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LOC121627885 Sharpr-MPRA regulatory region 164 [ Homo sapiens (human) ]

Gene ID: 121627885, updated on 12-Sep-2024

Summary

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Gene symbol
LOC121627885
Gene description
Sharpr-MPRA regulatory region 164
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. The major subregion was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in naive human embryonic stem cells, where it is marked by the H3K27ac and H3K4me1 histone modifications. Another subregion was validated as an enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 4:PromP, inactive/poised promoter, highly conserved). This locus also includes an accessible chromatin subregion that was validated as a silencer based on its ability to repress an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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See LOC121627885 in Genome Data Viewer
Location:
19q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (49017812..49018839)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (52012585..52013612)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (49521069..49522096)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14920 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:49473581-49474108 Neighboring gene CRISPRi-FlowFISH-validated FTL regulatory element 4 Neighboring gene glycogen synthase 1 Neighboring gene Sharpr-MPRA regulatory region 1809 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14921 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:49491709-49491891 Neighboring gene skeletal muscle cis-regulatory module in GYS1 intron Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14922 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10910 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14923 Neighboring gene RuvB like AAA ATPase 2 Neighboring gene Sharpr-MPRA regulatory region 732 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:49507585-49508084 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:49512697-49513198 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:49515021-49515195 Neighboring gene microRNA 6798 Neighboring gene uncharacterized LOC124904738 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14924 Neighboring gene luteinizing hormone subunit beta Neighboring gene stabilizer of axonemal microtubules 3 Neighboring gene chorionic gonadotropin subunit beta 3

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
  2. ATAC-STARR-seq reveals transcription factor-bound activators and silencers within chromatin-accessible regions of the human genome. Hansen TJ, et al. Genome Res, 2022 Aug 25. PMID 35858748, Free PMC Article
  3. Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells. Barakat TS, et al. Cell Stem Cell, 2018 Aug 2. PMID 30033119, 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)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid silent region 10911
  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:49521173-49522096

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_075076.2 

    Range
    101..1128
    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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    49017812..49018839
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    52012585..52013612
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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