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

KHDC3L Gene

protein-coding   GIFtS: 40
GCID: GC06P074073

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

(Previous name: chromosome 6 open reading frame 221)
(Previous symbol: C6orf221)
  See related disease
at  

(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
KH Domain Containing 3-Like, Subcortical Maternal Complex Member1 2     Chromosome 6 Open Reading Frame 2211
C6orf2211 2 3 5     ES Cell Associated Transcript 11
ECAT12 3 5     HYDM22
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, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

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. 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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000006.11  NC_018917.2  NT_007299.13  
Regulatory elements:
   Search SABiosciences Regulatory transcription factor binding sites for KHDC3L
         Other transcription factors

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

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 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 UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

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 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q587J8

  • KHDC3L Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    KHDC3L Protein Expression
    REFSEQ proteins: NP_001017361.1  
    ENSEMBL proteins: 
     ENSP00000359392  

    Human Recombinant Protein Products for KHDC3L: 
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    Browse Proteins at Cloud-Clone Corp. 

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005938cell cortex ----
    GO:0043234protein complex IEA--
    GO:0045179apical cortex IEA--

    KHDC3L for ontologies           About GeneDecksing



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

    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,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, 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, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

         Gene Ontology (GO): 1 molecular function term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding ----
         
    KHDC3L for ontologies           About GeneDecksing


    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 

    KHDC3L for phenotypes           About GeneDecksing

    Animal Models:
         MGI mouse knock-out Khdc3tm1Dean for KHDC3L

       inGenious Targeting Laboratory - Custom generated mouse model solutions for KHDC3L 
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    Inhib. RNA
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    (Pathways according to EMD Millipore, 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 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 Oct 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for KHDC3L

    3 Interacting proteins for KHDC3L (Q587J83) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    NLRP5P590473I2D: score=2 
    OOEPA6NGQ23I2D: score=1 
    TLE6Q9H8083I2D: score=1 
    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:0006468protein phosphorylation IEA--
    GO:0007094mitotic spindle assembly checkpoint IEA--
    GO:0090307spindle assembly involved in mitosis IEA--

    KHDC3L for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, 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 KHDC3L (KHD3L)

    Search CenterWatch for drugs/clinical trials and news about 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,
    Conferences by KenesGroup, 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, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    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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    Inhib. RNA
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    Primer
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    OriGene qPCR primer pairs and template standards for KHDC3L
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat KHDC3L
      QIAGEN 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:

    AA580965 BE550370 AI652239 AA872619 AA973759 AI917825 AI955057 AI631547 
    AA581033 AI651751 AI655845 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™, 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

    KHDC3L expression in normal human tissues (normalized intensities)      KHDC3L embryonic expression: see
    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 
     5/3 selected tissues (see all 3) fully expand
     
     Inner Cell Mass (Early Embryonic Tissues)    fully expand to see all 2 entries
             440A-3
     
     Ovary (Reproductive System)
             Secondary Oocyte Antral Follicle
     
     Gonad
             Secondary Oocyte Antral Follicle

    See KHDC3L Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for KHDC3L

    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

        SABiosciences Custom PCR Arrays for KHDC3L
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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)
    About This Section

    This gene was present in the common ancestor of human and mouse.

    Orthologs for KHDC3L gene from 1/5 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
    59.61(n)1
    40.39(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)
    About This Section
    Paralogs for KHDC3L gene
    OOEP2  
    2 SIMAP similar genes for KHDC3L using alignment to 1 protein entry:     KHD3L_HUMAN:
    DPPA5    OOEP

    KHDC3L for paralogs           About GeneDecksing


    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) 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

    10/113 SNPs in KHDC3L are shown (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
    SABiosciences Cancer Mutation 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, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    OMIM gene information: 611687    OMIM disorders: --

    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

  • 2 diseases for KHDC3L:    About MalaCards
    hydatidiform mole, recurrent    


    KHDC3L for disorders           About GeneDecksing


    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)
    About This Section

    PubMed articles for KHDC3L gene integrated from 9 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. (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. (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. (2003)
    4. Mutations in NLRP7 and KHDC3L confer a complete hydati diform mole phenotype on digynic triploid conceptions. (PubMed id 23125094)1 Fallahian M....Fisher R.A. (2013)
    5. 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. (2012)
    6. 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. (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. (2002)

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

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    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.)
    About This Section
    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, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 3 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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