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LOC124629356 Sharpr-MPRA regulatory region 12282 [ Homo sapiens (human) ]

Gene ID: 124629356, updated on 12-Sep-2024

Summary

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Gene symbol
LOC124629356
Gene description
Sharpr-MPRA regulatory region 12282
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 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Mar 2022]
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Genomic context

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See LOC124629356 in Genome Data Viewer
Location:
12q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (50550526..50550820)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (50513635..50513929)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (50944309..50944603)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene La ribonucleoprotein 4 Neighboring gene small nucleolar RNA, C/D box 133 Neighboring gene uncharacterized LOC124903127 Neighboring gene MPRA-validated peak1730 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4452 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6353 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4453 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6354 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6355 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6356 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:50923514-50924014 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:50924015-50924515 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6357 Neighboring gene fragile site, folic acid type, rare, fra(12)(q13.1) Neighboring gene disco interacting protein 2 homolog B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6358 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6359 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6360 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:51005279-51005780 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:51005781-51006280 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6361 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6362 Neighboring gene RNA, U6 small nuclear 769, pseudogene Neighboring gene RNA, U6 small nuclear 238, pseudogene

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_079726.1 

    Range
    101..395
    Download
    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
    50550526..50550820
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    50513635..50513929
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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