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

KXD1 Gene

protein-coding   GIFtS: 44
GCID: GC19P018669

KxDL Motif Containing 1

(Previous name: chromosome 19 open reading frame 50)
(Previous symbol: C19orf50)
  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
KxDL Motif Containing 11 2     MST0962
C19orf501 2 3     MSTP0962
Chromosome 19 Open Reading Frame 501     KxDL Motif-Containing Protein 12
KXDL2     UPF0459 Protein C19orf502

External Ids:    HGNC: 284201   Entrez Gene: 790362   Ensembl: ENSG000001057007   OMIM: 6151785   UniProtKB: Q9BQD33   

Export aliases for KXD1 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

GeneCards Summary for KXD1 Gene: 
KXD1 (KxDL motif containing 1) is a protein-coding gene. Diseases associated with KXD1 include gastric cancer. GO annotations related to this gene include protein binding.

UniProtKB/Swiss-Prot: KXDL1_HUMAN, Q9BQD3
Function: Involved in endosomal cargo sorting (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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000019.9  NT_011295.11  NC_018930.2  
Regulatory elements:
   Search SABiosciences Regulatory transcription factor binding sites for KXD1
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidKXD1 promoter sequence
   Search SABiosciences Chromatin IP Primers for KXD1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat KXD1


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

Entrez Gene cytogenetic band: 19p13.11   Ensembl cytogenetic band:  19p13.11   HGNC cytogenetic band: 19p13.11

KXD1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
KXD1 gene location

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19P018669:  view genomic region     (about GC identifiers)

Start:
18,668,572 bp from pter      End:
18,680,197 bp from pter
Size:
11,626 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: KXDL1_HUMAN, Q9BQD3 (See protein sequence)
Recommended Name: KxDL motif-containing protein 1  
Size: 176 amino acids; 19668 Da
Subunit: Associates with the BLOC-1 complex. Interacts with BLOC1S1. Interacts with DTNBP1/BLOC1S7 (via
coiled-coil domain) (By similarity)
Sequence caution: Sequence=AAC25583.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;
Secondary accessions: O76098

Explore the universe of human proteins at neXtProt for KXD1: NX_Q9BQD3

Explore proteomics data for KXD1 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q9BQD3

  • KXD1 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    KXD1 Protein Expression
    REFSEQ proteins (3 alternative transcripts): 
    NP_001165419.1  NP_001165420.1  NP_076974.2  

    ENSEMBL proteins: 
     ENSP00000222307   ENSP00000472268   ENSP00000469648   ENSP00000472535   ENSP00000471554  
     ENSP00000472678   ENSP00000469288   ENSP00000468990   ENSP00000469294   ENSP00000473057  
     ENSP00000472836   ENSP00000468857   ENSP00000468949   ENSP00000471127   ENSP00000443549  
     ENSP00000438903  

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    Novus Biologicals KXD1 Lysates
    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates 
    Browse ProSpec Recombinant Proteins
    Browse Proteins at Cloud-Clone Corp. 

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0031083colocalizes with BLOC-1 complex ISS--

    KXD1 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
    1 InterPro protein domain:
     IPR019371 Uncharacterised_KxDL

    Graphical View of Domain Structure for InterPro Entry Q9BQD3

    ProtoNet protein and cluster: Q9BQD3

    UniProtKB/Swiss-Prot: KXDL1_HUMAN, Q9BQD3
    Similarity: Belongs to the KXD1 family


    KXD1 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,
    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

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: KXDL1_HUMAN, Q9BQD3
    Function: Involved in endosomal cargo sorting (By similarity)

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding IPI16189514
         
    KXD1 for ontologies           About GeneDecksing


    Phenotypes:
         3 MGI mutant phenotypes (inferred from 1 allele(MGI details for Kxd1):
     hematopoietic system  pigmentation  vision/eye 

    KXD1 for phenotypes           About GeneDecksing

    Animal Models:
         MGI mouse knock-out Kxd1tm1Wli for KXD1

       inGenious Targeting Laboratory - Custom generated mouse model solutions for KXD1 
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    miRNA
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    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat KXD1
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    Inhib. RNA
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for KXD1


    (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 KXD1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    5/54 Interacting proteins for KXD1 (Q9BQD31, 2, 3 ENSP000002223074) via UniProtKB, MINT, STRING, and/or I2D (see all 54)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    IFT20Q8IY311, 2, 3, ENSP000003505704EBI-739657,EBI-744203 MINT-66901 I2D: score=5 STRING: ENSP00000350570
    RABGEF1Q9UJ411, 2, 3, ENSP000002849574EBI-739657,EBI-913954 MINT-67747 I2D: score=4 STRING: ENSP00000284957
    CEP19Q96LK02, 3, ENSP000003872094MINT-66218 I2D: score=4 STRING: ENSP00000387209
    FXR2P511162, 3, ENSP000002501134MINT-67476 I2D: score=4 STRING: ENSP00000250113
    LNX1Q8TBB12, 3, ENSP000002639254MINT-67890 I2D: score=4 STRING: ENSP00000263925
    About this table

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016192vesicle-mediated transport ISS--

    KXD1 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 KXD1 (KXDL1)

    Search CenterWatch for drugs/clinical trials and news about KXD1 / KXDL1

    (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 KXD1 gene (3 alternative transcripts): 
    NM_001171948.1  NM_001171949.1  NM_024069.3  

    Unigene Cluster for KXD1:

    KxDL motif containing 1
    Hs.714548  [show with all ESTs]
    Unigene Representative Sequence: NM_001171948
    17 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000222307(uc002njo.3 uc002njq.3) ENST00000600372 ENST00000600796
    ENST00000601630 ENST00000599000 ENST00000595073 ENST00000600654 ENST00000596785
    ENST00000599319 ENST00000597438 ENST00000596244 ENST00000602094 ENST00000598830
    ENST00000595870 ENST00000600099 ENST00000540691(uc021uqq.1) ENST00000539106(uc021uqr.1)

    miRNA
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    Inhib. RNA
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    Additional mRNA sequence: 

    AF173381.1 AK098346.1 BC001080.2 BC006479.1 

    19 DOTS entries:

    DT.100031545  DT.101983967  DT.100031547  DT.101983968  DT.100877696  DT.100877697  DT.91752226  DT.92329089 
    DT.95359253  DT.100877699  DT.80102067  DT.102820643  DT.121481855  DT.121481873  DT.446250  DT.121481845 
    DT.91662076  DT.95359250  DT.95359251 

    24/433 AceView cDNA sequences (see all 433):

    BQ674874 BM718773 AW235074 BQ549224 BP366510 BM887692 BI766302 AI636614 
    CA431389 BF446637 BQ668978 Z41157 BU683347 AI703068 BU186070 BU542393 
    BM450496 BX509496 CB215824 BU857250 BM997183 CB055204 AA789318 R57182 

    GeneLoc Exon Structure

    5/10 Alternative Splicing Database (ASD) splice patterns (SP) for KXD1 (see all 10)    About this scheme

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


    ECgene alternative splicing isoforms for KXD1

    (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

    KXD1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GAGCAAACGG
    KXD1 Expression
    About this image


    See KXD1 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for KXD1

    SOURCE GeneReport for Unigene cluster: Hs.714548
        SABiosciences Custom PCR Arrays for KXD1
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for KXD1

    (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 animals.

    Orthologs for KXD1 gene from 5/13 species (see all 13)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Kxd11 , 5 RIKEN cDNA 2810422J05 gene5
    KxDL motif containing 11
    84.09(n)1
    92.61(a)1
      8 (34.15 cM)5
    756201  NM_029366.21  NP_083642.11 
     705082725 
    chicken
    (Gallus gallus)
    Aves C28H19orf501 chromosome 28 open reading frame, human C19orf50 76.71(n)
    75.3(a)
      771070  XM_001233287.2  XP_001233288.2 
    zebrafish
    (Danio rerio)
    Actinopterygii Dr.158882 Transcribed sequence with weak similarity to protein refNP_076974.1 (H.sapiens) hypothetical protein MGC2749 [Homo sapiens] less 75.96(n)    CF998204.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG106811 CG10681 50.21(n)
    43.67(a)
      39425  NM_140323.2  NP_648580.1 
    worm
    (Caenorhabditis elegans)
    Secernentea C13F10.26
    Protein C13F10.2
    26(a)
    1 ↔ 1
    V(7221479-7222057)


    ENSEMBL Gene Tree for KXD1 (if available)
    TreeFam Gene Tree for KXD1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for KXD1 gene
    1 SIMAP similar gene for KXD1 using alignment to 8 protein entries:     KXDL1_HUMAN (see all proteins):
    MST096

    KXD1 for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for KXD1
    PGOHUM00000234540


    (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

    10/357 SNPs in KXD1 are shown (see all 357)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 19 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs105883991,2
    C--18232451(+) ttttt-/T/TTTT
            
    cagtt
    3 -- int11NA 2
    rs1140094691,2
    C,F--18666599(+) TAAAAG/AGACAC 3 -- us2k11Minor allele frequency- A:0.04WA 118
    rs1412004511,2
    --18666611(+) GGAGCG/TTATTT 3 -- us2k10--------
    rs1502322951,2
    --18666631(+) TTATTC/TATTTA 3 -- us2k10--------
    rs81126931,2
    C--18666707(+) gcttcA/Gcctcc 3 -- us2k10--------
    rs1819701811,2
    --18666780(+) CACGCC/TTGGCT 3 -- us2k10--------
    rs1493669561,2
    --18667013(+) GTTGTC/TGTTGT 3 -- us2k10--------
    rs81103711,2
    C,F,A,H--18667272(+) tccacC/Acgcct 3 -- us2k16Minor allele frequency- A:0.48NA CSA EA 250
    rs81103741,2
    C,F,A,H--18667281(+) ctggcC/Atccca 3 -- us2k17Minor allele frequency- A:0.49NA CSA EA 252
    rs1440442641,2
    --18667294(+) GTGCTA/GGGGTT 3 -- us2k10--------

    HapMap Linkage Disequilibrium report for KXD1 (18668572 - 18680197 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for KXD1: --
    SABiosciences Cancer Mutation PCR Assays
    SeqTarget long-range PCR primers for resequencing KXD1
    DNA2.0 Custom Variant and Variant Library Synthesis for KXD1

    (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: 615178    OMIM disorders: --

    2 diseases for KXD1:    About MalaCards
    gastric cancer    


    KXD1 for disorders           About GeneDecksing


    Export disorders for KXD1 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 KXD1 gene, integrated from 9 sources (see all 12):
    (articles sorted by number of sources associating them with KXD1)
        Utopia: connect your pdf to the dynamic
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    1. Yeast homologues of three BLOC-1 subunits highlight K xDL proteins as conserved interactors of BLOC-1. (PubMed id 21159114)1, 3 Hayes M.J....Levine T.P. (2011)
    2. Intersectin (ITSN) family of scaffolds function as mol ecular hubs in protein interaction networks. (PubMed id 22558309)1 Wong K.A....O'Bryan J.P. (2012)
    3. The BLOS1-interacting protein KXD1 is involved in the biogenesis of lysosome-related organelles. (PubMed id 22554196)1 Yang Q....Li W. (2012)
    4. Toward an understanding of the protein interaction net work of the human liver. (PubMed id 21988832)1 Wang J....Yang X. (2011)
    5. 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)
    6. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (2006)
    7. Towards a proteome-scale map of the human protein-protein interaction network. (PubMed id 16189514)1 Rual J.F....Vidal M. (2005)
    8. Transcriptome analysis of human gastric cancer. (PubMed id 16341674)1 Oh J.H....Kim N.S. (2005)
    9. 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)
    10. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1 Ota T.... Sugano S. (2004)

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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 79036 HGNC: 28420 AceView: MGC2749 Ensembl:ENSG00000105700 euGenes: HUgn79036
    ECgene: KXD1 H-InvDB: KXD1

    (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 KXD1 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 KXD1 gene:
    Search GeneIP for patents involving KXD1

    GeneCards and IP:
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