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ERVK3-1 endogenous retrovirus group K3 member 1 [ Homo sapiens (human) ]

Gene ID: 105372481, updated on 17-Sep-2024

Summary

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Official Symbol
ERVK3-1provided by HGNC
Official Full Name
endogenous retrovirus group K3 member 1provided by HGNC
Primary source
HGNC:HGNC:30466
See related
Ensembl:ENSG00000142396 AllianceGenome:HGNC:30466
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
Expression
Ubiquitous expression in bone marrow (RPKM 14.4), lymph node (RPKM 13.5) and 25 other tissues See more
Orthologs
all
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Genomic context

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See ERVK3-1 in Genome Data Viewer
Location:
19q13.43
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (58305377..58316812)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (61401792..61413227)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (58816743..58828178)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene zinc finger protein 544 Neighboring gene ZNF8 divergent transcript Neighboring gene ZNF8-ERVK3-1 readthrough (NMD candidate) Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15181 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15182 Neighboring gene zinc finger protein 8 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15183 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:58816949-58817449 Neighboring gene Sharpr-MPRA regulatory region 7439 Neighboring gene uncharacterized LOC105372480 Neighboring gene zinc finger protein 470 pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:58838245-58838987 Neighboring gene zinc finger and SCAN domain containing 22 Neighboring gene microRNA 6806

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Comprehensive Analysis of HERV Transcriptome in HIV+ Cells: Absence of HML2 Activation and General Downregulation of Individual HERV Loci. Grandi N, et al. Viruses, 2020 Apr 23. PMID 32340287, Free PMC Article
  2. Comprehensive Characterization of the Human Endogenous Retrovirus HERV-K(HML-6) Group: Overview of Structure, Phylogeny, and Contribution to the Human Genome. Pisano MP, et al. J Virol, 2019 Aug 15. PMID 31167914, Free PMC Article
  3. Comprehensive analysis of human endogenous retrovirus transcriptional activity in human tissues with a retrovirus-specific microarray. Seifarth W, et al. J Virol, 2005 Jan. PMID 15596828, Free PMC Article
  4. Expression analyses of human endogenous retroviruses (HERVs): tissue-specific and developmental stage-dependent expression of HERVs. Okahara G, et al. Genomics, 2004 Dec. PMID 15533715
  5. A revised nomenclature for transcribed human endogenous retroviral loci. Mayer J, et al. Mob DNA, 2011 May 4. PMID 21542922, Free PMC Article

See all (10) citations in PubMed

GeneRIFs: Gene References Into Functions

Phenotypes

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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)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Potential readthrough

Included gene: ZNF8

Readthrough ZNF8-ERVK3-1

Readthrough gene: ZNF8-ERVK3-1, Included gene: ZNF8

Homology

Clone Names

  • FLJ30306, MGC16737, DKFZp313J2310

General protein information

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Preferred Names
endogenous retrovirus group K3 member 1
Names
HERV-K(HML6-1)

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_001396080.1 → NP_001383009.1  endogenous retrovirus group K3 member 1

    Status: VALIDATED

    Source sequence(s)
    AC010642, AC020915
    Consensus CDS
    CCDS92702.1
    UniProtKB/TrEMBL
    A0A0U1RQV1, B3KNS4
    Related
    ENSP00000489018.1, ENST00000413518.6
    Conserved Domains (1) summary
    pfam15695
    Location:46 → 108
    HERV-K_REC; Rec (regulator of expression encoded by corf) of HERV-K-113

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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    58305377..58316812
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    61401792..61413227
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NR_144445.1: Suppressed sequence

    Description
    NR_144445.1: This RefSeq was removed because it is now thought that this gene does encode a protein.
Nucleotide Protein
Heading Accession and Version

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