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LOC123956135 Sharpr-MPRA regulatory region 13548 [ Homo sapiens (human) ]

Gene ID: 123956135, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123956135
Gene description
Sharpr-MPRA regulatory region 13548
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 non-DNase unmatched - State 23:Low, low signal proximal to active elements). [provided by RefSeq, Jan 2022]
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Genomic context

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See LOC123956135 in Genome Data Viewer
Location:
7p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (38182487..38182781)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (38323420..38323714)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (38222089..38222383)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18107 Neighboring gene Sharpr-MPRA regulatory region 10360 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:37987061-37987582 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:37987583-37988102 Neighboring gene ependymin related 1 Neighboring gene Sharpr-MPRA regulatory region 4879 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:38026488-38027240 Neighboring gene MPRA-validated peak6491 silencer Neighboring gene uncharacterized LOC105375236 Neighboring gene MPRA-validated peak6492 silencer Neighboring gene MPRA-validated peak6493 silencer Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:38110217-38110835 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18108 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr7:38214547-38215746 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25864 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18109 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25865 Neighboring gene STARD3 N-terminal like Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25866 Neighboring gene MPRA-validated peak6494 silencer Neighboring gene T cell receptor gamma constant 2 Neighboring gene T cell receptor gamma locus Neighboring gene T cell receptor gamma joining 2

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_078330.1 

    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
    38182487..38182781
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    38323420..38323714
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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