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LOC122861285 Sharpr-MPRA regulatory region 2767 [ Homo sapiens (human) ]

Gene ID: 122861285, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122861285
Gene description
Sharpr-MPRA regulatory region 2767
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 DNase matched - State 5:Enh, candidate strong enhancer, open chromatin) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 23:Low, low signal proximal to active elements). [provided by RefSeq, Oct 2021]
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Genomic context

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See LOC122861285 in Genome Data Viewer
Location:
2q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (207970165..207970459)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (208444416..208444710)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (208834889..208835183)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene cyclin Y like 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12284 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:208631909-208632465 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:208632466-208633023 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12285 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12286 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12287 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17045 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:208635695-208636515 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:208636987-208637462 Neighboring gene microRNA 4775 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:208647704-208648204 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:208660472-208661457 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:208661458-208662442 Neighboring gene frizzled class receptor 5 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:208666419-208666920 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:208666921-208667420 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:208675729-208676550 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17046 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17047 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17048 Neighboring gene pleckstrin homology domain containing M3 Neighboring gene HNF1 motif-containing MPRA enhancer 152 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:208713897-208714396 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr2:208772908-208774107 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:208835249-208835782 Neighboring gene RNA, U6 small nuclear 360, pseudogene Neighboring gene ribosomal protein L9 pseudogene 14

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_077100.1 

    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    207970165..207970459
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    208444416..208444710
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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