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LOC123924888 Sharpr-MPRA regulatory region 3173 [ Homo sapiens (human) ]

Gene ID: 123924888, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123924888
Gene description
Sharpr-MPRA regulatory region 3173
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 K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 14:Gen5', transcription transition, highly expressed genes towards 5' end). [provided by RefSeq, Jan 2022]
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Genomic context

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Location:
7p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (1454513..1454807)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (1566646..1566940)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (1494149..1494443)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene hESC enhancers GRCh37_chr7:1199449-1199961 and GRCh37_chr7:1199962-1200475 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:1200476-1200988 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:1209085-1210060 Neighboring gene ZFAND2A divergent transcript Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:1210061-1211034 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17848 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr7:1220431-1221630 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:1232959-1233460 Neighboring gene Sharpr-MPRA regulatory region 5475 Neighboring gene VISTA enhancer hs293 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:1273513-1274057 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:1274230-1275058 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:1281290-1282188 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:1288405-1288950 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:1294047-1294547 Neighboring gene MPRA-validated peak6338 silencer Neighboring gene UNC homeobox Neighboring gene MS31A repeat instability region Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:1329612-1330486 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:1341047-1341548 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:1360639-1361139 Neighboring gene MPRA-validated peak6340 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17849 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17850 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:1409793-1410317 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17851 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:1458534-1459206 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:1459207-1459877 Neighboring gene Sharpr-MPRA regulatory region 11952 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:1468179-1468734 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:1486489-1486993 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:1491449-1492000 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:1497060-1497782 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:1497783-1498505 Neighboring gene MICAL like 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17852 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:1499929-1500480 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:1500481-1501032 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:1505291-1505986 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:1505987-1506682 Neighboring gene MICALL2 divergent transcript Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:1509467-1510162 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17853 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:1533403-1533903 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17854 Neighboring gene integrator complex subunit 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_078280.1 

    Range
    101..395
    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
    1454513..1454807
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    1566646..1566940
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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