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LOC121009641 Sharpr-MPRA regulatory region 2966 [ Homo sapiens (human) ]

Gene ID: 121009641, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121009641
Gene description
Sharpr-MPRA regulatory region 2966
Gene type
biological region
Feature type(s)
regulatory: enhancer, silencer
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 HepG2 liver carcinoma cells (group: HepG2 Activating DNase matched - State 8:EnhW, candidate weak enhancer and open chromatin). This region also displayed repressive activity by Sharpr-MPRA in K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 14:Gen5', transcription transition, highly expressed genes towards 5' end). [provided by RefSeq, Mar 2021]
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Genomic context

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See LOC121009641 in Genome Data Viewer
Location:
3p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (12991929..12992223)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (12993449..12993743)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (13033429..13033723)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124909346 Neighboring gene microtubule affinity regulating kinase 4 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14071 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19455 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:12917663-12918176 Neighboring gene uncharacterized LOC105376956 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:12918177-12918689 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19456 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19457 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19458 Neighboring gene long intergenic non-protein coding RNA 2022 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:12969075-12969574 Neighboring gene IQ motif and Sec7 domain ArfGEF 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:12977492-12978056 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:12985145-12985725 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:12985857-12986542 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:12986543-12987228 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:12988583-12989084 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14073 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19459 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:12999703-13000203 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19460 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19461 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14074 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14075 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19462 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:13020550-13021749 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14076 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:13035123-13035681 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14078 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:13036241-13036799 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19463 Neighboring gene Sharpr-MPRA regulatory region 4746 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19464 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19465 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19466 Neighboring gene uncharacterized LOC124906214 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19467 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:13055383-13055884 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:13055885-13056384 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:13056642-13057410 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:13057411-13058178 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19470 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:13058755-13059554 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:13059555-13060352 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:13060353-13061150 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19472 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19471 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19473 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19474 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14080 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:13068313-13068814 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:13068815-13069314 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:13072358-13073358 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:13073359-13074357 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:13076449-13076949 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19475 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19476 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:13083243-13083838 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19477 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19478 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:13088478-13088996 Neighboring gene ribosomal protein L39 pseudogene 17

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_074038.1 

    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    12991929..12992223
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    12993449..12993743
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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