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LOC124403931 Sharpr-MPRA regulatory region 6088 [ Homo sapiens (human) ]

Gene ID: 124403931, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124403931
Gene description
Sharpr-MPRA regulatory region 6088
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 DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region). [provided by RefSeq, Feb 2022]
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Genomic context

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Location:
10p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (30553860..30554154)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (30584855..30585149)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (30842789..30843083)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2267 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3213 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3214 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:30724077-30724614 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:30724615-30725150 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3216 Neighboring gene mitogen-activated protein kinase kinase kinase 8 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3217 Neighboring gene heterogeneous nuclear ribonucleoprotein A1 pseudogene 32 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3218 Neighboring gene uncharacterized LOC105376478 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3219 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:30827242-30827742 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:30841700-30842312 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:30847997-30848576 Neighboring gene RNA, 7SL, cytoplasmic 63, pseudogene Neighboring gene NANOG hESC enhancer GRCh37_chr10:30862856-30863438 Neighboring gene uncharacterized LOC105376479

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_079011.1 

    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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    30553860..30554154
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    30584855..30585149
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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Other Literature Sources
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