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LOC124421502 Sharpr-MPRA regulatory region 5134 [ Homo sapiens (human) ]

Gene ID: 124421502, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124421502
Gene description
Sharpr-MPRA regulatory region 5134
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 matched - State 8:EnhW, candidate weak enhancer and open chromatin). [provided by RefSeq, Mar 2022]
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Genomic context

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Location:
11p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (17405642..17405936)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (17503236..17503530)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (17427189..17427483)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105376576 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:17373285-17373886 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:17373887-17374488 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4488 Neighboring gene natural killer cell cytotoxicity receptor 3 ligand 1 Neighboring gene MPRA-validated peak1220 silencer Neighboring gene NANOG hESC enhancer GRCh37_chr11:17397887-17398425 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr11:17399732-17400931 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:17408081-17408734 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:17408735-17409388 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3185 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3186 Neighboring gene potassium inwardly rectifying channel subfamily J member 11 Neighboring gene ATP binding cassette subfamily C member 8 Neighboring gene VISTA enhancer hs1977 Neighboring gene succinate dehydrogenase complex subunit C pseudogene 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:17497048-17497604 Neighboring gene uncharacterized LOC124902641

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_079191.1 

    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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    17405642..17405936
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    17503236..17503530
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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