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LOC121967067 Sharpr-MPRA regulatory region 13529 [ Homo sapiens (human) ]

Gene ID: 121967067, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121967067
Gene description
Sharpr-MPRA regulatory region 13529
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 both HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 19:H4K20, transcription, primarily H4K20me1, more intronic) and K562 erythroleukemia cells (group: K562 Repressive DNase matched - State 14:Gen5', transcription transition, highly expressed genes towards 5' end). [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 (8693170..8693464)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (8226647..8226941)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (8753229..8753523)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene arginine-glutamic acid dipeptide repeats Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:8562545-8563228 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:8564373-8565281 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:8569526-8570026 Neighboring gene small nucleolar RNA SNORA77 Neighboring gene small nucleolar RNA, C/D box 128 Neighboring gene Sharpr-MPRA regulatory region 8357 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:8658491-8658990 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 105 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 106 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 107 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 197 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 108 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 109 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 198 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:8750738-8751238 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 199 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 200 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:8770382-8770882 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:8781158-8781398 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:8790471-8790970 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:8791953-8792122 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 110 Neighboring gene ribosomal protein L7 pseudogene 11 Neighboring gene ribosomal protein L7 pseudogene 7

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_076207.1 

    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
    8693170..8693464
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    8226647..8226941
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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