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LOC123956278 Sharpr-MPRA regulatory region 10004 [ Homo sapiens (human) ]

Gene ID: 123956278, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123956278
Gene description
Sharpr-MPRA regulatory region 10004
Gene type
biological region
Feature type(s)
regulatory: 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. It was validated as a functional repressive element 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 Repressive DNase matched - State 4:PromP, inactive/poised promoter, highly conserved). [provided by RefSeq, Jan 2022]
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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 (155598815..155599109)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (156779399..156779693)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (155391509..155391803)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chr7:155262299-155262494 Neighboring gene VISTA enhancer hs1418 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr7:155274926-155276125 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:155277075-155277575 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:155282581-155283314 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18847 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:155286713-155287262 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:155290079-155290782 Neighboring gene engrailed homeobox 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18848 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr7:155301523-155302370 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr7:155302371-155303216 Neighboring gene canopy FGF signaling regulator 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:155334782-155335582 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:155340869-155341370 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26898 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:155382158-155382978 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:155386984-155387730 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:155436294-155437248 Neighboring gene RBM33 divergent transcript Neighboring gene RNA binding motif protein 33 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26899 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:155520719-155521219 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr7:155534138-155535337 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26901 Neighboring gene VISTA enhancer hs1268 Neighboring gene Sharpr-MPRA regulatory region 9615 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26902 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:155561116-155561309 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr7:155567610-155568809 Neighboring gene Sharpr-MPRA regulatory region 3765

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_078469.1 

    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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    155598815..155599109
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    156779399..156779693
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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