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LOC121053180 Sharpr-MPRA regulatory region 7030 [ Homo sapiens (human) ]

Gene ID: 121053180, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121053180
Gene description
Sharpr-MPRA regulatory region 7030
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 sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. It was validated as a functional enhancer by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in both HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 24:Quies, heterochromatin/dead zone) and K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 23:Low, low signal proximal to active elements). [provided by RefSeq, Apr 2021]
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Genomic context

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Location:
4q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (55768383..55768677)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (59256560..59256854)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (56634549..56634843)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15443 Neighboring gene neuromedin U Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr4:56501035-56501786 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr4:56501787-56502538 Neighboring gene uncharacterized LOC105377660 Neighboring gene CRISPRi-validated cis-regulatory element chr4.1623 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:56573715-56574216 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:56574217-56574716 Neighboring gene CRISPRi-validated cis-regulatory element chr4.1625 Neighboring gene CRISPRi-validated cis-regulatory element chr4.1626 Neighboring gene CRISPRi-validated cis-regulatory element chr4.1627 Neighboring gene CRISPRi-validated cis-regulatory element chr4.1628 Neighboring gene RNA, U6 small nuclear 276, pseudogene Neighboring gene uncharacterized LOC105377661 Neighboring gene exocyst complex component 1 like

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. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Ernst J, et al. Nat Biotechnol, 2016 Nov. PMID 27701403, 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_074120.1 

    Range
    101..395
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    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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    55768383..55768677
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NT_187541.1 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    94572..94866
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    59256560..59256854
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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