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LOC121053189 Sharpr-MPRA regulatory region 12770 [ Homo sapiens (human) ]

Gene ID: 121053189, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121053189
Gene description
Sharpr-MPRA regulatory region 12770
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 22:ReprW, weaker Polycomb repression) and K562 erythroleukemia cells (group: K562 Activating DNase matched - State 8:EnhW, candidate weak enhancer and open chromatin). [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 (98490878..98491172)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (101805837..101806131)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (99412029..99412323)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene Rap1 GTPase-GDP dissociation stimulator 1 Neighboring gene uncharacterized LOC124900919 Neighboring gene ribosomal protein L21 pseudogene 48 Neighboring gene tetraspanin 5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21734 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:99457519-99458032 Neighboring gene Sharpr-MPRA regulatory region 11258 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:99518736-99519334 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21735 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr4:99574420-99575619 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:99579327-99579486 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15578 Neighboring gene uncharacterized LOC112267901 Neighboring gene TSPAN5 divergent transcript Neighboring gene CRISPRi-validated cis-regulatory element chr4.2289 Neighboring gene CRISPRi-validated cis-regulatory element chr4.2290 Neighboring gene mitochondrial import receptor subunit TOM7 homolog

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_074129.1 

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

    Range
    98490878..98491172
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    101805837..101806131
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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