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LOC124310615 Sharpr-MPRA regulatory region 13033 [ Homo sapiens (human) ]

Gene ID: 124310615, updated on 12-Sep-2024

Summary

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Gene symbol
LOC124310615
Gene description
Sharpr-MPRA regulatory region 13033
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 8:EnhW, candidate weak enhancer and open chromatin). [provided by RefSeq, Feb 2022]
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Genomic context

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See LOC124310615 in Genome Data Viewer
Location:
9q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (100196267..100196561)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (112368025..112368319)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (102958549..102958843)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene inversin Neighboring gene DPPA3 pseudogene 10 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:102902488-102903061 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr9:102908301-102908959 Neighboring gene Nanog homeobox pseudogene 5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28722 Neighboring gene uncharacterized LOC124902235 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:103046218-103046718 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:103046719-103047219 Neighboring gene testis expressed 10 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:103103415-103103914 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28723 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:103114917-103115551

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 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_078897.1 

    Range
    101..395
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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
    100196267..100196561
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    112368025..112368319
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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