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LOC121392891 Sharpr-MPRA regulatory region 1666 [ Homo sapiens (human) ]

Gene ID: 121392891, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121392891
Gene description
Sharpr-MPRA regulatory region 1666
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 both HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 8:EnhW, candidate weak enhancer and open chromatin) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 8:EnhW). [provided by RefSeq, May 2021]
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Genomic context

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Location:
11p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (12599522..12599816)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (12691582..12691876)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (12621069..12621363)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene microtubule associated monooxygenase, calponin and LIM domain containing 2 Neighboring gene uncharacterized LOC124902634 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:12238418-12238918 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:12238919-12239419 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:12263505-12264029 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:12352017-12352518 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:12387753-12388325 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:12474119-12474620 Neighboring gene parvin alpha Neighboring gene Sharpr-MPRA regulatory region 15612/8581 Neighboring gene uncharacterized LOC105376556 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:12658187-12658688 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:12658689-12659188 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3162 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:12696795-12697609 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:12697610-12698423 Neighboring gene TEAD1 intron CAGE-defined low expression enhancer 1 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr11:12701865-12702582 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:12702583-12703300 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:12703301-12704018 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr11:12714955-12716154 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:12736558-12737398 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3163 Neighboring gene Sharpr-MPRA regulatory region 14023 Neighboring gene Sharpr-MPRA regulatory region 9596 Neighboring gene Sharpr-MPRA regulatory region 5264 Neighboring gene TEA domain transcription factor 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:12788587-12789086 Neighboring gene Sharpr-MPRA regulatory region 13244 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:12809225-12809732 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:12809733-12810240 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:12810874-12811512 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:12830522-12831193 Neighboring gene uncharacterized LOC107984313 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr11:12849868-12850506

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_074547.1 

    Range
    101..395
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    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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    12599522..12599816
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    12691582..12691876
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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