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LOC121587563 Sharpr-MPRA regulatory region 6091 [ Homo sapiens (human) ]

Gene ID: 121587563, updated on 12-Sep-2024

Summary

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Gene symbol
LOC121587563
Gene description
Sharpr-MPRA regulatory region 6091
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 4:PromP, inactive/poised promoter, highly conserved) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 4:PromP). [provided by RefSeq, Jun 2021]
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Genomic context

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See LOC121587563 in Genome Data Viewer
Location:
16q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (79600652..79600946)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (85656986..85657280)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (79634549..79634843)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene MAF bZIP transcription factor Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:79321285-79321785 Neighboring gene RNA, 5S ribosomal pseudogene 431 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:79332665-79333313 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr16:79333314-79333961 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr16:79362104-79362979 Neighboring gene MPRA-validated peak2651 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr16:79516400-79516610 Neighboring gene uncharacterized LOC124903729 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:79561711-79561812 Neighboring gene uncharacterized LOC101928230 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11158 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11159 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7737 Neighboring gene uncharacterized LOC105371356 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:79742031-79742530 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11160 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11161 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:79804516-79804714 Neighboring gene MAF transcriptional regulator RNA Neighboring gene long intergenic non-protein coding RNA 1229 Neighboring gene long intergenic non-protein coding RNA 1228

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_074850.1 

    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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    79600652..79600946
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    85656986..85657280
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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