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LOC124629334 Sharpr-MPRA regulatory region 2351 [ Homo sapiens (human) ]

Gene ID: 124629334, updated on 12-Sep-2024

Summary

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Gene symbol
LOC124629334
Gene description
Sharpr-MPRA regulatory region 2351
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, Mar 2022]
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Genomic context

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See LOC124629334 in Genome Data Viewer
Location:
12p
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (24911455..24911749)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (24781512..24781806)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (25064389..25064683)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105369699 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6102 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6103 Neighboring gene branched chain amino acid transaminase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4291 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6104 Neighboring gene uncharacterized LOC124902898 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:25055463-25055964 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr12:25057459-25058181 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:25078354-25078971 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:25080207-25080822 Neighboring gene defender against cell death 1 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6105 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4292 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6106 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6107 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6108 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6109 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6110 Neighboring gene uncharacterized LOC107984475

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_079613.1 

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

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    24911455..24911749
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    24781512..24781806
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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