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LOC132088953 Neanderthal introgressed variant-containing enhancer experimental_69363 [ Homo sapiens (human) ]

Gene ID: 132088953, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132088953
Gene description
Neanderthal introgressed variant-containing enhancer experimental_69363
Gene type
biological region
Feature type(s)
regulatory: enhancer
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic region contains a Neanderthal adaptively introgressed genetic variant, and was validated as an enhancer by massively parallel reporter assays (MPRAs) in K562 erythroleukemia cells, with activity observed for both the introgressed and non-introgressed 3:30312369 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132088953 in Genome Data Viewer
Location:
chromosome: 3
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (30270793..30270962)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (30273286..30273455)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (30312284..30312453)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene RNA binding motif single stranded interacting protein 3 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:30014055-30014647 Neighboring gene RBMS3 antisense RNA 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:30100685-30101217 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_69254 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:30125981-30126860 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:30126861-30127738 Neighboring gene uncharacterized LOC124906224 Neighboring gene uncharacterized LOC124909358 Neighboring gene small nucleolar RNA U3 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:30383595-30384794 Neighboring gene GATA motif-containing MPRA enhancer 299 Neighboring gene uncharacterized LOC101927995 Neighboring gene Sharpr-MPRA regulatory region 15230 Neighboring gene uncharacterized LOC105377013 Neighboring gene Sharpr-MPRA regulatory region 9798

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. Detection of Neanderthal Adaptively Introgressed Genetic Variants That Modulate Reporter Gene Expression in Human Immune Cells. Jagoda E, et al. Mol Biol Evol, 2022 Jan 7. PMID 34662402, Free PMC Article

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_229512.1 

    Range
    101..270
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    30270793..30270962
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    30273286..30273455
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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