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LOC121627890 Sharpr-MPRA regulatory region 10396 [ Homo sapiens (human) ]

Gene ID: 121627890, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121627890
Gene description
Sharpr-MPRA regulatory region 10396
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 unmatched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Jun 2021]
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Genomic context

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Location:
20p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (363225..363519)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (406586..406880)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (343869..344163)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12564 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12565 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12566 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12567 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12568 Neighboring gene Sharpr-MPRA regulatory region 7859/9812 Neighboring gene SRY-box transcription factor 12 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:326527-327290 Neighboring gene serine/arginine repetitive matrix protein 2-like Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:327291-328053 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:328054-328816 Neighboring gene Sharpr-MPRA regulatory region 10349 Neighboring gene Sharpr-MPRA regulatory region 12668 Neighboring gene neurensin 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:345627-346226 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12572 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12573 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:362523-363521 Neighboring gene tribbles pseudokinase 3 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:379646-380146 Neighboring gene CRISPRi-validated cis-regulatory element chr20.29 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:386661-386817 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12575 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:388888-389530 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:389531-390171 Neighboring gene RANBP2-type and C3HC4-type zinc finger containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12576 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:410614-411114 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:411115-411615

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_075081.1 

    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
    363225..363519
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    406586..406880
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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