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LOC113839549 Sharpr-MPRA regulatory region 3537 [ Homo sapiens (human) ]

Gene ID: 113839549, updated on 10-Dec-2024

Summary

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Gene symbol
LOC113839549
Gene description
Sharpr-MPRA regulatory region 3537
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 K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin), with weaker activity in HepG2 liver carcinoma cells (group: HepG2 Activating DNase matched - State 12:CtcfO). [provided by RefSeq, Jun 2021]
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Genomic context

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See LOC113839549 in Genome Data Viewer
Location:
9p
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (35193812..35194106)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (35212989..35213283)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (35193809..35194103)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902147 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:35157812-35158365 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19863 Neighboring gene zinc finger protein 492 pseudogene Neighboring gene unc-13 homolog B Neighboring gene MPRA-validated peak7230 silencer Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr9:35327315-35328514 Neighboring gene Sharpr-MPRA regulatory region 14419 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr9:35373268-35373820 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:35397379-35398578 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr9:35403221-35404420 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:35405745-35406290 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr9:35406291-35406836 Neighboring gene ATPase phospholipid transporting 8B5, pseudogene Neighboring gene zinc finger AN1-type containing 6 pseudogene 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:35481926-35482160 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19864 Neighboring gene uncharacterized LOC105376026 Neighboring gene RUN and SH3 domain containing 2

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_063159.1 

    Range
    101..395
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    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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
    35193812..35194106
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    35212989..35213283
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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