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LOC124252627 Sharpr-MPRA regulatory region 4081 [ Homo sapiens (human) ]

Gene ID: 124252627, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124252627
Gene description
Sharpr-MPRA regulatory region 4081
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 DNase matched - State 4:PromP, inactive/poised promoter, highly conserved). [provided by RefSeq, Feb 2022]
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Genomic context

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Location:
9p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (33401491..33401785)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (33420094..33420388)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (33401489..33401783)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene nuclear transcription factor, X-box binding 1 Neighboring gene uncharacterized LOC105376018 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:33372618-33373118 Neighboring gene uncharacterized LOC124902142 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:33380602-33381202 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:33381203-33381801 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:33383370-33383870 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:33383871-33384371 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr9:33385863-33387062 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:33390288-33391075 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:33391076-33391862 Neighboring gene uncharacterized LOC105376020 Neighboring gene aquaporin 7 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:33404334-33404891 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:33407721-33408222 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:33408223-33408722 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:33414572-33415103 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:33415104-33415634 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:33435285-33435786 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:33438678-33438916 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:33442744-33443943 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19834 Neighboring gene Sharpr-MPRA regulatory region 5008 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr9:33458152-33459351 Neighboring gene aquaporin 3 (Gill blood group) Neighboring gene microRNA 6851 Neighboring gene nucleolar protein 6

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_078805.1 

    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
    33401491..33401785
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    33420094..33420388
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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