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LOC122056855 Sharpr-MPRA regulatory region 12667 [ Homo sapiens (human) ]

Gene ID: 122056855, updated on 12-Sep-2024

Summary

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Gene symbol
LOC122056855
Gene description
Sharpr-MPRA regulatory region 12667
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 6:EnhF, candidate strong enhancer, flanking open chromatin). [provided by RefSeq, Jul 2021]
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Genomic context

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See LOC122056855 in Genome Data Viewer
Location:
1p
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (44723437..44723731)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (44594380..44594674)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (45189109..45189403)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene transmembrane protein 53 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:45139597-45140098 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 813 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 814 Neighboring gene small nucleolar RNA, C/D box 145 Neighboring gene armadillo like helical domain containing 1 Neighboring gene uncharacterized LOC105378690 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 815 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 816 Neighboring gene RNA, U5F small nuclear 1 Neighboring gene Sharpr-MPRA regulatory region 12642 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:45200330-45200889 Neighboring gene RNA, U5D small nuclear 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 943 Neighboring gene kinesin family member 2C Neighboring gene ATAC-STARR-seq lymphoblastoid active region 944 Neighboring gene small nucleolar RNA, C/D box 160

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_076311.1 

    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    44723437..44723731
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    44594380..44594674
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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