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LOC123477729 Sharpr-MPRA regulatory region 4886 [ Homo sapiens (human) ]

Gene ID: 123477729, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123477729
Gene description
Sharpr-MPRA regulatory region 4886
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 23:Low, low signal proximal to active elements) and K562 erythroleukemia cells (group: K562 Repressive DNase matched - State 8:EnhW, candidate weak enhancer and open chromatin). [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 (38157588..38157882)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (38126660..38126954)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (38159209..38159503)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene TBC1 domain family member 1 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr4:38021983-38023182 Neighboring gene mitochondrial ribosomal protein S33 pseudogene 2 Neighboring gene skeletal muscle cis-regulatory module in TBC1D1 intron Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr4:38055939-38057138 Neighboring gene uncharacterized LOC124900692 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_79330 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:38069109-38069610 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:38069611-38070110 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21421 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21422 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21423 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21424 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_79381 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:38107743-38108418 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:38119811-38120312 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:38129774-38130627 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:38130628-38131480 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15358 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_79448 Neighboring gene uncharacterized LOC124900693 Neighboring gene NANOG hESC enhancer GRCh37_chr4:38162468-38162969 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21427 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21428 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21429 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_79551 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_79567 Neighboring gene uncharacterized LOC105374408 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:38244857-38245358 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:38246135-38246332 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_79588 Neighboring gene uncharacterized LOC124900694 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_79608

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_077532.1 

    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
    38157588..38157882
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    38126660..38126954
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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