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LOC121967070 Sharpr-MPRA regulatory region 8161 [ Homo sapiens (human) ]

Gene ID: 121967070, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121967070
Gene description
Sharpr-MPRA regulatory region 8161
Gene type
biological region
Feature type(s)
regulatory: 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 repressive element 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 Repressive non-DNase unmatched - State 10:DNaseD, primarily Duke DNase, candidate regulatory elements in more likely repressive locations) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 20:ReprD, Polycomb repression w. Duke DNase/promoter and conservation enriched). [provided by RefSeq, Jul 2021]
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Genomic context

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Location:
1p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (9792431..9792725)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (9335217..9335511)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (9852489..9852783)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit delta Neighboring gene uncharacterized LOC124903839 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:9778914-9780113 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:9780296-9781272 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:9781273-9782247 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:9785121-9785329 Neighboring gene calsyntenin 1 Neighboring gene MPRA-validated peak58 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:9846382-9846882 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:9848516-9849304 Neighboring gene mitotic spindle organizing protein 1 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 232 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:9883897-9884613 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 137 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:9895719-9896320 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:9896321-9896920 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:9902151-9902692 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:9902693-9903232 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:9903774-9904313 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:9908375-9908876 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 138 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 139 Neighboring gene uncharacterized LOC105376717 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:9911316-9912116 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:9919701-9920595 Neighboring gene catenin beta interacting protein 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:9931412-9932340 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:9932341-9933268 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 236 Neighboring gene uncharacterized LOC124903838 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 140

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_076210.1 

    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    9792431..9792725
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    9335217..9335511
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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