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LOC121331318 Sharpr-MPRA regulatory region 3538 [ Homo sapiens (human) ]

Gene ID: 121331318, updated on 12-Sep-2024

Summary

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Gene symbol
LOC121331318
Gene description
Sharpr-MPRA regulatory region 3538
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 DNase matched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin) and K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 13:Ctcf, distal CTCF/candidate insulator without open chromatin). [provided by RefSeq, May 2021]
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Genomic context

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See LOC121331318 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 (4339389..4339683)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (4344025..4344319)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (4339389..4339683)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene GLIS family zinc finger 3 Neighboring gene uncharacterized LOC105375964 Neighboring gene uncharacterized LOC124902111 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr9:4136663-4137862 Neighboring gene GLIS3 intron CAGE-defined low expression enhancer Neighboring gene NANOG hESC enhancer GRCh37_chr9:4237960-4238479 Neighboring gene Sharpr-MPRA regulatory region 13837 Neighboring gene Sharpr-MPRA regulatory region 3194 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:4329035-4330234 Neighboring gene GLIS3 antisense RNA 2 Neighboring gene RNA, U6 small nuclear 694, pseudogene Neighboring gene Sharpr-MPRA regulatory region 14111 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28143 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28144 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28145 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19741 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28146 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19742 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28147 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr9:4514651-4515591 Neighboring gene solute carrier family 1 member 1

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_074342.1 

    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
    4339389..4339683
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    4344025..4344319
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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