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LOC122889060 Sharpr-MPRA regulatory region 2436 [ Homo sapiens (human) ]

Gene ID: 122889060, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122889060
Gene description
Sharpr-MPRA regulatory region 2436
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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Location:
3p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (31346617..31346911)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (31349088..31349382)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (31388109..31388403)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124909359 Neighboring gene H3 histone pseudogene 11 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:31398204-31399403 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:31418321-31419520 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19628 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:31453982-31455181 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14159 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:31490161-31490339 Neighboring gene THRAP3 pseudogene 1 Neighboring gene Sharpr-MPRA regulatory region 4459 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_69494 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:31568343-31568843 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14160 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19629 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14161 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14162 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14163 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19630 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:31576589-31577090 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:31577091-31577590 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_69540 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_69549 Neighboring gene STT3 oligosaccharyltransferase complex catalytic subunit B

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_077192.1 

    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    31346617..31346911
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    31349088..31349382
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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