
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Browse Tocris compounds for KHDC3L (KHD3L)



(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 KHDC3L gene: 
NM_001017361.2  

Unigene Cluster for KHDC3L:

KH domain containing 3-like, subcortical maternal complex member
Hs.128326  [show with all ESTs]
Unigene Representative Sequence: AB211062
1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000370367(uc003pgt.4)
miRNA
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  QuantiTect SYBR Green Assays in human, mouse, rat KHDC3L
  QuantiFast Probe-based Assays in human, mouse, rat KHDC3L

Additional mRNA sequence: 

AB211062.1 BC132844.1 BC137160.1 

1 DOTS entry:

DT.205070 

14 AceView cDNA sequences:

AI652239 AA580965 AA872619 BE550370 AA973759 AI917825 AI955057 AA581033 
AI631547 AI655845 AI651751 AW136207 AI371978 AI638315 

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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KHDC3L expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
KHDC3L Expression
About this image


KHDC3L expression in embryonic tissues and stem cells    About this table
Data from LifeMap, the Embryonic Development and Stem Cells Database
 selected tissues (see all 3) fully expand
 
 Inner Cell Mass (Early Embryonic Tissues)
         440A-3
 
 Ovary (Reproductive System)
         Secondary Oocyte Antral Follicle
 
 Gonad
         Secondary Oocyte Antral Follicle
KHDC3L Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

KHDC3L Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.128326

UniProtKB/Swiss-Prot: KHD3L_HUMAN, Q587J8
Tissue specificity: Expression appears to be maximal in germinal vesicle oocytes, it tails off through metaphase
II oocytes and is undetectable following the completion of the oocyte to embryo transition

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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for KHDC3L

(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 mouse.

Orthologs for KHDC3L gene from Selected species (see all 5)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Khdc31 , 5 RIKEN cDNA 2410004A20 gene5
KH domain containing 3, subcortical maternal complex more1
58.96(n)1
42.92(a)1
  9 (40.08 cM)5
669911  NM_025890.31  NP_080166.11 
 731018365 


ENSEMBL Gene Tree for KHDC3L (if available)
TreeFam Gene Tree for KHDC3L (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for KHDC3L gene
OOEP2  
2 SIMAP similar genes for KHDC3L using alignment to 1 protein entry:     KHD3L_HUMAN:
DPPA5    OOEP

Find genes that share paralogs with KHDC3L           About GenesLikeMe


1 Pseudogenes.org Pseudogene for KHDC3L
PGOHUM00000246124


(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 KHDC3L (see all 113)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 6 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs673969981,2
C--74071850(+) ATCCA-/TTTTTT 1 -- us2k11Minor allele frequency- T:0.00CSA 2
rs718455161,2
C--74071896(+) ACAGA-/AAAAAA 1 -- us2k10--------
rs1826318241,2
--74099648(+) GCCACC/TATGCC 1 -- us2k10--------
rs1180626821,2
C,F--74099692(+) TGTGAC/TTGGTG 1 -- us2k11Minor allele frequency- T:0.04NA 120
rs752477551,2
C--74099752(+) TGATGC/TGGAGC 1 -- us2k14Minor allele frequency- T:0.08WA NA EA 360
rs1429658871,2
--74099758(+) GGAGCA/GTTTTT 1 -- us2k10--------
rs1477520511,2
--74099847(+) TTTTGA/TGGAGA 1 -- us2k10--------
rs1870876181,2
--74099859(+) AGTCTC/TGCTCT 1 -- us2k10--------
rs1178984581,2
C,F--74099914(+) ACCTCC/TGCCTC 1 -- us2k11Minor allele frequency- T:0.11EA 120
rs5087701,2
C,F,A--74099927(+) GAGTTT/CAAGCG 1 -- us2k17Minor allele frequency- C:0.49NA CSA WA EA 365

HapMap Linkage Disequilibrium report for KHDC3L (74072400 - 74073898 bp)

Structural Variations
      Database of Genomic Variants (DGV) variations for KHDC3L: --
Human Gene Mutation Database (HGMD): KHDC3L
Site Specific Mutation Identification with PCR Assays
SeqTarget long-range PCR primers for resequencing KHDC3L
DNA2.0 Custom Variant and Variant Library Synthesis for KHDC3L

(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: 611687   
OMIM disorders: 614293  
UniProtKB/Swiss-Prot: KHD3L_HUMAN, Q587J8
  • Hydatidiform mole, recurrent, 2 (HYDM2) [MIM:614293]: A disorder characterized by excessive trophoblast
    development that produces a growing mass of tissue inside the uterus at the beginning of a pregnancy. It leads to
    abnormal pregnancies with no embryo, and cystic degeneration of the chorionic villi. Note=The disease is caused
    by mutations affecting the gene represented in this entry

  • 3 diseases for KHDC3L:    
    About MalaCards
    hydatidiform mole, recurrent, 2    gestational trophoblastic neoplasm    triploidy


    Find genes that share disorders with KHDC3L           About GenesLikeMe


    Export disorders for KHDC3L 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 KHDC3L gene integrated from 10 sources:
    (articles sorted by number of sources associating them with KHDC3L)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Mutations causing familial biparental hydatidiform mole implicate c6orf221 as a possible regulator of genomic imprinting in the human oocyte. (PubMed id 21885028)1, 2, 3 Parry D.A.... Sheridan E.G. (Am. J. Hum. Genet. 2011)
    2. Atypical structure and phylogenomic evolution of the new eutherian oocyte-and embryo-expressed KHDC1/DPPA5/ECAT1/OOEP gene family. (PubMed id 17913455)1, 2 Pierre A.... Monget P. (Genomics 2007)
    3. The homeoprotein Nanog is required for maintenance of pluripotency in mouse epiblast and ES cells. (PubMed id 12787504)1, 2 Mitsui K.... Yamanaka S. (Cell 2003)
    4. Absence of KHDC3L mutations in Chinese patients with recurrent and sporadic hydatidiform moles. (PubMed id 24215781)1 Zhao W....Qian J. (Cancer Genet 2013)
    5. Maternal NLRP7 and C6orf221 variants are not a common risk factor for androgenetic moles, triploidy and recurrent miscarriage. (PubMed id 23515668)1 Manokhina I....Robinson W.P. (Mol. Hum. Reprod. 2013)
    6. Report of four new patients with protein-truncating mutations in C6orf221/KHDC3L and colocalization with NLRP7. (PubMed id 23232697)1 Reddy R....Slim R. (Eur. J. Hum. Genet. 2013)
    7. Mutations in NLRP7 and KHDC3L confer a complete hydatidiform mole phenotype on digynic triploid conceptions. (PubMed id 23125094)1 Fallahian M....Fisher R.A. (Hum. Mutat. 2013)
    8. Mosaic moles and non-familial biparental moles are not caused by mutations in NLRP7, NLRP2 or C6orf221. (PubMed id 22909446)1 Andreasen L....Sunde L. (Mol. Hum. Reprod. 2012)
    9. 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)
    10. 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)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    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: 154288 HGNC: 33699 AceView: LOC154288 Ensembl:ENSG00000203908 euGenes: HUgn154288
    ECgene: KHDC3L H-InvDB: KHDC3L

    (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 KHDC3L 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 KHDC3L gene:
    Search GeneIP for patents involving KHDC3L

    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
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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