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LOC124310613 Sharpr-MPRA regulatory region 14650 [ Homo sapiens (human) ]

Gene ID: 124310613, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124310613
Gene description
Sharpr-MPRA regulatory region 14650
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, Feb 2022]
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Genomic context

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See LOC124310613 in Genome Data Viewer
Location:
9q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (98603047..98603341)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (110774682..110774976)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (101365329..101365623)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene ADP ribosylation factor like GTPase 8B pseudogene Neighboring gene TBC1 domain family member 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:101010111-101011028 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:101011029-101011945 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20119 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28695 Neighboring gene microRNA 6854 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28696 Neighboring gene MPRA-validated peak7303 silencer Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:101036136-101036669 Neighboring gene NANOG hESC enhancer GRCh37_chr9:101036702-101037236 Neighboring gene NANOG hESC enhancer GRCh37_chr9:101037237-101037769 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:101042021-101042706 Neighboring gene gamma-aminobutyric acid type B receptor subunit 2 Neighboring gene Sharpr-MPRA regulatory region 5055 Neighboring gene GATA motif-containing MPRA enhancer 175 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:101122073-101122573 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:101134501-101135189 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28697 Neighboring gene Sharpr-MPRA regulatory region 1904 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:101151090-101151268 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:101158435-101159110 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:101159111-101159786 Neighboring gene NANOG hESC enhancer GRCh37_chr9:101164028-101164529 Neighboring gene MPRA-validated peak7304 silencer Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:101257622-101258821 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:101270847-101271377 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_103859 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:101328229-101328729 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28698 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:101372736-101373728 Neighboring gene septin 7 pseudogene 7 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:101430118-101430303 Neighboring gene uncharacterized LOC124902228

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_078895.1 

    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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    98603047..98603341
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    110774682..110774976
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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