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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

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