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LOC123775392 Sharpr-MPRA regulatory region 9287 [ Homo sapiens (human) ]

Gene ID: 123775392, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123775392
Gene description
Sharpr-MPRA regulatory region 9287
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 22:ReprW, weaker Polycomb repression) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 7:EnhWF, candidate poised/weak enhancer, flanking open chromatin of candidate enhancers). [provided by RefSeq, Jan 2022]
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Genomic context

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Location:
6q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (106143574..106143868)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (107319432..107319726)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (106591449..106591743)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene RN7SK pseudogene 211 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17429 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:106441121-106441655 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:106442725-106443257 Neighboring gene NANOG hESC enhancer GRCh37_chr6:106462748-106463464 Neighboring gene PR/SET domain 1 Neighboring gene NANOG hESC enhancer GRCh37_chr6:106511809-106512319 Neighboring gene NANOG hESC enhancer GRCh37_chr6:106528405-106528951 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24877 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:106533839-106534558 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:106546043-106547242 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:106553364-106554077 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:106552649-106553363 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:106582537-106583736 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24878 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:106611080-106611926 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:106611927-106612773 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:106614661-106615396 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24883 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17430 Neighboring gene MPRA-validated peak6001 silencer Neighboring gene autophagy related 5 Neighboring gene RNA, 7SL, cytoplasmic 47, pseudogene Neighboring gene RNA, U6 small nuclear 344, pseudogene

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_078160.1 

    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    106143574..106143868
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    107319432..107319726
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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