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LOC124416856 Sharpr-MPRA regulatory region 907 [ Homo sapiens (human) ]

Gene ID: 124416856, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124416856
Gene description
Sharpr-MPRA regulatory region 907
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, Feb 2022]
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Genomic context

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See LOC124416856 in Genome Data Viewer
Location:
10q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (80462753..80463047)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (81331851..81332145)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (82222509..82222803)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene MPRA-validated peak1026 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr10:82123032-82123216 Neighboring gene DPY30 domain containing 1 Neighboring gene DPY30 domain containing 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:82163430-82163602 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2545 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:82168661-82169254 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:82170101-82170600 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr10:82177040-82177582 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3654 Neighboring gene peroxiredoxin like 2A Neighboring gene Sharpr-MPRA regulatory region 12974 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3655 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:82214375-82214892 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3657 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3658 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3659 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:82224527-82225098 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:82225099-82225670 Neighboring gene Sharpr-MPRA regulatory region 4556 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3660 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3661 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3662 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3663 Neighboring gene tetraspanin 14 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2547 Neighboring gene Sharpr-MPRA regulatory region 2609 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:82257110-82258073 Neighboring gene Sharpr-MPRA regulatory region 10623 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3664 Neighboring gene uncharacterized LOC124902471 Neighboring gene TSPAN14 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3665 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2548 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3666 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3667 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3668 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3669 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3670 Neighboring gene SH2 domain containing 4B Neighboring gene MPRA-validated peak1027 silencer Neighboring gene uncharacterized LOC105378387

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_079078.1 

    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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    80462753..80463047
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    81331851..81332145
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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