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LOC111188161 B3GALT5 ERV-L LTR promoter [ Homo sapiens (human) ]

Gene ID: 111188161, updated on 10-Oct-2023

Summary

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Gene symbol
LOC111188161
Gene description
B3GALT5 ERV-L LTR promoter
Gene type
biological region
Feature type(s)
mobile_element
protein_bind
regulatory: promoter, transcriptional_cis_regulatory_region
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This region represents a endogenous retroviral long terminal repeat that functions as an alternate promoter of the beta-1,3-galactosyltransferase 5 (B3GALT5) gene. This promoter is regulated by HNF1 and caudal type homeobox proteins. Treatment with a antagonist of DNA methylation (5-Aza-2'-deoxycytidine) decreased promoter activity, suggesting that activity of this region may be stimulated by DNA methylation. [provided by RefSeq, Sep 2017]
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Genomic context

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Location:
chromosome: 21
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (39657153..39657674)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (38041610..38042127)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (41029080..41029601)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:40899605-40900600 Neighboring gene H3K27ac hESC enhancer GRCh37_chr21:40907492-40908386 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:40909281-40910174 Neighboring gene JCAD pseudogene 1 Neighboring gene NANOG hESC enhancer GRCh37_chr21:40923594-40924095 Neighboring gene NANOG hESC enhancer GRCh37_chr21:40931347-40931936 Neighboring gene B3GALT5 antisense RNA 1 Neighboring gene beta-1,3-galactosyltransferase 5 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr21:41005119-41006318 Neighboring gene H3K27ac hESC enhancer GRCh37_chr21:41012219-41012718 Neighboring gene H3K27ac hESC enhancer GRCh37_chr21:41011717-41012218 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:41015167-41015667 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:41020756-41021302 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:41044997-41045632 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:41079003-41079814 Neighboring gene uncharacterized LOC107985499 Neighboring gene immunoglobulin superfamily member 5 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr21:41150548-41151747 Neighboring gene uncharacterized LOC107985500

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. Control of Glycosylation-Related Genes by DNA Methylation: the Intriguing Case of the B3GALT5 Gene and Its Distinct Promoters. Trinchera M, et al. Biology (Basel), 2014 Aug 4. PMID 25256425, Free PMC Article
  2. Transcriptional control of the B3GALT5 gene by a retroviral promoter and methylation of distant regulatory elements. Zulueta A, et al. FASEB J, 2014 Feb. PMID 24128890
  3. Comparative analysis of retroviral and native promoters driving expression of beta1,3-galactosyltransferase beta3Gal-T5 in human and mouse tissues. Mare L, et al. J Biol Chem, 2007 Jan 5. PMID 17107959
  4. An endogenous retroviral long terminal repeat is the dominant promoter for human beta1,3-galactosyltransferase 5 in the colon. Dunn CA, et al. Proc Natl Acad Sci U S A, 2003 Oct 28. PMID 14534330, Free PMC Article
  5. Endogenous retrovirus long terminal repeats as ready-to-use mobile promoters: the case of primate beta3GAL-T5. Dunn CA, et al. Gene, 2005 Dec 30. PMID 16112824

See all (8) 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 Variation Viewer (GRCh37.p13)

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.

Genomic

  1. NG_055563.1 

    Range
    101..622
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000021.9 Reference GRCh38.p14 Primary Assembly

    Range
    39657153..39657674
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060945.1 Alternate T2T-CHM13v2.0

    Range
    38041610..38042127
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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