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LOC122094890 Sharpr-MPRA regulatory region 14885 [ Homo sapiens (human) ]

Gene ID: 122094890, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122094890
Gene description
Sharpr-MPRA regulatory region 14885
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 HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 24:Quies, heterochromatin/dead zone). [provided by RefSeq, Jul 2021]
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Genomic context

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Location:
1p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (101371173..101371467)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (101220600..101220894)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (101836729..101837023)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1398 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1399 Neighboring gene uncharacterized LOC102723784 Neighboring gene Sharpr-MPRA regulatory region 6134 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1400 Neighboring gene peptidylprolyl isomerase A pseudogene 7 Neighboring gene long intergenic non-protein coding RNA 1307 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1401 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1125 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1402 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1403 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1404 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1405 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1407 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1406 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1408 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1409 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1410 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:101918390-101919589 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1126 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1411 Neighboring gene long intergenic non-protein coding RNA 1709 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:102129620-102130819 Neighboring gene RNA, U6 small nuclear 965, pseudogene Neighboring gene ribosomal protein SA pseudogene 19

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_076404.1 

    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    101371173..101371467
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    101220600..101220894
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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