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LOC121852944 Sharpr-MPRA regulatory region 3713 [ Homo sapiens (human) ]

Gene ID: 121852944, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121852944
Gene description
Sharpr-MPRA regulatory region 3713
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 14:Gen5', transcription transition, highly expressed genes towards 5' end). [provided by RefSeq, Jul 2021]
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Genomic context

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See LOC121852944 in Genome Data Viewer
Location:
17q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (65527911..65528205)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (66398558..66398852)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (63524029..63524323)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12609 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:63179396-63179932 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:63179933-63180469 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:63181573-63182096 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:63182097-63182620 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:63221253-63222057 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:63220448-63221252 Neighboring gene zinc finger protein 848, pseudogene Neighboring gene MPRA-validated peak2941 silencer Neighboring gene regulator of G protein signaling 9 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:63358670-63359869 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:63434615-63435115 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:63451995-63452494 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:63456111-63456744 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:63456745-63457378 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:63457379-63458011 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:63492294-63492926 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr17:63491028-63491660 Neighboring gene long intergenic non-protein coding RNA 2563 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:63519932-63520432 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:63526146-63526660 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:63526661-63527173 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:63527688-63528200 Neighboring gene MPRA-validated peak2942 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:63551316-63552089 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:63550543-63551315 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8863 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12610 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12611 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:63568601-63569439 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:63579618-63580152 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:63589757-63590572 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:63625333-63625832 Neighboring gene axin 2 Neighboring gene chloride intracellular channel 1 pseudogene Neighboring gene centrosomal protein 112

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_076051.1 

    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    65527911..65528205
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    66398558..66398852
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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