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LOC123864091 Sharpr-MPRA regulatory region 7657 [ Homo sapiens (human) ]

Gene ID: 123864091, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123864091
Gene description
Sharpr-MPRA regulatory region 7657
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 22:ReprW, weaker Polycomb repression). [provided by RefSeq, Jan 2022]
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Genomic context

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See LOC123864091 in Genome Data Viewer
Location:
6q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (144387673..144387967)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (145580306..145580600)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (144708809..144709103)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25213 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17639 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:144537315-144537779 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:144550475-144550694 Neighboring gene tRNA-Leu (anticodon TAA) 1-1 Neighboring gene MPRA-validated peak6183 silencer Neighboring gene MPRA-validated peak6184 silencer Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:144586575-144587308 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:144587309-144588042 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25214 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17640 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17641 Neighboring gene uncharacterized LOC124901418 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25215 Neighboring gene Sharpr-MPRA regulatory region 1397 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:144647748-144648492 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:144651868-144653067 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25216 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25217 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25218 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:144666170-144666670 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:144666671-144667171 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25219 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25220 Neighboring gene utrophin Neighboring gene rhomboid domain containing 1 pseudogene Neighboring gene small nucleolar RNA, H/ACA box 98

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_078223.1 

    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
    144387673..144387967
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    145580306..145580600
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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