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LOC124310652 Sharpr-MPRA regulatory region 9989 [ Homo sapiens (human) ]

Gene ID: 124310652, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124310652
Gene description
Sharpr-MPRA regulatory region 9989
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 HepG2 liver carcinoma cells (group: HepG2 Repressive DNase matched - State 4:PromP, inactive/poised promoter, highly conserved). [provided by RefSeq, Feb 2022]
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Genomic context

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Location:
9q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (128204010..128204304)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (140411090..140411384)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (130966289..130966583)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20327 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130916023-130916694 Neighboring gene MPRA-validated peak7335 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr9:130920069-130920264 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr9:130921445-130922398 and GRCh37_chr9:130922399-130923352 Neighboring gene lipocalin 2 Neighboring gene bublin coiled coil protein Neighboring gene CDKN1A interacting zinc finger protein 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130940513-130941204 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:130953834-130954001 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:130954889-130955404 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:130955405-130955919 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29074 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20331 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130966872-130967444 Neighboring gene dynamin 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr9:130980103-130981059 and GRCh37_chr9:130981060-130982015 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:130992962-130993210 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130995155-130995654 Neighboring gene microRNA 199b Neighboring gene microRNA 3154

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_078933.1 

    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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    128204010..128204304
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    140411090..140411384
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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