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FERD3L Gene

protein-coding   GIFtS: 47
GCID: GC07M019184

Fer3-Like BHLH Transcription Factor

(Previous name: Fer3-like (Drosophila))
  See 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
Fer3-Like BHLH Transcription Factor1 2     NTWIST2 3
Basic Helix-Loop-Helix Protein N-Twist2 3     bHLHa312 3
Class A Basic Helix-Loop-Helix Protein 312 3     Fer3-Like (Drosophila)1
Nephew Of Atonal 32 3     N-TWIST2
Neuronal Twist2 3     Fer3-Like Protein2
NATO32 3     BHLHA313

External Ids:    HGNC: 166601   Entrez Gene: 2228942   Ensembl: ENSG000001466187   UniProtKB: Q96RJ63   

Export aliases for FERD3L gene to outside databases

Previous GC identifers: GC07M018828 GC07M018928 GC07M018957 GC07M019150


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for FERD3L Gene:
FERD3L (Fer3-like bHLH transcription factor) is a protein-coding gene. Diseases associated with FERD3L include acrocephalosyndactylia, and saethre-chotzen syndrome. GO annotations related to this gene include protein dimerization activity. An important paralog of this gene is PTF1A.

UniProtKB/Swiss-Prot: FER3L_HUMAN, Q96RJ6
Function: Transcription factor that binds to the E-box and functions as inhibitor of transcription. DNA binding
requires dimerization with an E protein. Inhibits transcription activation by ASCL1/MASH1 by sequestering E
proteins (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:
NC_000007.14  NC_018918.2  NT_007819.18  
Regulatory elements:
   Regulatory transcription factor binding sites in the FERD3L gene promoter:
         AML1a   p53   ATF-2   HSF1 (long)   POU3F2   E47   PPAR-alpha   HSF1short   c-Jun   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidFERD3L promoter sequence
   Search Chromatin IP Primers for FERD3L

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat FERD3L


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

Entrez Gene cytogenetic band: 7p21.1   Ensembl cytogenetic band:  7p21.1   HGNC cytogenetic band: 7p21.3

FERD3L Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
FERD3L gene location

GeneLoc information about chromosome 7         GeneLoc Exon Structure

GeneLoc location for GC07M019184:  view genomic region     (about GC identifiers)

Start:
19,184,405 bp from pter      End:
19,185,044 bp from pter
Size:
640 bases      Orientation:
minus strand

1 alternative location:
Chr7-,CRA_TCAG 19,235,856-19,236,495     

(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, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: FER3L_HUMAN, Q96RJ6 (See protein sequence)
Recommended Name: Fer3-like protein  
Size: 166 amino acids; 19017 Da
Subunit: Heterodimer with TCF3/E12. Interacts with the bHLH domain of TCF3/E12 (By similarity)
Secondary accessions: Q495K0

Explore the universe of human proteins at neXtProt for FERD3L: NX_Q96RJ6

Explore proteomics data for FERD3L at MOPED


See FERD3L Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_690862.1  
ENSEMBL proteins: 
 ENSP00000275461  

FERD3L Human Recombinant Protein Products:

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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:
bHLH: Basic helix-loop-helix proteins

1 InterPro protein domain:
 IPR011598 bHLH_dom

Graphical View of Domain Structure for InterPro Entry Q96RJ6

ProtoNet protein and cluster: Q96RJ6

1 Blocks protein domain: IPB001092 Basic helix-loop-helix dimerization domain bHLH

UniProtKB/Swiss-Prot: FER3L_HUMAN, Q96RJ6
Similarity: Contains 1 bHLH (basic helix-loop-helix) domain


FERD3L for domains           About GeneDecksing


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

     UniProtKB/Swiss-Prot Summary: FER3L_HUMAN, Q96RJ6
Function: Transcription factor that binds to the E-box and functions as inhibitor of transcription. DNA binding
requires dimerization with an E protein. Inhibits transcription activation by ASCL1/MASH1 by sequestering E
proteins (By similarity)

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

GO IDQualified GO termEvidencePubMed IDs
GO:0003677DNA binding IEA--
GO:0046983protein dimerization activity IEA--
     
FERD3L for ontologies           About GeneDecksing


Phenotypes:
     3 MGI mutant phenotypes (inferred from 1 allele(MGI details for Ferd3l):
 cellular  embryogenesis  nervous system 

FERD3L for phenotypes           About GeneDecksing

Animal Models:
   inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for FERD3L
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miRNA
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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
FER3L_HUMAN, Q96RJ6: Nucleus (By similarity)
Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
nucleus4
cytosol1
extracellular1
mitochondrion1
peroxisome1
plasma membrane1

Gene Ontology (GO): 1 cellular component term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005634nucleus ISS--

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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 FERD3L
Interactions:

    Search GeneGlobe Interaction Network for FERD3L

STRING Interaction Network Preview (showing 1 interactants - click image to see more details)

1 Interacting protein for FERD3L (Q96RJ63 ENSP000002754614) via UniProtKB, MINT, STRING, and/or I2D
InteractantInteraction Details
GeneCardExternal ID(s)
TCF3P159233, ENSP000002629654I2D: score=1 STRING: ENSP00000262965
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Gene Ontology (GO): 5 biological process terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0006351transcription, DNA-templated IEA--
GO:0033504floor plate development IEA--
GO:0045892negative regulation of transcription, DNA-templated ISS--
GO:0048468cell development IEA--
GO:0050767regulation of neurogenesis IEA--

FERD3L for ontologies           About GeneDecksing



(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 FERD3L (FER3L)



(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,
Conferences by KenesGroup, 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, Primers from OriGene, and/or QIAGEN )
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REFSEQ mRNAs for FERD3L gene: 
NM_152898.2  

Unigene Cluster for FERD3L:

Fer3-like (Drosophila)
Hs.592168
Unigene Representative Sequence: AF517122
1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000275461(uc003suo.1)
miRNA
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Predesigned siRNA for gene silencing in human, mouse, rat FERD3L
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Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat FERD3L
Primer
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  QuantiFast Probe-based Assays in human, mouse, rat FERD3L

Additional mRNA sequence: 

AF517122.1 BC069147.1 BC101135.1 BC101136.1 BC101137.1 BC101138.2 

1 DOTS entry:

DT.100000413 

5 AceView cDNA sequences:

BC069147 BC043576 NM_152898 BI834521 AF517122 

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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FERD3L expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: ACCGAGCTCT
FERD3L Expression
About this image


FERD3L expression in embryonic tissues and stem cells    About this table
Data from LifeMap, the Embryonic Development and Stem Cells Database
 selected tissues (see all 2) fully expand
 
 Neural Tube (Nervous System)    fully expand to see all 5 entries
         Meso-diencephalic Dopaminergic Precursor Cells Mesencephalic Ventricular Zone
 
 Brain (Nervous System)    fully expand to see all 4 entries
         Meso-diencephalic Dopaminergic Precursor Cells Mesencephalic Ventricular Zone
FERD3L Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

FERD3L Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.592168
    Custom PCR Arrays for FERD3L
Primer
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QuantiFast Probe-based Assays in human, mouse, rat FERD3L
In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for FERD3L

(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 FERD3L gene from Selected species (see all 12)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Ferd3l1 , 5 Fer3-like (Drosophila)1, 5 78.59(n)1
78.79(a)1
  12 (14.79 cM)5
1147121  NM_033522.21  NP_277057.11 
 339284255 
chicken
(Gallus gallus)
Aves FERD3L1 Fer3-like (Drosophila) 69.91(n)
68.18(a)
  428429  XM_425989.2  XP_425989.1 
lizard
(Anolis carolinensis)
Reptilia FERD3L6
Fer3-like bHLH transcription factor
81(a)
1 ↔ 1
6(28678177-28678431)
zebrafish
(Danio rerio)
Actinopterygii ferd3l6
Fer3-like (Drosophila)
73(a)
1 ↔ 1
19(2463510-2463753) ENSDARG00000092160
fruit fly
(Drosophila melanogaster)
Insecta Fer36
48 related 3
32(a)
1 ↔ 1
3R(7519132-7519999)
worm
(Caenorhabditis elegans)
Secernentea hlh-136
Protein HLH-13 (hlh-13) mRNA, complete cds
26(a)
1 → many
X(4249249-4250764) WBGene00001957


ENSEMBL Gene Tree for FERD3L (if available)
TreeFam Gene Tree for FERD3L (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for FERD3L gene
PTF1A2  
6 SIMAP similar genes for FERD3L using alignment to 1 protein entry:     FER3L_HUMAN:
PTF1A    ATOH1    NEUROD4    NHLH1    NEUROD6    NEUROD2

FERD3L for paralogs           About GeneDecksing



(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 FERD3L (see all 84)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 7 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
VAR_0424394
A colorectal cancer sample4--see VAR_0424392 G R mis40--------
rs1126610151,2
F--19183913(+) CCTCAG/CTTCCT 1 -- ds50012Minor allele frequency- C:0.50CSA 4
rs102681601,2
C,F,A,H--19184059(+) CCCTTC/GAGGCT 1 -- ds500114Minor allele frequency- N:0.01EA NA NS WA CSA 989
rs1121916231,2
C--19184103(+) AAAAA-/ATGTAA 1 -- ds50011Minor allele frequency- A:0.50CSA 2
rs126724441,2
H--19184180(+) CACTTC/GCCACC 1 -- ds50010--------
rs1172117241,2
C,F--19184257(+) TTCCCC/GGCTCG 1 -- ds50011Minor allele frequency- G:0.23EA 120
rs1472776631,2
--19184320(+) AGCCAC/TTCTGC 1 -- ds50010--------
rs1112615191,2
C--19184427(+) GTGCCC/AGGTCC 1 -- ut311Minor allele frequency- A:0.50CSA 2
rs2015515771,2
--19184615(+) TCCGCA/GGCTGG 2 P L mis10--------
rs1418723441,2
C,F--19184631(+) GGCCTC/TGTTGA 2 K E mis12Minor allele frequency- T:0.00NA EU 5873

HapMap Linkage Disequilibrium report for FERD3L (19184405 - 19185044 bp)

Structural Variations
     Database of Genomic Variants (DGV) 1 variation for FERD3L:    About this table    
Variant IDTypeSubtypePubMed ID
nsv482940CNV Gain15286789

Site Specific Mutation Identification with PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing FERD3L
DNA2.0 Custom Variant and Variant Library Synthesis for FERD3L

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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9 diseases for FERD3L:    
About MalaCards
acrocephalosyndactylia    saethre-chotzen syndrome    learning disability    brachydactyly
breast and colorectal cancer    neuronitis    obesity    colorectal cancer
endotheliitis

1 disease from the University of Copenhagen DISEASES database for FERD3L:
Acrocephalosyndactylia

FERD3L for disorders           About GeneDecksing

Genetic Association Database (GAD): FERD3L

Export disorders for FERD3L 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 FERD3L gene, integrated from 10 sources (see all 15):
(articles sorted by number of sources associating them with FERD3L)
    Utopia: connect your pdf to the dynamic
world of online information

  1. N-twist, an evolutionarily conserved bHLH protein expressed in the developing CNS, functions as a transcriptional inhibitor. (PubMed id 12217327)1, 2, 3 Verzi M.P.... Black B.L. (Dev. Biol. 2002)
  2. Nato3 is an evolutionarily conserved bHLH transcription factor expressed in the CNS of Drosophila and mouse. (PubMed id 11472856)1, 2, 3 Segev E.... Ben-Arie N. (Mech. Dev. 2001)
  3. Human chromosome 7: DNA sequence and biology. (PubMed id 12690205)1, 2 Scherer S.W.... Tsui L.-C. (Science 2003)
  4. Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. (PubMed id 23251661)1 Comuzzie A.G....Butte N.F. (PLoS ONE 2012)
  5. Hundreds of variants clustered in genomic loci and biological pathways affect human height. (PubMed id 20881960)4 Lango Allen H....Hirschhorn J.N. (Nature 2010)
  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. Genetic correlates of brain aging on MRI and cognitive test measures: a genome-wide association and linkage analysis in the Framingham Study. (PubMed id 17903297)4 Seshadri S....Wolf P.A. (BMC Med. Genet. 2007)
  8. A genome-wide association study for blood lipid phenotypes in the Framingham Heart Study. (PubMed id 17903299)4 Kathiresan S....Cupples L.A. (BMC Med. Genet. 2007)
  9. Genome-wide association to body mass index and waist circumference: the Framingham Heart Study 100K project. (PubMed id 17903300)4 Fox C.S....Atwood L.D. (BMC Med. Genet. 2007)
  10. Genome-wide association of sleep and circadian phenotypes. (PubMed id 17903308)4 Gottlieb D.J....Wilk J.B. (BMC Med. Genet. 2007)

(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: 222894 HGNC: 16660 AceView: FERD3L Ensembl:ENSG00000146618 euGenes: HUgn222894
ECgene: FERD3L H-InvDB: FERD3L

(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 FERD3L 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 FERD3L gene:
Search GeneIP for patents involving FERD3L

GeneCards and IP:
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(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, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, 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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 Browse OriGene Antibodies   OriGene RNAi products in human, mouse, rat for FERD3L  
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 Block miRNA regulation of human, mouse, rat FERD3L using miScript Target Protectors SeqTarget long-range PCR primers for resequencing FERD3L
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 Novus Tissue Slides
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 Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat FERD3L
 inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for FERD3L
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GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014

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