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LOC123477720 Sharpr-MPRA regulatory region 5841 [ Homo sapiens (human) ]

Gene ID: 123477720, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123477720
Gene description
Sharpr-MPRA regulatory region 5841
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 K562 erythroleukemia cells (group: K562 Repressive DNase matched - State 23:Low, low signal proximal to active elements). [provided by RefSeq, Nov 2021]
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Genomic context

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Location:
4p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (26579107..26579401)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (26564184..26564478)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (26580729..26581023)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene recombination signal binding protein for immunoglobulin kappa J region Neighboring gene uncharacterized LOC105374542 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21393 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15334 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:26301633-26302396 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21394 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21395 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15335 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21396 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15336 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15337 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr4:26323092-26324013 Neighboring gene Sharpr-MPRA regulatory region 12863 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:26353747-26354248 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:26354249-26354748 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21397 Neighboring gene Sharpr-MPRA regulatory region 2944 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr4:26407341-26408540 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:26454493-26455031 Neighboring gene cholecystokinin A receptor Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr4:26569763-26570962 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21398 Neighboring gene TBC1 domain family member 19 Neighboring gene Sharpr-MPRA regulatory region 1278 Neighboring gene small nucleolar RNA SNORD74 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21399 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21400 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15338 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15339 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21401 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15340 Neighboring gene STIM2 antisense RNA 1

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_077524.1 

    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
    26579107..26579401
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    26564184..26564478
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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