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SDHAF1 Gene

protein-coding   GIFtS: 42
GCID: GC19P036486

Succinate Dehydrogenase Complex Assembly Factor 1

  See SDHAF1-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
Succinate Dehydrogenase Complex Assembly Factor 11 2
LYR Motif Containing 81 2
LYRM82 3
LYR Motif-Containing Protein 82 3
SDH Assembly Factor 12 3
Succinate Dehydrogenase Assembly Factor 1, Mitochondrial2

External Ids:    HGNC: 338671   Entrez Gene: 6440962   Ensembl: ENSG000002051387   OMIM: 6128485   UniProtKB: A6NFY73   

Export aliases for SDHAF1 gene to outside databases

Previous GC identifers: GC19P041178 GC19P032991


(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 SDHAF1 Gene:
The succinate dehydrogenase (SDH) complex (or complex II) of the mitochondrial respiratory chain is composed of 4
individual subunits. The protein encoded by this gene resides in the mitochondria, and is essential for SDH
assembly, but does not physically associate with the complex in vivo. Mutations in this gene are associated with
SDH-defective infantile leukoencephalopathy (mitochondrial complex II deficiency).(provided by RefSeq, Mar 2010)

GeneCards Summary for SDHAF1 Gene:
SDHAF1 (succinate dehydrogenase complex assembly factor 1) is a protein-coding gene. Diseases associated with SDHAF1 include mitochondrial complex ii deficiency, and mitochondrial respiratory chain complex ii deficiency, sdhaf1-related.

UniProtKB/Swiss-Prot: SDHF1_HUMAN, A6NFY7
Function: Plays an essential role in succinate dehydrogenase complex (SDH) assembly, a complex involved in complex
II of the mitochondrial electron transport chain. Probably acts by participating in mitochondrial biosynthesis of
iron-sulfur centers for complex II (Probable)




(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_000019.9  NC_018930.2  NT_011109.17  
Regulatory elements:
   Search for regulatory transcription factor binding sites for SDHAF1
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for SDHAF1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SDHAF1


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

Entrez Gene cytogenetic band: 19q13.12   Ensembl cytogenetic band:  19q13.12   HGNC cytogenetic band: 19q13.12

SDHAF1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SDHAF1 gene location

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19P036486:  view genomic region     (about GC identifiers)

Start:
36,486,090 bp from pter      End:
36,487,220 bp from pter
Size:
1,131 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: SDHF1_HUMAN, A6NFY7 (See protein sequence)
Recommended Name: Succinate dehydrogenase assembly factor 1, mitochondrial  
Size: 115 amino acids; 12806 Da
Secondary accessions: B2RPM7

Explore the universe of human proteins at neXtProt for SDHAF1: NX_A6NFY7

Explore proteomics data for SDHAF1 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See SDHAF1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_001036096.1  
    ENSEMBL proteins: 
     ENSP00000368165  

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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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    HGNC Gene Families:
    MITOAF: Mitochondrial respiratory chain complex assembly factors

    1 InterPro protein domain:
     IPR008011 Complex1_LYR

    Graphical View of Domain Structure for InterPro Entry A6NFY7

    ProtoNet protein and cluster: A6NFY7

    UniProtKB/Swiss-Prot: SDHF1_HUMAN, A6NFY7
    Similarity: Belongs to the complex I LYR family. SDHAF1 subfamily


    Find genes that share domains with SDHAF1           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: SDHF1_HUMAN, A6NFY7
    Function: Plays an essential role in succinate dehydrogenase complex (SDH) assembly, a complex involved in complex
    II of the mitochondrial electron transport chain. Probably acts by participating in mitochondrial biosynthesis of
    iron-sulfur centers for complex II (Probable)

    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 UniProtKB/Swiss-Prot
    SDHF1_HUMAN, A6NFY7: Mitochondrion matrix (Probable)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    mitochondrion5
    nucleus1

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005739mitochondrion IDA19465911
    GO:0005759mitochondrial matrix IEA--

    Find genes that share ontologies with SDHAF1           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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    UniProtKB/Swiss-Prot: SDHF1_HUMAN, A6NFY7
    Pathway: Cofactor biosynthesis; iron-sulfur cluster biosynthesis

        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for SDHAF1
    Interactions:

        Search GeneGlobe Interaction Network for SDHAF1

    STRING Interaction Network Preview (showing 2 interactants - click image to see more details)

    2 Interacting proteins for SDHAF1 (ENSP000003681654) via UniProtKB, MINT, STRING, and/or I2D

    InteractantInteraction Details
    GeneCardExternal ID(s)
    CLP1ENSP000003047044STRING: ENSP00000304704
    ZC3H14ENSP000002510384STRING: ENSP00000251038
    About this table

    Gene Ontology (GO): 2 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016226iron-sulfur cluster assembly NAS19465911
    GO:0034553mitochondrial respiratory chain complex II assembly IMP19465911

    Find genes that share ontologies with SDHAF1           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 Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for SDHAF1 (SDHF1)



    (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 SDHAF1 gene: 
    NM_001042631.2  

    Unigene Cluster for SDHAF1:

    Succinate dehydrogenase complex assembly factor 1
    Hs.356460  [show with all ESTs]
    Unigene Representative Sequence: BM802990
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000378887(uc002ocp.3)
    miRNA
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    hsa-miR-623 hsa-miR-3938 hsa-miR-204 hsa-miR-193a-5p hsa-miR-590-3p hsa-miR-211
    Browse SwitchGear 3'UTR luciferase reporter plasmids
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      QuantiFast Probe-based Assays in human, mouse, rat SDHAF1

    Additional mRNA sequence: 

    BC007205.1 BC064605.1 BC069054.1 BC137516.1 BC137517.1 

    3 DOTS entries:

    DT.97797048  DT.95374089  DT.97785795 

    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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    SDHAF1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: AGGAAGGGGT
    SDHAF1 Expression
    About this image

    SDHAF1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SDHAF1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.356460

    UniProtKB/Swiss-Prot: SDHF1_HUMAN, A6NFY7
    Tissue specificity: Ubiquitously expressed

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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SDHAF1

    (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 chordates.

    Orthologs for SDHAF1 gene from Selected species (see all 7)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Sdhaf11 , 5 succinate dehydrogenase complex assembly factor 11, 5 80.58(n)1
    80(a)1
      7 (17.39 cM)5
    683321  NM_001033140.31  NP_001028312.21 
     303214065 
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia LOC1017328731 succinate dehydrogenase assembly factor 1, mitochondrial-like 55.69(n)
    54.88(a)
      101732873  XM_004917352.1  XP_004917409.1 
    zebrafish
    (Danio rerio)
    Actinopterygii sdhaf11 succinate dehydrogenase complex assembly factor 1 56.44(n)
    53.33(a)
      606612  XM_002665941.3  XP_002665987.1 


    ENSEMBL Gene Tree for SDHAF1 (if available)
    TreeFam Gene Tree for SDHAF1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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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 SDHAF1 (see all 68)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 19 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0580984
    Mitochondrial complex II deficiency (MT-C2D)4--see VAR_0580982 G R mis40--------
    VAR_0580974
    Mitochondrial complex II deficiency (MT-C2D)4--see VAR_0580972 R P mis40--------
    rs1488179041,2
    --36643293(+) ATAGAC/TGTTTA 1 -- us2k10--------
    rs1844657801,2
    --36643426(+) AAAAAA/CTAAAT 1 -- us2k10--------
    rs1425285401,2
    --36643437(+) ATTTAA/CAATTC 1 -- us2k10--------
    rs748983701,2
    C,F--36643509(+) TTAGCC/TGGGTG 1 -- us2k12Minor allele frequency- T:0.12NA EA 240
    rs1509349851,2
    --36643528(+) TGTTCA/GCGTAA 1 -- us2k10--------
    rs72569161,2
    H--36643811(+) ttacaG/Tgtgtg 1 -- us2k14Minor allele frequency- T:0.00NS EA 414
    rs798196001,2
    C--36643894(+) TTCTCC/GCCTGA 1 -- us2k10--------
    rs1889238091,2
    --36643934(+) CTGACC/TAGCTT 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for SDHAF1 (36486090 - 36487220 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 3 variations for SDHAF1:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv911641CNV Loss21882294
    dgv51n68CNV Loss17160897
    nsv911638CNV Loss21882294

    Human Gene Mutation Database (HGMD): SDHAF1
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing SDHAF1
    DNA2.0 Custom Variant and Variant Library Synthesis for SDHAF1

    (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: 612848   
    OMIM disorders: 252011  
    UniProtKB/Swiss-Prot: SDHF1_HUMAN, A6NFY7
  • Mitochondrial complex II deficiency (MT-C2D) [MIM:252011]: A disorder of the mitochondrial respiratory
    chain with heterogeneous clinical manifestations. Clinical features include psychomotor regression in infants,
    poor growth with lack of speech development, severe spastic quadriplegia, dystonia, progressive
    leukoencephalopathy, muscle weakness, exercise intolerance, cardiomyopathy. Some patients manifest Leigh syndrome
    or Kearns-Sayre syndrome. Note=The disease is caused by mutations affecting the gene represented in this entry

  • 3 diseases for SDHAF1:    
    About MalaCards
    mitochondrial complex ii deficiency    mitochondrial respiratory chain complex ii deficiency, sdhaf1-related    leigh disease

    2 diseases from the University of Copenhagen DISEASES database for SDHAF1:
    Leigh disease     Paraganglioma

    Find genes that share disorders with SDHAF1           About GenesLikeMe


    Export disorders for SDHAF1 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 SDHAF1 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with SDHAF1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. SDHAF1, encoding a LYR complex-II specific assembly factor, is mutated in SDH-defective infantile leukoencephalopathy. (PubMed id 19465911)1, 2, 3 Ghezzi D.... Zeviani M. (Nat. Genet. 2009)
    2. The role of complex II in disease. (PubMed id 23174333)1 Hoekstra A.S. and Bayley J.P. (Biochim. Biophys. Acta 2013)
    3. Leukoencephalopathy with accumulated succinate is indicative of SDHAF1 related complex II deficiency. (PubMed id 22995659)1 Ohlenbusch A....Brockmann K. (Orphanet J Rare Dis 2012)
    4. Impact of a polymorphism in the IL-12p40 gene on the outcome of kidney transplantation. (PubMed id 19328947)1 Hoffmann T.W....Baron C. (Transplant. Proc. 2009)
    5. 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)
    6. The DNA sequence and biology of human chromosome 19. (PubMed id 15057824)2 Grimwood J.... Lucas S.M. (Nature 2004)
    7. 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)
    8. Normalization and subtraction: two approaches to facilitate gene discovery. (PubMed id 8889548)1 Bonaldo M.F.... Soares M.B. (Genome Res. 1996)

    (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: 644096 HGNC: 33867 Ensembl:ENSG00000205138 euGenes: HUgn644096 ECgene: SDHAF1
    H-InvDB: SDHAF1

    (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 SDHAF1 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 SDHAF1 gene:
    Search GeneIP for patents involving SDHAF1

    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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