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LOC122861301 Sharpr-MPRA regulatory region 2258 [ Homo sapiens (human) ]

Gene ID: 122861301, updated on 12-Sep-2024

Summary

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Gene symbol
LOC122861301
Gene description
Sharpr-MPRA regulatory region 2258
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 24:Quies, heterochromatin/dead zone). [provided by RefSeq, Oct 2021]
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Genomic context

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See LOC122861301 in Genome Data Viewer
Location:
2q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (223760912..223761206)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (224244084..224244378)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (224625629..224625923)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 12775 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr2:224482816-224483471 Neighboring gene secretogranin II Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:224561972-224563171 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:224563821-224565020 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:224590012-224591211 Neighboring gene MLX pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17172 Neighboring gene adaptor related protein complex 1 subunit sigma 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17173 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17174 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12377 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17175 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12376 Neighboring gene uncharacterized LOC124907988 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:224746345-224746846 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:224746847-224747346 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17176 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17177 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17178 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17179 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17180 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17181 Neighboring gene WD repeat and FYVE domain containing 1 Neighboring gene general transcription factor IIIA pseudogene 3

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_077116.1 

    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    223760912..223761206
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    224244084..224244378
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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