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LOC121627909 Sharpr-MPRA regulatory region 4283 [ Homo sapiens (human) ]

Gene ID: 121627909, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121627909
Gene description
Sharpr-MPRA regulatory region 4283
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 K562 erythroleukemia cells (group: K562 Activating DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Jun 2021]
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Genomic context

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Location:
20q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (50504292..50504586)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (52273902..52274196)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (49120829..49121123)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 10608 Neighboring gene RNA, 7SL, cytoplasmic 636, pseudogene Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr20:49056367-49057566 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:49065061-49066026 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:49074250-49074778 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:49076728-49077228 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13020 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18087 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18088 Neighboring gene cytochrome c oxidase subunit 6C pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18089 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18090 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:49126094-49126681 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18091 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13022 Neighboring gene protein tyrosine phosphatase non-receptor type 1 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr20:49157072-49158271 Neighboring gene Sharpr-MPRA regulatory region 13607 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr20:49177610-49178809 Neighboring gene RNA, 7SL, cytoplasmic 672, pseudogene Neighboring gene microRNA 645

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_075100.1 

    Range
    101..395
    Download
    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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    50504292..50504586
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    52273902..52274196
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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