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LOC121392893 Sharpr-MPRA regulatory region 11719 [ Homo sapiens (human) ]

Gene ID: 121392893, updated on 12-Sep-2024

Summary

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Gene symbol
LOC121392893
Gene description
Sharpr-MPRA regulatory region 11719
Gene type
biological region
Feature type(s)
regulatory: enhancer
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 matched - State 23:Low, low signal proximal to active elements). [provided by RefSeq, May 2021]
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Genomic context

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See LOC121392893 in Genome Data Viewer
Location:
11p
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (19277422..19277716)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (19397485..19397779)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (19298969..19299263)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene MED14-independent group 3 enhancer GRCh37_chr11:19253866-19255065 Neighboring gene CSRP3 and E2F8 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3198 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4515 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:19263697-19264268 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:19264269-19264838 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:19290948-19291137 Neighboring gene E2F transcription factor 8 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4516 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4517 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4518 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3199 Neighboring gene proliferating cell nuclear antigen pseudogene 4 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr11:19416525-19417056 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4519 Neighboring gene MPRA-validated peak1231 silencer Neighboring gene RNA, 5S ribosomal pseudogene 335 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr11:19463438-19464637 Neighboring gene neuron navigator 2 Neighboring gene NAV2 antisense RNA 5

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_074549.1 

    Range
    101..395
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    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
    19277422..19277716
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    19397485..19397779
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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