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LOC125424404 Sharpr-MPRA regulatory region 3066 [ Homo sapiens (human) ]

Gene ID: 125424404, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125424404
Gene description
Sharpr-MPRA regulatory region 3066
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 DNase matched - State 8:EnhW, candidate weak enhancer and open chromatin) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 14:Gen5', transcription transition, highly expressed genes towards 5' end). [provided by RefSeq, Jun 2022]
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Genomic context

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See LOC125424404 in Genome Data Viewer
Location:
22q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (26550303..26550597)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (27012670..27012964)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene MED14-independent group 3 enhancer GRCh37_chr22:26889254-26890453 Neighboring gene SRR1 domain containing Neighboring gene tuftelin interacting protein 11 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13570 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr22:26902046-26903245 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18792 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:26908724-26909261 Neighboring gene TFIP11 divergent transcript Neighboring gene tyrosylprotein sulfotransferase 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:26937311-26937812 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:26951753-26952722 Neighboring gene microRNA 548j Neighboring gene high mobility group box 1 pseudogene 10

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

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_081139.1 

    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_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    26550303..26550597
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    27012670..27012964
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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