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LOC121366036 Sharpr-MPRA regulatory region 6441 [ Homo sapiens (human) ]

Gene ID: 121366036, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121366036
Gene description
Sharpr-MPRA regulatory region 6441
Gene type
biological region
Feature type(s)
regulatory: enhancer
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 enhancer 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 Activating non-DNase unmatched - State 23:Low, low signal proximal to active elements) and K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 7:EnhWF, candidate poised/weak enhancer, flanking open chromatin of candidate enhancers). [provided by RefSeq, May 2021]
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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 (137632817..137633111)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (149884499..149884793)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (140527269..140527563)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902318 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20633 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20634 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20635 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29355 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20636 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:140513865-140514583 Neighboring gene ARRDC1 antisense RNA 1 Neighboring gene arrestin domain containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29356 Neighboring gene euchromatic histone lysine methyltransferase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29357 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140558803-140559307 Neighboring gene SET pseudogene 5 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140559363-140560044 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29358 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29359 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140569123-140569639 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr9:140573165-140573881 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140574605-140575206 Neighboring gene uncharacterized LOC124902319 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140575207-140575806 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140576860-140577836

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_074386.1 

    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
    137632817..137633111
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    149884499..149884793
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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