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    KHDC1 KH domain containing 1 [ Homo sapiens (human) ]

    Gene ID: 80759, updated on 10-Dec-2024

    Summary

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    Official Symbol
    KHDC1provided by HGNC
    Official Full Name
    KH domain containing 1provided by HGNC
    Primary source
    HGNC:HGNC:21366
    See related
    Ensembl:ENSG00000135314 MIM:611688; AllianceGenome:HGNC:21366
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    NDG1; C6orf147; C6orf148; bA257K9.4; Em:AC019205.8
    Summary
    Predicted to enable identical protein binding activity and poly(U) RNA binding activity. Predicted to be located in membrane. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Broad expression in brain (RPKM 1.7), thyroid (RPKM 1.1) and 23 other tissues See more
    Orthologs
    all
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    Genomic context

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    See KHDC1 in Genome Data Viewer
    Location:
    6q13
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (73241314..73310378, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (74417977..74487018, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (73951037..74020101, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene KH domain containing 1 pseudogene 1 Neighboring gene KHDC1-KHDC1L Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:73933575-73934774 Neighboring gene KH domain containing 1 like Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17332 Neighboring gene KHDC1 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:73978297-73978873 Neighboring gene chromosome 6 open reading frame 147 Neighboring gene ribosomal protein SA pseudogene 41 Neighboring gene EIF3E pseudogene 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:74017111-74017738 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24741 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24742 Neighboring gene syndecan binding protein 2 pseudogene 1 Neighboring gene phosphoribosylaminoimidazole carboxylase, phosphoribosylaminoimidazole succinocarboxamide synthetase pseudogene 3

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Atypical structure and phylogenomic evolution of the new eutherian oocyte- and embryo-expressed KHDC1/DPPA5/ECAT1/OOEP gene family. Pierre A, et al. Genomics, 2007 Nov. PMID 17913455
    2. Transcriptome analysis of human gastric cancer. Oh JH, et al. Mamm Genome, 2005 Dec. PMID 16341674
    3. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Kimura K, et al. Genome Res, 2006 Jan. PMID 16344560, Free PMC Article
    4. A reference map of the human binary protein interactome. Luck K, et al. Nature, 2020 Apr. PMID 32296183, Free PMC Article
    5. Complete sequencing and characterization of 21,243 full-length human cDNAs. Ota T, et al. Nat Genet, 2004 Jan. PMID 14702039

    See all (9) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Readthrough LOC122539213

    Readthrough gene: LOC122539213, Included gene: C6orf147, Included gene: KHDC1L

    Homology

    Clone Names

    • FLJ33665, MGC10818

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    KH homology domain-containing protein 1
    Names
    KH homology domain containing 1
    Putative KHDC1-like protein

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001251874.4 → NP_001238803.2  KH homology domain-containing protein 1

      Status: VALIDATED

      Source sequence(s)
      AC019205, AL365232

    2. NM_001395215.3 → NP_001382144.2  KH homology domain-containing protein 1

      Status: VALIDATED

      Source sequence(s)
      AC019205, AL365232
      Consensus CDS
      CCDS59027.1

    3. NM_001395216.1 → NP_001382145.1  KH homology domain-containing protein 1

      Status: VALIDATED

      Source sequence(s)
      AC019205, AL365232
      Consensus CDS
      CCDS43480.1
      Conserved Domains (1) summary
      cd12795
      Location:1 → 108
      FILIA_N_like; FILIA-N KH-like domain

    4. NM_030568.5 → NP_085045.3  KH homology domain-containing protein 1

      See identical proteins and their annotated locations for NP_085045.3

      Status: VALIDATED

      Source sequence(s)
      AL365232, BC022080, DA059235, DB473653
      Consensus CDS
      CCDS43480.1
      UniProtKB/Swiss-Prot
      Q4VXA5
      Related
      ENSP00000257765.5, ENST00000257765.10
      Conserved Domains (1) summary
      cd12795
      Location:1 → 108
      FILIA_N_like; FILIA-N KH-like domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      73241314..73310378 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      74417977..74487018 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q4VXA5.1 GenPept UniProtKB/Swiss-Prot:Q4VXA5

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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