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LOC121392929 Sharpr-MPRA regulatory region 9619 [ Homo sapiens (human) ]

Gene ID: 121392929, updated on 12-Sep-2024

Summary

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Gene symbol
LOC121392929
Gene description
Sharpr-MPRA regulatory region 9619
Gene type
biological region
Feature type(s)
regulatory: enhancer, 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 enhancer by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in HepG2 liver carcinoma cells (group: HepG2 Activating DNase unmatched - State 5:Enh, candidate strong enhancer, open chromatin). This region also displayed repressive activity by Sharpr-MPRA in K562 erythroleukemia cells (group: K562 Repressive DNase unmatched - State 5:Enh). [provided by RefSeq, May 2021]
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Genomic context

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See LOC121392929 in Genome Data Viewer
Location:
11q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (74138624..74138918)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (74067973..74068267)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (73849669..73849963)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene family with sequence similarity 91 member A1 pseudogene Neighboring gene MED14-independent group 3 enhancer GRCh37_chr11:73715060-73716259 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:73719425-73719605 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:73719739-73720378 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5249 Neighboring gene uncoupling protein 3 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr11:73747696-73748895 Neighboring gene C2 domain containing 3 centriole elongation regulator Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5250 Neighboring gene NANOG hESC enhancer GRCh37_chr11:73808354-73808901 Neighboring gene H3K27ac hESC enhancers GRCh37_chr11:73881282-73882205 and GRCh37_chr11:73882206-73883128 Neighboring gene protein phosphatase methylesterase 1 Neighboring gene uncharacterized LOC105369383 Neighboring gene RNA, 5S ribosomal pseudogene 343

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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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_074586.1 

    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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    74138624..74138918
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    74067973..74068267
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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