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LOC112529902 Sharpr-MPRA regulatory region 10516 [ Homo sapiens (human) ]

Gene ID: 112529902, updated on 17-Sep-2024

Summary

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Gene symbol
LOC112529902
Gene description
Sharpr-MPRA regulatory region 10516
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 HepG2 liver carcinoma cells (group: HepG2 Activating DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, May 2018]
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Genomic context

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See LOC112529902 in Genome Data Viewer
Location:
17q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (28698391..28698685)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (29641175..29641469)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (27025409..27025703)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene SPAG5 antisense RNA 1 Neighboring gene bridge-like lipid transfer protein family member 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:26954912-26955086 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8346 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8347 Neighboring gene stromal cell derived factor 2 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr17:26988611-26989810 Neighboring gene ribosomal protein S12 pseudogene 28 Neighboring gene SPT6 homolog, histone chaperone and transcription elongation factor Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr17:27037571-27038346 and GRCh37_chr17:27038347-27039122 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11936 Neighboring gene protein interacting with cyclin A1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8349 Neighboring gene RAB34, member RAS oncogene family

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_056892.1 

    Range
    101..395
    Download
    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    28698391..28698685
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    29641175..29641469
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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