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KLHDC9 Gene

protein-coding   GIFtS: 44
GCID: GC01P161068

Kelch Domain Containing 9

  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)
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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 91 2
Kelch/Ankyrin Repeat-Containing Cyclin A1-Interacting Protein2 3
KARCA12 3
Kelch/Ankyrin Repeat Containing Cyclin A1 Interacting Protein1
Kelch Domain-Containing Protein 92

External Ids:    HGNC: 284891   Entrez Gene: 1268232   Ensembl: ENSG000001627557   UniProtKB: Q8NEP73   
ORGUL members:         

Export aliases for KLHDC9 gene to outside databases

Previous GC identifers: GC01P159335 GC01P132425


(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 KLHDC9 Gene:
KLHDC9 (kelch domain containing 9) is a protein-coding gene. Diseases associated with KLHDC9 include retinitis.


(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_000001.11  NC_018912.2  NT_004487.20  
Regulatory elements:
   Regulatory transcription factor binding sites in the KLHDC9 gene promoter:
         Elk-1   Sp1   GATA-3   p53   POU3F1   Olf-1   AP-2gamma   AP-2beta   AP-2alpha   AP-2alphaA   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidKLHDC9 promoter sequence
   Search Chromatin IP Primers for KLHDC9

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat KLHDC9


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

Entrez Gene cytogenetic band: 1q23.3   Ensembl cytogenetic band:  1q23.3   HGNC cytogenetic band: 1q23.3

KLHDC9 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
KLHDC9 gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01P161068:  view genomic region     (about GC identifiers)

Start:
161,068,151 bp from pter      End:
161,070,138 bp from pter
Size:
1,988 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, 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, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: KLDC9_HUMAN, Q8NEP7 (See protein sequence)
Recommended Name: Kelch domain-containing protein 9  
Size: 349 amino acids; 37754 Da
Subunit: Interacts with CCNA1
Secondary accessions: Q5SY56 Q6NXT9 Q6PKN4 Q8N5E1 Q8NA16
Alternative splicing: 3 isoforms:  Q8NEP7-1   Q8NEP7-2   Q8NEP7-3   

Explore the universe of human proteins at neXtProt for KLHDC9: NX_Q8NEP7

Explore proteomics data for KLHDC9 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See KLHDC9 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_001007256.1  NP_689579.3  

    ENSEMBL proteins: 
     ENSP00000356990   ENSP00000376030  

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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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    2 InterPro protein domains:
     IPR011043 Gal_Oxase/kelch_b-propeller
     IPR015915 Kelch-typ_b-propeller

    Graphical View of Domain Structure for InterPro Entry Q8NEP7

    ProtoNet protein and cluster: Q8NEP7

    1 Blocks protein domain: IPB011498 Kelch

    UniProtKB/Swiss-Prot: KLDC9_HUMAN, Q8NEP7
    Similarity: Contains 3 Kelch repeats


    KLHDC9 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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    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for KLHDC9
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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 COMPARTMENTS: 

    CompartmentConfidence
    mitochondrion3
    cytosol2
    nucleus1
    peroxisome1

    (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 KLHDC9
    Interactions:

        Search GeneGlobe Interaction Network for KLHDC9

    STRING Interaction Network Preview (showing 4 interactants - click image to see more details)

    4 Interacting proteins for KLHDC9 (Q8NEP73 ENSP000003569904) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    CCNA1P783963, ENSP000002554654I2D: score=3 STRING: ENSP00000255465
    PPP1CAENSP000003260314STRING: ENSP00000326031
    PPP1CBENSP000002961224STRING: ENSP00000296122
    PPP1CCENSP000003350844STRING: ENSP00000335084
    About this table

    (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 KLHDC9 (KLDC9)



    (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, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for KLHDC9 gene (3 alternative transcripts): 
    NM_001007256.1  NM_001007255.2  NM_152366.4  

    Unigene Cluster for KLHDC9:

    Kelch domain containing 9
    Hs.507290  [show with all ESTs]
    Unigene Representative Sequence: NM_001007255
    8 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000490724 ENST00000469647 ENST00000471613 ENST00000368011(uc001fxq.3 uc001fxr.3)
    ENST00000392192(uc021pbt.1 uc001fxs.3) ENST00000392191 ENST00000494418
    ENST00000475934
    miRNA
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      QuantiTect SYBR Green Assays in human, mouse, rat KLHDC9
      QuantiFast Probe-based Assays in human, mouse, rat KLHDC9

    Additional mRNA sequence: 

    BC022077.1 BC066896.1 NR_033385.1 NR_033386.1 

    9 DOTS entries:

    DT.316111  DT.97798741  DT.102821325  DT.316112  DT.100752279  DT.100752278  DT.121398571  DT.121398579 
    DT.91674408 

    Selected AceView cDNA sequences (see all 96):

    AI279569 R46607 BI824441 AI884760 BC066896 AA459828 BX097392 AA679114 
    AA716344 AA405220 AA131591 BU173744 BQ638407 BQ654232 AI241682 AW296556 
    AA890405 AW664291 BQ008459 AA906885 BE675827 AA524491 AA937204 N54019 

    GeneLoc Exon Structure

    5 Alternative Splicing Database (ASD) splice patterns (SP) for KLHDC9    About this scheme

    ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5a · 5b · 5c ^ 6
    SP1:                    -                 -                     
    SP2:                                                            
    SP3:                                      -                     
    SP4:                                      -                     
    SP5:                    -           -     -                     


    ECgene alternative splicing isoforms for KLHDC9

    (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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    KLHDC9 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GGCCATCGCA
    KLHDC9 Expression
    About this image

    KLHDC9 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    KLHDC9 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.507290
        Custom PCR Arrays for KLHDC9
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    In Situ
    Assay Products:
     

     
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    (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 KLHDC9 gene from Selected species (see all 8)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Klhdc91 , 5 kelch domain containing 91, 5 82.52(n)1
    83.67(a)1
      1 (79.36 cM)5
    688741  NM_001033039.21  NP_001028211.11 
     1713584465 
    lizard
    (Anolis carolinensis)
    Reptilia KLHDC96
    kelch domain containing 9
    56(a)
    1 ↔ 1
    AAWZ02040441(21-6850)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia klhdc91 kelch domain containing 9 58.88(n)
    54.19(a)
      100486977  XM_004919344.1  XP_004919401.1 


    ENSEMBL Gene Tree for KLHDC9 (if available)
    TreeFam Gene Tree for KLHDC9 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for KLHDC9 gene
    1 SIMAP similar gene for KLHDC9 using alignment to 1 protein entry:     KLDC9_HUMAN:
    KARCA1

    KLHDC9 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 KLHDC9 (see all 104)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 1 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1879255671,2
    --132423600(+) ATATGA/GATTTG 2 -- us2k10--------
    rs1924730411,2
    --161066183(+) ATTTGA/GTTCAA 4 -- us2k10--------
    rs1822846271,2
    --161066219(+) AGGCAC/GTTCCT 4 -- us2k10--------
    rs1116582711,2
    F--161066335(+) TGTGAG/AGTTCA 4 -- us2k11Minor allele frequency- A:0.50CSA 2
    rs1473739881,2
    --161066422(+) GGCCCA/GTGGGG 4 -- us2k10--------
    rs46562881,2
    C,F,H--161066446(+) TTTCTA/CTCCAG 4 -- us2k116Minor allele frequency- C:0.12NS EA NA 2216
    rs1925768871,2
    --161066592(+) ATGACA/GGATCT 4 -- us2k10--------
    rs1848633871,2
    --161066616(+) GGGAGA/GTTAGC 4 -- us2k10--------
    rs1395858201,2
    --161066755(+) GGAAAC/GCTATA 4 -- us2k10--------
    rs1896613851,2
    --161066764(+) TAGTTA/GGGAGG 4 -- us2k10--------

    HapMap Linkage Disequilibrium report for KLHDC9 (161068151 - 161070138 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for KLHDC9: --
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing KLHDC9
    DNA2.0 Custom Variant and Variant Library Synthesis for KLHDC9

    (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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    1 disease for KLHDC9:    
    About MalaCards
    retinitis


    KLHDC9 for disorders           About GeneDecksing


    Export disorders for KLHDC9 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 KLHDC9 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with KLHDC9)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Identification of interaction partners and substrates of the cyclin A1-CDK2 complex. (PubMed id 15159402)1, 2, 3 Diederichs S.... Mueller-Tidow C. (J. Biol. Chem. 2004)
    2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    3. hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. (PubMed id 17207965)1 Lamesch P.... Vidal M. (Genomics 2007)
    4. The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)2 Gregory S.G.... Bentley D.R. (Nature 2006)
    5. Sequence comparison of human and mouse genes reveals a homologous block structure in the promoter regions. (PubMed id 15342556)1 Suzuki Y.... Sugano S. (Genome Res. 2004)
    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. (Genome Res. 2004)
    7. Expressed sequence tag analysis of human retina for the NEIBank project: retbindin, an abundant, novel retinal cDNA and alternative splicing of other retina-preferred gene transcripts. (PubMed id 12107411)1 Wistow G.... Peterson K. (Mol. Vis. 2002)
    8. 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: 126823 HGNC: 28489 AceView: KARCA1 Ensembl:ENSG00000162755 euGenes: HUgn126823
    ECgene: KLHDC9 H-InvDB: KLHDC9

    (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 KLHDC9 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 KLHDC9 gene:
    Search GeneIP for patents involving KLHDC9

    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, 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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