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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

KLHDC3 Gene

protein-coding   GIFtS: 51
GCID: GC06P042981

kelch domain containing 3

  Search for KLHDC3
in our new
 Human Malady Compendium 
Biological research products
for KLHDC3
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

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

Quality score for the ORGUL clustered with this gene is 3

Aliases
Kelch Domain Containing 31 2     HPeas1
PEAS1 2 3     RP1-20C7.32
DJ20C7.31     Kelch Domain-Containing Protein 32
Testis Intracellular Mediator Protein2 3     Protein Peas3

External Ids:    HGNC: 207041   Entrez Gene: 1161382   Ensembl: ENSG000001247027   OMIM: 6112485   UniProtKB: Q9BQ903   
ORGUL members:         
NONCODE:n411638    

Export aliases for KLHDC3 gene to outside databases

Previous GC identifers: GC06P042983 GC06P043030 GC06P043031 GC06P043089 GC06P042699


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

Entrez Gene summary for KLHDC3:
The protein encoded by this gene contains six repeated kelch motifs that are structurally similar to recombination
activating gene 2, a protein involved in the activation of the V(D)J recombination. In mouse, this gene is found to be
expressed specifically in testis. Its expression in pachytene spermatocytes is localized to cytoplasma and meiotic
chromatin, suggesting that this gene may be involved in meiotic recombination. (provided by RefSeq, Jun 2012)

UniProtKB/Swiss-Prot: KLDC3_HUMAN, Q9BQ90
Function: May be involved in meiotic recombination process

Gene Wiki entry for KLHDC3


(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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000006.11  NC_018917.1  NT_007592.15  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the KLHDC3 gene promoter:
         E2F-4   E2F-3a   E2F-5   E2F-2   Roaz   C/EBPalpha   Egr-2   CHOP-10   E2F   E2F-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidKLHDC3 promoter sequence
   Search SABiosciences Chromatin IP Primers for KLHDC3

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat KLHDC3


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

Entrez Gene cytogenetic band: 6p21.1   Ensembl cytogenetic band:  6p21.1   HGNC cytogenetic band: 6p21.1

KLHDC3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
KLHDC3 gene location

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06P042981:  view genomic region     (about GC identifiers)

Start:
42,981,951 bp from pter      End:
42,989,036 bp from pter
Size:
7,086 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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 Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: KLDC3_HUMAN, Q9BQ90 (See protein sequence)
Recommended Name: Kelch domain-containing protein 3  
Size: 382 amino acids; 43088 Da
Subcellular location: Cytoplasm. Note=Also found in meiotic chromatin (By similarity)
Secondary accessions: A8K2W9

Explore the universe of human proteins at neXtProt for KLHDC3: NX_Q9BQ90

KLHDC3 Protein expression data from MOPED and PaxDb:    About this image 
KLHDC3 Protein Expression

REFSEQ proteins: NP_476502.1  
ENSEMBL proteins: 
 ENSP00000313995   ENSP00000400876   ENSP00000331562   ENSP00000244670  
Reactome Protein details: Q9BQ90
Human Recombinant Protein Products for KLHDC3: 
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Uscn Proteins for KLHDC3

Gene Ontology (GO): 3 cellular component terms (GO ID links to tree view):    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0000790nuclear chromatin IDA12606021
GO:0005737cytoplasm IDA12606021
GO:0005829cytosol TAS--

KLHDC3 for ontologies           About GeneDecksing



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Uscn ELISAs and CLIAs for KLHDC3


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

KLHDC3 for domains           About GeneDecksing

2 InterPro domains/families:
 IPR011498 Kelch_2
 IPR015915 Kelch-typ_b-propeller

Graphical View of Domain Structure for InterPro Entry Q9BQ90

ProtoNet protein and cluster: Q9BQ90

1 Blocks protein family: IPB011498 Kelch

UniProtKB/Swiss-Prot: KLDC3_HUMAN, Q9BQ90
Similarity: Contains 5 Kelch repeats


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, Sirion Biotech, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, Sirion Biotech, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
About This Section

Molecular Function:

     UniProtKB/Swiss-Prot Summary: KLDC3_HUMAN, Q9BQ90
Function: May be involved in meiotic recombination process

     Gene Ontology (GO): 2 molecular function terms (GO ID links to tree view):    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0003682chromatin binding IDA12606021
GO:0005515protein binding IPI12482870
     
KLHDC3 for ontologies           About GeneDecksing


Phenotypes:
     1 GenomeRNAi human phenotype for KLHDC3:
 Increased gamma-H2AX phosphory 

Animal Models:
   inGenious Targeting Laboratory - Customizable classic, inducible, and humanized mouse model solutions for KLHDC3 

miRNA
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8/23 QIAGEN miScript miRNA Assays for microRNAs that regulate KLHDC3 (see all 23):
hsa-miR-4286 hsa-miR-513a-5p hsa-miR-202 hsa-miR-29c hsa-miR-29a hsa-miR-181a-2* hsa-miR-340 hsa-miR-449a
SwitchGear 3'UTR luciferase reporter plasmidKLHDC3 3' UTR sequence
Inhib. RNA
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In Situ Assay
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(Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, 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 Mar 2013 via Entrez Gene).
About This Section

Unified GeneCards pathways  About this table 
See pathways by source

Super-pathwaycontained gene-specific pathways
1Activation of Chaperone Genes by XBP1(S)
Activation of Chaperone Genes by XBP1(S)1.00
Unfolded Protein Response0.71
Activation of Chaperones by IRE1alpha0.94
2Expression of KLHDC3
Expression of KLHDC31.00
3Asparagine N-linked glycosylation
Metabolism of proteins0.15

Pathway sources
See GeneCards unified pathways
Show all pathways


5        Reactome Pathways for KLHDC3
    Expression of KLHDC3
Activation of Chaperone Genes by XBP1(S)
Metabolism of proteins
Activation of Chaperones by IRE1alpha
Unfolded Protein Response



KLHDC3 for pathways           About GeneDecksing

Interactions:

    Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for KLHDC3

STRING Interaction Network Preview (showing 5 interactants - click image to see 9)

5/9 Interacting proteins for KLHDC3 (Q9BQ903 ENSP000003139954) via UniProtKB, MINT, STRING, and/or I2D (see all 9)
InteractantInteraction Details
GeneCardExternal ID(s)
DLG3Q927963, ENSP000003634804I2D: score=2 STRING: ENSP00000363480
UBXN7O948883, ENSP000002963284I2D: score=2 STRING: ENSP00000296328
TCEB2ENSP000002623064STRING: ENSP00000262306
TCEB1ENSP000002848114STRING: ENSP00000284811
CUL2ENSP000003638804STRING: ENSP00000363880
About this table

Gene Ontology (GO): 3 biological process terms (GO ID links to tree view):    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0006987activation of signaling protein activity involved in unfolded protein response TAS--
GO:0007131reciprocal meiotic recombination NAS12606021
GO:0030968endoplasmic reticulum unfolded protein response TAS--

KLHDC3 for ontologies           About GeneDecksing



(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section
Browse Small Molecules at EMD Millipore
Browse drugs & compounds from Enzo Life Sciences

Browse Tocris compounds for KLHDC3
Search CenterWatch for drugs/clinical trials and news about KLHDC3 / KLDC3 

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 235 Homo sapiens; Mar 10 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,
RNAi Products from EMD Millipore,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, Sirion Biotech, microRNA from QIAGEN,
Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section

REFSEQ mRNAs for KLHDC3 gene (2 alternative transcripts): 
NM_057161.3  NM_001242872.1  

Unigene Cluster for KLHDC3:

Kelch domain containing 3
Hs.412468  [show with all ESTs]
Unigene Representative Sequence: NM_057161
4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000326974(uc003otl.3 uc003otn.3 uc003otm.3 uc021yzr.1)
ENST00000432243 ENST00000332245(uc003oto.3) ENST00000244670

miRNA
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QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat KLHDC3
8/23 QIAGEN miScript miRNA Assays for microRNAs that regulate KLHDC3 (see all 23):
hsa-miR-4286 hsa-miR-513a-5p hsa-miR-202 hsa-miR-29c hsa-miR-29a hsa-miR-181a-2* hsa-miR-340 hsa-miR-449a
SwitchGear 3'UTR luciferase reporter plasmidKLHDC3 3' UTR sequence
Inhib. RNA
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Sirion Biotech Custom design and validation of potent shRNA sequences against KLHDC3 
Clone
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  QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat KLHDC3
  QIAGEN QuantiFast Probe-based Assays in human, mouse, rat KLHDC3

Additional cDNA sequence: 

AB055925.1 AK097719.1 AK290384.1 BC000295.2 BC001789.1 BC001793.2 BC007296.1 BC021546.1 
BC041793.1 BC045612.1 NR_040101.1 

24/31 DOTS entries (see all 31):

DT.100802149  DT.100892388  DT.455288  DT.87017301  DT.121385652  DT.100892383  DT.100892375  DT.121385680 
DT.121385719  DT.95331722  DT.100892356  DT.100892389  DT.121385672  DT.121385666  DT.92467136  DT.95340143 
DT.100045338  DT.40223712  DT.95339998  DT.100759070  DT.121385592  DT.121385620  DT.121385626  DT.121385653 

24/971 AceView cDNA sequences (see all 971):

CR612447 BU185210 AL047473 AI968233 BC001793 AU279911 BM972160 BQ056358 
AW138370 AW296542 CR599856 BM670875 BE270075 BC012987 BG179476 AI891023 
BC007296 BM795240 BU734755 BM753820 AW292070 AA417366 BC001175 CK300860 

GeneLoc Exon Structure

5/10 Alternative Splicing Database (ASD) splice patterns (SP) for KLHDC3 (see all 10)    About this scheme

ExUns: 1a · 1b · 1c ^ 2a · 2b ^ 3 ^ 4a · 4b ^ 5a · 5b ^ 6a · 6b · 6c · 6d · 6e ^ 7 ^ 8a · 8b ^ 9 ^ 10 ^ 11a · 11b · 11c
SP1:                                      -                                                                                                   
SP2:                                      -                                                                                                   
SP3:                                -     -                                                                                                   
SP4:                                      -     -                                                                                             
SP5:                    -     -           -                 -     -     -     -     -     -     -     -     -     -     -     -               


ECgene alternative splicing isoforms for KLHDC3

(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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

KLHDC3 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: AGACCTCCTT
KLHDC3 Expression
About this image
See KLHDC3 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for KLHDC3

SOURCE GeneReport for Unigene cluster: Hs.412468
    SABiosciences Custom PCR Arrays for KLHDC3

Primer
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for KLHDC3

(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 KLHDC3 gene from 7/23 species (see all 23)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
chicken
(Gallus gallus)
Aves KLHDC31 kelch domain containing 3 77.57(n)
86.65(a)
  421251  XM_419323.3  XP_419323.3 
lizard
(Anolis carolinensis)
Reptilia KLHDC36
--
88(a)
1 ↔ 1
2(144729711-144758687)
African clawed frog
(Xenopus laevis)
Amphibia klhdc3-prov2 kelch domain containing 3 74.66(n)    BC056132.1 
zebrafish
(Danio rerio)
Actinopterygii Dr.167352 Transcribed sequence with moderate similarity to protein more 77.89(n)    CK030046.1 
fruit fly
(Drosophila melanogaster)
Insecta CG120811 CG12081 54.87(n)
50.4(a)
  31799  NM_132266.1  NP_572494.1 
worm
(Caenorhabditis elegans)
Secernentea F53E4.11 Protein F53E4.1 51.1(n)
45.6(a)
  180050  NM_074494.4  NP_506895.1 
thale cress
(Arabidopsis thaliana)
eudicotyledons AT1G186101 galactose oxidase/kelch repeat domain-containing protein 44.19(n)
31.61(a)
  838442  NM_101719.6  NP_173296.3 


ENSEMBL Gene Tree for KLHDC3 (if available)
TreeFam Gene Tree for KLHDC3 (if available) 

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
Paralogs for KLHDC3 gene
KLHDC22  HCFC12  KLHDC12  LZTR12  RABEPK2  KLHDC102  HCFC22  

KLHDC3 for paralogs           About GeneDecksing



(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section

10/68 NCBI SNPs in KLHDC3 are shown (see all 68    About this table
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 6 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1878021781,2
--42983780(+) GCAATA/TCTCCT 2 -- int10--------
rs1923782841,2
--42983792(+) CCTCAA/GCCTCC 2 -- int10--------
rs1847793031,2
--42984157(+) ACATAC/TCTTTC 2 -- int10--------
rs1435357861,2
--42984178(+) CCTGGC/TAGCAT 2 -- int10--------
rs1471279471,2
--42984209(+) GAACTC/GCTTGT 2 -- int10--------
rs1394883951,2
--42984291(+) CCAACC/TGCGGT 2 -- int10--------
rs1896108701,2
--42984294(+) ACCGCA/GGTAAC 2 -- int10--------
rs1918502321,2
--42984328(+) GTCCCA/GCCCTA 2 -- int10--------
rs1843273471,2
--42984525(+) CAAGAC/GAATAT 2 -- int10--------
rs1890503601,2
--42984532(+) ATATAC/TCGTTT 2 -- int10--------

HapMap Linkage Disequilibrium report for KLHDC3 (42981951 - 42989036 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
      Database of Genomic Variants (DGV) variations for KLHDC3: --

SABiosciences Cancer Mutation PCR Assays
QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing KLHDC3
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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.)
About This Section

KLHDC3 for disorders           About MalaCards

KLHDC3 for disorders           About GeneDecksing

OMIM gene information: 611248    OMIM disorders: --


Export disorders for KLHDC3 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 KLHDC3 gene, integrated from 9 sources (see all 17):
(articles sorted by number of sources associating them with KLHDC3)
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  1. A novel testis-specific RAG2-like protein, Peas: its expression in pachytene spermatocyte cytoplasm and meiotic chromatin. (PubMed id 12606021)1, 2, 3, 9 Ohinata Y....Mitsui Y. (2003)
  2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
  4. The DNA sequence and analysis of human chromosome 6. (PubMed id 14574404)1, 2 Mungall A.J.... Beck S. (2003)
  5. Male-enhanced antigen-1 gene flanked by two overlappi ng genes is expressed in late spermatogenesis. (PubMed id 12444059)1, 3 Ohinata Y....Mitsui Y. (2002)
  6. Mass spectrometric analysis of lysine ubiquitylation r eveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (2011)
  7. Dynamics of cullin-RING ubiquitin ligase network revea led by systematic quantitative proteomics. (PubMed id 21145461)1 Bennett E.J....Harper J.W. (2010)
  8. UBXD7 binds multiple ubiquitin ligases and implicates p97 in HIF1alpha turnover. (PubMed id 18775313)1 Alexandru G....Deshaies R.J. (2008)
  9. Characterization of Cullin-box sequences that direct recruitment of Cul2-Rbx1 and Cul5-Rbx2 modules to Elongin BC-based ubiquitin ligases. (PubMed id 18187417)1 Mahrour N....Conaway J.W. (2008)
  10. hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. (PubMed id 17207965)1 Lamesch P.... Vidal M. (2007)

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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: 116138 HGNC: 20704 AceView: PPP2R5D Ensembl:ENSG00000124702 euGenes: HUgn116138
ECgene: KLHDC3 H-InvDB: KLHDC3

(According to HUGE)
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(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
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NameDescription
PharmGKB entry for KLHDC3 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 KLHDC3 gene:
Search GeneIP for patents involving KLHDC3

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