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LOC124310636 Sharpr-MPRA regulatory region 3775 [ Homo sapiens (human) ]

Gene ID: 124310636, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124310636
Gene description
Sharpr-MPRA regulatory region 3775
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 21:Repr, strong Polycomb repression). [provided by RefSeq, Feb 2022]
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Genomic context

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Location:
9q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (121763730..121764024)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (133959718..133960012)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (124526009..124526303)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107987016 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20237 Neighboring gene Sharpr-MPRA regulatory region 14365 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:124359845-124360812 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:124360813-124361778 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:124366827-124367614 Neighboring gene DAB2 interacting protein Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:124393797-124394545 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:124396647-124397309 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28924 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:124411655-124412490 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:124416949-124417448 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:124446578-124447078 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28925 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20238 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:124468887-124469686 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:124480397-124480994 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:124482472-124482999 Neighboring gene uncharacterized LOC105376257 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:124500148-124500924 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:124504941-124505640 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:124510791-124511314 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:124514713-124515213 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:124516632-124517247 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:124517370-124517953 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:124543874-124544863 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr9:124552172-124552712 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:124556939-124557676 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr9:124558413-124559150 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:124573577-124574096 Neighboring gene uncharacterized LOC107987125 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:124578825-124579621 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:124589529-124590300 Neighboring gene tubulin tyrosine ligase like 11 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:124650231-124650789 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:124659227-124659916 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:124688418-124688918 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:124748015-124748516 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr9:124801206-124802405 Neighboring gene uncharacterized LOC124902262

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_078917.1 

    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
    121763730..121764024
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    133959718..133960012
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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