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LOC112935955 Sharpr-MPRA regulatory region 14465 [ Homo sapiens (human) ]

Gene ID: 112935955, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112935955
Gene description
Sharpr-MPRA regulatory region 14465
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 24:Quies, heterochromatin/dead zone). [provided by RefSeq, Aug 2018]
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Genomic context

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See LOC112935955 in Genome Data Viewer
Location:
3p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (61985035..61985329)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (62028392..62028686)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (61970709..61971003)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene protein tyrosine phosphatase receptor type G Neighboring gene uncharacterized LOC124906245 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:61657567-61658404 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:61665901-61666400 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:61671542-61672277 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:61673811-61674444 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:61676017-61676556 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:61677824-61678324 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:61678325-61678825 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:61678925-61679473 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:61680893-61681393 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:61685048-61685943 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:61686839-61687733 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:61690681-61691408 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:61689953-61690680 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:61700687-61701188 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:61701189-61701688 Neighboring gene ribosomal protein L10a pseudogene 6 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr3:61815091-61815694 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr3:61815695-61816299 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:61852378-61852880 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:61852881-61853381 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:61857459-61858243 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:61860549-61861255 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:61932324-61933045 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:62026884-62028083 Neighboring gene RNA, U2 small nuclear 10, pseudogene Neighboring gene inhibitor of DNA binding 2B (pseudogene)

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_061470.1 

    Range
    101..395
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    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    61985035..61985329
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    62028392..62028686
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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