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LOC121740699 Sharpr-MPRA regulatory region 2521 [ Homo sapiens (human) ]

Gene ID: 121740699, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121740699
Gene description
Sharpr-MPRA regulatory region 2521
Gene type
biological region
Feature type(s)
regulatory: enhancer, silencer
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. A subregion was validated as a functional enhancer by Sharpr-MPRA (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). An overlapping accessible chromatin subregion was used in a lentiviral ReSE (repressive ability of silencer elements) screen that assays for cell survival based on transcriptional repression of an apoptosis-inducing fusion protein. That subregion was identified as a functional silencer in HepG2 cells. [provided by RefSeq, Jun 2023]
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Genomic context

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Location:
7q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (130899790..130900233)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (132217299..132217742)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (130584549..130584843)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene MED14-independent group 3 enhancer GRCh37_chr7:130571236-130572435 Neighboring gene long intergenic non-protein coding RNA, p53 induced transcript Neighboring gene microRNA 29b-1 Neighboring gene microRNA 29a Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr7:130588151-130589350 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancers GRCh37_chr7:130595421-130595954 and GRCh37_chr7:130595955-130596488 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr7:130597482-130598681 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18651 Neighboring gene long intergenic non-protein coding RNA 513 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:130635654-130635822 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18652 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26659 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr7:130644756-130645955 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26662 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26663 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26664 Neighboring gene Sharpr-MPRA regulatory region 13565 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26665 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26666 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26667 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 7:130729465 Neighboring gene RNA, U6 small nuclear 1010, pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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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)

General gene information

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Other Names

  • ReSE screen-validated silencer GRCh37_chr7:130584789-130584992

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_075761.2 

    Range
    101..544
    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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    130899790..130900233
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    132217299..132217742
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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